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Wang HY, Louis HMS, Costello CL, Murray SS, Dell'Aquila ML. A CD10-negative adult B-lymphoblastic leukaemia with amplification of KMT2A without rearrangement: A case report and review of the English literature. Br J Haematol 2024. [PMID: 38735761 DOI: 10.1111/bjh.19520] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2024] [Accepted: 04/27/2024] [Indexed: 05/14/2024]
Affiliation(s)
- Huan-You Wang
- Division of Laboratory and Genomic Medicine, Department of Pathology, University of California San Diego Health Sciences, La Jolla, California, USA
| | - Hailee M St Louis
- Division of Laboratory and Genomic Medicine, Department of Pathology, University of California San Diego Health Sciences, La Jolla, California, USA
| | - Caitlin L Costello
- Division of Blood and Marrow Transplant, Department of Medicine, University of California San Diego Health Sciences, La Jolla, California, USA
| | - Sarah S Murray
- Division of Laboratory and Genomic Medicine, Department of Pathology, University of California San Diego Health Sciences, La Jolla, California, USA
| | - Marie L Dell'Aquila
- Division of Laboratory and Genomic Medicine, Department of Pathology, University of California San Diego Health Sciences, La Jolla, California, USA
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2
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Lee TD, Aisner DL, David MP, Eno CC, Gagan J, Gocke CD, Guseva NV, Haley L, Jajosky AN, Jones D, Mansukhani MM, Mroz P, Murray SS, Newsom KJ, Paulson V, Roy S, Rushton C, Segal JP, Senaratne TN, Siddon AJ, Starostik P, Van Ziffle JAG, Wu D, Xian RR, Yohe S, Kim AS. Current clinical practices and challenges in molecular testing: a GOAL Consortium Hematopathology Working Group report. Blood Adv 2023; 7:4599-4607. [PMID: 37236162 PMCID: PMC10425685 DOI: 10.1182/bloodadvances.2023010149] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2023] [Revised: 05/02/2023] [Accepted: 05/18/2023] [Indexed: 05/28/2023] Open
Abstract
While molecular testing of hematologic malignancies is now standard of care, there is variability in practice and testing capabilities between different academic laboratories, with common questions arising on how to best meet clinical expectations. A survey was sent to hematopathology subgroup members of the Genomics Organization for Academic Laboratories consortium to assess current and future practice and potentially establish a reference for peer institutions. Responses were received from 18 academic tertiary-care laboratories regarding next-generation sequencing (NGS) panel design, sequencing protocols and metrics, assay characteristics, laboratory operations, case reimbursement, and development plans. Differences in NGS panel size, use, and gene content were reported. Gene content for myeloid processes was reported to be generally excellent, while genes for lymphoid processes were less well covered. The turnaround time (TAT) for acute cases, including acute myeloid leukemia, was reported to range from 2 to 7 calendar days to 15 to 21 calendar days, with different approaches to achieving rapid TAT described. To help guide NGS panel design and standardize gene content, consensus gene lists based on current and future NGS panels in development were generated. Most survey respondents expected molecular testing at academic laboratories to continue to be viable in the future, with rapid TAT for acute cases likely to remain an important factor. Molecular testing reimbursement was reported to be a major concern. The results of this survey and subsequent discussions improve the shared understanding of differences in testing practices for hematologic malignancies between institutions and will help provide a more consistent level of patient care.
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Affiliation(s)
- Thomas D. Lee
- Department of Pathology and Laboratory Medicine, David Geffen School of Medicine at University of California Los Angeles, Los Angeles, CA
| | - Dara L. Aisner
- Department of Pathology, University of Colorado, Aurora, CO
| | - Marjorie P. David
- Department of Pathology and Laboratory Medicine, University of Texas Health Science Center at San Antonio, San Antonio, TX
| | - Celeste C. Eno
- Department of Pathology and Lab Medicine, Cedars-Sinai Medical Center, Los Angeles, CA
| | - Jeffrey Gagan
- Department of Pathology, University of Texas Southwestern, Dallas, TX
| | - Christopher D. Gocke
- Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, MD
| | | | - Lisa Haley
- Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, MD
| | - Audrey N. Jajosky
- Department of Pathology & Laboratory Medicine, University of Rochester Medical Center, Rochester, NY
| | - Daniel Jones
- The Ohio State University Comprehensive Cancer Center, The Ohio State University, Columbus, OH
| | - Mahesh M. Mansukhani
- Department of Pathology and Cell Biology, Columbia University Irving Medical Center, New York, NY
| | - Pawel Mroz
- Department of Laboratory Medicine and Pathology, University of Minnesota, Minneapolis, MN
| | - Sarah S. Murray
- Department of Pathology, University of California San Diego, La Jolla, CA
| | - Kimberly J. Newsom
- Department of Pathology, Immunology and Laboratory Medicine, University of Florida, Gainesville, FL
| | - Vera Paulson
- Department of Laboratory Medicine and Pathology, University of Washington, Seattle, WA
| | - Somak Roy
- Department of Pathology, Cincinnati Children’s Hospital Medical Center, Cincinnati, OH
| | - Chase Rushton
- Department of Pathology and Laboratory Medicine, Perelman School of Medicine at University of Pennsylvania, Philadelphia, PA
| | | | - T. Niroshini Senaratne
- Department of Pathology and Laboratory Medicine, David Geffen School of Medicine at University of California Los Angeles, Los Angeles, CA
| | - Alexa J. Siddon
- Departments of Laboratory Medicine & Pathology, Yale School of Medicine, New Haven, CT
| | - Petr Starostik
- Department of Pathology, Immunology and Laboratory Medicine, University of Florida, Gainesville, FL
| | | | - David Wu
- Department of Laboratory Medicine and Pathology, University of Washington, Seattle, WA
| | - Rena R. Xian
- Department of Pathology, Johns Hopkins University School of Medicine, Baltimore, MD
| | - Sophia Yohe
- Department of Laboratory Medicine and Pathology, University of Minnesota, Minneapolis, MN
| | - Annette S. Kim
- Department of Pathology, Brigham and Women’s Hospital/Harvard Medical School, Boston, MA
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3
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Li P, Brown S, Williams M, White T, Xie W, Cui W, Peker D, Lei L, Kunder CA, Wang HY, Murray SS, Vagher J, Kovacsovics T, Patel JL. The genetic landscape of germline DDX41 variants predisposing to myeloid neoplasms. Blood 2022; 140:716-755. [PMID: 35671390 PMCID: PMC9389629 DOI: 10.1182/blood.2021015135] [Citation(s) in RCA: 39] [Impact Index Per Article: 19.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2021] [Accepted: 04/09/2022] [Indexed: 11/20/2022] Open
Abstract
Germline DDX41 variants are the most common mutations predisposing to acute myeloid leukemia (AML)/myelodysplastic syndrome (MDS) in adults, but the causal variant (CV) landscape and clinical spectrum of hematologic malignancies (HMs) remain unexplored. Here, we analyzed the genomic profiles of 176 patients with HM carrying 82 distinct presumably germline DDX41 variants among a group of 9821 unrelated patients. Using our proposed DDX41-specific variant classification, we identified features distinguishing 116 patients with HM with CV from 60 patients with HM with variant of uncertain significance (VUS): an older age (median 69 years), male predominance (74% in CV vs 60% in VUS, P = .03), frequent concurrent somatic DDX41 variants (79% in CV vs 5% in VUS, P < .0001), a lower somatic mutation burden (1.4 ± 0.1 in CV vs 2.9 ± 0.04 in VUS, P = .012), near exclusion of canonical recurrent genetic abnormalities including mutations in NPM1, CEBPA, and FLT3 in AML, and favorable overall survival (OS) in patients with AML/MDS. This superior OS was determined independent of blast count, abnormal karyotypes, and concurrent variants, including TP53 in patients with AML/MDS, regardless of patient's sex, age, or specific germline CV, suggesting that germline DDX41 variants define a distinct clinical entity. Furthermore, unrelated patients with myeloproliferative neoplasm and B-cell lymphoma were linked by DDX41 CV, thus expanding the known disease spectrum. This study outlines the CV landscape, expands the phenotypic spectrum in unrelated DDX41-mutated patients, and underscores the urgent need for gene-specific diagnostic and clinical management guidelines.
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Affiliation(s)
- Peng Li
- Division of Hematopathology, Department of Pathology, University of Utah Health, Salt Lake City, UT
- Genomics Laboratory, ARUP Laboratories, Salt Lake City, UT
| | - Sara Brown
- Genomics Laboratory, ARUP Laboratories, Salt Lake City, UT
| | - Margaret Williams
- Division of Hematopathology, Department of Pathology, University of Utah Health, Salt Lake City, UT
- Genomics Laboratory, ARUP Laboratories, Salt Lake City, UT
| | - Thomas White
- Genomics Laboratory, ARUP Laboratories, Salt Lake City, UT
| | - Wei Xie
- Department of Pathology, School of Medicine, Oregon Health and Science University, Portland, OR
| | - Wei Cui
- Department of Pathology and Laboratory Medicine, University of Kansas Medical Center, Kansas City, KS
| | - Deniz Peker
- Division of Hematopathology, Department of Pathology and Laboratory Medicine, Emory University, Atlanta, GA
| | - Li Lei
- Department of Pathology and Laboratory Medicine, University of California, Davis, Sacramento, CA
- Department of Pathology, Stanford University, School of Medicine, Stanford, CA
| | - Christian A Kunder
- Department of Pathology, Stanford University, School of Medicine, Stanford, CA
| | - Huan-You Wang
- Department of Pathology & Immunology, University of California San Diego Health System, La Jolla, CA
| | - Sarah S Murray
- Department of Pathology & Immunology, University of California San Diego Health System, La Jolla, CA
| | - Jennie Vagher
- Department of Internal Medicine, University of Utah Health, Salt Lake City, UT; and
- Huntsman Cancer Institute, Salt Lake City, UT
| | - Tibor Kovacsovics
- Department of Internal Medicine, University of Utah Health, Salt Lake City, UT; and
- Huntsman Cancer Institute, Salt Lake City, UT
| | - Jay L Patel
- Division of Hematopathology, Department of Pathology, University of Utah Health, Salt Lake City, UT
- Genomics Laboratory, ARUP Laboratories, Salt Lake City, UT
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Wang HY, Murray SS, Bejar R. Indolent T-cell prolymphocytic leukemia with no expression of surface T-cell receptors or surface CD3. Int J Lab Hematol 2021; 43:O224-O226. [PMID: 33855780 DOI: 10.1111/ijlh.13529] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2021] [Revised: 02/16/2021] [Accepted: 03/03/2021] [Indexed: 11/29/2022]
Affiliation(s)
- Huan-You Wang
- Division of Laboratory and Genomic Medicine, Department of Pathology, University of California San Diego Health System, La Jolla, CA, USA
| | - Sarah S Murray
- Division of Laboratory and Genomic Medicine, Department of Pathology, University of California San Diego Health System, La Jolla, CA, USA
| | - Rafael Bejar
- Division of Hematology and Oncology, Department of Medicine, University of California San Diego Health System, La Jolla, CA, USA
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5
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Bevins N, Sun S, Gaieb Z, Thorson JA, Murray SS. Comparison of commonly used solid tumor targeted gene sequencing panels for estimating tumor mutation burden shows analytical and prognostic concordance within the cancer genome atlas cohort. J Immunother Cancer 2020; 8:e000613. [PMID: 32217764 PMCID: PMC7174068 DOI: 10.1136/jitc-2020-000613] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 02/27/2020] [Indexed: 12/22/2022] Open
Abstract
BACKGROUND Tumor mutation burden (TMB) is a biomarker frequently reported by clinical laboratories, which is derived by quantifying of the number of single nucleotide or indel variants (mutations) identified by next-generation sequencing of tumors. TMB values can inform prognosis or predict the response of a patient's tumor to immune checkpoint inhibitor therapy. Methods for the calculation of TMB are not standardized between laboratories, with significant variables being the gene content of the panels sequenced and the inclusion or exclusion of synonymous variants in the calculations. The impact of these methodological differences has not been investigated and the concordance of reported TMB values between laboratories is unknown. METHODS Sequence variant lists from more than 9000 tumors of various types were downloaded from The Cancer Genome Atlas. Variant lists were filtered to include only appropriate variant types (ie, non-synonymous only or synonymous and non-synonymous variants) within the genes found in five commonly used targeted solid tumor gene panels as well as an in-house gene panel. Calculated TMB was paired with corresponding overall survival (OS) data of each patient. RESULTS Regression analysis indicates high concordance of TMB as derived from the examined panels. TMB derived from panels was consistently and significantly lower than that derived from a whole exome. TMB, as derived from whole exome or the examined panels, showed a significant correlation with OS in the examined data. CONCLUSIONS TMB derived from the examined gene panels was analytically equivalent between panels, but not between panels and whole-exome sequencing. Correlation between TMB and OS is significant if TMB method-specific cut-offs are used. These results suggest that TMB values, as derived from the gene panels examined, are analytically and prognostically equivalent.
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Affiliation(s)
| | - Shulei Sun
- Pathology, UC San Diego, La Jolla, California, USA
| | - Zied Gaieb
- Chemistry and Biochemistry, UC San Diego, La Jolla, California, USA
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6
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Saloner R, Paolillo EW, Kohli M, Murray SS, Moore DJ, Grant I, Cherner M. Genetic variation in alcohol dehydrogenase is associated with neurocognition in men with HIV and history of alcohol use disorder: preliminary findings. J Neurovirol 2020; 26:214-225. [PMID: 31933193 DOI: 10.1007/s13365-019-00825-z] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2019] [Revised: 11/22/2019] [Accepted: 12/17/2019] [Indexed: 12/12/2022]
Abstract
The co-occurrence of HIV and alcohol use disorder (AUD) amplifies risk for neural injury and neurocognitive deficits. However, the substantial neurocognitive heterogeneity across HIV+/AUD+ individuals suggests inter-individual differences in vulnerability to the neurotoxicity of comorbid HIV/AUD. Genetic variation in alcohol dehydrogenase (ADH), which metabolizes ethanol, may contribute to inter-individual neurocognitive variability. We evaluated associations between five ADH single-nucleotide polymorphisms (SNPs) and neurocognition in men stratified by HIV and lifetime AUD status. Neurobehavioral assessments were administered to 153 men. Three-way ANOVAs examined the interaction of HIV, AUD, and ADH SNPs on global and domain-specific demographically corrected T scores. Follow-up ANCOVAs adjusted for age, estimated verbal IQ, depression, and remote non-alcohol substance use disorders. HIV/AUD groups differed globally and for verbal fluency, working memory, executive function, and processing speed T scores specifically, with HIV+/AUD+ exhibiting the poorest performance. ADH4 (rs1126671) was associated with large effects on working memory (d = - 1.16, p = .001) and executive function (d = - 0.77, p = .028) selectively in HIV+/AUD+, which remained significant in ANCOVA models. ADH1A (rs3819197) moderated the deleterious effects of HIV+/AUD+ on processing speed such that HIV+/AUD+ related to slower information processing in A allele carriers but not GG homozygotes (ps < 0.03). Preliminary findings suggest genetic variation in the ADH pathway moderates the deleterious neurocognitive effects of comorbid HIV/AUD. Differential metabolism of heavy ethanol exposure may compromise neurocognition under conditions of neurobiological stress, such as in HIV infection. The functional effects on ethanol metabolism of ADH SNPs examined in this study remain poorly understood, warranting further examination of pharmacokinetic mechanisms mediating ADH gene-neurobehavior relationships in HIV.
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Affiliation(s)
- Rowan Saloner
- Joint Doctoral Program in Clinical Psychology, San Diego State University/University of California San Diego, San Diego, CA, USA. .,Department of Psychiatry, HIV Neurobehavioral Research Program, University of California San Diego, San Diego, CA, USA.
| | - Emily W Paolillo
- Joint Doctoral Program in Clinical Psychology, San Diego State University/University of California San Diego, San Diego, CA, USA.,Department of Psychiatry, HIV Neurobehavioral Research Program, University of California San Diego, San Diego, CA, USA
| | - Maulika Kohli
- Joint Doctoral Program in Clinical Psychology, San Diego State University/University of California San Diego, San Diego, CA, USA.,Department of Psychiatry, HIV Neurobehavioral Research Program, University of California San Diego, San Diego, CA, USA
| | - Sarah S Murray
- Department of Pathology, University of California San Diego, La Jolla, CA, USA
| | - David J Moore
- Department of Psychiatry, HIV Neurobehavioral Research Program, University of California San Diego, San Diego, CA, USA
| | - Igor Grant
- Department of Psychiatry, HIV Neurobehavioral Research Program, University of California San Diego, San Diego, CA, USA
| | - Mariana Cherner
- Department of Psychiatry, HIV Neurobehavioral Research Program, University of California San Diego, San Diego, CA, USA
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7
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Cherner M, Watson CWM, Saloner R, Halpin LE, Minassian A, Murray SS, Vaida F, Bousman C, Everall I. Adverse effect of catechol-O-methyltransferase (COMT) Val158Met met/met genotype in methamphetamine-related executive dysfunction. Addict Behav 2019; 98:106023. [PMID: 31301644 PMCID: PMC6733518 DOI: 10.1016/j.addbeh.2019.06.012] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2018] [Revised: 06/03/2019] [Accepted: 06/10/2019] [Indexed: 01/19/2023]
Abstract
INTRODUCTION The Val allele of the Val158Met single-nucleotide polymorphism of the catechol-o-methyltransferase gene (COMT) confers greater catabolism of dopamine (DA) in the prefrontal cortex (PFC) than the Met allele. Met/Met homozygotes typically outperform Val-carriers on tests of executive function (EF), perhaps resulting from increased DA bioavailability. Methamphetamine (METH) causes large releases of DA, which is associated with neurotoxicity and executive dysfunction in chronic METH users. We hypothesized that, contrary to its effect in non-METH-using populations, slower DA clearance conferred by Met/Met will relate to worse EF in METH users. METHODS 149 non-Hispanic White men, stratified by METH dependence (METH+/-) and COMT (Val/Val, Val/Met, Met/Met), completed three tests of EF: Wisconsin Card Sorting Test (WCST), Stroop Color-Word Test (Stroop), and Trail Making Test Part B (Trails B). Demographically-adjusted test scores were averaged to create an EF composite T-score. We examined the interaction of METH and COMT on the EF composite and individual test T-scores, controlling for premorbid functioning and alcohol use. RESULTS METH group differences in EF were evident only among Met/Met carriers (beta = -9.36, p < .001) but not among Val carriers: Val/Met (beta = -1.38, p = .44) and Val/Val (beta = -4.34, p = .10). These effects were most salient on the WCST. CONCLUSIONS In the pre-frontal hyperdopaminergic state triggered by methamphetamine, greater DA inactivation conferred by the Val allele may protect against METH-related executive dysfunction, suggesting genetically-driven differences in vulnerability to METH.
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Affiliation(s)
- Mariana Cherner
- Department of Psychiatry, University of California San Diego, United States.
| | - Caitlin W-M Watson
- Department of Psychiatry, University of California San Diego, United States
| | - Rowan Saloner
- Department of Psychiatry, University of California San Diego, United States
| | - Laura E Halpin
- Department of Psychiatry and Behavioral Sciences, University of California Los Angeles, United States
| | - Arpi Minassian
- Department of Psychiatry, University of California San Diego, United States
| | - Sarah S Murray
- Department of Pathology, University of California San Diego, United States
| | - Florin Vaida
- Department of Family & Preventive Medicine, University of California San Diego, United States
| | - Chad Bousman
- Department of Medical Genetics, University of Calgary, Canada
| | - Ian Everall
- Institute of Psychiatry, Psychology & Neuroscience, King's College, United Kingdom
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8
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Thorson JA, Murray SS. Library Preparation Using FFPE-Derived Tumor DNA for High-Throughput Hybridization-Based Targeted or Exome Sequencing. Methods Mol Biol 2019; 1908:19-36. [PMID: 30649718 DOI: 10.1007/978-1-4939-9004-7_2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
The use of next generation sequencing (NGS) to profile tumor genomes for the presence of diagnostic, prognostic, or therapeutically targetable variants is revolutionizing the practice of oncology and is increasingly utilized in clinical laboratory settings. Beginning with the isolation of DNA of sufficient quality and quantity from a tumor specimen, the creation of a library of genomic fragments representing the portion of the genome of interest, ranging from a few genes to the entire exome, is the first step required in the sequencing process. Fixed tumor tissue in the form of a tissue block is the most commonly encountered specimen for analysis in a clinical setting. Special precautions must be employed to ensure that material isolated from these specimens is suitable for use. Once DNA is obtained, one of the most commonly used methods for library preparation involves fluid phase hybridization-based capture of the genomic regions to be interrogated. This multistep process involves fragmentation of the DNA to a uniform size distribution, ligating adapter molecules which are labeled with specific barcodes to enable downstream sequencing and sample identification, and the use of a multiplexed pool of biotinylated single stranded RNA or DNA hybridization probes to recognize and capture the targeted genomic regions. Fragments which are not specifically captured during the hybridization process are removed via a series of wash steps, and a final low cycle amplification is used to prepare the library of captured fragments for sequencing. In this chapter, we provide a step-by-step guide to the preparation of fixed tissue-derived DNA libraries for sequencing via the Illumina process and highlight some of the precautions necessary when working with these types of specimens.
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Affiliation(s)
- John A Thorson
- Department of Pathology, University of California San Diego, La Jolla, CA, USA.
- Center for Advanced Laboratory Medicine, University of California San Diego Health, La Jolla, CA, USA.
| | - Sarah S Murray
- Department of Pathology, University of California San Diego, La Jolla, CA, USA
- Center for Advanced Laboratory Medicine, University of California San Diego Health, La Jolla, CA, USA
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9
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Sun S, Murray SS. Bioinformatics Basics for High-Throughput Hybridization-Based Targeted DNA Sequencing from FFPE-Derived Tumor Specimens: From Reads to Variants. Methods Mol Biol 2019; 1908:37-48. [PMID: 30649719 DOI: 10.1007/978-1-4939-9004-7_3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
The use of next-generation sequencing and hybridization-based capture for target enrichment have enabled the interrogation of coding regions of several clinically significant cancer genes in tumor specimens using both targeted panels of a few to hundreds of genes, to whole-exome panels encompassing coding regions of all genes in the genome. Next-generation sequencing (NGS) technologies produce millions of relatively short segments of sequences or reads that require bioinformatics tools to map reads back to a reference genome using various read alignment tools, as well as to determine differences between single bases (single nucleotide variants or SNVs) or multiple bases (insertions and deletions or indels) between the aligned reads and the reference genome to call variants. In addition to single nucleotide changes or small insertions and deletions, high copy gains and losses can also be gleaned from NGS data to call gene amplifications and deletions. Throughout these processes, numerous quality control metrics can be assessed at each step to ensure that the resulting called variants are of high quality and are accurate. In this chapter we review common tools used to generate reads from Illumina-derived sequence data, align reads, and call variants from hybridization-based targeted NGS panel data generated from tumor FFPE-derived DNA specimens as well as basic quality metrics to assess for each assayed specimen.
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Affiliation(s)
- Shulei Sun
- Center for Advanced Laboratory Medicine, University of California San Diego Health, La Jolla, CA, USA
| | - Sarah S Murray
- Center for Advanced Laboratory Medicine, University of California San Diego Health, La Jolla, CA, USA.
- Department of Pathology, University of California San Diego, La Jolla, CA, USA.
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10
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Budde M, Friedrichs S, Alliey-Rodriguez N, Ament S, Badner JA, Berrettini WH, Bloss CS, Byerley W, Cichon S, Comes AL, Coryell W, Craig DW, Degenhardt F, Edenberg HJ, Foroud T, Forstner AJ, Frank J, Gershon ES, Goes FS, Greenwood TA, Guo Y, Hipolito M, Hood L, Keating BJ, Koller DL, Lawson WB, Liu C, Mahon PB, McInnis MG, McMahon FJ, Meier SM, Mühleisen TW, Murray SS, Nievergelt CM, Nurnberger JI, Nwulia EA, Potash JB, Quarless D, Rice J, Roach JC, Scheftner WA, Schork NJ, Shekhtman T, Shilling PD, Smith EN, Streit F, Strohmaier J, Szelinger S, Treutlein J, Witt SH, Zandi PP, Zhang P, Zöllner S, Bickeböller H, Falkai PG, Kelsoe JR, Nöthen MM, Rietschel M, Schulze TG, Malzahn D. Efficient region-based test strategy uncovers genetic risk factors for functional outcome in bipolar disorder. Eur Neuropsychopharmacol 2019; 29:156-170. [PMID: 30503783 DOI: 10.1016/j.euroneuro.2018.10.005] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/12/2018] [Revised: 10/16/2018] [Accepted: 10/23/2018] [Indexed: 11/21/2022]
Abstract
Genome-wide association studies of case-control status have advanced the understanding of the genetic basis of psychiatric disorders. Further progress may be gained by increasing sample size but also by new analysis strategies that advance the exploitation of existing data, especially for clinically important quantitative phenotypes. The functionally-informed efficient region-based test strategy (FIERS) introduced herein uses prior knowledge on biological function and dependence of genotypes within a powerful statistical framework with improved sensitivity and specificity for detecting consistent genetic effects across studies. As proof of concept, FIERS was used for the first genome-wide single nucleotide polymorphism (SNP)-based investigation on bipolar disorder (BD) that focuses on an important aspect of disease course, the functional outcome. FIERS identified a significantly associated locus on chromosome 15 (hg38: chr15:48965004 - 49464789 bp) with consistent effect strength between two independent studies (GAIN/TGen: European Americans, BOMA: Germans; n = 1592 BD patients in total). Protective and risk haplotypes were found on the most strongly associated SNPs. They contain a CTCF binding site (rs586758); CTCF sites are known to regulate sets of genes within a chromatin domain. The rs586758 - rs2086256 - rs1904317 haplotype is located in the promoter flanking region of the COPS2 gene, close to microRNA4716, and the EID1, SHC4, DTWD1 genes as plausible biological candidates. While implication with BD is novel, COPS2, EID1, and SHC4 are known to be relevant for neuronal differentiation and function and DTWD1 for psychopharmacological side effects. The test strategy FIERS that enabled this discovery is equally applicable for tag SNPs and sequence data.
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Affiliation(s)
- Monika Budde
- Institute of Psychiatric Phenomics and Genomics, University Hospital, LMU Munich, Nussbaumstr. 7, Munich 80336, Germany
| | - Stefanie Friedrichs
- Department of Genetic Epidemiology, University Medical Center Göttingen, Georg-August-University, Göttingen 37099, Germany
| | - Ney Alliey-Rodriguez
- Department of Psychiatry and Behavioral Neuroscience, University of Chicago, Chicago, IL 60637, United States
| | - Seth Ament
- Institute for Systems Biology, Seattle, WA 98109, United States
| | - Judith A Badner
- Department of Psychiatry, Rush University Medical Center, Chicago, IL 60612, United States
| | - Wade H Berrettini
- Department of Psychiatry, University of Pennsylvania, Philadelphia, PA 19104, United States
| | - Cinnamon S Bloss
- University of California San Diego, La Jolla, CA 92093, United States
| | - William Byerley
- Department of Psychiatry, University of California at San Francisco, San Francisco, CA 94103, United States
| | - Sven Cichon
- Human Genomics Research Group, Department of Biomedicine, University of Basel, Basel 4031, Switzerland; Institute of Medical Genetics and Pathology, University Hospital Basel, Basel 4031, Switzerland; Institute of Neuroscience and Medicine (INM-1), Research Centre Jülich, Jülich 52425, Germany
| | - Ashley L Comes
- Institute of Psychiatric Phenomics and Genomics, University Hospital, LMU Munich, Nussbaumstr. 7, Munich 80336, Germany; International Max Planck Research School for Translational Psychiatry, Max Planck Institute of Psychiatry, Munich 80804, Germany
| | - William Coryell
- University of Iowa Hospitals and Clinics, Iowa City, IA 52242, United States
| | - David W Craig
- The Translational Genomics Research Institute, Phoenix, AZ 85004, United States
| | - Franziska Degenhardt
- Institute of Human Genetics, School of Medicine & University Hospital Bonn, University of Bonn, Bonn 53127, Germany; Department of Genomics, Life & Brain Center, University of Bonn, Bonn 53127, Germany
| | - Howard J Edenberg
- Department of Biochemistry and Molecular Biology, Indiana University School of Medicine, Indianapolis, IN 46202, United States; Department of Medical and Molecular Genetics, Indiana University School of Medicine, Indianapolis, IN 46202, United States
| | - Tatiana Foroud
- Department of Medical and Molecular Genetics, Indiana University School of Medicine, Indianapolis, IN 46202, United States
| | - Andreas J Forstner
- Institute of Human Genetics, School of Medicine & University Hospital Bonn, University of Bonn, Bonn 53127, Germany; Department of Genomics, Life & Brain Center, University of Bonn, Bonn 53127, Germany; Human Genomics Research Group, Department of Biomedicine, University of Basel, Basel 4031, Switzerland; Department of Psychiatry (UPK), University of Basel, Basel 4012, Switzerland
| | - Josef Frank
- Department of Genetic Epidemiology in Psychiatry, Central Institute of Mental Health, Medical Faculty Mannheim, University of Heidelberg, Mannheim 68159, Germany
| | - Elliot S Gershon
- Department of Psychiatry and Behavioral Neuroscience, University of Chicago, Chicago, IL 60637, United States
| | - Fernando S Goes
- Department of Psychiatry and Behavioral Sciences, Johns Hopkins School of Medicine, Baltimore, MD 21287, United States
| | - Tiffany A Greenwood
- Department of Psychiatry, University of California San Diego, San Diego, CA 92093, United States
| | - Yiran Guo
- Center for Applied Genomics, Children's Hospital of Philadelphia, Abramson Research Center, Philadelphia, PA 19104, United States; Beijing Genomics Institute at Shenzhen, Shenzhen 518083, China
| | - Maria Hipolito
- Department of Psychiatry and Behavioral Sciences, Howard University Hospital, Washington, DC 20060, United States
| | - Leroy Hood
- Institute for Systems Biology, Seattle, WA 98109, United States
| | - Brendan J Keating
- Cardiovascular Institute, University of Pennsylvania School of Medicine, Philadelphia, PA 19104-5159, United States; Institute for Translational Medicine and Therapeutics, School of Medicine, University of Pennsylvania, Philadelphia, PA 19104-5158, United States
| | - Daniel L Koller
- Department of Medical and Molecular Genetics, Indiana University School of Medicine, Indianapolis, IN 46202, United States
| | - William B Lawson
- Dell Medical School, University of Texas at Austin, Austin, TX 78723, United States
| | - Chunyu Liu
- SUNY Upstate Medical University, Syracuse, NY 13210, United States
| | - Pamela B Mahon
- Department of Psychiatry and Behavioral Sciences, Johns Hopkins School of Medicine, Baltimore, MD 21287, United States
| | - Melvin G McInnis
- Department of Psychiatry, University of Michigan, Ann Arbor, MI 48105, United States
| | - Francis J McMahon
- U.S. Department of Health & Human Services, Intramural Research Program, National Institute of Mental Health, National Institutes of Health, Bethesda, MD 20894, United States
| | - Sandra M Meier
- Department of Genetic Epidemiology in Psychiatry, Central Institute of Mental Health, Medical Faculty Mannheim, University of Heidelberg, Mannheim 68159, Germany; National Centre for Register-Based Research, Aarhus University, Aarhus V 8210, Denmark
| | - Thomas W Mühleisen
- Institute of Neuroscience and Medicine (INM-1), Research Centre Jülich, Jülich 52425, Germany; Human Genomics Research Group, Department of Biomedicine, University of Basel, Basel 4031, Switzerland
| | - Sarah S Murray
- Scripps Genomic Medicine & The Scripps Translational Sciences Institute (STSI), La Jolla, CA 92037, United States; Department of Pathology, University of California San Diego, La Jolla, CA 92093, United States
| | - Caroline M Nievergelt
- Department of Psychiatry, University of California San Diego, San Diego, CA 92093, United States
| | - John I Nurnberger
- Department of Psychiatry, Indiana University School of Medicine, Indianapolis, IN 46202, United States
| | - Evaristus A Nwulia
- Department of Psychiatry and Behavioral Sciences, Howard University Hospital, Washington, DC 20060, United States
| | - James B Potash
- Department of Psychiatry, Carver College of Medicine, University of Iowa School of Medicine, Iowa City, IA 52242, United States
| | - Danjuma Quarless
- J. Craig Venter Institute, La Jolla, CA 92037, United States; University of California San Diego, La Jolla, CA 92093, United States
| | - John Rice
- Department of Psychiatry, Washington University School of Medicine in St. Louis, St. Louis, MO 63110, United States
| | - Jared C Roach
- Institute for Systems Biology, Seattle, WA 98109, United States
| | | | - Nicholas J Schork
- J. Craig Venter Institute, La Jolla, CA 92037, United States; The Translational Genomics Research Institute, Phoenix, AZ 85004, United States; University of California San Diego, La Jolla, CA 92093, United States
| | - Tatyana Shekhtman
- Department of Psychiatry, University of California San Diego, San Diego, CA 92093, United States
| | - Paul D Shilling
- Department of Psychiatry, University of California San Diego, San Diego, CA 92093, United States
| | - Erin N Smith
- Scripps Genomic Medicine & The Scripps Translational Sciences Institute (STSI), La Jolla, CA 92037, United States; Department of Pediatrics and Rady's Children's Hospital, School of Medicine, University of California San Diego, La Jolla, CA 92037, United States
| | - Fabian Streit
- Department of Genetic Epidemiology in Psychiatry, Central Institute of Mental Health, Medical Faculty Mannheim, University of Heidelberg, Mannheim 68159, Germany
| | - Jana Strohmaier
- Department of Genetic Epidemiology in Psychiatry, Central Institute of Mental Health, Medical Faculty Mannheim, University of Heidelberg, Mannheim 68159, Germany
| | - Szabolcs Szelinger
- The Translational Genomics Research Institute, Phoenix, AZ 85004, United States
| | - Jens Treutlein
- Department of Genetic Epidemiology in Psychiatry, Central Institute of Mental Health, Medical Faculty Mannheim, University of Heidelberg, Mannheim 68159, Germany
| | - Stephanie H Witt
- Department of Genetic Epidemiology in Psychiatry, Central Institute of Mental Health, Medical Faculty Mannheim, University of Heidelberg, Mannheim 68159, Germany
| | - Peter P Zandi
- Department of Mental Health, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD 21205, United States
| | - Peng Zhang
- Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI 48109, United States
| | - Sebastian Zöllner
- Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI 48109, United States; Department of Psychiatry, University of Michigan, Ann Arbor, MI 48105, United States
| | - Heike Bickeböller
- Department of Genetic Epidemiology, University Medical Center Göttingen, Georg-August-University, Göttingen 37099, Germany
| | - Peter G Falkai
- Department of Psychiatry and Psychotherapy, University Hospital, LMU Munich, Munich 80336, Germany
| | - John R Kelsoe
- Department of Psychiatry, University of California San Diego, San Diego, CA 92093, United States
| | - Markus M Nöthen
- Institute of Human Genetics, School of Medicine & University Hospital Bonn, University of Bonn, Bonn 53127, Germany; Department of Genomics, Life & Brain Center, University of Bonn, Bonn 53127, Germany
| | - Marcella Rietschel
- Department of Genetic Epidemiology in Psychiatry, Central Institute of Mental Health, Medical Faculty Mannheim, University of Heidelberg, Mannheim 68159, Germany
| | - Thomas G Schulze
- Institute of Psychiatric Phenomics and Genomics, University Hospital, LMU Munich, Nussbaumstr. 7, Munich 80336, Germany; Department of Genetic Epidemiology in Psychiatry, Central Institute of Mental Health, Medical Faculty Mannheim, University of Heidelberg, Mannheim 68159, Germany; Department of Psychiatry and Behavioral Sciences, Johns Hopkins School of Medicine, Baltimore, MD 21287, United States; U.S. Department of Health & Human Services, Intramural Research Program, National Institute of Mental Health, National Institutes of Health, Bethesda, MD 20894, United States.
| | - Dörthe Malzahn
- Department of Genetic Epidemiology, University Medical Center Göttingen, Georg-August-University, Göttingen 37099, Germany.
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11
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Sun S, Thorson JA, Murray SS. Annotation of Variant Data from High-Throughput DNA Sequencing from Tumor Specimens: Filtering Strategies to Identify Driver Mutations. Methods Mol Biol 2019; 1908:49-60. [PMID: 30649720 DOI: 10.1007/978-1-4939-9004-7_4] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
The use of next-generation sequencing technologies has enabled the analysis of a wide spectrum of somatic mutations in tumors. This analysis can be carried out using various strategies including the use of small panels of focused, clinically actionable genes, large panels of cancer-related genes, whole exomes, and the entire genome. One of the main goals in these analyses is to identify key mutations in these tumors that drive the oncogenic process. Depending on the gene, mutations can have altering effects, such as loss of function mutations in tumor suppressor genes, to mutations that activate genes such as kinases involved with cell cycle progression or proliferation. Once the sequencing process is complete, and the alignment of the large collection of reads to the reference genome and variant calling has been carried out, one is left with a large collection of variants. The challenge then becomes assigning where the variant resides in the genome with respect to coding regions, splice site regions, regulatory regions, and what potential functional effect these variants may have on the resulting protein. Other helpful information includes determining if the variant has been identified before, and if so, the tumor type associated with the variant. In addition, if the tumor profiling experiment is not conducted with a matched specimen representing the inherited genome, various tools are helpful to determine if the variant is likely to be an inherited polymorphism or a somatic event. In this chapter, we review the various tools available for annotating variants to assist in filtering down and prioritizing the hundreds to thousands of variants down to the key variants likely to be driver mutations and relevant to the tumor being profiled.
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Affiliation(s)
- Shulei Sun
- Center for Advanced Laboratory Medicine, University of California San Diego Health, La Jolla, CA, USA
| | - John A Thorson
- Center for Advanced Laboratory Medicine, University of California San Diego Health, La Jolla, CA, USA
- Department of Pathology, University of California San Diego, La Jolla, CA, USA
| | - Sarah S Murray
- Center for Advanced Laboratory Medicine, University of California San Diego Health, La Jolla, CA, USA.
- Department of Pathology, University of California San Diego, La Jolla, CA, USA.
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12
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Ligthart S, Vaez A, Võsa U, Stathopoulou MG, de Vries PS, Prins BP, Van der Most PJ, Tanaka T, Naderi E, Rose LM, Wu Y, Karlsson R, Barbalic M, Lin H, Pool R, Zhu G, Macé A, Sidore C, Trompet S, Mangino M, Sabater-Lleal M, Kemp JP, Abbasi A, Kacprowski T, Verweij N, Smith AV, Huang T, Marzi C, Feitosa MF, Lohman KK, Kleber ME, Milaneschi Y, Mueller C, Huq M, Vlachopoulou E, Lyytikäinen LP, Oldmeadow C, Deelen J, Perola M, Zhao JH, Feenstra B, Amini M, Lahti J, Schraut KE, Fornage M, Suktitipat B, Chen WM, Li X, Nutile T, Malerba G, Luan J, Bak T, Schork N, Del Greco M F, Thiering E, Mahajan A, Marioni RE, Mihailov E, Eriksson J, Ozel AB, Zhang W, Nethander M, Cheng YC, Aslibekyan S, Ang W, Gandin I, Yengo L, Portas L, Kooperberg C, Hofer E, Rajan KB, Schurmann C, den Hollander W, Ahluwalia TS, Zhao J, Draisma HHM, Ford I, Timpson N, Teumer A, Huang H, Wahl S, Liu Y, Huang J, Uh HW, Geller F, Joshi PK, Yanek LR, Trabetti E, Lehne B, Vozzi D, Verbanck M, Biino G, Saba Y, Meulenbelt I, O'Connell JR, Laakso M, Giulianini F, Magnusson PKE, Ballantyne CM, Hottenga JJ, Montgomery GW, Rivadineira F, Rueedi R, Steri M, Herzig KH, Stott DJ, Menni C, Frånberg M, St Pourcain B, Felix SB, Pers TH, Bakker SJL, Kraft P, Peters A, Vaidya D, Delgado G, Smit JH, Großmann V, Sinisalo J, Seppälä I, Williams SR, Holliday EG, Moed M, Langenberg C, Räikkönen K, Ding J, Campbell H, Sale MM, Chen YDI, James AL, Ruggiero D, Soranzo N, Hartman CA, Smith EN, Berenson GS, Fuchsberger C, Hernandez D, Tiesler CMT, Giedraitis V, Liewald D, Fischer K, Mellström D, Larsson A, Wang Y, Scott WR, Lorentzon M, Beilby J, Ryan KA, Pennell CE, Vuckovic D, Balkau B, Concas MP, Schmidt R, Mendes de Leon CF, Bottinger EP, Kloppenburg M, Paternoster L, Boehnke M, Musk AW, Willemsen G, Evans DM, Madden PAF, Kähönen M, Kutalik Z, Zoledziewska M, Karhunen V, Kritchevsky SB, Sattar N, Lachance G, Clarke R, Harris TB, Raitakari OT, Attia JR, van Heemst D, Kajantie E, Sorice R, Gambaro G, Scott RA, Hicks AA, Ferrucci L, Standl M, Lindgren CM, Starr JM, Karlsson M, Lind L, Li JZ, Chambers JC, Mori TA, de Geus EJCN, Heath AC, Martin NG, Auvinen J, Buckley BM, de Craen AJM, Waldenberger M, Strauch K, Meitinger T, Scott RJ, McEvoy M, Beekman M, Bombieri C, Ridker PM, Mohlke KL, Pedersen NL, Morrison AC, Boomsma DI, Whitfield JB, Strachan DP, Hofman A, Vollenweider P, Cucca F, Jarvelin MR, Jukema JW, Spector TD, Hamsten A, Zeller T, Uitterlinden AG, Nauck M, Gudnason V, Qi L, Grallert H, Borecki IB, Rotter JI, März W, Wild PS, Lokki ML, Boyle M, Salomaa V, Melbye M, Eriksson JG, Wilson JF, Penninx BWJH, Becker DM, Worrall BB, Gibson G, Krauss RM, Ciullo M, Zaza G, Wareham NJ, Oldehinkel AJ, Palmer LJ, Murray SS, Pramstaller PP, Bandinelli S, Heinrich J, Ingelsson E, Deary IJ, Mägi R, Vandenput L, van der Harst P, Desch KC, Kooner JS, Ohlsson C, Hayward C, Lehtimäki T, Shuldiner AR, Arnett DK, Beilin LJ, Robino A, Froguel P, Pirastu M, Jess T, Koenig W, Loos RJF, Evans DA, Schmidt H, Smith GD, Slagboom PE, Eiriksdottir G, Morris AP, Psaty BM, Tracy RP, Nolte IM, Boerwinkle E, Visvikis-Siest S, Reiner AP, Gross M, Bis JC, Franke L, Franco OH, Benjamin EJ, Chasman DI, Dupuis J, Snieder H, Dehghan A, Alizadeh BZ. Genome Analyses of >200,000 Individuals Identify 58 Loci for Chronic Inflammation and Highlight Pathways that Link Inflammation and Complex Disorders. Am J Hum Genet 2018; 103:691-706. [PMID: 30388399 PMCID: PMC6218410 DOI: 10.1016/j.ajhg.2018.09.009] [Citation(s) in RCA: 250] [Impact Index Per Article: 41.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2018] [Accepted: 09/20/2018] [Indexed: 02/07/2023] Open
Abstract
C-reactive protein (CRP) is a sensitive biomarker of chronic low-grade inflammation and is associated with multiple complex diseases. The genetic determinants of chronic inflammation remain largely unknown, and the causal role of CRP in several clinical outcomes is debated. We performed two genome-wide association studies (GWASs), on HapMap and 1000 Genomes imputed data, of circulating amounts of CRP by using data from 88 studies comprising 204,402 European individuals. Additionally, we performed in silico functional analyses and Mendelian randomization analyses with several clinical outcomes. The GWAS meta-analyses of CRP revealed 58 distinct genetic loci (p < 5 × 10-8). After adjustment for body mass index in the regression analysis, the associations at all except three loci remained. The lead variants at the distinct loci explained up to 7.0% of the variance in circulating amounts of CRP. We identified 66 gene sets that were organized in two substantially correlated clusters, one mainly composed of immune pathways and the other characterized by metabolic pathways in the liver. Mendelian randomization analyses revealed a causal protective effect of CRP on schizophrenia and a risk-increasing effect on bipolar disorder. Our findings provide further insights into the biology of inflammation and could lead to interventions for treating inflammation and its clinical consequences.
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Affiliation(s)
- Symen Ligthart
- Department of Epidemiology, Erasmus University Medical Center, Rotterdam 3000 CA, the Netherlands
| | - Ahmad Vaez
- Department of Epidemiology, University of Groningen, University Medical Center Groningen, Groningen 9700 RB, the Netherlands; Department of Bioinformatics, Isfahan University of Medical Sciences, Isfahan 81746-73461, Iran
| | - Urmo Võsa
- Department of Genetics, University of Groningen, University Medical Center Groningen, Groningen 9700 RB, the Netherlands; Estonian Genome Center, Institute of Genomics, University of Tartu, Tartu 51010, Estonia
| | | | - Paul S de Vries
- Department of Epidemiology, Erasmus University Medical Center, Rotterdam 3000 CA, the Netherlands; Human Genetics Center, Department of Epidemiology, Human Genetics, and Environmental Sciences, School of Public Health, University of Texas Health Science Center at Houston, Houston, TX 77030, USA
| | - Bram P Prins
- Department of Human Genetics, Wellcome Trust Sanger Institute, Hinxton CB10 1SA, UK
| | - Peter J Van der Most
- Department of Epidemiology, University of Groningen, University Medical Center Groningen, Groningen 9700 RB, the Netherlands
| | - Toshiko Tanaka
- Translational Gerontology Branch, National Institute on Aging, Baltimore, MD 21224, USA
| | - Elnaz Naderi
- Department of Epidemiology, University of Groningen, University Medical Center Groningen, Groningen 9700 RB, the Netherlands; Department of Radiation Oncology, University of Groningen, University Medical Center Groningen, Groningen 9713 GZ, the Netherlands
| | - Lynda M Rose
- Division of Preventive Medicine, Brigham and Women's Hospital, Boston, MA 02215, USA
| | - Ying Wu
- Department of Genetics, University of North Carolina, Chapel Hill, NC 27599, USA
| | - Robert Karlsson
- Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, Stockholm 17177, Sweden
| | - Maja Barbalic
- University of Split School of Medicine, Split 21000, Croatia
| | - Honghuang Lin
- Department of Medicine, Boston University School of Medicine, Boston, MA 02118, USA
| | - René Pool
- Department of Biological Psychology, Netherlands Twin Register, Vrije Universiteit, Amsterdam 1081 BT, the Netherlands; Amsterdam Public Health research institute, VU University Medical Center, Amsterdam 1081 BT, the Netherlands
| | - Gu Zhu
- QIMR Berghofer Medical Research Institute, Brisbane, QLD 4006, Australia
| | - Aurélien Macé
- Department of Computational Biology, University of Lausanne, Lausanne 1010, Switzerland; Swiss Institute of Bioinformatics, Lausanne 1015, Switzerland; Institute of Social and Preventive Medicine, University Hospital of Lausanne, Lausanne 1010, Switzerland
| | - Carlo Sidore
- Istituto di Ricerca Genetica e Biomedica, Consiglio Nazionale delle Ricerche, Sardinia 08045, Italy
| | - Stella Trompet
- Department of Cardiology, Leiden University Medical Center, Leiden 2300 RC, the Netherlands; Department of Gerontology and Geriatrics, Leiden University Medical Center, Leiden 2333 ZA, the Netherlands
| | - Massimo Mangino
- Department of Twin Research & Genetic Epidemiology, King's College London, London SE1 7EH, UK; NIHR Biomedical Research Centre at Guy's and St. Thomas' Foundation Trust, London SE1 9RT, UK
| | - Maria Sabater-Lleal
- Unit of Genomics of Complex Diseases, Institut d'Investigació Biomèdica Sant Pau, Barcelona 08025, Spain; Cardiovascular Medicine Unit, Department of Medicine, Center for Molecular Medicine, Karolinska Institutet, Stockholm 17176, Sweden
| | - John P Kemp
- University of Queensland Diamantina Institute, Translational Research Institute, Brisbane, QLD 4102, Australia; MRC Integrative Epidemiology Unit, Bristol Medical School, University of Bristol, Bristol BS8 2BN, UK
| | - Ali Abbasi
- Department of Epidemiology, University of Groningen, University Medical Center Groningen, Groningen 9700 RB, the Netherlands; Department of Internal Medicine, University of Groningen, University Medical Center Groningen, Groningen 9713 GZ, the Netherlands; MRC Epidemiology Unit, University of Cambridge School of Medicine, Institute of Metabolic Science, Cambridge Biomedical Campus, Addenbrooke's Hospital, Cambridge CB2 0QQ, UK
| | - Tim Kacprowski
- Department of Functional Genomics, Interfaculty Institute for Genetics and Functional Genomics, University Medicine and Ernst-Moritz-Arndt University Greifswald, Greifswald 17475, Germany; German Centre for Cardiovascular Research, Partner Site Greifswald, Greifswald 17475, Germany
| | - Niek Verweij
- University of Groningen, University Medical Center Groningen, Department of Cardiology, Groningen 9713 AV, the Netherlands
| | - Albert V Smith
- Icelandic Heart Association, Kopavogur 201, Iceland; Faculty of Medicine, University of Iceland, Reykjavik 101, Iceland
| | - Tao Huang
- Department of Epidemiology and Biostatistics, School of Public Health, Peking University, Beijing 100191, China; Department of Nutrition, Harvard T.H. Chan School of Public Health, Boston, MA 02115, USA
| | - Carola Marzi
- Institute of Epidemiology II, Research Unit of Molecular Epidemiology, Helmholtz Zentrum München, German Research Center for Environmental Health, Neuherberg 85764, Germany; German Center for Diabetes Research, Partner Site Munich, Munich 85764, Germany
| | - Mary F Feitosa
- Division of Statistical Genomics, Department of Genetics, Washington University School of Medicine, St. Louis, MO 63108-2212, USA
| | - Kurt K Lohman
- Department of Epidemiology and Prevention, Public Health Sciences, Wake Forest University Health Sciences, Winston-Salem, NC 27157, USA
| | - Marcus E Kleber
- Vth Department of Medicine, Medical Faculty Mannheim, Heidelberg University, Mannheim 68167, Germany
| | - Yuri Milaneschi
- Department of Psychiatry, Amsterdam Neuroscience and Amsterdam Public Health Research Institute, Amsterdam University Medical Center/GGZ inGeest Research & Innovation, Amsterdam 1081 HJ, the Netherlands
| | - Christian Mueller
- Department of General and Interventional Cardiology, University Heart Center Hamburg, Hamburg 20246, Germany; Institute of Medical Biometry and Statistics, University Medical Center Schleswig-Holstein, Campus Luebeck, Lübeck 23562, Germany; German Center for Cardiovascular Research, Partner Site RhineMain, 55131 Mainz, Germany
| | - Mahmudul Huq
- Department of Epidemiology, University of Groningen, University Medical Center Groningen, Groningen 9700 RB, the Netherlands
| | - Efthymia Vlachopoulou
- Transplantation Laboratory, Medicum, University of Helsinki, Helsinki 00014, Finland
| | - Leo-Pekka Lyytikäinen
- Department of Clinical Chemistry, Fimlab Laboratories, Tampere 33014, Finland; Department of Clinical Chemistry, Finnish Cardiovascular Research Center - Tampere, Faculty of Medicine and Life Sciences, University of Tampere, Tampere 33520, Finland
| | - Christopher Oldmeadow
- Hunter Medical Research Institute, New Lambon Heights, NSW 2305, Australia; Centre for Clinical Epidemiology & Biostatistics, Faculty of Health and Medicine, University of Newcastle, Callaghan, NSW 2308, Australia
| | - Joris Deelen
- Molecular Epidemiology, Leiden University Medical Center, Leiden 2333 ZC, the Netherlands; Max Planck Institute for Biology of Ageing, Cologne 50931, Germany
| | - Markus Perola
- National Institute for Health and Welfare, Helsinki 00271, Finland
| | - Jing Hua Zhao
- MRC Epidemiology Unit, University of Cambridge School of Clinical Medicine, Institute of Metabolic Science, Cambridge CB2 0QQ, UK
| | - Bjarke Feenstra
- Department of Epidemiology Research, Statens Serum Institut, Copenhagen 2300, Denmark
| | - Marzyeh Amini
- Department of Epidemiology, University of Groningen, University Medical Center Groningen, Groningen 9700 RB, the Netherlands
| | - Jari Lahti
- Helsinki Collegium for Advanced Studies, University of Helsinki, Helsinki 00014, Finland; Department of Psychology and Logopedics, Faculty of Medicine, University of Helsinki, Helsinki 00014, Finland; Folkhälsan Research Centre, Helsinki 00250, Finland
| | - Katharina E Schraut
- Centre for Global Health Research, Usher Institute of Population Health Sciences and Informatics, University of Edinburgh, Teviot Place, Edinburgh EH16 4UX, UK
| | - Myriam Fornage
- Human Genetics Center, School of Public Health and Brown Foundation Institute of Molecular Medicine, University of Texas Health Science Center at Houston, Houston, TX 77030, USA
| | - Bhoom Suktitipat
- Department of Biochemistry, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok 10700, Thailand
| | - Wei-Min Chen
- Center for Public Health Genomics, University of Virginia, Charlottesville, VA 22908, USA
| | - Xiaohui Li
- Institute for Translational Genomics and Population Sciences, Department of Pediatrics, Los Angeles Biomedical Research Institute at Harbor-UCLA Medical Center, Torrance, CA 90502, USA
| | - Teresa Nutile
- Institute of Genetics and Biophysics "A. Buzzati-Traverso," Consiglio Nazionale delle Ricerche, Napoli 80131, Italy
| | - Giovanni Malerba
- Department of Neurosciences, Biomedicine and Movement Sciences, University of Verona, Verona 37134, Italy
| | - Jian'an Luan
- MRC Epidemiology Unit, University of Cambridge School of Clinical Medicine, Institute of Metabolic Science, Cambridge CB2 0QQ, UK
| | - Tom Bak
- Interdisciplinary Center Psychopathology and Emotion regulation, University Medical Center Groningen, University of Groningen, Groningen 9700 RB, the Netherlands
| | - Nicholas Schork
- Human Biology, J. Craig Venter Institute, La Jolla, CA 92037, USA; Quantitative Medicine, Translational Genomics Research Institute, Phoenix, AZ 85004, USA
| | - Fabiola Del Greco M
- Institute for Biomedicine, Eurac Research, Affiliated Institute of the University of Lübeck, Bolzano 39100, Italy
| | - Elisabeth Thiering
- Institute of Epidemiology, Helmholtz Zentrum München - German Research Centre for Environmental Health, Neuherberg 85764, Germany; Ludwig Maximilian University of Munich, Dr. von Hauner Children's Hospital, Munich 80337, Germany
| | - Anubha Mahajan
- Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford OX3 7BN, UK
| | - Riccardo E Marioni
- Centre for Cognitive Ageing and Cognitive Epidemiology, University of Edinburgh, Edinburgh EH8 9JZ, UK; Centre for Genomic and Experimental Medicine, Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh EH4 2XU, UK
| | - Evelin Mihailov
- Estonian Genome Center, Institute of Genomics, University of Tartu, Tartu 51010, Estonia
| | - Joel Eriksson
- Department of Internal Medicine and Clinical Nutrition, University of Gothenburg, Gothenburg 41345, Sweden
| | - Ayse Bilge Ozel
- Department of Human Genetics, University of Michigan, Ann Arbor, MI 48109-5618, USA
| | - Weihua Zhang
- Department of Epidemiology and Biostatistics, Imperial College London, London W2 1PG, UK; Department of Cardiology, Ealing Hospital, Middlesex UB1 3HW, UK
| | - Maria Nethander
- Bioinformatics Core Facility, Sahlgrenska Academy, University of Gothenburg, Gothenburg 413 90, Sweden
| | - Yu-Ching Cheng
- Division of Endocrinology, Diabetes and Nutrition, Department of Medicine, University of Maryland School of Medicine, Baltimore, MD 21201, USA
| | - Stella Aslibekyan
- Department of Epidemiology, University of Alabama at Birmingham, Birmingham, AL 35294-0022, USA
| | - Wei Ang
- Medical School, University of Western Australia, Perth, WA 6009, Australia
| | | | - Loïc Yengo
- Centre National de la Recherche Scientifique UMR 8199, University of Lille, Institut Pasteur de Lille, European Genomic Institute for Diabetes, FR 3508, 59000 Lille, France; Program in Complex Trait Genomics, Institute for Molecular Bioscience, University of Queensland, St. Lucia, Brisbane, QLD 4072, Australia
| | - Laura Portas
- Support OU, Institute of Genetic and Biomedic Research, Consiglio Nazionale delle Ricerche, Sassari 7100, Italy
| | - Charles Kooperberg
- Fred Hutchinson Cancer Research Center, Public Health Sciences Division, Mail Stop M3-A410, 1100 Fairview Ave. N., Seattle, WA, USA
| | - Edith Hofer
- Clinical Division of Neurogeriatrics, Department of Neurology, Medical University Graz, Graz 8036, Austria; Institute of Medical Informatics, Statistics and Documentation, Medical University Graz, Graz 8036, Austria
| | - Kumar B Rajan
- Department of Internal Medicine, Rush University Medical Center, Chicago, IL 60612, USA
| | - Claudia Schurmann
- Charles Bronfman Institute for Personalized Medicine, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; Genetics of Obesity and Related Metabolic Traits Program, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Wouter den Hollander
- Department of Medical Statistics and Bio-informatics, Section Molecular Epidemiology, Leiden University Medical Center, Leiden 2333 ZC, the Netherlands
| | - Tarunveer S Ahluwalia
- Steno Diabetes Center Copenhagen, Gentofte 2820, Denmark; Novo Nordisk Foundation Centre for Basic Metabolic Research, Section of Metabolic Genetics, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen 2100, Denmark
| | - Jing Zhao
- Center for Integrative Genomics, School of Biology, Georgia Institute of Technology, Atlanta, GA 30332, USA
| | - Harmen H M Draisma
- Department of Biological Psychology, Netherlands Twin Register, Vrije Universiteit, Amsterdam 1081 BT, the Netherlands; Amsterdam Public Health research institute, VU University Medical Center, Amsterdam 1081 BT, the Netherlands; Neuroscience Campus Amsterdam, Amsterdam 1081 HV, the Netherlands
| | - Ian Ford
- Robertson Centre for Biostatistics, University of Glasgow, Glasgow G12 8QQ, UK
| | - Nicholas Timpson
- MRC Integrative Epidemiology Unit, Bristol Medical School, University of Bristol, Bristol BS8 2BN, UK
| | - Alexander Teumer
- Department SHIP-KEF, Institute for Community Medicine, University Medicine Greifswald, Greifswald 17475, Germany
| | - Hongyan Huang
- Program in Genetic Epidemiology and Statistical Genetics, Harvard T.H. Chan School of Public Health, Boston, MA 02115, USA
| | - Simone Wahl
- Institute of Epidemiology II, Research Unit of Molecular Epidemiology, Helmholtz Zentrum München, German Research Center for Environmental Health, Neuherberg 85764, Germany; German Center for Diabetes Research, Partner Site Munich, Munich 85764, Germany
| | - YongMei Liu
- Department of Epidemiology and Prevention, Public Health Sciences, Wake Forest University Health Sciences, Winston-Salem, NC 27157, USA
| | - Jie Huang
- Boston VA Research Institute, Inc., Boston, MA 02130, USA
| | - Hae-Won Uh
- Medical Statistics and Bioinformatics, Leiden University Medical Center, Leiden 2333 ZC, the Netherlands
| | - Frank Geller
- Department of Epidemiology Research, Statens Serum Institut, Copenhagen 2300, Denmark
| | - Peter K Joshi
- Centre for Global Health Research, Usher Institute of Population Health Sciences and Informatics, University of Edinburgh, Teviot Place, Edinburgh EH16 4UX, UK
| | - Lisa R Yanek
- GeneSTAR Research Center, Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA
| | - Elisabetta Trabetti
- Department of Neurosciences, Biomedicine and Movement Sciences, University of Verona, Verona 37134, Italy
| | - Benjamin Lehne
- Department of Epidemiology and Biostatistics, Imperial College London, London W2 1PG, UK
| | - Diego Vozzi
- Institute for Maternal and Child Health, IRCCS "Burlo Garofolo," Trieste 34140, Italy
| | - Marie Verbanck
- Centre National de la Recherche Scientifique UMR 8199, University of Lille, Institut Pasteur de Lille, European Genomic Institute for Diabetes, FR 3508, 59000 Lille, France
| | - Ginevra Biino
- Institute of Molecular Genetics, Consiglio Nazionale delle Ricerche, Pavia 27100, Italy
| | - Yasaman Saba
- Gottfried Schatz Research Center, Institute for Molecular Biology and Biochemistry, 8010 Graz, Austria
| | - Ingrid Meulenbelt
- Department of Medical Statistics and Bio-informatics, Section Molecular Epidemiology, Leiden University Medical Center, Leiden 2333 ZC, the Netherlands
| | - Jeff R O'Connell
- Division of Endocrinology, Diabetes and Nutrition, Department of Medicine, University of Maryland School of Medicine, Baltimore, MD 21201, USA
| | - Markku Laakso
- Institute of Clinical Medicine, Internal Medicine, University of Eastern Finland and Kuopio University Hospital, Kuopio 70210, Finland
| | - Franco Giulianini
- Division of Preventive Medicine, Brigham and Women's Hospital, Boston, MA 02215, USA
| | - Patrik K E Magnusson
- Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, Stockholm 17177, Sweden
| | - Christie M Ballantyne
- Department of Medicine, Baylor College of Medicine, Houston, TX 77030, USA; Methodist DeBakey Heart and Vascular Center, Houston, TX 77030, USA
| | - Jouke Jan Hottenga
- Department of Biological Psychology, Netherlands Twin Register, Vrije Universiteit, Amsterdam 1081 BT, the Netherlands
| | - Grant W Montgomery
- QIMR Berghofer Medical Research Institute, Brisbane, QLD 4006, Australia
| | - Fernando Rivadineira
- Department of Internal Medicine, Erasmus University Medical Center, Rotterdam 3015 CN, the Netherlands
| | - Rico Rueedi
- Department of Computational Biology, University of Lausanne, Lausanne 1010, Switzerland; Swiss Institute of Bioinformatics, Lausanne 1015, Switzerland
| | - Maristella Steri
- Istituto di Ricerca Genetica e Biomedica, Consiglio Nazionale delle Ricerche, Sardinia 08045, Italy
| | - Karl-Heinz Herzig
- Department of Physiology, Institute of Biomedicine, University of Oulu, Medical Research Center Oulu and Oulu University Hospital, Oulu 90014, Finland; Biocenter Oulu, University of Oulu, Oulu 90220, Finland; Department of Gastroenterology and Metabolism, Poznan University of Medical Sciences, Poznan 60-512, Poland
| | - David J Stott
- Institute of Cardiovascular and Medical Sciences, Faculty of Medicine, University of Glasgow, Glasgow G12 8QQ, UK
| | - Cristina Menni
- Department of Twin Research & Genetic Epidemiology, King's College London, London SE1 7EH, UK
| | - Mattias Frånberg
- Cardiovascular Medicine Unit, Department of Medicine, Center for Molecular Medicine, Karolinska Institutet, Stockholm 17176, Sweden; Department of Numerical Analysis and Computer Science, Stockholm University, Stockholm 100 44, Sweden
| | - Beate St Pourcain
- MRC Integrative Epidemiology Unit, Bristol Medical School, University of Bristol, Bristol BS8 2BN, UK; Donders Institute, Radboud University, Nijmegen 6525 XD, the Netherlands
| | - Stephan B Felix
- German Centre for Cardiovascular Research, Partner Site Greifswald, Greifswald 17475, Germany; Department for Internal Medicine B, University Medicine Greifswald, Greifswald 17475, Germany
| | - Tune H Pers
- Department of Epidemiology Research, Statens Serum Institut, Copenhagen 2300, Denmark; Novo Nordisk Foundation Centre for Basic Metabolic Research, Section of Metabolic Genetics, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen 2100, Denmark
| | - Stephan J L Bakker
- Department of Internal Medicine, University of Groningen, University Medical Center Groningen, Groningen 9713 GZ, the Netherlands
| | - Peter Kraft
- Program in Genetic Epidemiology and Statistical Genetics, Harvard T.H. Chan School of Public Health, Boston, MA 02115, USA
| | - Annette Peters
- Institute of Epidemiology II, Helmholtz Zentrum München, German Research Center for Environmental Health, Neuherber 85764, Germany
| | - Dhananjay Vaidya
- GeneSTAR Research Center, Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA
| | - Graciela Delgado
- Vth Department of Medicine, Medical Faculty Mannheim, Heidelberg University, Mannheim 68167, Germany
| | - Johannes H Smit
- Department of Psychiatry, Amsterdam Neuroscience and Amsterdam Public Health Research Institute, Amsterdam University Medical Center/GGZ inGeest Research & Innovation, Amsterdam 1081 HJ, the Netherlands
| | - Vera Großmann
- Center for Thrombosis and Hemostasis, University Medical Center of the Johannes Gutenberg University Mainz, Mainz 55131, Germany
| | - Juha Sinisalo
- Heart and Lung Center, Helsinki University Hospital and Helsinki University, Helsinki 00029, Finland
| | - Ilkka Seppälä
- Department of Clinical Chemistry, Fimlab Laboratories, Tampere 33014, Finland; Department of Clinical Chemistry, Finnish Cardiovascular Research Center - Tampere, Faculty of Medicine and Life Sciences, University of Tampere, Tampere 33520, Finland
| | - Stephen R Williams
- Department of Neurology, University of Virginia, Charlottesville, VA 22908, USA
| | - Elizabeth G Holliday
- Hunter Medical Research Institute, New Lambon Heights, NSW 2305, Australia; Centre for Clinical Epidemiology & Biostatistics, Faculty of Health and Medicine, University of Newcastle, Callaghan, NSW 2308, Australia
| | - Matthijs Moed
- Molecular Epidemiology, Leiden University Medical Center, Leiden 2333 ZC, the Netherlands
| | - Claudia Langenberg
- MRC Epidemiology Unit, University of Cambridge School of Clinical Medicine, Institute of Metabolic Science, Cambridge CB2 0QQ, UK
| | - Katri Räikkönen
- Department of Psychology and Logopedics, Faculty of Medicine, University of Helsinki, Helsinki 00014, Finland
| | - Jingzhong Ding
- Department of Internal Medicine/Geriatrics, Wake Forest University Health Sciences, Winston-Salem, NC 27157, USA
| | - Harry Campbell
- Centre for Global Health Research, Usher Institute of Population Health Sciences and Informatics, University of Edinburgh, Teviot Place, Edinburgh EH16 4UX, UK
| | - Michele M Sale
- Center for Public Health Genomics, University of Virginia, Charlottesville, VA 22908, USA
| | - Yii-Der I Chen
- Institute for Translational Genomics and Population Sciences, Department of Pediatrics, Los Angeles Biomedical Research Institute at Harbor-UCLA Medical Center, Torrance, CA 90502, USA
| | - Alan L James
- Busselton Population Medical Research Institute, Sir Charles Gairdner Hospital, Nedlands, WA 6009, Australia; Department of Pulmonary Physiology and Sleep Medicine, Sir Charles Gairdner Hospital, Nedlands, WA 6009, Australia
| | - Daniela Ruggiero
- Institute of Genetics and Biophysics "A. Buzzati-Traverso," Consiglio Nazionale delle Ricerche, Napoli 80131, Italy; IRCCS Neuromed, Pozzilli (IS) 86077, Italy
| | - Nicole Soranzo
- Sanger Institute, Wellcome Trust Genome Campus, Hinxton CB10 1SA, UK
| | - Catharina A Hartman
- Interdisciplinary Center Psychopathology and Emotion regulation, University Medical Center Groningen, University of Groningen, Groningen 9700 RB, the Netherlands
| | - Erin N Smith
- Department of Pediatrics and Rady Children's Hospital, School of Medicine, University of California, San Diego, La Jolla, CA 92037, USA
| | - Gerald S Berenson
- Center for Cardiovascular Health, Tulane University, New Orleans, LA 70112, USA
| | - Christian Fuchsberger
- Institute for Biomedicine, Eurac Research, Affiliated Institute of the University of Lübeck, Bolzano 39100, Italy
| | - Dena Hernandez
- Laboratory of Neurogenetics, National Institute on Aging, Bethesda, MD 20892, USA
| | - Carla M T Tiesler
- Institute of Epidemiology, Helmholtz Zentrum München - German Research Centre for Environmental Health, Neuherberg 85764, Germany; Ludwig Maximilian University of Munich, Dr. von Hauner Children's Hospital, Munich 80337, Germany
| | - Vilmantas Giedraitis
- Department of Public Health and Caring Sciences, Molecular Geriatrics, Uppsala University, Uppsala 752 37, Sweden
| | - David Liewald
- Centre for Cognitive Ageing and Cognitive Epidemiology, University of Edinburgh, Edinburgh EH8 9JZ, UK
| | - Krista Fischer
- Estonian Genome Center, Institute of Genomics, University of Tartu, Tartu 51010, Estonia
| | - Dan Mellström
- Department of Internal Medicine and Clinical Nutrition, University of Gothenburg, Gothenburg 41345, Sweden
| | - Anders Larsson
- Department of Medical Sciences, Uppsala University, Uppsala 751 41, Sweden
| | - Yunmei Wang
- Department of Medicine, Case Cardiovascular Research Institute, Case Western Reserve University, Harrington Heart & Vascular Institute, University Hospitals, Cleveland, OH 44106, USA
| | - William R Scott
- Department of Epidemiology and Biostatistics, Imperial College London, London W2 1PG, UK
| | - Matthias Lorentzon
- Department of Internal Medicine and Clinical Nutrition, University of Gothenburg, Gothenburg 41345, Sweden; Geriatric Medicine, Sahlgrenska University Hospital, Mölndal 431 80, Sweden
| | - John Beilby
- PathWest Laboratory Medicine WA, Nedlands, WA 6009, Australia; School of Biomedical Sciences, University of Western Australia, Crawley, Perth, WA 6009, Australia
| | - Kathleen A Ryan
- Division of Endocrinology, Diabetes and Nutrition, Department of Medicine, University of Maryland School of Medicine, Baltimore, MD 21201, USA
| | - Craig E Pennell
- Medical School, University of Western Australia, Perth, WA 6009, Australia
| | - Dragana Vuckovic
- Medical Sciences, Surgical and Health Department, University of Trieste, Trieste 34137, Italy
| | - Beverly Balkau
- INSERM U1018, Centre de Recherche en Epidémiologie et Santé des Populations, Team 5 (EpReC, Renal, and Cardiovascular Epidemiology), Université de Versailles Saint-Quentin-en-Yvelines, Université Paris-Saclay, Villejuif 94807, France
| | - Maria Pina Concas
- Institute for Maternal and Child Health, IRCCS "Burlo Garofolo," Trieste 34140, Italy
| | - Reinhold Schmidt
- Clinical Division of Neurogeriatrics, Department of Neurology, Medical University Graz, Graz 8036, Austria
| | - Carlos F Mendes de Leon
- Department of Epidemiology, School of Public Health, University of Michigan, Ann Arbor, MI 48109, USA
| | - Erwin P Bottinger
- Charles Bronfman Institute for Personalized Medicine, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; Department of Pharmacology and Systems Therapeutics, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Margreet Kloppenburg
- Department of Rheumatology, Leiden University Medical Center, Leiden 2300 RC, the Netherlands; Department of Clinical Epidemiology, Leiden University Medical Center, Leiden 2333 ZC, the Netherlands
| | - Lavinia Paternoster
- MRC Integrative Epidemiology Unit, Bristol Medical School, University of Bristol, Bristol BS8 2BN, UK
| | - Michael Boehnke
- Department of Biostatistics and Center for Statistical Genetics, University of Michigan, Ann Arbor, MI 48109, USA
| | - A W Musk
- Busselton Population Medical Research Institute, Sir Charles Gairdner Hospital, Nedlands, WA 6009, Australia; Department of Respiratory Medicine, Sir Charles Gairdner Hospital, Nedlands, WA 6009, Australia
| | - Gonneke Willemsen
- Department of Biological Psychology, Netherlands Twin Register, Vrije Universiteit, Amsterdam 1081 BT, the Netherlands
| | - David M Evans
- University of Queensland Diamantina Institute, Translational Research Institute, Brisbane, QLD 4102, Australia; MRC Integrative Epidemiology Unit, Bristol Medical School, University of Bristol, Bristol BS8 2BN, UK
| | - Pamela A F Madden
- Department of Psychiatry, Washington University School of Medicine, 4560 Clayton Ave., Suite 1000, St. Louis, MO 63110, USA
| | - Mika Kähönen
- Department of Clinical Physiology, Tampere University Hospital, Tampere 33520, Finland; Department of Clinical Physiology, Finnish Cardiovascular Research Center - Tampere, Faculty of Medicine and Life Sciences, University of Tampere, Tampere 33520, Finland
| | - Zoltán Kutalik
- Swiss Institute of Bioinformatics, Lausanne 1015, Switzerland; Institute of Social and Preventive Medicine, University Hospital of Lausanne, Lausanne 1010, Switzerland
| | - Magdalena Zoledziewska
- Istituto di Ricerca Genetica e Biomedica, Consiglio Nazionale delle Ricerche, Sardinia 08045, Italy
| | - Ville Karhunen
- Center for Life Course Health Research, Faculty of Medicine, University of Oulu, 90014 Oulun yliopisto, Finland
| | - Stephen B Kritchevsky
- Gerontology and Geriatric Medicine, Sticht Center on Aging and Rehabilitation, Wake Forest University Health Sciences, Winston-Salem, NC 27157, USA
| | - Naveed Sattar
- BHF Glasgow Cardiovascular Research Centre, Faculty of Medicine, Glasgow G12 8TA, UK
| | - Genevieve Lachance
- Department of Twin Research & Genetic Epidemiology, King's College London, London SE1 7EH, UK
| | - Robert Clarke
- Clinical Trial Service Unit, Nuffield Department of Population Health, University of Oxford, Oxford OX3 7LF, UK
| | - Tamara B Harris
- Laboratory of Epidemiology and Population Sciences, National Institute on Aging, Intramural Research Program, National Institutes of Health, Bethesda, MD 20892, USA
| | - Olli T Raitakari
- Department of Clinical Physiology and Nuclear Medicine, Turku University Hospital, Turku 20520, Finland; Research Centre of Applied and Preventive Cardiovascular Medicine, University of Turku, Turku 20520, Finland
| | - John R Attia
- Hunter Medical Research Institute, New Lambon Heights, NSW 2305, Australia; Centre for Clinical Epidemiology & Biostatistics, Faculty of Health and Medicine, University of Newcastle, Callaghan, NSW 2308, Australia; John Hunter Hospital, New Lambton Heights, NWS 2305, Australia
| | - Diana van Heemst
- Department of Gerontology and Geriatrics, Leiden University Medical Center, Leiden 2333 ZA, the Netherlands
| | - Eero Kajantie
- Chronic Disease Prevention Unit, National Institute for Health and Welfare, Helsinki 00014, Finland; Hospital for Children and Adolescents, Helsinki University Central Hospital and University of Helsinki, Helsinki 00290, Finland; Department of Obstetrics and Gynaecology, MRC Oulu, Oulu University Hospital and University of Oulu, Oulu 90014, Finland
| | - Rossella Sorice
- Institute of Genetics and Biophysics "A. Buzzati-Traverso," Consiglio Nazionale delle Ricerche, Napoli 80131, Italy
| | - Giovanni Gambaro
- Division of Nephrology and Dialysis, Columbus-Gemelli University Hospital, Università Cattolica del Sacro Cuore, Roma 168, Italy
| | - Robert A Scott
- MRC Epidemiology Unit, University of Cambridge School of Clinical Medicine, Institute of Metabolic Science, Cambridge CB2 0QQ, UK
| | - Andrew A Hicks
- Institute for Biomedicine, Eurac Research, Affiliated Institute of the University of Lübeck, Bolzano 39100, Italy
| | - Luigi Ferrucci
- Translational Gerontology Branch, National Institute on Aging, Baltimore, MD 21224, USA
| | - Marie Standl
- Institute of Epidemiology, Helmholtz Zentrum München - German Research Centre for Environmental Health, Neuherberg 85764, Germany
| | - Cecilia M Lindgren
- Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford OX3 7BN, UK; Big Data Institute, Li Ka Shing Centre for Health Information and Discovery, University of Oxford, Oxford OX3 7FZ, UK; Program in Medical and Population Genetics, Broad Institute, Cambridge, MA 02142, USA
| | - John M Starr
- Centre for Cognitive Ageing and Cognitive Epidemiology, University of Edinburgh, Edinburgh EH8 9JZ, UK; Alzheimer's Scotland Dementia Research Centre, University of Edinburgh, Edinburgh EH8 9JZ, UK
| | - Magnus Karlsson
- Department of Clinical Sciences and Orthopaedic Surgery, Lund University, Malmo 20502, Sweden
| | - Lars Lind
- Department of Medical Sciences, Uppsala University, Uppsala 751 41, Sweden
| | - Jun Z Li
- Department of Human Genetics, University of Michigan, Ann Arbor, MI 48109-5618, USA
| | - John C Chambers
- Department of Epidemiology and Biostatistics, Imperial College London, London W2 1PG, UK; Department of Cardiology, Ealing Hospital, Middlesex UB1 3HW, UK; Imperial College Healthcare NHS Trust, London W12 0HS, UK; Lee Kong Chian School of Medicine, Nanyang Technological University, Singapore 308232, Singapore; MRC-PHE Centre for Environment and Health, Imperial College London, London W2 1PG, UK
| | - Trevor A Mori
- Medical School, University of Western Australia, Perth, WA 6009, Australia
| | - Eco J C N de Geus
- Department of Biological Psychology, Netherlands Twin Register, Vrije Universiteit, Amsterdam 1081 BT, the Netherlands; Amsterdam Public Health research institute, VU University Medical Center, Amsterdam 1081 BT, the Netherlands
| | - Andrew C Heath
- Department of Psychiatry, Washington University School of Medicine, 4560 Clayton Ave., Suite 1000, St. Louis, MO 63110, USA
| | - Nicholas G Martin
- QIMR Berghofer Medical Research Institute, Brisbane, QLD 4006, Australia
| | - Juha Auvinen
- Center for Life Course Health Research, Faculty of Medicine, University of Oulu, 90014 Oulun yliopisto, Finland; Unit of Primary Health Care, Oulu University Hospital, Oulu 90220, Finland
| | - Brendan M Buckley
- Department of Epidemiology and Public Health, University College Cork, Cork T12 K8AF, Ireland
| | - Anton J M de Craen
- Department of Gerontology and Geriatrics, Leiden University Medical Center, Leiden 2333 ZA, the Netherlands
| | - Melanie Waldenberger
- Institute of Epidemiology II, Research Unit of Molecular Epidemiology, Helmholtz Zentrum München, German Research Center for Environmental Health, Neuherberg 85764, Germany; German Center for Cardiovascular Research, Partner Site Munich Heart Alliance, 80636 Munich, Germany
| | - Konstantin Strauch
- Institute of Genetic Epidemiology, Helmholtz Zentrum München, German Research Center for Environmental Health, Neuherberg 85764, Germany; Genetic Epidemiology, Institute of Medical Informatics, Biometry, and Epidemiology, Faculty of Medicine, Ludwig Maximilian University of Munich, Neuherberg 85764, Germany
| | - Thomas Meitinger
- Institute of Human Genetics, Technische Universität München, Munich 85764, Germany; Institute of Human Genetics, Helmholtz Zentrum München, Neuherberg 85764, Germany; Munich Cluster for Systems Neurology (SyNergy), Munich 81377, Germany
| | - Rodney J Scott
- Hunter Medical Research Institute, New Lambon Heights, NSW 2305, Australia; Information-Based Medicine Stream, Hunter Medical Research Institute, New Lambton Heights, NSW 2305, Australia
| | - Mark McEvoy
- Hunter Medical Research Institute, New Lambon Heights, NSW 2305, Australia; Centre for Clinical Epidemiology & Biostatistics, Faculty of Health and Medicine, University of Newcastle, Callaghan, NSW 2308, Australia
| | - Marian Beekman
- Molecular Epidemiology, Leiden University Medical Center, Leiden 2333 ZC, the Netherlands
| | - Cristina Bombieri
- Department of Neurosciences, Biomedicine and Movement Sciences, University of Verona, Verona 37134, Italy
| | - Paul M Ridker
- Division of Preventive Medicine, Brigham and Women's Hospital, Boston, MA 02215, USA; Harvard Medical School, Boston, MA 02115, USA
| | - Karen L Mohlke
- Department of Genetics, University of North Carolina, Chapel Hill, NC 27599, USA
| | - Nancy L Pedersen
- Department of Medical Epidemiology and Biostatistics, Karolinska Institutet, Stockholm 17177, Sweden
| | - Alanna C Morrison
- Human Genetics Center, Department of Epidemiology, Human Genetics, and Environmental Sciences, School of Public Health, University of Texas Health Science Center at Houston, Houston, TX 77030, USA
| | - Dorret I Boomsma
- Department of Biological Psychology, Netherlands Twin Register, Vrije Universiteit, Amsterdam 1081 BT, the Netherlands
| | - John B Whitfield
- QIMR Berghofer Medical Research Institute, Brisbane, QLD 4006, Australia
| | - David P Strachan
- Population Health Research Institute, St. George's, University of London, London SW17 0RE, UK
| | - Albert Hofman
- Department of Epidemiology, Erasmus University Medical Center, Rotterdam 3000 CA, the Netherlands
| | - Peter Vollenweider
- Department of Internal Medicine, Centre Hospitalier Universitaire Vaudois, Lausanne 1011, Switzerland
| | - Francesco Cucca
- Istituto di Ricerca Genetica e Biomedica, Consiglio Nazionale delle Ricerche, Sardinia 08045, Italy
| | - Marjo-Riitta Jarvelin
- Biocenter Oulu, University of Oulu, Oulu 90220, Finland; Center for Life Course Health Research, Faculty of Medicine, University of Oulu, 90014 Oulun yliopisto, Finland; Unit of Primary Health Care, Oulu University Hospital, Oulu 90220, Finland; Department of Epidemiology and Biostatistics, MRC-PHE Centre for Environment & Health, School of Public Health, Imperial College London, London W2 1PG, UK; Department of Life Sciences, College of Health and Life Sciences, Brunel University London, Kingston Lane, Uxbridge, Middlesex UB8 3PH, UK
| | - J Wouter Jukema
- Department of Cardiology, Leiden University Medical Center, Leiden 2300 RC, the Netherlands; Durrer Center for Cardiogenetic Research, Amsterdam 3501 DG, the Netherlands; Interuniversity Cardiology Institute of the Netherlands, Utrecht 3511 EP, the Netherlands
| | - Tim D Spector
- Department of Twin Research & Genetic Epidemiology, King's College London, London SE1 7EH, UK
| | - Anders Hamsten
- Cardiovascular Medicine Unit, Department of Medicine, Center for Molecular Medicine, Karolinska Institutet, Stockholm 17176, Sweden
| | - Tanja Zeller
- Department of General and Interventional Cardiology, University Heart Center Hamburg, Hamburg 20246, Germany; German Center for Cardiovascular Research, Partner Site RhineMain, 55131 Mainz, Germany
| | - André G Uitterlinden
- Department of Epidemiology, Erasmus University Medical Center, Rotterdam 3000 CA, the Netherlands; Department of Internal Medicine, Erasmus University Medical Center, Rotterdam 3015 CN, the Netherlands
| | - Matthias Nauck
- German Centre for Cardiovascular Research, Partner Site Greifswald, Greifswald 17475, Germany; Institute for Clinical Chemistry and Laboratory Medicine, University Medicine Greifswald, Greifswald 17475, Germany
| | - Vilmundur Gudnason
- Icelandic Heart Association, Kopavogur 201, Iceland; Faculty of Medicine, University of Iceland, Reykjavik 101, Iceland
| | - Lu Qi
- Department of Nutrition, Harvard T.H. Chan School of Public Health, Boston, MA 02115, USA; Department of Epidemiology, Tulane University School of Public Health and Tropical Medicine, New Orleans, LA 70112, USA
| | - Harald Grallert
- Institute of Epidemiology II, Research Unit of Molecular Epidemiology, Helmholtz Zentrum München, German Research Center for Environmental Health, Neuherberg 85764, Germany; German Center for Diabetes Research, Partner Site Munich, Munich 85764, Germany
| | - Ingrid B Borecki
- Analytical Genetics Group, Regeneron Genetics Center, Regeneron Pharmaceuticals, Inc., Tarrytown, NY 10591, USA
| | - Jerome I Rotter
- Institute for Translational Genomics and Population Sciences, Departments of Pediatrics and Medicine, Los Angeles Biomedical Research Institute at Harbor-UCLA Medical Center, Torrance, CA 90502, USA
| | - Winfried März
- Vth Department of Medicine, Medical Faculty Mannheim, Heidelberg University, Mannheim 68167, Germany; Synlab Academy, Synlab Holding Deutschland GmbH, Mannheim 68161, Germany; Clinical Institute of Medical and Chemical Laboratory Diagnostics, Medical University of Graz, Graz 8036, Austria
| | - Philipp S Wild
- German Center for Cardiovascular Research, Partner Site RhineMain, 55131 Mainz, Germany; Center for Thrombosis and Hemostasis, University Medical Center of the Johannes Gutenberg University Mainz, Mainz 55131, Germany; Preventive Cardiology and Preventive Medicine, Center for Cardiology, University Medical Center of the Johannes Gutenberg-University Mainz, Mainz 55131, Germany
| | - Marja-Liisa Lokki
- Transplantation Laboratory, Medicum, University of Helsinki, Helsinki 00014, Finland
| | - Michael Boyle
- John Hunter Hospital, New Lambton Heights, NWS 2305, Australia
| | - Veikko Salomaa
- National Institute for Health and Welfare, Helsinki 00271, Finland
| | - Mads Melbye
- Department of Epidemiology Research, Statens Serum Institut, Copenhagen 2300, Denmark; Department of Clinical Medicine, University of Copenhagen, Copenhagen 2300, Denmark; Department of Medicine, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Johan G Eriksson
- National Institute for Health and Welfare, Helsinki 00271, Finland; Folkhälsan Research Centre, Helsinki 00250, Finland; Department of General Practice and Primary Health Care, University of Helsinki and Helsinki University Hospital, Helsinki 00014, Finland
| | - James F Wilson
- Centre for Global Health Research, Usher Institute of Population Health Sciences and Informatics, University of Edinburgh, Teviot Place, Edinburgh EH16 4UX, UK; MRC Human Genetics Unit, Institute for Genetics and Molecular Medicine, University of Edinburgh, Western General Hospital, Edinburgh EH4 2XU, UK
| | - Brenda W J H Penninx
- Department of Psychiatry, Amsterdam Neuroscience and Amsterdam Public Health Research Institute, Amsterdam University Medical Center/GGZ inGeest Research & Innovation, Amsterdam 1081 HJ, the Netherlands
| | - Diane M Becker
- GeneSTAR Research Center, Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA
| | - Bradford B Worrall
- Departments of Neurology and Public Health Sciences, University of Virginia Charlottesville, Charlottesville, VA 22908-0394, USA
| | - Greg Gibson
- Center for Integrative Genomics, School of Biology, Georgia Institute of Technology, Atlanta, GA 30332, USA
| | - Ronald M Krauss
- Children's Hospital Oakland Research Institute, Oakland, CA 94609, USA
| | - Marina Ciullo
- Institute of Genetics and Biophysics "A. Buzzati-Traverso," Consiglio Nazionale delle Ricerche, Napoli 80131, Italy; IRCCS Neuromed, Pozzilli (IS) 86077, Italy
| | - Gianluigi Zaza
- Renal Unit, Department of Medicine, Verona University Hospital, Verona 37126, Italy
| | - Nicholas J Wareham
- MRC Epidemiology Unit, University of Cambridge School of Clinical Medicine, Institute of Metabolic Science, Cambridge CB2 0QQ, UK
| | - Albertine J Oldehinkel
- Interdisciplinary Center Psychopathology and Emotion regulation, University Medical Center Groningen, University of Groningen, Groningen 9700 RB, the Netherlands
| | - Lyle J Palmer
- School of Public Health, University of Adelaide, Adelaide, SA 5000, Australia
| | - Sarah S Murray
- Department of Pathology, University of California, San Diego, San Diego, CA 92121, USA
| | - Peter P Pramstaller
- Institute for Biomedicine, Eurac Research, Affiliated Institute of the University of Lübeck, Bolzano 39100, Italy; General Central Hospital, Department of Neurology, Bolzano 39100, Italy; Department of Neurology, University of Lübeck, Lübeck 23538, Germany
| | | | - Joachim Heinrich
- Institute of Epidemiology, Helmholtz Zentrum München - German Research Centre for Environmental Health, Neuherberg 85764, Germany; Institute and Clinic for Occupational, Social and Environmental Medicine, University Hospital, LMU Munich, Comprehensive Pneumology Center Munich, Member DZL, German Center for Lung Research, 81377 Munich, Germany
| | - Erik Ingelsson
- Department of Medical Sciences, Molecular Epidemiology and Science for Life Laboratory, Uppsala University, Uppsala 751 41, Sweden; Department of Medicine, Division of Cardiovascular Medicine, Stanford University School of Medicine, Stanford, CA 94305, USA; Stanford Cardiovascular Institute, Stanford University, Stanford, CA 94305, USA
| | - Ian J Deary
- Centre for Cognitive Ageing and Cognitive Epidemiology, University of Edinburgh, Edinburgh EH8 9JZ, UK; Department of Psychology, University of Edinburgh, Edinburgh EH8 9JZ, UK
| | - Reedik Mägi
- Estonian Genome Center, Institute of Genomics, University of Tartu, Tartu 51010, Estonia
| | - Liesbeth Vandenput
- Department of Internal Medicine and Clinical Nutrition, University of Gothenburg, Gothenburg 41345, Sweden
| | - Pim van der Harst
- University of Groningen, University Medical Center Groningen, Department of Cardiology, Groningen 9713 AV, the Netherlands
| | - Karl C Desch
- Department of Pediatrics and Communicable Diseases, University of Michigan, Ann Arbor, MI 48109, USA
| | - Jaspal S Kooner
- Department of Cardiology, Ealing Hospital, Middlesex UB1 3HW, UK; Imperial College Healthcare NHS Trust, London W12 0HS, UK; MRC-PHE Centre for Environment and Health, Imperial College London, London W2 1PG, UK; National Heart and Lung Institute, Imperial College London, London W12 0NN, UK
| | - Claes Ohlsson
- Department of Internal Medicine and Clinical Nutrition, University of Gothenburg, Gothenburg 41345, Sweden
| | - Caroline Hayward
- MRC Human Genetics Unit, Institute for Genetics and Molecular Medicine, University of Edinburgh, Western General Hospital, Edinburgh EH4 2XU, UK
| | - Terho Lehtimäki
- Department of Clinical Chemistry, Fimlab Laboratories, Tampere 33014, Finland; Department of Clinical Chemistry, Finnish Cardiovascular Research Center - Tampere, Faculty of Medicine and Life Sciences, University of Tampere, Tampere 33520, Finland
| | - Alan R Shuldiner
- Division of Endocrinology, Diabetes and Nutrition, Department of Medicine, University of Maryland School of Medicine, Baltimore, MD 21201, USA
| | - Donna K Arnett
- University of Kentucky, College of Public Health, Lexington, KY 40508, USA
| | - Lawrence J Beilin
- Medical School, University of Western Australia, Perth, WA 6009, Australia
| | - Antonietta Robino
- Institute for Maternal and Child Health, IRCCS "Burlo Garofolo," Trieste 34140, Italy
| | - Philippe Froguel
- Centre National de la Recherche Scientifique UMR 8199, University of Lille, Institut Pasteur de Lille, European Genomic Institute for Diabetes, FR 3508, 59000 Lille, France; Department of Genomics of Common Disease, School of Public Health, Imperial College London, London SW7 2AZ, UK
| | - Mario Pirastu
- Support OU, Institute of Genetic and Biomedic Research, Consiglio Nazionale delle Ricerche, Sassari 7100, Italy
| | - Tine Jess
- Center for Clinical Research and Prevention, Bispebjerg and Frederiksberg Hospital, Frederiksberg 2200, Denmark
| | - Wolfgang Koenig
- German Center for Cardiovascular Research, Partner Site Munich Heart Alliance, 80636 Munich, Germany; Department of Internal Medicine II-Cardiology, University of Ulm Medical Center, 80801 Ulm, Germany; Deutsches Herzzentrum München, Technische Universität München, 80636 Munich, Germany
| | - Ruth J F Loos
- Charles Bronfman Institute for Personalized Medicine, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; Genetics of Obesity and Related Metabolic Traits Program, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; Mindich Child Health and Development Institute, Icahn School of Medicine at Mount Sinai, New York, NY 10029-6542, USA
| | - Denis A Evans
- Department of Internal Medicine, Rush University Medical Center, Chicago, IL 60612, USA
| | - Helena Schmidt
- Department of Neurology, Medical University Graz, Graz 8010, Austria; Institute of Molecular Biology and Biochemistry, Centre for Molecular Medicine, Medical University of Graz, Graz 8010, Austria
| | - George Davey Smith
- MRC Integrative Epidemiology Unit, Bristol Medical School, University of Bristol, Bristol BS8 2BN, UK
| | - P Eline Slagboom
- Molecular Epidemiology, Leiden University Medical Center, Leiden 2333 ZC, the Netherlands
| | | | - Andrew P Morris
- Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford OX3 7BN, UK; Department of Biostatistics, University of Liverpool, Liverpool L69 3GL, UK
| | - Bruce M Psaty
- Cardiovascular Health Research Unit, Department of Medicine, University of Washington, Seattle, WA 98101, USA; Department of Epidemiology, University of Washington, Seattle, WA 98101, USA; Department of Health Services, University of Washington, Seattle, WA 98195-7660, USA; Kaiser Permanente Washington Health Research Institute, Seattle, WA 98101, USA
| | - Russell P Tracy
- Department of Pathology, University of Vermont, Colchester, VT 05405, USA
| | - Ilja M Nolte
- Department of Epidemiology, University of Groningen, University Medical Center Groningen, Groningen 9700 RB, the Netherlands
| | - Eric Boerwinkle
- Human Genetics Center, School of Public Health, University of Texas Health Science Center at Houston, Houston, TX 77030, USA; Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX 77030, USA
| | | | - Alex P Reiner
- Department of Epidemiology, University of Washington, Seattle, WA 98101, USA
| | - Myron Gross
- Department of Lab Medicine and Pathology, University of Minnesota, Minneapolis, MN 55455, USA
| | - Joshua C Bis
- Cardiovascular Health Research Unit, Department of Medicine, University of Washington, Seattle, WA 98101, USA
| | - Lude Franke
- Department of Genetics, University of Groningen, University Medical Center Groningen, Groningen 9700 RB, the Netherlands
| | - Oscar H Franco
- Department of Epidemiology, Erasmus University Medical Center, Rotterdam 3000 CA, the Netherlands; Institute of Social and Preventive Medicine, University of Bern, 3012 Bern, Switzerland
| | - Emelia J Benjamin
- Department of Medicine, Boston University School of Medicine, Boston, MA 02118, USA; National Heart, Lung, and Blood Institute's Framingham Heart Study, Framingham, MA 01702, USA
| | - Daniel I Chasman
- Division of Preventive Medicine, Brigham and Women's Hospital, Boston, MA 02215, USA; Harvard Medical School, Boston, MA 02115, USA
| | - Josée Dupuis
- National Heart, Lung, and Blood Institute's Framingham Heart Study, Framingham, MA 01702, USA; Department of Biostatistics, Boston University School of Public Health, Boston, MA 02118, USA
| | - Harold Snieder
- Department of Epidemiology, University of Groningen, University Medical Center Groningen, Groningen 9700 RB, the Netherlands
| | - Abbas Dehghan
- Department of Epidemiology, Erasmus University Medical Center, Rotterdam 3000 CA, the Netherlands; Department of Epidemiology and Biostatistics, MRC-PHE Centre for Environment & Health, School of Public Health, Imperial College London, London W2 1PG, UK.
| | - Behrooz Z Alizadeh
- Department of Epidemiology, University of Groningen, University Medical Center Groningen, Groningen 9700 RB, the Netherlands.
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13
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Wang HY, Dell'Aquila ML, Dvanajscak Z, Bejar R, Broome HE, Hsi E, Murray SS, Thorson JA. JAK2 double minutes with resultant simultaneous amplification of JAK2 and CD274 in a therapy-related myelodysplastic syndrome evolving into an acute myeloid leukaemia. Br J Haematol 2018; 185:566-570. [PMID: 30132795 DOI: 10.1111/bjh.15538] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Huan-You Wang
- Division of Laboratory and Genomic Medicine, Department of Pathology, University of California San Diego, La Jolla, CA, USA
| | - Marie L Dell'Aquila
- Division of Medical Genetics, Department of Medicine, University of California San Diego, La Jolla, CA, USA
| | - Zeljko Dvanajscak
- Division of Laboratory and Genomic Medicine, Department of Pathology, University of California San Diego, La Jolla, CA, USA
| | - Rafael Bejar
- Division of Hematology and Oncology, Department of Medicine, University of California San Diego, La Jolla, CA, USA
| | - H Elizabeth Broome
- Division of Laboratory and Genomic Medicine, Department of Pathology, University of California San Diego, La Jolla, CA, USA
| | - Eric Hsi
- Department of Pathology and Clinical Medicine, Cleveland Clinic Foundation, Cleveland, OH, USA
| | - Sarah S Murray
- Division of Laboratory and Genomic Medicine, Department of Pathology, University of California San Diego, La Jolla, CA, USA
| | - John A Thorson
- Division of Laboratory and Genomic Medicine, Department of Pathology, University of California San Diego, La Jolla, CA, USA
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14
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Murray SS, Wong AW, Yang J, Li Y, Putz U, Tan SS, Howitt J. Ubiquitin Regulation of Trk Receptor Trafficking and Degradation. Mol Neurobiol 2018; 56:1628-1636. [PMID: 29911254 DOI: 10.1007/s12035-018-1179-5] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2018] [Accepted: 06/04/2018] [Indexed: 10/28/2022]
Abstract
The regulation of Trk receptors is critical for orchestrating multiple signalling pathways required for developing and maintaining neuronal networks. Activation of Trk receptors results in signalling, internalisation and subsequent degradation of the protein. Although ubiquitination of TrkA by Nedd4-2 has been identified as an important degradation pathway, much less is known about the pathways regulating the degradation of TrkB and TrkC. Critical to the interaction between TrkA and Nedd4-2 is a PPxY motif present within TrkA but absent in TrkB and TrkC. Given the absence of this interaction motif, it remains to be determined how TrkB and TrkC are ubiquitinated. Here we report that the adaptor protein Ndfip1 can interact with all three Trk receptors and show for TrkB the recruitment of Nedd4-2 through PPxY motifs present in Ndfip1. Ndfip1 mediates the ubiquitination of TrkB, resulting in receptor trafficking predominantly on Rab7 containing late endosomes, highlighting a pathway for TrkB degradation at the lysosome. In vitro, overexpression of Ndfip1 increased TrkB ubiquitination and decreased viability of BDNF-dependent primary neurons. In vivo, conditional genetic deletion of Ndfip1 increased TrkB in the brain and resulted in enlargement of the granular cell layer of the dentate gyrus.
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Affiliation(s)
- S S Murray
- Department of Anatomy and Neuroscience, The University of Melbourne, Parkville, Australia
| | - A W Wong
- Department of Anatomy and Neuroscience, The University of Melbourne, Parkville, Australia
| | - J Yang
- Florey Institute of Neuroscience and Mental Health, The University of Melbourne, Parkville, Australia
| | - Y Li
- Florey Institute of Neuroscience and Mental Health, The University of Melbourne, Parkville, Australia
| | - U Putz
- Florey Institute of Neuroscience and Mental Health, The University of Melbourne, Parkville, Australia
| | - S-S Tan
- Florey Institute of Neuroscience and Mental Health, The University of Melbourne, Parkville, Australia
| | - J Howitt
- Florey Institute of Neuroscience and Mental Health, The University of Melbourne, Parkville, Australia. .,Department of Health and Medical Sciences, Iverson Health Innovation Institute, Swinburne University of Technology, Hawthorn, Australia.
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15
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Gonias SL, Karimi-Mostowfi N, Murray SS, Mantuano E, Gilder AS. Expression of LDL receptor-related proteins (LRPs) in common solid malignancies correlates with patient survival. PLoS One 2017; 12:e0186649. [PMID: 29088295 PMCID: PMC5663383 DOI: 10.1371/journal.pone.0186649] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2017] [Accepted: 10/04/2017] [Indexed: 01/06/2023] Open
Abstract
LDL receptor-related proteins (LRPs) are transmembrane receptors involved in endocytosis, cell-signaling, and trafficking of other cellular proteins. Considerable work has focused on LRPs in the fields of vascular biology and neurobiology. How these receptors affect cancer progression in humans remains largely unknown. Herein, we mined provisional databases in The Cancer Genome Atlas (TCGA) to compare expression of thirteen LRPs in ten common solid malignancies in patients. Our first goal was to determine the abundance of LRP mRNAs in each type of cancer. Our second goal was to determine whether expression of LRPs is associated with improved or worsened patient survival. In total, data from 4,629 patients were mined. In nine of ten cancers studied, the most abundantly expressed LRP was LRP1; however, a correlation between LRP1 mRNA expression and patient survival was observed only in bladder urothelial carcinoma. In this malignancy, high levels of LRP1 mRNA were associated with worsened patient survival. High levels of LDL receptor (LDLR) mRNA were associated with decreased patient survival in pancreatic adenocarcinoma. High levels of LRP10 mRNA were associated with decreased patient survival in hepatocellular carcinoma, lung adenocarcinoma, and pancreatic adenocarcinoma. LRP2 was the only LRP for which high levels of mRNA expression correlated with improved patient survival. This correlation was observed in renal clear cell carcinoma. Insights into LRP gene expression in human cancers and their effects on patient survival should guide future research.
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Affiliation(s)
- Steven L. Gonias
- Department of Pathology, University of California San Diego, La Jolla, California, United States of America
- * E-mail:
| | - Nicki Karimi-Mostowfi
- Department of Pathology, University of California San Diego, La Jolla, California, United States of America
| | - Sarah S. Murray
- Department of Pathology, University of California San Diego, La Jolla, California, United States of America
| | - Elisabetta Mantuano
- Department of Pathology, University of California San Diego, La Jolla, California, United States of America
- The Department of Experimental Medicine, Sapienza University of Rome, Rome, Italy
| | - Andrew S. Gilder
- Department of Pathology, University of California San Diego, La Jolla, California, United States of America
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16
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Eicher JD, Montgomery AM, Akshoomoff N, Amaral DG, Bloss CS, Libiger O, Schork NJ, Darst BF, Casey BJ, Chang L, Ernst T, Frazier J, Kaufmann WE, Keating B, Kenet T, Kennedy D, Mostofsky S, Murray SS, Sowell ER, Bartsch H, Kuperman JM, Brown TT, Hagler DJ, Dale AM, Jernigan TL, Gruen JR. Dyslexia and language impairment associated genetic markers influence cortical thickness and white matter in typically developing children. Brain Imaging Behav 2016; 10:272-82. [PMID: 25953057 PMCID: PMC4639472 DOI: 10.1007/s11682-015-9392-6] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Abstract
Dyslexia and language impairment (LI) are complex traits with substantial genetic components. We recently completed an association scan of the DYX2 locus, where we observed associations of markers in DCDC2, KIAA0319, ACOT13, and FAM65B with reading-, language-, and IQ-related traits. Additionally, the effects of reading-associated DYX3 markers were recently characterized using structural neuroimaging techniques. Here, we assessed the neuroimaging implications of associated DYX2 and DYX3 markers, using cortical volume, cortical thickness, and fractional anisotropy. To accomplish this, we examined eight DYX2 and three DYX3 markers in 332 subjects in the Pediatrics Imaging Neurocognition Genetics study. Imaging-genetic associations were examined by multiple linear regression, testing for influence of genotype on neuroimaging. Markers in DYX2 genes KIAA0319 and FAM65B were associated with cortical thickness in the left orbitofrontal region and global fractional anisotropy, respectively. KIAA0319 and ACOT13 were suggestively associated with overall fractional anisotropy and left pars opercularis cortical thickness, respectively. DYX3 markers showed suggestive associations with cortical thickness and volume measures in temporal regions. Notably, we did not replicate association of DYX3 markers with hippocampal measures. In summary, we performed a neuroimaging follow-up of reading-, language-, and IQ-associated DYX2 and DYX3 markers. DYX2 associations with cortical thickness may reflect variations in their role in neuronal migration. Furthermore, our findings complement gene expression and imaging studies implicating DYX3 markers in temporal regions. These studies offer insight into where and how DYX2 and DYX3 risk variants may influence neuroimaging traits. Future studies should further connect the pathways to risk variants associated with neuroimaging/neurocognitive outcomes.
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Affiliation(s)
- John D Eicher
- Department of Genetics, Yale University, New Haven, CT, 06520, USA
| | - Angela M Montgomery
- Department of Pediatrics, Yale University School of Medicine, New Haven, CT, 06520, USA
| | - Natacha Akshoomoff
- Center for Human Development, University of California, La Jolla, San Diego, CA, 92037, USA
- Department of Psychiatry, University of California, La Jolla, San Diego, CA, 92037, USA
| | - David G Amaral
- Department of Psychiatry and Behavioral Sciences, University of California, Davis, CA, 95817, USA
| | - Cinnamon S Bloss
- Scripps Genomic Medicine, Scripps Health, Scripps Translational Science Institute, La Jolla, CA, 92037, USA
| | - Ondrej Libiger
- Scripps Genomic Medicine, Scripps Health, Scripps Translational Science Institute, La Jolla, CA, 92037, USA
| | - Nicholas J Schork
- Scripps Genomic Medicine, Scripps Health, Scripps Translational Science Institute, La Jolla, CA, 92037, USA
| | - Burcu F Darst
- Scripps Genomic Medicine, Scripps Health, Scripps Translational Science Institute, La Jolla, CA, 92037, USA
| | - B J Casey
- Sackler Institute for Developmental Psychobiology, Weil Cornell Medical College, New York, NY, 10065, USA
| | - Linda Chang
- Department of Medicine, Queen's Medical Center, University of Hawaii, Honolulu, HI, 96813, USA
| | - Thomas Ernst
- Department of Medicine, Queen's Medical Center, University of Hawaii, Honolulu, HI, 96813, USA
| | - Jean Frazier
- Department of Psychiatry, University of Massachusetts Medical School, Boston, MA, 01655, USA
| | - Walter E Kaufmann
- Kennedy Krieger Institute, 707 N. Broadway, Baltimore, MD, 21205, USA
- Department of Neurology, Harvard Medical School, Children's Hospital Boston, Boston, MA, 02115, USA
| | - Brian Keating
- Department of Medicine, Queen's Medical Center, University of Hawaii, Honolulu, HI, 96813, USA
| | - Tal Kenet
- Department of Neurology and Athinoula A. Martinos Center for Biomedical Imaging, Massachusetts General Hospital, Charlestown, MA, 02129, USA
| | - David Kennedy
- Department of Psychiatry, University of Massachusetts Medical School, Boston, MA, 01655, USA
| | - Stewart Mostofsky
- Kennedy Krieger Institute, 707 N. Broadway, Baltimore, MD, 21205, USA
| | - Sarah S Murray
- Scripps Genomic Medicine, Scripps Health, Scripps Translational Science Institute, La Jolla, CA, 92037, USA
| | - Elizabeth R Sowell
- Department of Pediatrics, University of Southern California, Los Angeles, CA, 90027, USA
- Developmental Cognitive Neuroimaging Laboratory Children's Hospital, Los Angeles, CA, 90027, USA
| | - Hauke Bartsch
- Multimodal Imaging Laboratory, University of California, La Jolla, San Diego, CA, 92037, USA
| | - Joshua M Kuperman
- Multimodal Imaging Laboratory, University of California, La Jolla, San Diego, CA, 92037, USA
- Department of Neurosciences, University of California, La Jolla, San Diego, CA, 92037, USA
| | - Timothy T Brown
- Center for Human Development, University of California, La Jolla, San Diego, CA, 92037, USA
- Multimodal Imaging Laboratory, University of California, La Jolla, San Diego, CA, 92037, USA
- Department of Neurosciences, University of California, La Jolla, San Diego, CA, 92037, USA
| | - Donald J Hagler
- Multimodal Imaging Laboratory, University of California, La Jolla, San Diego, CA, 92037, USA
- Radiology University of California, La Jolla, San Diego, CA, 92037, USA
| | - Anders M Dale
- Department of Psychiatry, University of California, La Jolla, San Diego, CA, 92037, USA
- Multimodal Imaging Laboratory, University of California, La Jolla, San Diego, CA, 92037, USA
- Department of Neurosciences, University of California, La Jolla, San Diego, CA, 92037, USA
- Radiology University of California, La Jolla, San Diego, CA, 92037, USA
- Cognitive Science University of California, La Jolla, San Diego, CA, 92037, USA
| | - Terry L Jernigan
- Center for Human Development, University of California, La Jolla, San Diego, CA, 92037, USA
- Department of Psychiatry, University of California, La Jolla, San Diego, CA, 92037, USA
- Radiology University of California, La Jolla, San Diego, CA, 92037, USA
- Cognitive Science University of California, La Jolla, San Diego, CA, 92037, USA
| | - Jeffrey R Gruen
- Department of Genetics, Yale University, New Haven, CT, 06520, USA.
- Department of Pediatrics, Yale University School of Medicine, New Haven, CT, 06520, USA.
- Department of Investigative, School of Medicine, Medicine Yale University, New Haven, CT, 06520, USA.
- Department of Pediatrics, Genetics, and Investigative Medicine, Yale Child Health Research Center, 464 Congress Avenue, New Haven, CT, 06520-8081, USA.
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17
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Evans DS, Avery CL, Nalls MA, Li G, Barnard J, Smith EN, Tanaka T, Butler AM, Buxbaum SG, Alonso A, Arking DE, Berenson GS, Bis JC, Buyske S, Carty CL, Chen W, Chung MK, Cummings SR, Deo R, Eaton CB, Fox ER, Heckbert SR, Heiss G, Hindorff LA, Hsueh WC, Isaacs A, Jamshidi Y, Kerr KF, Liu F, Liu Y, Lohman KK, Magnani JW, Maher JF, Mehra R, Meng YA, Musani SK, Newton-Cheh C, North KE, Psaty BM, Redline S, Rotter JI, Schnabel RB, Schork NJ, Shohet RV, Singleton AB, Smith JD, Soliman EZ, Srinivasan SR, Taylor HA, Van Wagoner DR, Wilson JG, Young T, Zhang ZM, Zonderman AB, Evans MK, Ferrucci L, Murray SS, Tranah GJ, Whitsel EA, Reiner AP, Sotoodehnia N. Fine-mapping, novel loci identification, and SNP association transferability in a genome-wide association study of QRS duration in African Americans. Hum Mol Genet 2016; 25:4350-4368. [PMID: 27577874 PMCID: PMC5291202 DOI: 10.1093/hmg/ddw284] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2016] [Revised: 08/03/2016] [Accepted: 08/19/2016] [Indexed: 12/14/2022] Open
Abstract
The electrocardiographic QRS duration, a measure of ventricular depolarization and conduction, is associated with cardiovascular mortality. While single nucleotide polymorphisms (SNPs) associated with QRS duration have been identified at 22 loci in populations of European descent, the genetic architecture of QRS duration in non-European populations is largely unknown. We therefore performed a genome-wide association study (GWAS) meta-analysis of QRS duration in 13,031 African Americans from ten cohorts and a transethnic GWAS meta-analysis with additional results from populations of European descent. In the African American GWAS, a single genome-wide significant SNP association was identified (rs3922844, P = 4 × 10-14) in intron 16 of SCN5A, a voltage-gated cardiac sodium channel gene. The QRS-prolonging rs3922844 C allele was also associated with decreased SCN5A RNA expression in human atrial tissue (P = 1.1 × 10-4). High density genotyping revealed that the SCN5A association region in African Americans was confined to intron 16. Transethnic GWAS meta-analysis identified novel SNP associations on chromosome 18 in MYL12A (rs1662342, P = 4.9 × 10-8) and chromosome 1 near CD1E and SPTA1 (rs7547997, P = 7.9 × 10-9). The 22 QRS loci previously identified in populations of European descent were enriched for significant SNP associations with QRS duration in African Americans (P = 9.9 × 10-7), and index SNP associations in or near SCN5A, SCN10A, CDKN1A, NFIA, HAND1, TBX5 and SETBP1 replicated in African Americans. In summary, rs3922844 was associated with QRS duration and SCN5A expression, two novel QRS loci were identified using transethnic meta-analysis, and a significant proportion of QRS-SNP associations discovered in populations of European descent were transferable to African Americans when adequate power was achieved.
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Affiliation(s)
- Daniel S Evans
- California Pacific Medical Center Research Institute, San Francisco, CA, USA .
| | - Christy L Avery
- Department of Epidemiology, Gillings School of Global Public Health, University of North Carolina, Chapel Hill, NC, USA
| | - Mike A Nalls
- Laboratory of Neurogenetics, National Institute on Aging, National Institutes of Health, Bethesda, MD, USA
| | - Guo Li
- Cardiovascular Health Research Unit, Department of Medicine, University of Washington, Seattle, WA, USA
| | - John Barnard
- Department of Quantitative Health Sciences, Lerner Research Institute, Cleveland Clinic, Cleveland, OH, USA
| | - Erin N Smith
- Department of Pediatrics and Rady Children's Hospital, University of California at San Diego, School of Medicine, La Jolla, CA, USA
| | - Toshiko Tanaka
- Translational Gerontology Branch, National Institute on Aging, National Institutes of Health, Baltimore, MD, USA
| | - Anne M Butler
- Department of Epidemiology, Gillings School of Global Public Health, University of North Carolina, Chapel Hill, NC, USA
| | - Sarah G Buxbaum
- Center of Excellence in Minority Health and Health Disparities, Jackson State University, Jackson, MS, USA
- Department of Epidemiology and Biostatistics, Jackson State University School of Public Health (Initiative), Jackson, MS, USA
| | - Alvaro Alonso
- Department of Epidemiology, Rollins School of Public Health, Emory University, Atlanta, GA, USA
| | - Dan E Arking
- McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - Gerald S Berenson
- Department of Medicine and Cardiology, Tulane University, New Orleans, LA, USA
| | - Joshua C Bis
- Cardiovascular Health Research Unit, Department of Medicine, University of Washington, Seattle, WA, USA
| | - Steven Buyske
- Department of Statistics and Biostatistics and Department of Genetics, Rutgers University, Piscataway, NJ, USA
| | - Cara L Carty
- Division of Public Health Sciences, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - Wei Chen
- Department of Epidemiology, Tulane University, New Orleans, LA, USA
| | - Mina K Chung
- Department of Cardiovascular Medicine, Heart and Vascular Institute, Cleveland Clinic, Cleveland, OH, USA
- Department of Molecular Cardiology, Lerner Research Institute, Cleveland Clinic, Cleveland, OH, USA
- Cleveland Clinic Lerner College of Medicine of Case Western Reserve University, Cleveland, OH, USA
| | - Steven R Cummings
- California Pacific Medical Center Research Institute, San Francisco, CA, USA
| | - Rajat Deo
- Division of Cardiovascular Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Charles B Eaton
- Departments of Family Medicine and Epidemiology, Alpert Medical School, Brown University, Providence, RI, USA
| | - Ervin R Fox
- Department of Medicine, Division of Cardiovascular Disease, University of Mississippi Medical Center, Jackson, MS, USA
| | - Susan R Heckbert
- Cardiovascular Health Research Unit, Department of Medicine, University of Washington, Seattle, WA, USA
- Department of Epidemiology, University of Washington, Seattle, WA, USA
- Group Health Research Institute, Group Health Cooperative, Seattle, WA, USA
| | - Gerardo Heiss
- Department of Epidemiology, Gillings School of Global Public Health, University of North Carolina, Chapel Hill, NC, USA
| | - Lucia A Hindorff
- National Institutes of Health, National Human Genome Research Institute, Office of Population Genomics, Bethesda, MD, USA
| | - Wen-Chi Hsueh
- Phoenix Epidemiology and Clinical Research Branch, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Phoenix, AZ, USA
| | - Aaron Isaacs
- Genetic Epidemiology Unit, Department of Epidemiology, Erasmus University Medical Center, Rotterdam, the Netherlands
- CARIM School for Cardiovascular Diseases, Maastricht Centre for Systems Biology (MaCSBio), Dept. of Biochemistry, Maastricht University, Maastricht, the Netherlands
| | - Yalda Jamshidi
- Cardiogenetics Lab, Institute of Cardiovascular and Cell Sciences, St George's University of London, UK
| | - Kathleen F Kerr
- Department of Biostatistics, School of Public Health, University of Washington, Seattle, WA, USA
| | - Felix Liu
- Department of Epidemiology and Biostatistics, University of California, San Francisco, CA, USA
| | - Yongmei Liu
- Department of Epidemiology and Prevention, Division of Public Health Sciences, Wake Forest University, Winston-Salem, NC, USA
| | - Kurt K Lohman
- Department of Epidemiology and Prevention, Division of Public Health Sciences, Wake Forest University, Winston-Salem, NC, USA
| | - Jared W Magnani
- Department of Medicine, Division of Cardiology, University of Pittsburgh Medical Center Heart and Vascular Institute, University of Pittsburgh, Pittsburgh, PA, USA
| | - Joseph F Maher
- Department of Medicine, University of Mississippi Medical Center, Jackson, MS, USA
| | - Reena Mehra
- Program for Medical and Population Genetics, Broad Institute of Harvard and Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Yan A Meng
- Jackson Heart Study, University of Mississippi Medical Center, Jackson, MS, USA
| | - Solomon K Musani
- Cardiovascular Research Center and Center for Human Genetic Research, Massachusetts General Hospital and Harvard Medical School, Boston,MA, USA
| | - Christopher Newton-Cheh
- Jackson Heart Study, University of Mississippi Medical Center, Jackson, MS, USA
- Carolina Center for Genome Sciences, University of North Carolina, Chapel Hill, NC, USA
| | - Kari E North
- Department of Epidemiology, Gillings School of Global Public Health, University of North Carolina, Chapel Hill, NC, USA
- Department of Health Services, University of Washington, Seattle, WA, USA
| | - Bruce M Psaty
- Cardiovascular Health Research Unit, Department of Medicine, University of Washington, Seattle, WA, USA
- Department of Epidemiology, University of Washington, Seattle, WA, USA
- Group Health Research Institute, Group Health Cooperative, Seattle, WA, USA
- Department of Medicine, Division of Sleep Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | - Susan Redline
- Institute for Translational Genomics and Population Sciences, Los Angeles Biomedical Research Institute and Departments of Medicine and Pediatrics, Harbor-UCLA Medical Center, Torrance, CA, USA
| | - Jerome I Rotter
- University Heart Center Hamburg and German Center for Cardiovascular Research, Hamburg, Germany
| | | | - Nicholas J Schork
- Center for Cardiovascular Research, John A. Burns School of Medicine, University of Hawaii, Honolulu, HI, USA
| | - Ralph V Shohet
- Department of Cellular and Molecular Medicine, Cleveland Clinic, Cleveland, OH, USA
| | - Andrew B Singleton
- Laboratory of Neurogenetics, National Institute on Aging, National Institutes of Health, Bethesda, MD, USA
| | - Jonathan D Smith
- Epidemiological Cardiology Research Center (EPICARE), Department of Epidemiology and Prevention, Division of Public Health Sciences, Wake Forest School of Medicine, Winston-Salem, NC, USA
| | - Elsayed Z Soliman
- Department of Physiology and Biophysics, University of Mississippi Medical Center, Jackson, MS, USA
| | | | - Herman A Taylor
- Department of Medicine, University of Mississippi Medical Center, Jackson, MS, USA
| | - David R Van Wagoner
- Department of Molecular Cardiology, Lerner Research Institute, Cleveland Clinic, Cleveland, OH, USA
| | - James G Wilson
- Laboratory of Epidemiology and Population Science, National Institute on Aging, National Institutes of Health, Baltimore, MD, USA
| | - Taylor Young
- Jackson Heart Study, University of Mississippi Medical Center, Jackson, MS, USA
| | - Zhu-Ming Zhang
- Department of Physiology and Biophysics, University of Mississippi Medical Center, Jackson, MS, USA
| | - Alan B Zonderman
- Department of Pathology, University of California San Diego, La Jolla, CA, USA
| | - Michele K Evans
- Department of Pathology, University of California San Diego, La Jolla, CA, USA
| | - Luigi Ferrucci
- Translational Gerontology Branch, National Institute on Aging, National Institutes of Health, Baltimore, MD, USA
| | - Sarah S Murray
- Department of Medicine, School of Medicine, University of North Carolina, Chapel Hill, NC, USA
| | - Gregory J Tranah
- California Pacific Medical Center Research Institute, San Francisco, CA, USA
| | - Eric A Whitsel
- Department of Epidemiology, Gillings School of Global Public Health, University of North Carolina, Chapel Hill, NC, USA
- Membership of the CHARGE QRS Consortium is provided in the acknowledgements and
| | - Alex P Reiner
- Cardiovascular Health Research Unit, Department of Medicine, University of Washington, Seattle, WA, USA
- Division of Public Health Sciences, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - Nona Sotoodehnia
- Department of Epidemiology, University of Washington, Seattle, WA, USA .
- Division of Cardiology, University of Washington, Seattle, WA, USA
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18
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Chang L, Douet V, Bloss C, Lee K, Pritchett A, Jernigan TL, Akshoomoff N, Murray SS, Frazier J, Kennedy DN, Amaral DG, Gruen J, Kaufmann WE, Casey BJ, Sowell E, Ernst T. Gray matter maturation and cognition in children with different APOE ε genotypes. Neurology 2016; 87:585-94. [PMID: 27412137 DOI: 10.1212/wnl.0000000000002939] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2015] [Accepted: 03/28/2016] [Indexed: 01/15/2023] Open
Abstract
OBJECTIVE The aims of the current study were to determine whether children with the 6 different APOE ε genotypes show differences in gray matter maturation, particularly for those with ε4 and ε2 alleles, which are associated with poorer outcomes in many neurologic disorders. METHODS A total of 1,187 healthy children (aged 3-20 years, 52.1% boys, 47.9% girls) with acceptable data from the cross-sectional Pediatric Imaging Neurocognition and Genetics Study were evaluated for the effects of 6 APOE ε genotypes on macroscopic and microscopic cortical and subcortical gray matter structures (measured with 3-tesla MRI and FreeSurfer for automated morphometry) and on cognition (NIH Toolbox). RESULTS Among APOE ε4 carriers, age-related changes in brain structures and cognition varied depending on genotype, with the smallest hippocampi in ε2ε4 children, the lowest hippocampal fractional anisotropy in younger ε4ε4 children, the largest medial orbitofrontal cortical areas in ε3ε4 children, and age-dependent thinning of the entorhinal cortex in ε4ε4 children. Younger ε4ε4 children had the lowest scores on executive function and working memory, while younger ε2ε4 children performed worse on attention tasks. Larger parietal gyri in the younger ε2ε4 children, and thinner temporal and cingulate isthmus cortices or smaller hippocampi in the younger ε4ε4 children, predicted poorer performance on attention or working memory. CONCLUSIONS Our findings validated and extended prior smaller studies that showed altered brain development in APOE ε4-carrier children. The ε4ε4 and ε2ε4 genotypes may negatively influence brain development and brain aging at the extremes of age. Studying APOE ε polymorphisms in young children may provide the earliest indicators for individuals who might benefit from early interventions or preventive measures for future brain injuries and dementia.
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Affiliation(s)
- Linda Chang
- From the Department of Medicine (L.C., V.D., K.L., A.P., T.E.), John A. Burns School of Medicine, University of Hawaii and The Queen's Medical Center, Honolulu; Department of Psychiatry, School of Medicine (C.B.), Departments of Psychiatry and Cognitive Science (T.L.J., N.A.), and Department of Pathology (S.S.M.), University of California San Diego, La Jolla; Department of Psychiatry (J.F., D.N.K.), University of Massachusetts Medical School, Boston; Department of Psychiatry and Behavioral Sciences (D.G.A.), University of California, Davis; Departments of Pediatrics and Investigative Medicine (J.G.), Yale Child Health Research Center, Yale University School of Medicine, New Haven, CT; Boston Children's Hospital (W.E.K.), Harvard Medical School, Boston, MA; Sackler Institute for Developmental Psychobiology (B.J.C.), Weil Cornell Medical College, New York, NY; Department of Pediatrics (E.S.), University of Southern California, Los Angeles; and Children's Hospital (E.S.), Los Angeles, CA.
| | - Vanessa Douet
- From the Department of Medicine (L.C., V.D., K.L., A.P., T.E.), John A. Burns School of Medicine, University of Hawaii and The Queen's Medical Center, Honolulu; Department of Psychiatry, School of Medicine (C.B.), Departments of Psychiatry and Cognitive Science (T.L.J., N.A.), and Department of Pathology (S.S.M.), University of California San Diego, La Jolla; Department of Psychiatry (J.F., D.N.K.), University of Massachusetts Medical School, Boston; Department of Psychiatry and Behavioral Sciences (D.G.A.), University of California, Davis; Departments of Pediatrics and Investigative Medicine (J.G.), Yale Child Health Research Center, Yale University School of Medicine, New Haven, CT; Boston Children's Hospital (W.E.K.), Harvard Medical School, Boston, MA; Sackler Institute for Developmental Psychobiology (B.J.C.), Weil Cornell Medical College, New York, NY; Department of Pediatrics (E.S.), University of Southern California, Los Angeles; and Children's Hospital (E.S.), Los Angeles, CA
| | - Cinnamon Bloss
- From the Department of Medicine (L.C., V.D., K.L., A.P., T.E.), John A. Burns School of Medicine, University of Hawaii and The Queen's Medical Center, Honolulu; Department of Psychiatry, School of Medicine (C.B.), Departments of Psychiatry and Cognitive Science (T.L.J., N.A.), and Department of Pathology (S.S.M.), University of California San Diego, La Jolla; Department of Psychiatry (J.F., D.N.K.), University of Massachusetts Medical School, Boston; Department of Psychiatry and Behavioral Sciences (D.G.A.), University of California, Davis; Departments of Pediatrics and Investigative Medicine (J.G.), Yale Child Health Research Center, Yale University School of Medicine, New Haven, CT; Boston Children's Hospital (W.E.K.), Harvard Medical School, Boston, MA; Sackler Institute for Developmental Psychobiology (B.J.C.), Weil Cornell Medical College, New York, NY; Department of Pediatrics (E.S.), University of Southern California, Los Angeles; and Children's Hospital (E.S.), Los Angeles, CA
| | - Kristin Lee
- From the Department of Medicine (L.C., V.D., K.L., A.P., T.E.), John A. Burns School of Medicine, University of Hawaii and The Queen's Medical Center, Honolulu; Department of Psychiatry, School of Medicine (C.B.), Departments of Psychiatry and Cognitive Science (T.L.J., N.A.), and Department of Pathology (S.S.M.), University of California San Diego, La Jolla; Department of Psychiatry (J.F., D.N.K.), University of Massachusetts Medical School, Boston; Department of Psychiatry and Behavioral Sciences (D.G.A.), University of California, Davis; Departments of Pediatrics and Investigative Medicine (J.G.), Yale Child Health Research Center, Yale University School of Medicine, New Haven, CT; Boston Children's Hospital (W.E.K.), Harvard Medical School, Boston, MA; Sackler Institute for Developmental Psychobiology (B.J.C.), Weil Cornell Medical College, New York, NY; Department of Pediatrics (E.S.), University of Southern California, Los Angeles; and Children's Hospital (E.S.), Los Angeles, CA
| | - Alexandra Pritchett
- From the Department of Medicine (L.C., V.D., K.L., A.P., T.E.), John A. Burns School of Medicine, University of Hawaii and The Queen's Medical Center, Honolulu; Department of Psychiatry, School of Medicine (C.B.), Departments of Psychiatry and Cognitive Science (T.L.J., N.A.), and Department of Pathology (S.S.M.), University of California San Diego, La Jolla; Department of Psychiatry (J.F., D.N.K.), University of Massachusetts Medical School, Boston; Department of Psychiatry and Behavioral Sciences (D.G.A.), University of California, Davis; Departments of Pediatrics and Investigative Medicine (J.G.), Yale Child Health Research Center, Yale University School of Medicine, New Haven, CT; Boston Children's Hospital (W.E.K.), Harvard Medical School, Boston, MA; Sackler Institute for Developmental Psychobiology (B.J.C.), Weil Cornell Medical College, New York, NY; Department of Pediatrics (E.S.), University of Southern California, Los Angeles; and Children's Hospital (E.S.), Los Angeles, CA
| | - Terry L Jernigan
- From the Department of Medicine (L.C., V.D., K.L., A.P., T.E.), John A. Burns School of Medicine, University of Hawaii and The Queen's Medical Center, Honolulu; Department of Psychiatry, School of Medicine (C.B.), Departments of Psychiatry and Cognitive Science (T.L.J., N.A.), and Department of Pathology (S.S.M.), University of California San Diego, La Jolla; Department of Psychiatry (J.F., D.N.K.), University of Massachusetts Medical School, Boston; Department of Psychiatry and Behavioral Sciences (D.G.A.), University of California, Davis; Departments of Pediatrics and Investigative Medicine (J.G.), Yale Child Health Research Center, Yale University School of Medicine, New Haven, CT; Boston Children's Hospital (W.E.K.), Harvard Medical School, Boston, MA; Sackler Institute for Developmental Psychobiology (B.J.C.), Weil Cornell Medical College, New York, NY; Department of Pediatrics (E.S.), University of Southern California, Los Angeles; and Children's Hospital (E.S.), Los Angeles, CA
| | - Natacha Akshoomoff
- From the Department of Medicine (L.C., V.D., K.L., A.P., T.E.), John A. Burns School of Medicine, University of Hawaii and The Queen's Medical Center, Honolulu; Department of Psychiatry, School of Medicine (C.B.), Departments of Psychiatry and Cognitive Science (T.L.J., N.A.), and Department of Pathology (S.S.M.), University of California San Diego, La Jolla; Department of Psychiatry (J.F., D.N.K.), University of Massachusetts Medical School, Boston; Department of Psychiatry and Behavioral Sciences (D.G.A.), University of California, Davis; Departments of Pediatrics and Investigative Medicine (J.G.), Yale Child Health Research Center, Yale University School of Medicine, New Haven, CT; Boston Children's Hospital (W.E.K.), Harvard Medical School, Boston, MA; Sackler Institute for Developmental Psychobiology (B.J.C.), Weil Cornell Medical College, New York, NY; Department of Pediatrics (E.S.), University of Southern California, Los Angeles; and Children's Hospital (E.S.), Los Angeles, CA
| | - Sarah S Murray
- From the Department of Medicine (L.C., V.D., K.L., A.P., T.E.), John A. Burns School of Medicine, University of Hawaii and The Queen's Medical Center, Honolulu; Department of Psychiatry, School of Medicine (C.B.), Departments of Psychiatry and Cognitive Science (T.L.J., N.A.), and Department of Pathology (S.S.M.), University of California San Diego, La Jolla; Department of Psychiatry (J.F., D.N.K.), University of Massachusetts Medical School, Boston; Department of Psychiatry and Behavioral Sciences (D.G.A.), University of California, Davis; Departments of Pediatrics and Investigative Medicine (J.G.), Yale Child Health Research Center, Yale University School of Medicine, New Haven, CT; Boston Children's Hospital (W.E.K.), Harvard Medical School, Boston, MA; Sackler Institute for Developmental Psychobiology (B.J.C.), Weil Cornell Medical College, New York, NY; Department of Pediatrics (E.S.), University of Southern California, Los Angeles; and Children's Hospital (E.S.), Los Angeles, CA
| | - Jean Frazier
- From the Department of Medicine (L.C., V.D., K.L., A.P., T.E.), John A. Burns School of Medicine, University of Hawaii and The Queen's Medical Center, Honolulu; Department of Psychiatry, School of Medicine (C.B.), Departments of Psychiatry and Cognitive Science (T.L.J., N.A.), and Department of Pathology (S.S.M.), University of California San Diego, La Jolla; Department of Psychiatry (J.F., D.N.K.), University of Massachusetts Medical School, Boston; Department of Psychiatry and Behavioral Sciences (D.G.A.), University of California, Davis; Departments of Pediatrics and Investigative Medicine (J.G.), Yale Child Health Research Center, Yale University School of Medicine, New Haven, CT; Boston Children's Hospital (W.E.K.), Harvard Medical School, Boston, MA; Sackler Institute for Developmental Psychobiology (B.J.C.), Weil Cornell Medical College, New York, NY; Department of Pediatrics (E.S.), University of Southern California, Los Angeles; and Children's Hospital (E.S.), Los Angeles, CA
| | - David N Kennedy
- From the Department of Medicine (L.C., V.D., K.L., A.P., T.E.), John A. Burns School of Medicine, University of Hawaii and The Queen's Medical Center, Honolulu; Department of Psychiatry, School of Medicine (C.B.), Departments of Psychiatry and Cognitive Science (T.L.J., N.A.), and Department of Pathology (S.S.M.), University of California San Diego, La Jolla; Department of Psychiatry (J.F., D.N.K.), University of Massachusetts Medical School, Boston; Department of Psychiatry and Behavioral Sciences (D.G.A.), University of California, Davis; Departments of Pediatrics and Investigative Medicine (J.G.), Yale Child Health Research Center, Yale University School of Medicine, New Haven, CT; Boston Children's Hospital (W.E.K.), Harvard Medical School, Boston, MA; Sackler Institute for Developmental Psychobiology (B.J.C.), Weil Cornell Medical College, New York, NY; Department of Pediatrics (E.S.), University of Southern California, Los Angeles; and Children's Hospital (E.S.), Los Angeles, CA
| | - David G Amaral
- From the Department of Medicine (L.C., V.D., K.L., A.P., T.E.), John A. Burns School of Medicine, University of Hawaii and The Queen's Medical Center, Honolulu; Department of Psychiatry, School of Medicine (C.B.), Departments of Psychiatry and Cognitive Science (T.L.J., N.A.), and Department of Pathology (S.S.M.), University of California San Diego, La Jolla; Department of Psychiatry (J.F., D.N.K.), University of Massachusetts Medical School, Boston; Department of Psychiatry and Behavioral Sciences (D.G.A.), University of California, Davis; Departments of Pediatrics and Investigative Medicine (J.G.), Yale Child Health Research Center, Yale University School of Medicine, New Haven, CT; Boston Children's Hospital (W.E.K.), Harvard Medical School, Boston, MA; Sackler Institute for Developmental Psychobiology (B.J.C.), Weil Cornell Medical College, New York, NY; Department of Pediatrics (E.S.), University of Southern California, Los Angeles; and Children's Hospital (E.S.), Los Angeles, CA
| | - Jeffrey Gruen
- From the Department of Medicine (L.C., V.D., K.L., A.P., T.E.), John A. Burns School of Medicine, University of Hawaii and The Queen's Medical Center, Honolulu; Department of Psychiatry, School of Medicine (C.B.), Departments of Psychiatry and Cognitive Science (T.L.J., N.A.), and Department of Pathology (S.S.M.), University of California San Diego, La Jolla; Department of Psychiatry (J.F., D.N.K.), University of Massachusetts Medical School, Boston; Department of Psychiatry and Behavioral Sciences (D.G.A.), University of California, Davis; Departments of Pediatrics and Investigative Medicine (J.G.), Yale Child Health Research Center, Yale University School of Medicine, New Haven, CT; Boston Children's Hospital (W.E.K.), Harvard Medical School, Boston, MA; Sackler Institute for Developmental Psychobiology (B.J.C.), Weil Cornell Medical College, New York, NY; Department of Pediatrics (E.S.), University of Southern California, Los Angeles; and Children's Hospital (E.S.), Los Angeles, CA
| | - Walter E Kaufmann
- From the Department of Medicine (L.C., V.D., K.L., A.P., T.E.), John A. Burns School of Medicine, University of Hawaii and The Queen's Medical Center, Honolulu; Department of Psychiatry, School of Medicine (C.B.), Departments of Psychiatry and Cognitive Science (T.L.J., N.A.), and Department of Pathology (S.S.M.), University of California San Diego, La Jolla; Department of Psychiatry (J.F., D.N.K.), University of Massachusetts Medical School, Boston; Department of Psychiatry and Behavioral Sciences (D.G.A.), University of California, Davis; Departments of Pediatrics and Investigative Medicine (J.G.), Yale Child Health Research Center, Yale University School of Medicine, New Haven, CT; Boston Children's Hospital (W.E.K.), Harvard Medical School, Boston, MA; Sackler Institute for Developmental Psychobiology (B.J.C.), Weil Cornell Medical College, New York, NY; Department of Pediatrics (E.S.), University of Southern California, Los Angeles; and Children's Hospital (E.S.), Los Angeles, CA
| | - B J Casey
- From the Department of Medicine (L.C., V.D., K.L., A.P., T.E.), John A. Burns School of Medicine, University of Hawaii and The Queen's Medical Center, Honolulu; Department of Psychiatry, School of Medicine (C.B.), Departments of Psychiatry and Cognitive Science (T.L.J., N.A.), and Department of Pathology (S.S.M.), University of California San Diego, La Jolla; Department of Psychiatry (J.F., D.N.K.), University of Massachusetts Medical School, Boston; Department of Psychiatry and Behavioral Sciences (D.G.A.), University of California, Davis; Departments of Pediatrics and Investigative Medicine (J.G.), Yale Child Health Research Center, Yale University School of Medicine, New Haven, CT; Boston Children's Hospital (W.E.K.), Harvard Medical School, Boston, MA; Sackler Institute for Developmental Psychobiology (B.J.C.), Weil Cornell Medical College, New York, NY; Department of Pediatrics (E.S.), University of Southern California, Los Angeles; and Children's Hospital (E.S.), Los Angeles, CA
| | - Elizabeth Sowell
- From the Department of Medicine (L.C., V.D., K.L., A.P., T.E.), John A. Burns School of Medicine, University of Hawaii and The Queen's Medical Center, Honolulu; Department of Psychiatry, School of Medicine (C.B.), Departments of Psychiatry and Cognitive Science (T.L.J., N.A.), and Department of Pathology (S.S.M.), University of California San Diego, La Jolla; Department of Psychiatry (J.F., D.N.K.), University of Massachusetts Medical School, Boston; Department of Psychiatry and Behavioral Sciences (D.G.A.), University of California, Davis; Departments of Pediatrics and Investigative Medicine (J.G.), Yale Child Health Research Center, Yale University School of Medicine, New Haven, CT; Boston Children's Hospital (W.E.K.), Harvard Medical School, Boston, MA; Sackler Institute for Developmental Psychobiology (B.J.C.), Weil Cornell Medical College, New York, NY; Department of Pediatrics (E.S.), University of Southern California, Los Angeles; and Children's Hospital (E.S.), Los Angeles, CA
| | - Thomas Ernst
- From the Department of Medicine (L.C., V.D., K.L., A.P., T.E.), John A. Burns School of Medicine, University of Hawaii and The Queen's Medical Center, Honolulu; Department of Psychiatry, School of Medicine (C.B.), Departments of Psychiatry and Cognitive Science (T.L.J., N.A.), and Department of Pathology (S.S.M.), University of California San Diego, La Jolla; Department of Psychiatry (J.F., D.N.K.), University of Massachusetts Medical School, Boston; Department of Psychiatry and Behavioral Sciences (D.G.A.), University of California, Davis; Departments of Pediatrics and Investigative Medicine (J.G.), Yale Child Health Research Center, Yale University School of Medicine, New Haven, CT; Boston Children's Hospital (W.E.K.), Harvard Medical School, Boston, MA; Sackler Institute for Developmental Psychobiology (B.J.C.), Weil Cornell Medical College, New York, NY; Department of Pediatrics (E.S.), University of Southern California, Los Angeles; and Children's Hospital (E.S.), Los Angeles, CA
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19
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Pramparo T, Lombardo MV, Campbell K, Barnes CC, Marinero S, Solso S, Young J, Mayo M, Dale A, Ahrens-Barbeau C, Murray SS, Lopez L, Lewis N, Pierce K, Courchesne E. Cell cycle networks link gene expression dysregulation, mutation, and brain maldevelopment in autistic toddlers. Mol Syst Biol 2015; 11:841. [PMID: 26668231 PMCID: PMC4704485 DOI: 10.15252/msb.20156108] [Citation(s) in RCA: 55] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023] Open
Abstract
Genetic mechanisms underlying abnormal early neural development in toddlers with Autism Spectrum Disorder (ASD) remain uncertain due to the impossibility of direct brain gene expression measurement during critical periods of early development. Recent findings from a multi‐tissue study demonstrated high expression of many of the same gene networks between blood and brain tissues, in particular with cell cycle functions. We explored relationships between blood gene expression and total brain volume (TBV) in 142 ASD and control male toddlers. In control toddlers, TBV variation significantly correlated with cell cycle and protein folding gene networks, potentially impacting neuron number and synapse development. In ASD toddlers, their correlations with brain size were lost as a result of considerable changes in network organization, while cell adhesion gene networks significantly correlated with TBV variation. Cell cycle networks detected in blood are highly preserved in the human brain and are upregulated during prenatal states of development. Overall, alterations were more pronounced in bigger brains. We identified 23 candidate genes for brain maldevelopment linked to 32 genes frequently mutated in ASD. The integrated network includes genes that are dysregulated in leukocyte and/or postmortem brain tissue of ASD subjects and belong to signaling pathways regulating cell cycle G1/S and G2/M phase transition. Finally, analyses of the CHD8 subnetwork and altered transcript levels from an independent study of CHD8 suppression further confirmed the central role of genes regulating neurogenesis and cell adhesion processes in ASD brain maldevelopment.
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Affiliation(s)
- Tiziano Pramparo
- Department of Neurosciences, UC San Diego Autism Center, School of Medicine University of California San Diego, La Jolla, CA, USA
| | - Michael V Lombardo
- Department of Psychology, University of Cyprus, Nicosia, Cyprus Center for Applied Neuroscience, University of Cyprus, Nicosia, Cyprus Autism Research Centre, Department of Psychiatry, University of Cambridge, Cambridge, UK
| | - Kathleen Campbell
- Department of Neurosciences, UC San Diego Autism Center, School of Medicine University of California San Diego, La Jolla, CA, USA
| | - Cynthia Carter Barnes
- Department of Neurosciences, UC San Diego Autism Center, School of Medicine University of California San Diego, La Jolla, CA, USA
| | - Steven Marinero
- Department of Neurosciences, UC San Diego Autism Center, School of Medicine University of California San Diego, La Jolla, CA, USA
| | - Stephanie Solso
- Department of Neurosciences, UC San Diego Autism Center, School of Medicine University of California San Diego, La Jolla, CA, USA
| | - Julia Young
- Department of Neurosciences, UC San Diego Autism Center, School of Medicine University of California San Diego, La Jolla, CA, USA
| | - Maisi Mayo
- Department of Neurosciences, UC San Diego Autism Center, School of Medicine University of California San Diego, La Jolla, CA, USA
| | - Anders Dale
- Department of Neurosciences, UC San Diego Autism Center, School of Medicine University of California San Diego, La Jolla, CA, USA
| | - Clelia Ahrens-Barbeau
- Department of Neurosciences, UC San Diego Autism Center, School of Medicine University of California San Diego, La Jolla, CA, USA
| | - Sarah S Murray
- Scripps Genomic Medicine & The Scripps Translational Sciences Institute (STSI), La Jolla, CA, USA Department of Pathology, University of California San Diego, La Jolla, CA, USA
| | - Linda Lopez
- Department of Neurosciences, UC San Diego Autism Center, School of Medicine University of California San Diego, La Jolla, CA, USA
| | - Nathan Lewis
- Novo Nordisk Foundation Center for Biosustainability at the UCSD School of Medicine, and Department of Pediatrics, University of California San Diego, La Jolla, CA, USA
| | - Karen Pierce
- Department of Neurosciences, UC San Diego Autism Center, School of Medicine University of California San Diego, La Jolla, CA, USA
| | - Eric Courchesne
- Department of Neurosciences, UC San Diego Autism Center, School of Medicine University of California San Diego, La Jolla, CA, USA
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20
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Newman E, Thompson WK, Bartsch H, Hagler DJ, Chen CH, Brown TT, Kuperman JM, McCabe C, Chung Y, Libiger O, Akshoomoff N, Bloss CS, Casey BJ, Chang L, Ernst TM, Frazier JA, Gruen JR, Kennedy DN, Murray SS, Sowell ER, Schork N, Kenet T, Kaufmann WE, Mostofsky S, Amaral DG, Dale AM, Jernigan TL. Anxiety is related to indices of cortical maturation in typically developing children and adolescents. Brain Struct Funct 2015; 221:3013-25. [PMID: 26183468 DOI: 10.1007/s00429-015-1085-9] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2015] [Accepted: 07/07/2015] [Indexed: 12/19/2022]
Abstract
Anxiety is a risk factor for many adverse neuropsychiatric and socioeconomic outcomes, and has been linked to functional and structural changes in the ventromedial prefrontal cortex (VMPFC). However, the nature of these differences, as well as how they develop in children and adolescents, remains poorly understood. More effective interventions to minimize the negative consequences of anxiety require better understanding of its neurobiology in children. Recent research suggests that structural imaging studies may benefit from clearly delineating between cortical surface area and thickness when examining these associations, as these distinct cortical phenotypes are influenced by different cellular mechanisms and genetic factors. The present study examined relationships between cortical surface area and thickness of the VMPFC and a self-report measure of anxiety (SCARED-R) in 287 youths aged 7-20 years from the Pediatric Imaging, Neurocognition, and Genetics (PING) study. Age and gender interactions were examined for significant associations in order to test for developmental differences. Cortical surface area and thickness were also examined simultaneously to determine whether they contribute independently to the prediction of anxiety. Anxiety was negatively associated with relative cortical surface area of the VMPFC as well as with global cortical thickness, but these associations diminished with age. The two cortical phenotypes contributed additively to the prediction of anxiety. These findings suggest that higher anxiety in children may be characterized by both delayed expansion of the VMPFC and an altered trajectory of global cortical thinning. Further longitudinal studies will be needed to confirm these findings.
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Affiliation(s)
- Erik Newman
- Center for Human Development, University of California, San Diego, 9500 Gilman Drive, MC 0115, La Jolla, CA, 92093, USA. .,Department of Psychiatry, University of California, San Diego, La Jolla, CA, USA.
| | - Wesley K Thompson
- Department of Psychiatry, University of California, San Diego, La Jolla, CA, USA.,Stein Institute for Research on Aging, University of California, San Diego, La Jolla, CA, USA
| | - Hauke Bartsch
- Multimodal Imaging Laboratory, University of California, San Diego, La Jolla, CA, USA
| | - Donald J Hagler
- Multimodal Imaging Laboratory, University of California, San Diego, La Jolla, CA, USA.,Department of Radiology, University of California, San Diego, La Jolla, CA, USA
| | - Chi-Hua Chen
- Department of Psychiatry, University of California, San Diego, La Jolla, CA, USA.,Multimodal Imaging Laboratory, University of California, San Diego, La Jolla, CA, USA
| | - Timothy T Brown
- Multimodal Imaging Laboratory, University of California, San Diego, La Jolla, CA, USA.,Department of Neurosciences, University of California, San Diego, La Jolla, CA, USA
| | - Joshua M Kuperman
- Multimodal Imaging Laboratory, University of California, San Diego, La Jolla, CA, USA.,Department of Radiology, University of California, San Diego, La Jolla, CA, USA
| | - Connor McCabe
- Center for Human Development, University of California, San Diego, 9500 Gilman Drive, MC 0115, La Jolla, CA, 92093, USA.,Department of Psychology, University of Washington, Seattle, WA, USA
| | - Yoonho Chung
- Center for Human Development, University of California, San Diego, 9500 Gilman Drive, MC 0115, La Jolla, CA, 92093, USA.,Multimodal Imaging Laboratory, University of California, San Diego, La Jolla, CA, USA.,Department of Psychology, Yale University, New Haven, CT, USA
| | - Ondrej Libiger
- Scripps Genomic Medicine, Scripps Translational Science Institute and Scripps Health, La Jolla, CA, USA
| | - Natacha Akshoomoff
- Center for Human Development, University of California, San Diego, 9500 Gilman Drive, MC 0115, La Jolla, CA, 92093, USA.,Department of Psychiatry, University of California, San Diego, La Jolla, CA, USA
| | - Cinnamon S Bloss
- Scripps Genomic Medicine, Scripps Translational Science Institute and Scripps Health, La Jolla, CA, USA
| | - B J Casey
- Sackler Institute for Developmental Psychobiology, Weil Cornell Medical College, New York, NY, USA
| | - Linda Chang
- Department of Medicine, University of Hawaii and Queen's Medical Center, Honolulu, HI, USA
| | - Thomas M Ernst
- Department of Medicine, University of Hawaii and Queen's Medical Center, Honolulu, HI, USA
| | - Jean A Frazier
- Department of Psychiatry, University of Massachusetts Medical School, Boston, MA, USA
| | - Jeffrey R Gruen
- Department of Pediatrics, Yale University School of Medicine, New Haven, CT, USA.,Department of Genetics, Yale University School of Medicine, New Haven, CT, USA
| | - David N Kennedy
- Department of Psychiatry, University of Massachusetts Medical School, Boston, MA, USA
| | - Sarah S Murray
- Department of Pathology, University of California, San Diego, La Jolla, CA, USA
| | - Elizabeth R Sowell
- Department of Pediatrics, University of Southern California, Los Angeles, CA, USA.,Children's Hospital, Los Angeles, CA, USA
| | - Nicholas Schork
- Scripps Genomic Medicine, Scripps Translational Science Institute and Scripps Health, La Jolla, CA, USA
| | - Tal Kenet
- Department of Neurology and Athinoula A. Martinos Center for Biomedical Imaging, Massachusetts General Hospital, Charlestown, MA, USA
| | - Walter E Kaufmann
- Boston Children's Hospital and Harvard Medical School, Boston, MA, USA
| | - Stewart Mostofsky
- Kennedy Krieger Institute and Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - David G Amaral
- Department of Psychiatry and Behavioral Sciences, University of California, Davis, Davis, CA, USA
| | - Anders M Dale
- Multimodal Imaging Laboratory, University of California, San Diego, La Jolla, CA, USA.,Department of Radiology, University of California, San Diego, La Jolla, CA, USA.,Department of Neurosciences, University of California, San Diego, La Jolla, CA, USA.,Department of Cognitive Science, University of California, San Diego, La Jolla, CA, USA
| | - Terry L Jernigan
- Center for Human Development, University of California, San Diego, 9500 Gilman Drive, MC 0115, La Jolla, CA, 92093, USA.,Department of Psychiatry, University of California, San Diego, La Jolla, CA, USA.,Department of Radiology, University of California, San Diego, La Jolla, CA, USA.,Department of Cognitive Science, University of California, San Diego, La Jolla, CA, USA
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21
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Jernigan TL, Brown TT, Hagler DJ, Akshoomoff N, Bartsch H, Newman E, Thompson WK, Bloss CS, Murray SS, Schork N, Kennedy DN, Kuperman JM, McCabe C, Chung Y, Libiger O, Maddox M, Casey BJ, Chang L, Ernst TM, Frazier JA, Gruen JR, Sowell ER, Kenet T, Kaufmann WE, Mostofsky S, Amaral DG, Dale AM. The Pediatric Imaging, Neurocognition, and Genetics (PING) Data Repository. Neuroimage 2015; 124:1149-1154. [PMID: 25937488 DOI: 10.1016/j.neuroimage.2015.04.057] [Citation(s) in RCA: 182] [Impact Index Per Article: 20.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2015] [Revised: 04/26/2015] [Accepted: 04/27/2015] [Indexed: 11/16/2022] Open
Abstract
The main objective of the multi-site Pediatric Imaging, Neurocognition, and Genetics (PING) study was to create a large repository of standardized measurements of behavioral and imaging phenotypes accompanied by whole genome genotyping acquired from typically-developing children varying widely in age (3 to 20 years). This cross-sectional study produced sharable data from 1493 children, and these data have been described in several publications focusing on brain and cognitive development. Researchers may gain access to these data by applying for an account on the PING portal and filing a data use agreement. Here we describe the recruiting and screening of the children and give a brief overview of the assessments performed, the imaging methods applied, the genetic data produced, and the numbers of cases for whom different data types are available. We also cite sources of more detailed information about the methods and data. Finally we describe the procedures for accessing the data and for using the PING data exploration portal.
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Affiliation(s)
- Terry L Jernigan
- Center for Human Development, University of California, San Diego, La Jolla, CA, USA; Department of Cognitive Science, University of California, San Diego, La Jolla, CA, USA; Department of Psychiatry, University of California, San Diego, La Jolla, CA, USA.
| | - Timothy T Brown
- Multimodal Imaging Laboratory, University of California, San Diego, La Jolla, CA, USA; Department of Neurosciences, University of California, San Diego, La Jolla, CA, USA
| | - Donald J Hagler
- Multimodal Imaging Laboratory, University of California, San Diego, La Jolla, CA, USA; Department of Radiology, University of California, San Diego, La Jolla, CA, USA
| | - Natacha Akshoomoff
- Center for Human Development, University of California, San Diego, La Jolla, CA, USA; Department of Psychiatry, University of California, San Diego, La Jolla, CA, USA
| | - Hauke Bartsch
- Multimodal Imaging Laboratory, University of California, San Diego, La Jolla, CA, USA
| | - Erik Newman
- Center for Human Development, University of California, San Diego, La Jolla, CA, USA; Department of Psychiatry, University of California, San Diego, La Jolla, CA, USA
| | - Wesley K Thompson
- Department of Psychiatry, University of California, San Diego, La Jolla, CA, USA; Stein Institute for Research on Aging, University of California, San Diego, La Jolla, CA, USA
| | - Cinnamon S Bloss
- The Qualcomm Institute, University of California, San Diego, La Jolla, CA, USA
| | - Sarah S Murray
- Department of Pathology, University of California, San Diego, La Jolla, CA, USA
| | | | - David N Kennedy
- Department of Psychiatry, University of Massachusetts Medical School, Boston, MA, USA
| | - Joshua M Kuperman
- Multimodal Imaging Laboratory, University of California, San Diego, La Jolla, CA, USA; Department of Radiology, University of California, San Diego, La Jolla, CA, USA
| | - Connor McCabe
- Department of Psychology, University of Washington, Seattle, WA, USA
| | - Yoonho Chung
- Department of Psychology, Yale University, New Haven, CT, USA
| | - Ondrej Libiger
- The Qualcomm Institute, University of California, San Diego, La Jolla, CA, USA
| | - Melanie Maddox
- Center for Human Development, University of California, San Diego, La Jolla, CA, USA
| | - B J Casey
- Sackler Institute for Developmental Psychobiology, Weil Cornell Medical College, New York, NY, USA
| | - Linda Chang
- Department of Medicine, University of Hawaii, Queen's Medical Center, Honolulu, HI, USA
| | - Thomas M Ernst
- Department of Medicine, University of Hawaii, Queen's Medical Center, Honolulu, HI, USA
| | - Jean A Frazier
- Department of Psychiatry, University of Massachusetts Medical School, Boston, MA, USA
| | - Jeffrey R Gruen
- Departments of Pediatrics and Genetics, Yale University, School of Medicine, New Haven, CT, USA
| | - Elizabeth R Sowell
- Department of Pediatrics, University of Southern California, Children's Hospital Los Angeles, Los Angeles, CA, USA
| | - Tal Kenet
- Department of Neurology, Athinoula A. Martinos Center for Biomedical Imaging, Massachusetts General Hospital, Charlestown, MA, USA
| | | | - Stewart Mostofsky
- Kennedy Krieger Institute, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | - David G Amaral
- Department of Psychiatry and Behavioral Sciences, University of California-Davis, Davis, CA, USA
| | - Anders M Dale
- Department of Cognitive Science, University of California, San Diego, La Jolla, CA, USA; Multimodal Imaging Laboratory, University of California, San Diego, La Jolla, CA, USA; Department of Neurosciences, University of California, San Diego, La Jolla, CA, USA; Department of Radiology, University of California, San Diego, La Jolla, CA, USA
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22
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Pramparo T, Pierce K, Lombardo MV, Carter Barnes C, Marinero S, Ahrens-Barbeau C, Murray SS, Lopez L, Xu R, Courchesne E. Prediction of autism by translation and immune/inflammation coexpressed genes in toddlers from pediatric community practices. JAMA Psychiatry 2015; 72:386-94. [PMID: 25739104 DOI: 10.1001/jamapsychiatry.2014.3008] [Citation(s) in RCA: 65] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/14/2022]
Abstract
IMPORTANCE The identification of genomic signatures that aid early identification of individuals at risk for autism spectrum disorder (ASD) in the toddler period remains a major challenge because of the genetic and phenotypic heterogeneity of the disorder. Generally, ASD is not diagnosed before the fourth to fifth birthday. OBJECTIVE To apply a functional genomic approach to identify a biologically relevant signature with promising performance in the diagnostic classification of infants and toddlers with ASD. DESIGN, SETTING, AND PARTICIPANTS Proof-of-principle study of leukocyte RNA expression levels from 2 independent cohorts of children aged 1 to 4 years (142 discovery participants and 73 replication participants) using Illumina microarrays. Coexpression analysis of differentially expressed genes between Discovery ASD and control toddlers were used to define gene modules and eigengenes used in a diagnostic classification analysis. Independent validation of the classifier performance was tested on the replication cohort. Pathway enrichment and protein-protein interaction analyses were used to confirm biological relevance of the functional networks in the classifier. Participant recruitment occurred in general pediatric clinics and community settings. Male infants and toddlers (age range, 1-4 years) were enrolled in the study. Recruitment criteria followed the 1-Year Well-Baby Check-Up Approach. Diagnostic judgment followed DSM-IV-TR and Autism Diagnostic Observation Schedule criteria for autism. Participants with ASD were compared with control groups composed of typically developing toddlers as well as toddlers with global developmental or language delay. MAIN OUTCOMES AND MEASURES Logistic regression and receiver operating characteristic curve analysis were used in a classification test to establish the accuracy, specificity, and sensitivity of the module-based classifier. RESULTS Our signature of differentially coexpressed genes was enriched in translation and immune/inflammation functions and produced 83% accuracy. In an independent test with approximately half of the sample and a different microarray, the diagnostic classification of ASD vs control samples was 75% accurate. Consistent with its ASD specificity, our signature did not distinguish toddlers with global developmental or language delay from typically developing toddlers (62% accuracy). CONCLUSIONS AND RELEVANCE This proof-of-principle study demonstrated that genomic biomarkers with very good sensitivity and specificity for boys with ASD in general pediatric settings can be identified. It also showed that a blood-based clinical test for at-risk male infants and toddlers could be refined and routinely implemented in pediatric diagnostic settings.
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Affiliation(s)
- Tiziano Pramparo
- UC San Diego Autism Center of Excellence, Department of Neuroscience, University of California, San Diego School of Medicine, La Jolla
| | - Karen Pierce
- UC San Diego Autism Center of Excellence, Department of Neuroscience, University of California, San Diego School of Medicine, La Jolla
| | - Michael V Lombardo
- Autism Research Centre, Department of Psychiatry, University of Cambridge, Cambridge, United Kingdom3Department of Psychology, University of Cyprus, Nicosia, Cyprus4Center for Applied Neuroscience, University of Cyprus, Nicosia, Cyprus
| | - Cynthia Carter Barnes
- UC San Diego Autism Center of Excellence, Department of Neuroscience, University of California, San Diego School of Medicine, La Jolla
| | - Steven Marinero
- UC San Diego Autism Center of Excellence, Department of Neuroscience, University of California, San Diego School of Medicine, La Jolla
| | - Clelia Ahrens-Barbeau
- UC San Diego Autism Center of Excellence, Department of Neuroscience, University of California, San Diego School of Medicine, La Jolla
| | - Sarah S Murray
- Scripps Genomic Medicine and Scripps Translational Sciences Institute, La Jolla, California6Department of Pathology, University of California, San Diego, La Jolla
| | - Linda Lopez
- UC San Diego Autism Center of Excellence, Department of Neuroscience, University of California, San Diego School of Medicine, La Jolla
| | - Ronghui Xu
- Department of Family and Preventive Medicine, University of California, San Diego, La Jolla8Department of Mathematics, University of California, San Diego, La Jolla
| | - Eric Courchesne
- UC San Diego Autism Center of Excellence, Department of Neuroscience, University of California, San Diego School of Medicine, La Jolla
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23
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Noble KG, Houston SM, Brito NH, Bartsch H, Kan E, Kuperman JM, Akshoomoff N, Amaral DG, Bloss CS, Libiger O, Schork NJ, Murray SS, Casey BJ, Chang L, Ernst TM, Frazier JA, Gruen JR, Kennedy DN, Van Zijl P, Mostofsky S, Kaufmann WE, Kenet T, Dale AM, Jernigan TL, Sowell ER. Family income, parental education and brain structure in children and adolescents. Nat Neurosci 2015; 18:773-8. [PMID: 25821911 PMCID: PMC4414816 DOI: 10.1038/nn.3983] [Citation(s) in RCA: 663] [Impact Index Per Article: 73.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2014] [Accepted: 02/27/2015] [Indexed: 01/18/2023]
Abstract
Socioeconomic disparities are associated with differences in cognitive development. The extent to which this translates to disparities in brain structure is unclear. Here, we investigated relationships between socioeconomic factors and brain morphometry, independently of genetic ancestry, among a cohort of 1099 typically developing individuals between 3 and 20 years. Income was logarithmically associated with brain surface area. Specifically, among children from lower income families, small differences in income were associated with relatively large differences in surface area, whereas, among children from higher income families, similar income increments were associated with smaller differences in surface area. These relationships were most prominent in regions supporting language, reading, executive functions and spatial skills; surface area mediated socioeconomic differences in certain neurocognitive abilities. These data indicate that income relates most strongly to brain structure among the most disadvantaged children. Potential implications are discussed.
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Affiliation(s)
- Kimberly G Noble
- 1] College of Physicians and Surgeons, Columbia University, New York, New York, USA. [2] Teachers College, Columbia University, New York, New York, USA
| | - Suzanne M Houston
- 1] Department of Psychology, University of Southern California, Los Angeles, California, USA. [2] The Saban Research Institute of Children's Hospital, Los Angeles, California, USA. [3] Department of Pediatrics of the Keck School of Medicine, University of Southern California, Los Angeles, California, USA
| | - Natalie H Brito
- Robert Wood Johnson Health and Society Scholar Program, Columbia University, New York, New York, USA
| | - Hauke Bartsch
- Stein Institute for Research on Aging, University of California, San Diego, La Jolla, California, USA
| | - Eric Kan
- 1] The Saban Research Institute of Children's Hospital, Los Angeles, California, USA. [2] Department of Pediatrics of the Keck School of Medicine, University of Southern California, Los Angeles, California, USA
| | - Joshua M Kuperman
- 1] Multimodal Imaging Laboratory, University of California, San Diego, La Jolla, California, USA. [2] Department of Radiology, University of California, San Diego, La Jolla, California, USA. [3] The Pediatric Imaging, Neurocognition, and Genetics Study, San Diego, California, USA
| | - Natacha Akshoomoff
- 1] The Pediatric Imaging, Neurocognition, and Genetics Study, San Diego, California, USA. [2] Center for Human Development, University of California, San Diego, La Jolla, California, USA. [3] Department of Psychiatry, University of California, San Diego, La Jolla, California, USA
| | - David G Amaral
- 1] The Pediatric Imaging, Neurocognition, and Genetics Study, San Diego, California, USA. [2] The MIND Institute, University of California at Davis, Davis, California, USA
| | - Cinnamon S Bloss
- 1] The Pediatric Imaging, Neurocognition, and Genetics Study, San Diego, California, USA. [2] The Qualcomm Institute, University of California, San Diego, La Jolla, California, USA
| | | | - Nicholas J Schork
- Human Biology, J. Craig Venter Institute, University of California, San Diego, La Jolla, California, USA
| | - Sarah S Murray
- 1] The Pediatric Imaging, Neurocognition, and Genetics Study, San Diego, California, USA. [2] Department of Pathology, University of California, San Diego, La Jolla, California, USA
| | - B J Casey
- 1] The Pediatric Imaging, Neurocognition, and Genetics Study, San Diego, California, USA. [2] Weill Medical College of Cornell University, New York, New York, USA
| | - Linda Chang
- 1] The Pediatric Imaging, Neurocognition, and Genetics Study, San Diego, California, USA. [2] Department of Medicine, John A. Burns School of Medicine, University of Hawaii and the Queen's Medical Center, Honolulu, Hawaii, USA
| | - Thomas M Ernst
- 1] The Pediatric Imaging, Neurocognition, and Genetics Study, San Diego, California, USA. [2] Department of Medicine, John A. Burns School of Medicine, University of Hawaii and the Queen's Medical Center, Honolulu, Hawaii, USA
| | - Jean A Frazier
- 1] The Pediatric Imaging, Neurocognition, and Genetics Study, San Diego, California, USA. [2] University of Massachusetts Medical School, Worcester, Massachusetts, USA
| | - Jeffrey R Gruen
- 1] The Pediatric Imaging, Neurocognition, and Genetics Study, San Diego, California, USA. [2] Department of Pediatrics, Yale University School of Medicine, New Haven, Connecticut, USA. [3] Department of Genetics, Yale University School of Medicine, New Haven, Connecticut, USA. [4] Department of Investigative Medicine, Yale University School of Medicine, New Haven, Connecticut, USA
| | - David N Kennedy
- 1] The Pediatric Imaging, Neurocognition, and Genetics Study, San Diego, California, USA. [2] University of Massachusetts Medical School, Worcester, Massachusetts, USA
| | - Peter Van Zijl
- 1] The Pediatric Imaging, Neurocognition, and Genetics Study, San Diego, California, USA. [2] Department of Radiology, Johns Hopkins University, Baltimore, Maryland, USA. [3] Kennedy Krieger Institute, Baltimore, Maryland, USA
| | - Stewart Mostofsky
- 1] The Pediatric Imaging, Neurocognition, and Genetics Study, San Diego, California, USA. [2] Kennedy Krieger Institute, Baltimore, Maryland, USA
| | - Walter E Kaufmann
- 1] The Pediatric Imaging, Neurocognition, and Genetics Study, San Diego, California, USA. [2] Department of Neurology, Boston Children's Hospital, Boston, Massachusetts, USA. [3] Harvard Medical School, Boston, Massachusetts, USA
| | - Tal Kenet
- 1] The Pediatric Imaging, Neurocognition, and Genetics Study, San Diego, California, USA. [2] Harvard Medical School, Boston, Massachusetts, USA. [3] Department of Neurology, Massachusetts General Hospital, Massachusetts, USA
| | - Anders M Dale
- 1] Multimodal Imaging Laboratory, University of California, San Diego, La Jolla, California, USA. [2] Department of Radiology, University of California, San Diego, La Jolla, California, USA. [3] The Pediatric Imaging, Neurocognition, and Genetics Study, San Diego, California, USA. [4] Department of Cognitive Science, University of California, San Diego, La Jolla, California, USA. [5] Department of Neurology, Department of Neurosciences, University of California, San Diego, La Jolla, California, USA. [6] Center for Translational Imaging and Personalized Medicine, University of California San Diego, La Jolla, California, USA
| | - Terry L Jernigan
- 1] The Pediatric Imaging, Neurocognition, and Genetics Study, San Diego, California, USA. [2] Center for Human Development, University of California, San Diego, La Jolla, California, USA. [3] Department of Psychiatry, University of California, San Diego, La Jolla, California, USA. [4] Department of Cognitive Science, University of California, San Diego, La Jolla, California, USA
| | - Elizabeth R Sowell
- 1] The Saban Research Institute of Children's Hospital, Los Angeles, California, USA. [2] Department of Pediatrics of the Keck School of Medicine, University of Southern California, Los Angeles, California, USA. [3] The Pediatric Imaging, Neurocognition, and Genetics Study, San Diego, California, USA
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Kripke DF, Kline LE, Nievergelt CM, Murray SS, Shadan FF, Dawson A, Poceta JS, Cronin J, Jamil SM, Tranah GJ, Loving RT, Grizas AP, Hahn EK. Genetic variants associated with sleep disorders. Sleep Med 2015; 16:217-24. [PMID: 25660813 PMCID: PMC4352103 DOI: 10.1016/j.sleep.2014.11.003] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/11/2014] [Revised: 10/30/2014] [Accepted: 11/14/2014] [Indexed: 12/31/2022]
Abstract
OBJECTIVE The diagnostic boundaries of sleep disorders are under considerable debate. The main sleep disorders are partly heritable; therefore, defining heritable pathophysiologic mechanisms could delineate diagnoses and suggest treatment. We collected clinical data and DNA from consenting patients scheduled to undergo clinical polysomnograms, to expand our understanding of the polymorphisms associated with the phenotypes of particular sleep disorders. METHODS Patients at least 21 years of age were recruited to contribute research questionnaires, and to provide access to their medical records, saliva for deoxyribonucleic acid (DNA), and polysomnographic data. From these complex data, 38 partly overlapping phenotypes were derived indicating complaints, subjective and objective sleep timing, and polysomnographic disturbances. A custom chip was used to genotype 768 single-nucleotide polymorphisms (SNPs). Additional assays derived ancestry-informative markers (eg, 751 participants of European ancestry). Linear regressions controlling for age, gender, and ancestry were used to assess the associations of each phenotype with each of the SNPs, highlighting those with Bonferroni-corrected significance. RESULTS In peroxisome proliferator-activated receptor gamma, coactivator 1 beta (PPARGC1B), rs6888451 was associated with several markers of obstructive sleep apnea. In aryl hydrocarbon receptor nuclear translocator-like (ARNTL), rs10766071 was associated with decreased polysomnographic sleep duration. The association of rs3923809 in BTBD9 with periodic limb movements in sleep was confirmed. SNPs in casein kinase 1 delta (CSNK1D rs11552085), cryptochrome 1 (CRY1 rs4964515), and retinoic acid receptor-related orphan receptor A (RORA rs11071547) were less persuasively associated with sleep latency and time of falling asleep. CONCLUSIONS SNPs associated with several sleep phenotypes were suggested, but due to risks of false discovery, independent replications are needed before the importance of these associations can be assessed, followed by investigation of molecular mechanisms.
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Affiliation(s)
- Daniel F Kripke
- Viterbi Family Sleep Center, Scripps Clinic, La Jolla, CA, USA; Department of Psychiatry, University of California, San Diego, La Jolla, CA, USA.
| | | | | | - Sarah S Murray
- Department of Pathology, Center for Advanced Laboratory Medicine, University of California, San Diego, CA, USA
| | - Farhad F Shadan
- Viterbi Family Sleep Center, Scripps Clinic, La Jolla, CA, USA
| | - Arthur Dawson
- Viterbi Family Sleep Center, Scripps Clinic, La Jolla, CA, USA
| | - J Steven Poceta
- Viterbi Family Sleep Center, Scripps Clinic, La Jolla, CA, USA
| | - John Cronin
- Viterbi Family Sleep Center, Scripps Clinic, La Jolla, CA, USA
| | - Shazia M Jamil
- Viterbi Family Sleep Center, Scripps Clinic, La Jolla, CA, USA
| | - Gregory J Tranah
- California Pacific Medical Center Research Institute, San Francisco, CA, USA
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25
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Kripke DF, Klimecki WT, Nievergelt CM, Rex KM, Murray SS, Shekhtman T, Tranah GJ, Loving RT, Lee HJ, Rhee MK, Shadan FF, Poceta JS, Jamil SM, Kline LE, Kelsoe JR. Circadian polymorphisms in night owls, in bipolars, and in non-24-hour sleep cycles. Psychiatry Investig 2014; 11:345-62. [PMID: 25395965 PMCID: PMC4225198 DOI: 10.4306/pi.2014.11.4.345] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/15/2014] [Revised: 04/18/2014] [Accepted: 04/18/2014] [Indexed: 12/13/2022] Open
Abstract
People called night owls habitually have late bedtimes and late times of arising, sometimes suffering a heritable circadian disturbance called delayed sleep phase syndrome (DSPS). Those with DSPS, those with more severe progressively-late non-24-hour sleep-wake cycles, and those with bipolar disorder may share genetic tendencies for slowed or delayed circadian cycles. We searched for polymorphisms associated with DSPS in a case-control study of DSPS research participants and a separate study of Sleep Center patients undergoing polysomnography. In 45 participants, we resequenced portions of 15 circadian genes to identify unknown polymorphisms that might be associated with DSPS, non-24-hour rhythms, or bipolar comorbidities. We then genotyped single nucleotide polymorphisms (SNPs) in both larger samples, using Illumina Golden Gate assays. Associations of SNPs with the DSPS phenotype and with the morningness-eveningness parametric phenotype were computed for both samples, then combined for meta-analyses. Delayed sleep and "eveningness" were inversely associated with loci in circadian genes NFIL3 (rs2482705) and RORC (rs3828057). A group of haplotypes overlapping BHLHE40 was associated with non-24-hour sleep-wake cycles, and less robustly, with delayed sleep and bipolar disorder (e.g., rs34883305, rs34870629, rs74439275, and rs3750275 were associated with n=37, p=4.58E-09, Bonferroni p=2.95E-06). Bright light and melatonin can palliate circadian disorders, and genetics may clarify the underlying circadian photoperiodic mechanisms. After further replication and identification of the causal polymorphisms, these findings may point to future treatments for DSPS, non-24-hour rhythms, and possibly bipolar disorder or depression.
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Affiliation(s)
- Daniel F. Kripke
- Department of Psychiatry, University of California, San Diego, CA, USA
- Viterbi Family Sleep Center, Scripps Clinic, La Jolla, CA, USA
| | - Walter T. Klimecki
- Department of Pharmacology and Toxicology, University of Arizona, Tucson, AZ, USA
| | | | - Katharine M. Rex
- Department of Psychiatry, University of California, San Diego, CA, USA
| | - Sarah S. Murray
- Department of Pathology, Center for Advanced Laboratory Medicine, University of California, San Diego, CA, USA
| | - Tatyana Shekhtman
- Department of Psychiatry, University of California, San Diego, CA, USA
- VA San Diego Healthcare System, San Diego, CA, USA
| | - Gregory J. Tranah
- California Pacific Medical Center Research Institute, San Francisco, CA, USA
| | | | - Heon-Jeong Lee
- Department of Psychiatry, Korea University College of Medicine, Seoul, Republic of Korea
| | - Min Kyu Rhee
- Department of Psychology, Gyeongsang National University, Jinju, Republic of Korea
| | | | | | - Shazia M. Jamil
- Viterbi Family Sleep Center, Scripps Clinic, La Jolla, CA, USA
| | | | - John R. Kelsoe
- Department of Psychiatry, University of California, San Diego, CA, USA
- VA San Diego Healthcare System, San Diego, CA, USA
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26
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Voros S, Maurovich-Horvat P, Marvasty IB, Bansal AT, Barnes MR, Vazquez G, Murray SS, Voros V, Merkely B, Brown BO, Warnick GR. Precision phenotyping, panomics, and system-level bioinformatics to delineate complex biologies of atherosclerosis: rationale and design of the "Genetic Loci and the Burden of Atherosclerotic Lesions" study. J Cardiovasc Comput Tomogr 2014; 8:442-51. [PMID: 25439791 DOI: 10.1016/j.jcct.2014.08.006] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/29/2014] [Revised: 08/25/2014] [Accepted: 08/27/2014] [Indexed: 01/24/2023]
Abstract
BACKGROUND Complex biological networks of atherosclerosis are largely unknown. OBJECTIVE The main objective of the Genetic Loci and the Burden of Atherosclerotic Lesions study is to assemble comprehensive biological networks of atherosclerosis using advanced cardiovascular imaging for phenotyping, a panomic approach to identify underlying genomic, proteomic, metabolomic, and lipidomic underpinnings, analyzed by systems biology-driven bioinformatics. METHODS By design, this is a hypothesis-free unbiased discovery study collecting a large number of biologically related factors to examine biological associations between genomic, proteomic, metabolomic, lipidomic, and phenotypic factors of atherosclerosis. The Genetic Loci and the Burden of Atherosclerotic Lesions study (NCT01738828) is a prospective, multicenter, international observational study of atherosclerotic coronary artery disease. Approximately 7500 patients are enrolled and undergo non-contrast-enhanced coronary calcium scanning by CT for the detection and quantification of coronary artery calcium, as well as coronary artery CT angiography for the detection and quantification of plaque, stenosis, and overall coronary artery disease burden. In addition, patients undergo whole genome sequencing, DNA methylation, whole blood-based transcriptome sequencing, unbiased proteomics based on mass spectrometry, as well as metabolomics and lipidomics on a mass spectrometry platform. The study is analyzed in 3 subsequent phases, and each phase consists of a discovery cohort and an independent validation cohort. For the primary analysis, the primary phenotype will be the presence of any atherosclerotic plaque, as detected by cardiac CT. Additional phenotypic analyses will include per patient maximal luminal stenosis defined as 50% and 70% diameter stenosis. Single-omic and multi-omic associations will be examined for each phenotype; putative biomarkers will be assessed for association, calibration, discrimination, and reclassification.
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Affiliation(s)
- Szilard Voros
- Global Genomics Group, LLC, 737 N. 5th Street, Richmond, VA 23219, USA.
| | | | - Idean B Marvasty
- Global Genomics Group, LLC, 737 N. 5th Street, Richmond, VA 23219, USA
| | | | | | | | - Sarah S Murray
- University of California at San Diego, San Diego, CA, USA
| | - Viktor Voros
- Global Genomics Group, LLC, 737 N. 5th Street, Richmond, VA 23219, USA
| | | | - Bradley O Brown
- Global Genomics Group, LLC, 737 N. 5th Street, Richmond, VA 23219, USA
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27
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Yoneyama S, Guo Y, Lanktree MB, Barnes MR, Elbers CC, Karczewski KJ, Padmanabhan S, Bauer F, Baumert J, Beitelshees A, Berenson GS, Boer JM, Burke G, Cade B, Chen W, Cooper-Dehoff RM, Gaunt TR, Gieger C, Gong Y, Gorski M, Heard-Costa N, Johnson T, Lamonte MJ, Mcdonough C, Monda KL, Onland-Moret NC, Nelson CP, O'Connell JR, Ordovas J, Peter I, Peters A, Shaffer J, Shen H, Smith E, Speilotes L, Thomas F, Thorand B, Monique Verschuren WM, Anand SS, Dominiczak A, Davidson KW, Hegele RA, Heid I, Hofker MH, Huggins GS, Illig T, Johnson JA, Kirkland S, König W, Langaee TY, Mccaffery J, Melander O, Mitchell BD, Munroe P, Murray SS, Papanicolaou G, Redline S, Reilly M, Samani NJ, Schork NJ, Van Der Schouw YT, Shimbo D, Shuldiner AR, Tobin MD, Wijmenga C, Yusuf S, Hakonarson H, Lange LA, Demerath EW, Fox CS, North KE, Reiner AP, Keating B, Taylor KC. Gene-centric meta-analyses for central adiposity traits in up to 57 412 individuals of European descent confirm known loci and reveal several novel associations. Hum Mol Genet 2014; 23:2498-510. [PMID: 24345515 PMCID: PMC3988452 DOI: 10.1093/hmg/ddt626] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2013] [Revised: 11/18/2013] [Accepted: 12/09/2013] [Indexed: 12/15/2022] Open
Abstract
Waist circumference (WC) and waist-to-hip ratio (WHR) are surrogate measures of central adiposity that are associated with adverse cardiovascular events, type 2 diabetes and cancer independent of body mass index (BMI). WC and WHR are highly heritable with multiple susceptibility loci identified to date. We assessed the association between SNPs and BMI-adjusted WC and WHR and unadjusted WC in up to 57 412 individuals of European descent from 22 cohorts collaborating with the NHLBI's Candidate Gene Association Resource (CARe) project. The study population consisted of women and men aged 20-80 years. Study participants were genotyped using the ITMAT/Broad/CARE array, which includes ∼50 000 cosmopolitan tagged SNPs across ∼2100 cardiovascular-related genes. Each trait was modeled as a function of age, study site and principal components to control for population stratification, and we conducted a fixed-effects meta-analysis. No new loci for WC were observed. For WHR analyses, three novel loci were significantly associated (P < 2.4 × 10(-6)). Previously unreported rs2811337-G near TMCC1 was associated with increased WHR (β ± SE, 0.048 ± 0.008, P = 7.7 × 10(-9)) as was rs7302703-G in HOXC10 (β = 0.044 ± 0.008, P = 2.9 × 10(-7)) and rs936108-C in PEMT (β = 0.035 ± 0.007, P = 1.9 × 10(-6)). Sex-stratified analyses revealed two additional novel signals among females only, rs12076073-A in SHC1 (β = 0.10 ± 0.02, P = 1.9 × 10(-6)) and rs1037575-A in ATBDB4 (β = 0.046 ± 0.01, P = 2.2 × 10(-6)), supporting an already established sexual dimorphism of central adiposity-related genetic variants. Functional analysis using ENCODE and eQTL databases revealed that several of these loci are in regulatory regions or regions with differential expression in adipose tissue.
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Affiliation(s)
| | - Yiran Guo
- Center for Applied Genomics, Children's Hospital of Philadelphia, 3615 Civic Center Boulevard, Abramson Research Center, Philadelphia, PA 19104, USA
- BGI-Shenzhen, Beishan Beishan Industrial Zone,Yantian District, Shenzhen 518083, China
| | | | - Michael R. Barnes
- National Institute for Health Biomedical Research Unit
- London School of Medicine
| | - Clara C. Elbers
- Julius Center for Health Sciences and Primary Care, UMC Utrecht, PO Box 85500, 3508 GA, Utrecht, The Netherlands
| | | | | | - Florianne Bauer
- Julius Center for Health Sciences and Primary Care, UMC Utrecht, PO Box 85500, 3508 GA, Utrecht, The Netherlands
| | | | | | - Gerald S. Berenson
- Department of Epidemiology, Tulane University, New Orleans, LA 70112, USA
| | - Jolanda M.A. Boer
- Center for Nutrition, Prevention and Health Services, National Institute for Public Health and the Environment, 3720 BA Bilthoven, The Netherlands
| | | | - Brian Cade
- Division of Sleep Medicine, Harvard Medical School, Boston, MA 02115, USA
- Division of Sleep Medicine, Department of Medicine, Brigham and Women's Hospital, Boston, MA 02115, USA
| | - Wei Chen
- Department of Epidemiology, Tulane University, New Orleans, LA 70112, USA
| | - Rhonda M. Cooper-Dehoff
- Department of Pharmacotherapy and Translational Research
- Center for Pharmacogenomics, University of Florida, Gainesville, FL 32610, USA
| | - Tom R. Gaunt
- MRC Integrative Epidemiology Unit, School of Social and Community Medicine, Bristol BS8 2BN, UK
| | | | - Yan Gong
- Department of Pharmacotherapy and Translational Research
- Center for Pharmacogenomics, University of Florida, Gainesville, FL 32610, USA
| | - Mathias Gorski
- Department of Genetic Epidemiology, Institute of Epidemiology and Preventive Medicine, University of Regensburg, 93053 Regensburg, Germany
- Department of Internal Medicine II, University Medical Center Regensburg, 93053 Regensburg, Germany
| | | | - Toby Johnson
- Clinical Pharmacology and The Genome Centre, William Harvey Research Institute, Barts
- London School of Medicine and Dentistry, Queen Mary University of London, London EC1M 6BQ, UK
| | - Michael J. Lamonte
- Department of Social and Preventive Medicine, SUNY-Buffalo School of Public Health and Health Professions, Buffalo, NY 14214, USA
| | - Caitrin Mcdonough
- Department of Pharmacotherapy and Translational Research
- Center for Pharmacogenomics, University of Florida, Gainesville, FL 32610, USA
| | - Keri L. Monda
- Gillings School of Global Public Health
- The Center for Observational Research, Amgen, Inc., Thousand Oaks, CA 91320, USA
| | - N. Charlotte Onland-Moret
- Julius Center for Health Sciences and Primary Care, UMC Utrecht, PO Box 85500, 3508 GA, Utrecht, The Netherlands
| | - Christopher P. Nelson
- Department of Cardiovascular Science, University of Leicester, Leicester LE3 9QP, UK
- Leicester NIHR Biomedical Research Unit in Cardiovascular Disease, Glenfield Hospital, Leicester LE3 9QP, UK
| | | | - Jose Ordovas
- Nutrition and Genomics Laboratory, Tufts University, Boston, MA 02111, USA
| | - Inga Peter
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | | | - Jonathan Shaffer
- Division of General Medicine, Center for Behavioral Cardiovascular Health, Columbia University Medical Center, New York, NY 10032, USA
| | | | - Erin Smith
- Department of Pediatrics and Rady's Children's Hospital, University of California at San Diego, School of Medicine, La Jolla, CA 92093, USA
| | - Liz Speilotes
- Division of Gastroenterology, Massachusetts General Hospital, Boston, MA 02114, USA
- Department of Internal Medicine, Division of Gastroenterology
- Center for Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI 48109, USA
- The Broad Institute, Cambridge, MA 02141, USA
| | - Fridtjof Thomas
- Department of Preventive Medicine, University of Tennessee Health Science Center, Memphis, TN 38163, USA
| | | | - W. M. Monique Verschuren
- Center for Nutrition, Prevention and Health Services, National Institute for Public Health and the Environment, 3720 BA Bilthoven, The Netherlands
| | - Sonia S. Anand
- Population Health Research Institute, Hamilton Health Sciences, Department of Medicine, and
- Population Genomics Program, Department of Clinical Epidemiology, McMaster University, Hamilton, ON, CanadaL8S4L8
| | - Anna Dominiczak
- College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow G12 8QQ, UK
| | - Karina W. Davidson
- Division of General Medicine, Center for Behavioral Cardiovascular Health, Columbia University Medical Center, New York, NY 10032, USA
| | - Robert A. Hegele
- Robarts Research Institute, Schulich School of Medicine & Dentistry, University of Western Ontario, London, ON, CanadaN6A 5C1
| | - Iris Heid
- Institute of Genetic Epidemiology
- Department of Genetic Epidemiology, Institute of Epidemiology and Preventive Medicine, University of Regensburg, 93053 Regensburg, Germany
| | - Marten H. Hofker
- Department of Molecular Genetics, University Medical Center Groningen, Groningen University, 9700 AB Groningen, The Netherlands
| | - Gordon S. Huggins
- Center for Translational Genomics, Molecular Cardiology Research Institute, Tufts Medical Center, Boston, MA 02111, USA
| | - Thomas Illig
- Research Unit for Molecular Epidemiology, Helmholtz Zentrum München, German Research Centre for Environmental Health, 85764 Neuherberg, Germany
- Hannover Unified Biobank, Hannover Medical School, 30625 Hannover, Germany
| | - Julie A. Johnson
- Department of Pharmacotherapy and Translational Research
- Center for Pharmacogenomics, University of Florida, Gainesville, FL 32610, USA
| | - Susan Kirkland
- Department of Community Health & Epidemiology, Dalhousie University, Halifax, NS, Canada
| | | | - Wolfgang König
- Department of Internal Medicine II, Cardiology, University of Ulm Medical Center, Ulm 89081, Germany
| | - Taimour Y. Langaee
- Department of Pharmacotherapy and Translational Research
- Center for Pharmacogenomics, University of Florida, Gainesville, FL 32610, USA
| | - Jeanne Mccaffery
- Weight Control and Diabetes Research Center, The Miriam Hospital and
- Warren Alpert School of Medicine at Brown University, Providence, RI 02906, USA
| | - Olle Melander
- Department of Clinical Sciences, Hypertension & Cardiovascular Disease, Lund University, SE 20502 Malmo, Sweden
| | | | - Patricia Munroe
- Clinical Pharmacology and The Genome Centre, William Harvey Research Institute, Barts
- London School of Medicine and Dentistry, Queen Mary University of London, London EC1M 6BQ, UK
| | - Sarah S. Murray
- The Scripps Research Institute, Scripps Health, La Jolla, CA 92037, USA
| | - George Papanicolaou
- Division of Prevention and Population Sciences, NHLBI, NIH, Bethesda, MD 20824, USA
| | - Susan Redline
- Division of Sleep Medicine, Harvard Medical School, Boston, MA 02115, USA
- Division of Sleep Medicine, Department of Medicine, Brigham and Women's Hospital, Boston, MA 02115, USA
| | - Muredach Reilly
- Cardiovascular Institute, University of Pennsylvania Medical Center, Philadelphia, PA 19104, USA
| | - Nilesh J. Samani
- Department of Cardiovascular Science, University of Leicester, Leicester LE3 9QP, UK
- Leicester NIHR Biomedical Research Unit in Cardiovascular Disease, Glenfield Hospital, Leicester LE3 9QP, UK
| | - Nicholas J. Schork
- The Scripps Research Institute, Scripps Health, La Jolla, CA 92037, USA
- Scripps Translational Science Institute, La Jolla, CA 92037, USA
| | - Yvonne T. Van Der Schouw
- Julius Center for Health Sciences and Primary Care, UMC Utrecht, PO Box 85500, 3508 GA, Utrecht, The Netherlands
| | - Daichi Shimbo
- Division of General Medicine, Center for Behavioral Cardiovascular Health, Columbia University Medical Center, New York, NY 10032, USA
| | - Alan R. Shuldiner
- Department of Medicine and Program for Personalized and Genomic Medicine, University of Maryland School of Medicine, Baltimore, MD 21201, USA
- Geriatric Research and Education Clinical Center, Veterans Administration Medical Center, Baltimore, MD 21201, USA
| | - Martin D. Tobin
- Department of Health Sciences
- Department of Genetics, University of Leicester, Leicester LE1 7RH, UK
| | - Cisca Wijmenga
- Department of Genetics, University Medical Center Groningen, University of Groningen, Groningen 9700 RB, The Netherlands
| | - Salim Yusuf
- Population Health Research Institute, Hamilton Health Sciences, Department of Medicine, and
- Population Genomics Program, Department of Clinical Epidemiology, McMaster University, Hamilton, ON, CanadaL8S4L8
| | | | | | - Hakon Hakonarson
- Center for Applied Genomics, Children's Hospital of Philadelphia, 3615 Civic Center Boulevard, Abramson Research Center, Philadelphia, PA 19104, USA
| | - Leslie A. Lange
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Ellen W Demerath
- Division of Epidemiology and Community Health, University of Minnesota, Minneapolis, MN 55454, USA
| | - Caroline S. Fox
- Framingham Heart Study, Boston University School of Medicine, Boston, MA 02118, USA
| | - Kari E North
- Gillings School of Global Public Health
- Carolina Center for Genome Sciences, Chapel Hill, NC 27599, USA
| | - Alex P. Reiner
- Department of Epidemiology, University of Washington School of Public Health, Seattle, WA 98195, USA
| | - Brendan Keating
- Center for Applied Genomics, Children's Hospital of Philadelphia, 3615 Civic Center Boulevard, Abramson Research Center, Philadelphia, PA 19104, USA
| | - Kira C. Taylor
- Department of Epidemiology and Population Health, School of Public Health and Information Sciences, University of Louisville, Louisville, KY 40202, USA
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28
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Tragante V, Barnes MR, Ganesh SK, Lanktree MB, Guo W, Franceschini N, Smith EN, Johnson T, Holmes MV, Padmanabhan S, Karczewski KJ, Almoguera B, Barnard J, Baumert J, Chang YPC, Elbers CC, Farrall M, Fischer ME, Gaunt TR, Gho JMIH, Gieger C, Goel A, Gong Y, Isaacs A, Kleber ME, Mateo Leach I, McDonough CW, Meijs MFL, Melander O, Nelson CP, Nolte IM, Pankratz N, Price TS, Shaffer J, Shah S, Tomaszewski M, van der Most PJ, Van Iperen EPA, Vonk JM, Witkowska K, Wong COL, Zhang L, Beitelshees AL, Berenson GS, Bhatt DL, Brown M, Burt A, Cooper-DeHoff RM, Connell JM, Cruickshanks KJ, Curtis SP, Davey-Smith G, Delles C, Gansevoort RT, Guo X, Haiqing S, Hastie CE, Hofker MH, Hovingh GK, Kim DS, Kirkland SA, Klein BE, Klein R, Li YR, Maiwald S, Newton-Cheh C, O'Brien ET, Onland-Moret NC, Palmas W, Parsa A, Penninx BW, Pettinger M, Vasan RS, Ranchalis JE, M Ridker P, Rose LM, Sever P, Shimbo D, Steele L, Stolk RP, Thorand B, Trip MD, van Duijn CM, Verschuren WM, Wijmenga C, Wyatt S, Young JH, Zwinderman AH, Bezzina CR, Boerwinkle E, Casas JP, Caulfield MJ, Chakravarti A, Chasman DI, Davidson KW, Doevendans PA, Dominiczak AF, FitzGerald GA, Gums JG, Fornage M, Hakonarson H, Halder I, Hillege HL, Illig T, Jarvik GP, Johnson JA, Kastelein JJP, Koenig W, Kumari M, März W, Murray SS, O'Connell JR, Oldehinkel AJ, Pankow JS, Rader DJ, Redline S, Reilly MP, Schadt EE, Kottke-Marchant K, Snieder H, Snyder M, Stanton AV, Tobin MD, Uitterlinden AG, van der Harst P, van der Schouw YT, Samani NJ, Watkins H, Johnson AD, Reiner AP, Zhu X, de Bakker PIW, Levy D, Asselbergs FW, Munroe PB, Keating BJ. Gene-centric meta-analysis in 87,736 individuals of European ancestry identifies multiple blood-pressure-related loci. Am J Hum Genet 2014; 94:349-60. [PMID: 24560520 DOI: 10.1016/j.ajhg.2013.12.016] [Citation(s) in RCA: 129] [Impact Index Per Article: 12.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2013] [Accepted: 12/20/2013] [Indexed: 11/29/2022] Open
Abstract
Blood pressure (BP) is a heritable risk factor for cardiovascular disease. To investigate genetic associations with systolic BP (SBP), diastolic BP (DBP), mean arterial pressure (MAP), and pulse pressure (PP), we genotyped ~50,000 SNPs in up to 87,736 individuals of European ancestry and combined these in a meta-analysis. We replicated findings in an independent set of 68,368 individuals of European ancestry. Our analyses identified 11 previously undescribed associations in independent loci containing 31 genes including PDE1A, HLA-DQB1, CDK6, PRKAG2, VCL, H19, NUCB2, RELA, HOXC@ complex, FBN1, and NFAT5 at the Bonferroni-corrected array-wide significance threshold (p < 6 × 10(-7)) and confirmed 27 previously reported associations. Bioinformatic analysis of the 11 loci provided support for a putative role in hypertension of several genes, such as CDK6 and NUCB2. Analysis of potential pharmacological targets in databases of small molecules showed that ten of the genes are predicted to be a target for small molecules. In summary, we identified previously unknown loci associated with BP. Our findings extend our understanding of genes involved in BP regulation, which may provide new targets for therapeutic intervention or drug response stratification.
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Affiliation(s)
- Vinicius Tragante
- Department of Cardiology, Division Heart and Lungs, University Medical Center Utrecht, 3584 CX Utrecht, the Netherlands; Department of Medical Genetics, Biomedical Genetics, University Medical Center Utrecht, 3584 CX Utrecht, the Netherlands
| | - Michael R Barnes
- William Harvey Research Institute National Institute for Health Biomedical Research Unit, Barts and the London School of Medicine, Queen Mary University of London, London EC1M 6BQ, UK
| | - Santhi K Ganesh
- Division of Cardiovascular Medicine, Departments of Internal Medicine and Human Genetics, University of Michigan Health System, Ann Arbor, MI 48109, USA
| | - Matthew B Lanktree
- Department of Medicine, McMaster University, Hamilton, ON L8S 4L8, Canada
| | - Wei Guo
- Department of Epidemiology and Biostatistics, Case Western Reserve University, Cleveland, OH 44106, USA
| | - Nora Franceschini
- Department of Epidemiology, University of North Carolina, Chapel Hill, NC 27599, USA
| | - Erin N Smith
- Department of Pediatrics and Rady's Children's Hospital, University of California at San Diego, School of Medicine, La Jolla, CA 92093, USA
| | - Toby Johnson
- Clinical Pharmacology and Barts and The London Genome Centre, William Harvey Research Institute, Barts and The London School of Medicine and Dentistry, Queen Mary University of London, London EC1M 6BQ, UK
| | - Michael V Holmes
- Department of Surgery, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Sandosh Padmanabhan
- BHF Glasgow Cardiovascular Research Centre, University of Glasgow, Glasgow G12 8TA, UK
| | - Konrad J Karczewski
- Department of Genetics, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Berta Almoguera
- Center for Applied Genomics, Abramson Research Center, The Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA
| | - John Barnard
- Department of Quantitative Health Sciences, Lerner Research Institute, Cleveland Clinic, Cleveland, OH 44195, USA
| | - Jens Baumert
- Institute of Epidemiology II, Helmholtz Zentrum München, German Research Center for Environmental Health, Neuherberg 85764, Germany
| | - Yen-Pei Christy Chang
- Departments of Medicine and Epidemiology & Public Health, University of Maryland School of Medicine, Baltimore, MD 21201, USA
| | - Clara C Elbers
- Department of Medical Genetics, Biomedical Genetics, University Medical Center Utrecht, 3584 CX Utrecht, the Netherlands; Julius Center for Health Sciences and Primary Care, University Medical Center Utrecht, 3584 CX Utrecht, the Netherlands
| | - Martin Farrall
- Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford OX3 7BN, UK; Division of Cardiovascular Medicine, Radcliffe Department of Medicine, University of Oxford, Oxford OX3 9DU, UK
| | - Mary E Fischer
- Department of Ophthalmology and Visual Sciences, University of Wisconsin, Madison, WI 53726, USA
| | - Tom R Gaunt
- MRC Integrative Epidemiology Unit, School of Social and Community Medicine, University of Bristol, Oakfield House, Oakfield Grove, Bristol BS8 2BN, UK
| | - Johannes M I H Gho
- Department of Cardiology, Division Heart and Lungs, University Medical Center Utrecht, 3584 CX Utrecht, the Netherlands
| | - Christian Gieger
- Institute of Genetic Epidemiology, Helmholtz Zentrum München, German Research Center for Environmental Health, Neuherberg 85764, Germany
| | - Anuj Goel
- Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford OX3 7BN, UK; Division of Cardiovascular Medicine, Radcliffe Department of Medicine, University of Oxford, Oxford OX3 9DU, UK
| | - Yan Gong
- Department of Pharmacotherapy and Translational Research and Center for Pharmacogenomics, University of Florida, Gainesville, FL 32610, USA
| | - Aaron Isaacs
- Genetic Epidemiology Unit, Department of Epidemiology, Erasmus Medical Center, 3015 GE Rotterdam, the Netherlands
| | - Marcus E Kleber
- Medical Clinic V, Medical Faculty Mannheim, Heidelberg University, Mannheim 68167, Germany
| | - Irene Mateo Leach
- Department of Cardiology, University of Groningen, University Medical Center Groningen, 9700 RB Groningen, the Netherlands
| | - Caitrin W McDonough
- Department of Pharmacotherapy and Translational Research and Center for Pharmacogenomics, University of Florida, Gainesville, FL 32610, USA
| | - Matthijs F L Meijs
- Department of Cardiology, Division Heart and Lungs, University Medical Center Utrecht, 3584 CX Utrecht, the Netherlands
| | - Olle Melander
- Hypertension and Cardiovascular Disease, Department of Clinical Sciences, Lund University, Malmö 20502, Sweden; Centre of Emergency Medicine, Skåne University Hospital, Malmö 20502, Sweden
| | - Christopher P Nelson
- Department of Cardiovascular Sciences, University of Leicester, Leicester LE3 9QP, UK; NIHR Leicester Cardiovascular Biomedical Research Unit, Glenfield Hospital, Groby Road, Leicester LE3 9QP, UK
| | - Ilja M Nolte
- Department of Epidemiology, University of Groningen, University Medical Center Groningen, 9700 RB Groningen, the Netherlands
| | - Nathan Pankratz
- Institute of Human Genetics, Department of Laboratory Medicine and Pathology, University of Minnesota, Minneapolis, MN 55455, USA
| | - Tom S Price
- MRC SGDP Centre, Institute of Psychiatry, London SE5 8AF, UK
| | - Jonathan Shaffer
- Department of Medicine, Columbia University, New York, NY 10032, USA
| | - Sonia Shah
- UCL Genetics Institute, Department of Genetics, Evolution and Environment, University College London, Kathleen Lonsdale Building, Gower Place, London WC1E 6BT, UK
| | - Maciej Tomaszewski
- Department of Cardiovascular Sciences, University of Leicester, Leicester LE3 9QP, UK
| | - Peter J van der Most
- Department of Epidemiology, University of Groningen, University Medical Center Groningen, 9700 RB Groningen, the Netherlands
| | - Erik P A Van Iperen
- Durrer Center for Cardiogenetic Research, ICIN-Netherlands Heart Institute, 3511 GC Utrecht, the Netherlands; Department of Clinical Epidemiology, Biostatistics and Bioinformatics, Academic Medical Center, 1105 AZ Amsterdam, the Netherlands
| | - Judith M Vonk
- Department of Epidemiology, University of Groningen, University Medical Center Groningen, 9700 RB Groningen, the Netherlands
| | - Kate Witkowska
- Clinical Pharmacology and Barts and The London Genome Centre, William Harvey Research Institute, Barts and The London School of Medicine and Dentistry, Queen Mary University of London, London EC1M 6BQ, UK
| | - Caroline O L Wong
- Clinical Pharmacology and Barts and The London Genome Centre, William Harvey Research Institute, Barts and The London School of Medicine and Dentistry, Queen Mary University of London, London EC1M 6BQ, UK
| | - Li Zhang
- Department of Quantitative Health Sciences, Lerner Research Institute, Cleveland Clinic, Cleveland, OH 44195, USA
| | - Amber L Beitelshees
- Division of Endocrinology, Diabetes, and Nutrition, University of Maryland School of Medicine, Baltimore, MD 21201, USA
| | - Gerald S Berenson
- Department of Epidemiology, Tulane University, New Orleans, LA 70118, USA
| | - Deepak L Bhatt
- Brigham and Women's Hospital and Harvard Medical School, Boston, MA 02115, USA
| | - Morris Brown
- Clinical Pharmacology Unit, University of Cambridge, Addenbrookes Hospital, Hills Road, Cambridge CB2 2QQ, UK
| | - Amber Burt
- Department of Medicine (Medical Genetics), University of Washington, Seattle, WA 98195, USA
| | - Rhonda M Cooper-DeHoff
- Department of Pharmacotherapy and Translational Research and Center for Pharmacogenomics, University of Florida, Gainesville, FL 32610, USA
| | - John M Connell
- University of Dundee, Ninewells Hospital &Medical School, Dundee DD1 9SY, UK
| | - Karen J Cruickshanks
- Department of Ophthalmology and Visual Sciences, University of Wisconsin, Madison, WI 53726, USA; Department of Population Health Sciences, University of Wisconsin, Madison, WI 53726, USA
| | - Sean P Curtis
- Merck Research Laboratories, P.O. Box 2000, Rahway, NJ 07065, USA
| | - George Davey-Smith
- MRC Integrative Epidemiology Unit, School of Social and Community Medicine, University of Bristol, Oakfield House, Oakfield Grove, Bristol BS8 2BN, UK
| | - Christian Delles
- Institute of Cardiovascular and Medical Sciences, University of Glasgow, Glasgow G12 8TA, UK
| | - Ron T Gansevoort
- Division of Nephrology, Department of Medicine, University of Groningen, University Medical Center Groningen, 9700 RB Groningen, the Netherlands
| | - Xiuqing Guo
- Cedars-Sinai Med Ctr-PEDS, Los Angeles, CA 90048, USA
| | - Shen Haiqing
- Division of Endocrinology, Diabetes, and Nutrition, University of Maryland School of Medicine, Baltimore, MD 21201, USA
| | - Claire E Hastie
- Institute of Cardiovascular and Medical Sciences, University of Glasgow, Glasgow G12 8TA, UK
| | - Marten H Hofker
- Julius Center for Health Sciences and Primary Care, University Medical Center Utrecht, 3584 CX Utrecht, the Netherlands; Department Pathology and Medical Biology, Medical Biology Division, Molecular Genetics, University of Groningen, University Medical Center Groningen, 9700 RB Groningen, the Netherlands
| | - G Kees Hovingh
- Department of Vascular Medicine, Academic Medical Center, 1105 AZ Amsterdam, the Netherlands
| | - Daniel S Kim
- Departments of Medicine (Medical Genetics) and Genome Sciences, University of Washington, Seattle, WA 98195, USA
| | - Susan A Kirkland
- Department of Community Health and Epidemiology, Dalhousie University, Halifax, NS B3H 1V7, Canada
| | - Barbara E Klein
- Department of Ophthalmology and Visual Sciences, University of Wisconsin, Madison, WI 53726, USA
| | - Ronald Klein
- Department of Ophthalmology and Visual Sciences, University of Wisconsin, Madison, WI 53726, USA
| | - Yun R Li
- Center for Applied Genomics, Abramson Research Center, The Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA
| | - Steffi Maiwald
- Department of Vascular Medicine, Academic Medical Center, 1105 AZ Amsterdam, the Netherlands
| | | | - Eoin T O'Brien
- Conway Institute of Biomolecular and Biomedical Research, University College Dublin, Belfield, Dublin 4, Ireland
| | - N Charlotte Onland-Moret
- Department of Medical Genetics, Biomedical Genetics, University Medical Center Utrecht, 3584 CX Utrecht, the Netherlands; Julius Center for Health Sciences and Primary Care, University Medical Center Utrecht, 3584 CX Utrecht, the Netherlands
| | - Walter Palmas
- Department of Medicine, Columbia University, New York, NY 10032, USA
| | - Afshin Parsa
- Division of Endocrinology, Diabetes, and Nutrition, University of Maryland School of Medicine, Baltimore, MD 21201, USA
| | - Brenda W Penninx
- Department of Psychiatry/EMGO Institute, VU University Medical Centre, 1081 BT Amsterdam, the Netherlands
| | - Mary Pettinger
- Division of Public Health Sciences, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA
| | - Ramachandran S Vasan
- Department of Medicine, Boston University School of Medicine, Framingham, MA 02118, USA
| | - Jane E Ranchalis
- Department of Medicine (Medical Genetics), University of Washington, Seattle, WA 98195, USA
| | - Paul M Ridker
- Division of Preventive Medicine, Brigham and Women's Hospital, Boston, MA 02115, USA; Harvard Medical School, Boston, MA 02115, USA
| | - Lynda M Rose
- Division of Preventive Medicine, Brigham and Women's Hospital, Boston, MA 02115, USA
| | - Peter Sever
- International Centre for Circulatory Health, Imperial College London, W2 1LA UK
| | - Daichi Shimbo
- Department of Medicine, Columbia University, New York, NY 10032, USA
| | - Laura Steele
- Department of Surgery, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Ronald P Stolk
- Department of Epidemiology, University of Groningen, University Medical Center Groningen, 9700 RB Groningen, the Netherlands
| | - Barbara Thorand
- Institute of Epidemiology II, Helmholtz Zentrum München, German Research Center for Environmental Health, Neuherberg 85764, Germany
| | - Mieke D Trip
- Department of Cardiology, Academic Medical Center, 1105 AZ Amsterdam, the Netherlands
| | - Cornelia M van Duijn
- Genetic Epidemiology Unit, Department of Epidemiology, Erasmus Medical Center, 3015 GE Rotterdam, the Netherlands
| | - W Monique Verschuren
- Julius Center for Health Sciences and Primary Care, University Medical Center Utrecht, 3584 CX Utrecht, the Netherlands; National Institute for Public Health and the Environment (RIVM), 3720 BA Bilthoven, the Netherlands
| | - Cisca Wijmenga
- Department of Genetics, University of Groningen, University Medical Center Groningen, 9700 RB Groningen, the Netherlands
| | - Sharon Wyatt
- Schools of Nursing and Medicine, University of Mississippi Medical Center, Jackson, MS 39216, USA
| | - J Hunter Young
- Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Aeilko H Zwinderman
- Department of Clinical Epidemiology, Biostatistics and Bioinformatics, Academic Medical Center, 1105 AZ Amsterdam, the Netherlands
| | - Connie R Bezzina
- Heart Failure Research Center, Department of Clinical and Experimental Cardiology, Academic Medical Center, 1105 AZ Amsterdam, the Netherlands; Molecular and Experimental Cardiology Group, Academic Medical Centre, 1105 AZ Amsterdam, the Netherlands
| | - Eric Boerwinkle
- Human Genetics Center and Institute of Molecular Medicine and Division of Epidemiology, University of Texas Health Science Center, Houston, TX 77030, USA
| | - Juan P Casas
- Faculty of Epidemiology and Population Health, London School of Hygiene and Tropical Medicine, London WC1E 7HT, UK; Genetic Epidemiology Group, Department of Epidemiology and Public Health, University College London, London WC1E 6BT, UK
| | - Mark J Caulfield
- Clinical Pharmacology and Barts and The London Genome Centre, William Harvey Research Institute, Barts and The London School of Medicine and Dentistry, Queen Mary University of London, London EC1M 6BQ, UK
| | - Aravinda Chakravarti
- Center for Complex Disease Genomics, McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Daniel I Chasman
- Division of Preventive Medicine, Brigham and Women's Hospital, Boston, MA 02115, USA; Harvard Medical School, Boston, MA 02115, USA
| | - Karina W Davidson
- Departments of Medicine & Psychiatry, Columbia University, New York, NY 10032, USA
| | - Pieter A Doevendans
- Department of Cardiology, Division Heart and Lungs, University Medical Center Utrecht, 3584 CX Utrecht, the Netherlands
| | - Anna F Dominiczak
- BHF Glasgow Cardiovascular Research Centre, University of Glasgow, Glasgow G12 8TA, UK
| | - Garret A FitzGerald
- The Institute for Translational Medicine and Therapeutics, School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - John G Gums
- Departments of Pharmacotherapy and Translational Research and Community Health and Family Medicine, University of Florida, Gainesville, FL 32610, USA
| | - Myriam Fornage
- Institute of Molecular Medicine and School of Public Health Division of Epidemiology Human Genetics and Environmental Sciences, University of Texas Health Science Center at Houston, Houston, TX 77030, USA
| | - Hakon Hakonarson
- Center for Applied Genomics, Abramson Research Center, The Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA; Department of Pediatrics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Indrani Halder
- School of Medicine, University of Pittsburgh, PA 15261, USA
| | - Hans L Hillege
- Department of Cardiology, University of Groningen, University Medical Center Groningen, 9700 RB Groningen, the Netherlands
| | - Thomas Illig
- Research Unit of Molecular Epidemiology, Helmholtz Zentrum München, German Research Center for Environmental Health, Neuherberg 85764, Germany; Hannover Unified Biobank, Hannover Medical School, Hannover 30625, Germany
| | - Gail P Jarvik
- International Centre for Circulatory Health, Imperial College London, W2 1LA UK
| | - Julie A Johnson
- Department of Pharmacotherapy and Translational Research and Center for Pharmacogenomics, University of Florida, Gainesville, FL 32610, USA
| | - John J P Kastelein
- Department of Vascular Medicine, Academic Medical Center, 1105 AZ Amsterdam, the Netherlands
| | - Wolfgang Koenig
- Department of Internal Medicine II - Cardiology, University of Ulm Medical Centre, Ulm 89081, Germany
| | - Meena Kumari
- Department of Epidemiology and Public Health, Division of Population Health, University College London, Torrington Place, London WC1E 7HB, UK
| | - Winfried März
- Medical Clinic V, Medical Faculty Mannheim, Heidelberg University, Mannheim 68167, Germany; Synlab Academy, Synlab Services GmbH, Mannheim 69214, Germany; Clinical Institute of Medical and Chemical Laboratory Diagnostics, Medical University of Graz, Graz 8036, Austria
| | - Sarah S Murray
- Department of Pathology, University of California San Diego, La Jolla, CA 92037, USA
| | - Jeffery R O'Connell
- Division of Endocrinology, Diabetes, and Nutrition, University of Maryland School of Medicine, Baltimore, MD 21201, USA
| | - Albertine J Oldehinkel
- Interdisciplinary Center Psychopathology and Emotion Regulation, University of Groningen, University Medical Center Groningen, 9700 RB Groningen, the Netherlands
| | - James S Pankow
- Division of Epidemiology and Community Health, University of Minnesota, Minneapolis, MN 55454, USA
| | - Daniel J Rader
- Cardiovascular Institute, the Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Susan Redline
- Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA 02215, USA
| | - Muredach P Reilly
- Cardiovascular Institute, the Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Eric E Schadt
- Department of Genetics and Genomic Sciences, Mount Sinai School of Medicine, New York, NY 10029, USA
| | | | - Harold Snieder
- Department of Epidemiology, University of Groningen, University Medical Center Groningen, 9700 RB Groningen, the Netherlands
| | - Michael Snyder
- Department of Genetics, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Alice V Stanton
- Molecular & Cellular Therapeutics, Royal College of Surgeons in Ireland, 123 St Stephens Green, Dublin 2, Ireland
| | - Martin D Tobin
- Department of Health Sciences, University of Leicester, Leicester LE1 7RH, UK
| | - André G Uitterlinden
- Departments of Epidemiology and Internal Medicine, Erasmus Medical Center, 3015 GE Rotterdam, the Netherlands
| | - Pim van der Harst
- Department of Cardiology, University of Groningen, University Medical Center Groningen, 9700 RB Groningen, the Netherlands; Durrer Center for Cardiogenetic Research, ICIN-Netherlands Heart Institute, 3511 GC Utrecht, the Netherlands; Department of Genetics, University of Groningen, University Medical Center Groningen, 9700 RB Groningen, the Netherlands
| | - Yvonne T van der Schouw
- Julius Center for Health Sciences and Primary Care, University Medical Center Utrecht, 3584 CX Utrecht, the Netherlands
| | - Nilesh J Samani
- Department of Cardiovascular Sciences, University of Leicester, Leicester LE3 9QP, UK; NIHR Leicester Cardiovascular Biomedical Research Unit, Glenfield Hospital, Groby Road, Leicester LE3 9QP, UK
| | - Hugh Watkins
- Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford OX3 7BN, UK; Division of Cardiovascular Medicine, Radcliffe Department of Medicine, University of Oxford, Oxford OX3 9DU, UK
| | - Andrew D Johnson
- National Heart, Lung and Blood Institute Framingham Heart Study, Framingham, MA 01702, USA
| | - Alex P Reiner
- Division of Public Health Sciences, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA
| | - Xiaofeng Zhu
- Department of Epidemiology and Biostatistics, Case Western Reserve University, Cleveland, OH 44106, USA
| | - Paul I W de Bakker
- Department of Medical Genetics, Biomedical Genetics, University Medical Center Utrecht, 3584 CX Utrecht, the Netherlands; Julius Center for Health Sciences and Primary Care, University Medical Center Utrecht, 3584 CX Utrecht, the Netherlands; Division of Genetics, Brigham and Women's Hospital, Harvard Medical School, Boston, MA and Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Daniel Levy
- Center for Population Studies, National Heart, Lung, and Blood Institute, Framingham, MA 01702, USA
| | - Folkert W Asselbergs
- Department of Cardiology, Division Heart and Lungs, University Medical Center Utrecht, 3584 CX Utrecht, the Netherlands; Durrer Center for Cardiogenetic Research, ICIN-Netherlands Heart Institute, 3511 GC Utrecht, the Netherlands; Institute of Cardiovascular Science, Faculty of Population Health Sciences, University College London, London WC1E 6BT, UK
| | - Patricia B Munroe
- Clinical Pharmacology and Barts and The London Genome Centre, William Harvey Research Institute, Barts and The London School of Medicine and Dentistry, Queen Mary University of London, London EC1M 6BQ, UK.
| | - Brendan J Keating
- Department of Surgery, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA; Center for Applied Genomics, Abramson Research Center, The Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA; Department of Pediatrics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA.
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Akshoomoff N, Newman E, Thompson WK, McCabe C, Bloss CS, Chang L, Amaral DG, Casey BJ, Ernst TM, Frazier JA, Gruen JR, Kaufmann WE, Kenet T, Kennedy DN, Libiger O, Mostofsky S, Murray SS, Sowell ER, Schork N, Dale AM, Jernigan TL. The NIH Toolbox Cognition Battery: results from a large normative developmental sample (PING). Neuropsychology 2014; 28:1-10. [PMID: 24219608 PMCID: PMC3925365 DOI: 10.1037/neu0000001] [Citation(s) in RCA: 130] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022] Open
Abstract
OBJECTIVE The NIH Toolbox Cognition Battery (NTCB) was designed to provide a brief, efficient computerized test of key neuropsychological functions appropriate for use in children as young as 3 years of age. This report describes the performance of a large group of typically developing children and adolescents and examines the impact of age and sociocultural variables on test performance. METHOD The NTCB was administered to a sample of 1,020 typically developing males and females ranging in age from 3 to 20 years, diverse in terms of socioeconomic status (SES) and race/ethnicity, as part of the new publicly accessible Pediatric Imaging, Neurocognition, and Genetics (PING) data resource, at 9 sites across the United States. RESULTS General additive models of nonlinear age-functions were estimated from age-differences in test performance on the 8 NTCB subtests while controlling for family SES and genetic ancestry factors (GAFs). Age accounted for the majority of the variance across all NTCB scores, with additional significant contributions of gender on some measures, and of SES and race/ethnicity (GAFs) on all. After adjusting for age and gender, SES and GAFs explained a substantial proportion of the remaining unexplained variance in Picture Vocabulary scores. CONCLUSIONS The results highlight the sensitivity to developmental effects and efficiency of this new computerized assessment battery for neurodevelopmental research. Limitations are observed in the form of some ceiling effects in older children, some floor effects, particularly on executive function tests in the youngest participants, and evidence for variable measurement sensitivity to cultural/socioeconomic factors.
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Affiliation(s)
- Natacha Akshoomoff
- Department of Psychiatry, University of California, San Diego, La Jolla, CA
- Center for Human Development, University of California, San Diego, La Jolla, CA
| | - Erik Newman
- Department of Psychiatry, University of California, San Diego, La Jolla, CA
| | - Wesley K. Thompson
- Department of Psychiatry, University of California, San Diego, La Jolla, CA
- Stein Institute for Research on Aging, University of California, San Diego, La Jolla, CA
| | - Connor McCabe
- Center for Human Development, University of California, San Diego, La Jolla, CA
| | - Cinnamon S. Bloss
- Scripps Genomic Medicine, Scripps Translational Science Institute and Scripps Health, La Jolla, CA
| | - Linda Chang
- Department of Medicine, University of Hawaii and Queen’s Medical Center, Honolulu, HI
| | - David G. Amaral
- Department of Psychiatry and Behavioral Sciences and The M.I.N.D. Institute, University of California, Davis, Sacramento, CA
| | - B. J. Casey
- Sackler Institute for Developmental Psychobiology, Weil Cornell Medical College, New York, NY
| | - Thomas M. Ernst
- Department of Medicine, University of Hawaii and Queen’s Medical Center, Honolulu, HI
| | - Jean A. Frazier
- Department of Psychiatry, University of Massachusetts Medical School, Boston, MA
| | - Jeffrey R. Gruen
- Departments of Pediatrics and Genetics, Yale University School of Medicine, New Haven, CT
| | - Walter E. Kaufmann
- Kennedy Krieger Institute and Johns Hopkins University School of Medicine, Baltimore, MD
| | - Tal Kenet
- Department of Neurology and Athinoula A. Martinos Center for Biomedical Imaging, Massachusetts General Hospital, Charlestown, MA
| | - David N. Kennedy
- Department of Psychiatry, University of Massachusetts Medical School, Boston, MA
| | - Ondrej Libiger
- Scripps Genomic Medicine, Scripps Translational Science Institute and Scripps Health, La Jolla, CA
| | - Stewart Mostofsky
- Kennedy Krieger Institute and Johns Hopkins University School of Medicine, Baltimore, MD
| | - Sarah S. Murray
- Scripps Genomic Medicine, Scripps Translational Science Institute and Scripps Health, La Jolla, CA
| | - Elizabeth R. Sowell
- Department of Pediatrics, University of Southern California, Los Angeles, CA and Children’s Hospital, Los Angeles, CA
| | - Nicholas Schork
- Scripps Genomic Medicine, Scripps Translational Science Institute and Scripps Health, La Jolla, CA
| | - Anders M. Dale
- Department of Neurosciences, University of California, San Diego, La Jolla, CA
- Department of Radiology, University of California, San Diego, La Jolla, CA
| | - Terry L. Jernigan
- Department of Psychiatry, University of California, San Diego, La Jolla, CA
- Center for Human Development, University of California, San Diego, La Jolla, CA
- Department of Radiology, University of California, San Diego, La Jolla, CA
- Department of Cognitive Science, University of California, San Diego, La Jolla, CA
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30
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Eicher JD, Powers NR, Miller LL, Akshoomoff N, Amaral DG, Bloss CS, Libiger O, Schork NJ, Darst BF, Casey BJ, Chang L, Ernst T, Frazier J, Kaufmann WE, Keating B, Kenet T, Kennedy D, Mostofsky S, Murray SS, Sowell ER, Bartsch H, Kuperman JM, Brown TT, Hagler DJ, Dale AM, Jernigan TL, St Pourcain B, Davey Smith G, Ring SM, Gruen JR. Genome-wide association study of shared components of reading disability and language impairment. Genes Brain Behav 2013; 12:792-801. [PMID: 24024963 PMCID: PMC3904347 DOI: 10.1111/gbb.12085] [Citation(s) in RCA: 79] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/21/2013] [Revised: 08/16/2013] [Accepted: 09/09/2013] [Indexed: 11/29/2022]
Abstract
Written and verbal languages are neurobehavioral traits vital to the development of communication skills. Unfortunately, disorders involving these traits-specifically reading disability (RD) and language impairment (LI)-are common and prevent affected individuals from developing adequate communication skills, leaving them at risk for adverse academic, socioeconomic and psychiatric outcomes. Both RD and LI are complex traits that frequently co-occur, leading us to hypothesize that these disorders share genetic etiologies. To test this, we performed a genome-wide association study on individuals affected with both RD and LI in the Avon Longitudinal Study of Parents and Children. The strongest associations were seen with markers in ZNF385D (OR = 1.81, P = 5.45 × 10(-7) ) and COL4A2 (OR = 1.71, P = 7.59 × 10(-7) ). Markers within NDST4 showed the strongest associations with LI individually (OR = 1.827, P = 1.40 × 10(-7) ). We replicated association of ZNF385D using receptive vocabulary measures in the Pediatric Imaging Neurocognitive Genetics study (P = 0.00245). We then used diffusion tensor imaging fiber tract volume data on 16 fiber tracts to examine the implications of replicated markers. ZNF385D was a predictor of overall fiber tract volumes in both hemispheres, as well as global brain volume. Here, we present evidence for ZNF385D as a candidate gene for RD and LI. The implication of transcription factor ZNF385D in RD and LI underscores the importance of transcriptional regulation in the development of higher order neurocognitive traits. Further study is necessary to discern target genes of ZNF385D and how it functions within neural development of fluent language.
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Affiliation(s)
- J D Eicher
- Department of Genetics, Yale UniversityNew Haven, CT, USA
| | - N R Powers
- Department of Genetics, Yale UniversityNew Haven, CT, USA
| | - L L Miller
- MRC Integrative Epidemiology Unit (IEU), School of Social and Community Medicine, University of BristolBristol, UK
| | - N Akshoomoff
- Center for Human Development, University of California at San DiegoLa Jolla, CA, USA
- Department of Psychiatry, University of California at San DiegoLa Jolla, CA, USA
| | - D G Amaral
- Department of Psychiatry and Behavioral Sciences, University of CaliforniaDavis, CA, USA
| | - C S Bloss
- Scripps Genomic Medicine, Scripps Translational Science Institute and Scripps HealthLa Jolla, CA, USA
| | - O Libiger
- Scripps Genomic Medicine, Scripps Translational Science Institute and Scripps HealthLa Jolla, CA, USA
| | - N J Schork
- Scripps Genomic Medicine, Scripps Translational Science Institute and Scripps HealthLa Jolla, CA, USA
| | - B F Darst
- Scripps Genomic Medicine, Scripps Translational Science Institute and Scripps HealthLa Jolla, CA, USA
| | - B J Casey
- Sackler Institute for Developmental Psychobiology, Weil Cornell Medical CollegeNew York, NY, USA
| | - L Chang
- Department of Medicine, University of Hawaii and Queen's Medical CenterHonolulu, HI, USA
| | - T Ernst
- Department of Medicine, University of Hawaii and Queen's Medical CenterHonolulu, HI, USA
| | - J Frazier
- Department of Psychiatry, University of Massachusetts Medical SchoolBoston, MA, USA
| | - W E Kaufmann
- Kennedy Krieger InstituteBaltimore, MD, USA
- Department of Neurology, Children's Hospital Boston, Harvard Medical SchoolBoston, MA, USA
| | - B Keating
- Department of Medicine, University of Hawaii and Queen's Medical CenterHonolulu, HI, USA
| | - T Kenet
- Department of Neurology and Athinoula A. Martinos Center for Biomedical Imaging, Massachusetts General HospitalCharlestown, MA, USA
| | - D Kennedy
- Department of Psychiatry, University of Massachusetts Medical SchoolBoston, MA, USA
| | | | - S S Murray
- Scripps Genomic Medicine, Scripps Translational Science Institute and Scripps HealthLa Jolla, CA, USA
| | - E R Sowell
- Department of Pediatrics, University of Southern CaliforniaLos Angeles, CA, USA
- Developmental Cognitive Neuroimaging Laboratory, Children's HospitalLos Angeles, CA, USA
| | - H Bartsch
- Multimodal Imaging Laboratory, University of California at San DiegoLa Jolla, CA, USA
| | - J M Kuperman
- Multimodal Imaging Laboratory, University of California at San DiegoLa Jolla, CA, USA
- Department of Neurosciences, University of California at San DiegoLa Jolla, CA, USA
| | - T T Brown
- Center for Human Development, University of California at San DiegoLa Jolla, CA, USA
- Multimodal Imaging Laboratory, University of California at San DiegoLa Jolla, CA, USA
- Department of Neurosciences, University of California at San DiegoLa Jolla, CA, USA
| | - D J Hagler
- Multimodal Imaging Laboratory, University of California at San DiegoLa Jolla, CA, USA
- Department of Radiology, University of California at San DiegoLa Jolla, CA, USA
| | - A M Dale
- Department of Psychiatry, University of California at San DiegoLa Jolla, CA, USA
- Multimodal Imaging Laboratory, University of California at San DiegoLa Jolla, CA, USA
- Department of Neurosciences, University of California at San DiegoLa Jolla, CA, USA
- Department of Radiology, University of California at San DiegoLa Jolla, CA, USA
- Department of Cognitive Science, University of California at San DiegoLa Jolla, CA, USA
| | - T L Jernigan
- Center for Human Development, University of California at San DiegoLa Jolla, CA, USA
- Department of Psychiatry, University of California at San DiegoLa Jolla, CA, USA
- Department of Radiology, University of California at San DiegoLa Jolla, CA, USA
- Department of Cognitive Science, University of California at San DiegoLa Jolla, CA, USA
| | - B St Pourcain
- MRC Integrative Epidemiology Unit (IEU), School of Social and Community Medicine, University of BristolBristol, UK
- School of Oral and Dental Sciences, University of BristolBristol, UK
- School of Experimental Psychology, University of BristolBristol, UK
| | - G Davey Smith
- MRC Integrative Epidemiology Unit (IEU), School of Social and Community Medicine, University of BristolBristol, UK
| | - S M Ring
- MRC Integrative Epidemiology Unit (IEU), School of Social and Community Medicine, University of BristolBristol, UK
| | - J R Gruen
- Department of Genetics, Yale UniversityNew Haven, CT, USA
- Departments of Pediatrics and Investigative Medicine, Yale University School of MedicineNew Haven, CT, USA
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31
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Franceschini N, Fox E, Zhang Z, Edwards TL, Nalls MA, Sung YJ, Tayo BO, Sun YV, Gottesman O, Adeyemo A, Johnson AD, Young JH, Rice K, Duan Q, Chen F, Li Y, Tang H, Fornage M, Keene KL, Andrews JS, Smith JA, Faul JD, Guangfa Z, Guo W, Liu Y, Murray SS, Musani SK, Srinivasan S, Velez Edwards DR, Wang H, Becker LC, Bovet P, Bochud M, Broeckel U, Burnier M, Carty C, Chasman DI, Ehret G, Chen WM, Chen G, Chen W, Ding J, Dreisbach AW, Evans MK, Guo X, Garcia ME, Jensen R, Keller MF, Lettre G, Lotay V, Martin LW, Moore JH, Morrison AC, Mosley TH, Ogunniyi A, Palmas W, Papanicolaou G, Penman A, Polak JF, Ridker PM, Salako B, Singleton AB, Shriner D, Taylor KD, Vasan R, Wiggins K, Williams SM, Yanek LR, Zhao W, Zonderman AB, Becker DM, Berenson G, Boerwinkle E, Bottinger E, Cushman M, Eaton C, Nyberg F, Heiss G, Hirschhron JN, Howard VJ, Karczewsk KJ, Lanktree MB, Liu K, Liu Y, Loos R, Margolis K, Snyder M, Psaty BM, Schork NJ, Weir DR, Rotimi CN, Sale MM, Harris T, Kardia SLR, Hunt SC, Arnett D, Redline S, Cooper RS, Risch NJ, Rao DC, Rotter JI, Chakravarti A, Reiner AP, Levy D, Keating BJ, Zhu X. Genome-wide association analysis of blood-pressure traits in African-ancestry individuals reveals common associated genes in African and non-African populations. Am J Hum Genet 2013; 93:545-54. [PMID: 23972371 DOI: 10.1016/j.ajhg.2013.07.010] [Citation(s) in RCA: 148] [Impact Index Per Article: 13.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2013] [Revised: 05/20/2013] [Accepted: 07/03/2013] [Indexed: 01/11/2023] Open
Abstract
High blood pressure (BP) is more prevalent and contributes to more severe manifestations of cardiovascular disease (CVD) in African Americans than in any other United States ethnic group. Several small African-ancestry (AA) BP genome-wide association studies (GWASs) have been published, but their findings have failed to replicate to date. We report on a large AA BP GWAS meta-analysis that includes 29,378 individuals from 19 discovery cohorts and subsequent replication in additional samples of AA (n = 10,386), European ancestry (EA) (n = 69,395), and East Asian ancestry (n = 19,601). Five loci (EVX1-HOXA, ULK4, RSPO3, PLEKHG1, and SOX6) reached genome-wide significance (p < 1.0 × 10(-8)) for either systolic or diastolic BP in a transethnic meta-analysis after correction for multiple testing. Three of these BP loci (EVX1-HOXA, RSPO3, and PLEKHG1) lack previous associations with BP. We also identified one independent signal in a known BP locus (SOX6) and provide evidence for fine mapping in four additional validated BP loci. We also demonstrate that validated EA BP GWAS loci, considered jointly, show significant effects in AA samples. Consequently, these findings suggest that BP loci might have universal effects across studied populations, demonstrating that multiethnic samples are an essential component in identifying, fine mapping, and understanding their trait variability.
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Affiliation(s)
- Nora Franceschini
- Department of Epidemiology, University of North Carolina at Chapel Hill, NC 27599, USA.
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32
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Demerath EW, Liu CT, Franceschini N, Chen G, Palmer JR, Smith EN, Chen CTL, Ambrosone CB, Arnold AM, Bandera EV, Berenson GS, Bernstein L, Britton A, Cappola AR, Carlson CS, Chanock SJ, Chen W, Chen Z, Deming SL, Elks CE, Evans MK, Gajdos Z, Henderson BE, Hu JJ, Ingles S, John EM, Kerr KF, Kolonel LN, Le Marchand L, Lu X, Millikan RC, Musani SK, Nock NL, North K, Nyante S, Press MF, Rodriquez-Gil JL, Ruiz-Narvaez EA, Schork NJ, Srinivasan SR, Woods NF, Zheng W, Ziegler RG, Zonderman A, Heiss G, Gwen Windham B, Wellons M, Murray SS, Nalls M, Pastinen T, Rajkovic A, Hirschhorn J, Adrienne Cupples L, Kooperberg C, Murabito JM, Haiman CA. Genome-wide association study of age at menarche in African-American women. Hum Mol Genet 2013; 22:3329-46. [PMID: 23599027 DOI: 10.1093/hmg/ddt181] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
African-American (AA) women have earlier menarche on average than women of European ancestry (EA), and earlier menarche is a risk factor for obesity and type 2 diabetes among other chronic diseases. Identification of common genetic variants associated with age at menarche has a potential value in pointing to the genetic pathways underlying chronic disease risk, yet comprehensive genome-wide studies of age at menarche are lacking for AA women. In this study, we tested the genome-wide association of self-reported age at menarche with common single-nucleotide polymorphisms (SNPs) in a total of 18 089 AA women in 15 studies using an additive genetic linear regression model, adjusting for year of birth and population stratification, followed by inverse-variance weighted meta-analysis (Stage 1). Top meta-analysis results were then tested in an independent sample of 2850 women (Stage 2). First, while no SNP passed the pre-specified P < 5 × 10(-8) threshold for significance in Stage 1, suggestive associations were found for variants near FLRT2 and PIK3R1, and conditional analysis identified two independent SNPs (rs339978 and rs980000) in or near RORA, strengthening the support for this suggestive locus identified in EA women. Secondly, an investigation of SNPs in 42 previously identified menarche loci in EA women demonstrated that 25 (60%) of them contained variants significantly associated with menarche in AA women. The findings provide the first evidence of cross-ethnic generalization of menarche loci identified to date, and suggest a number of novel biological links to menarche timing in AA women.
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Affiliation(s)
- Ellen W Demerath
- Division of Epidemiology and Community Health, School of Public Health, University of Minnesota, Minneapolis, MN, USA.
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Ganesh SK, Tragante V, Guo W, Guo Y, Lanktree MB, Smith EN, Johnson T, Castillo BA, Barnard J, Baumert J, Chang YPC, Elbers CC, Farrall M, Fischer ME, Franceschini N, Gaunt TR, Gho JM, Gieger C, Gong Y, Isaacs A, Kleber ME, Leach IM, McDonough CW, Meijs MF, Mellander O, Molony CM, Nolte IM, Padmanabhan S, Price TS, Rajagopalan R, Shaffer J, Shah S, Shen H, Soranzo N, van der Most PJ, Van Iperen EP, Van Setten JA, Vonk JM, Zhang L, Beitelshees AL, Berenson GS, Bhatt DL, Boer JM, Boerwinkle E, Burkley B, Burt A, Chakravarti A, Chen W, Cooper-DeHoff RM, Curtis SP, Dreisbach A, Duggan D, Ehret GB, Fabsitz RR, Fornage M, Fox E, Furlong CE, Gansevoort RT, Hofker MH, Hovingh GK, Kirkland SA, Kottke-Marchant K, Kutlar A, LaCroix AZ, Langaee TY, Li YR, Lin H, Liu K, Maiwald S, Malik R, Murugesan G, Newton-Cheh C, O'Connell JR, Onland-Moret NC, Ouwehand WH, Palmas W, Penninx BW, Pepine CJ, Pettinger M, Polak JF, Ramachandran VS, Ranchalis J, Redline S, Ridker PM, Rose LM, Scharnag H, Schork NJ, Shimbo D, Shuldiner AR, Srinivasan SR, Stolk RP, Taylor HA, Thorand B, Trip MD, van Duijn CM, Verschuren WM, Wijmenga C, Winkelmann BR, Wyatt S, Young JH, Boehm BO, Caulfield MJ, Chasman DI, Davidson KW, Doevendans PA, FitzGerald GA, Gums JG, Hakonarson H, Hillege HL, Illig T, Jarvik GP, Johnson JA, Kastelein JJ, Koenig W, März W, Mitchell BD, Murray SS, Oldehinkel AJ, Rader DJ, Reilly MP, Reiner AP, Schadt EE, Silverstein RL, Snieder H, Stanton AV, Uitterlinden AG, van der Harst P, van der Schouw YT, Samani NJ, Johnson AD, Munroe PB, de Bakker PI, Zhu X, Levy D, Keating BJ, Asselbergs FW. Loci influencing blood pressure identified using a cardiovascular gene-centric array. Hum Mol Genet 2013; 22:1663-78. [PMID: 23303523 PMCID: PMC3657476 DOI: 10.1093/hmg/dds555] [Citation(s) in RCA: 120] [Impact Index Per Article: 10.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2012] [Revised: 11/30/2012] [Accepted: 12/27/2012] [Indexed: 01/11/2023] Open
Abstract
Blood pressure (BP) is a heritable determinant of risk for cardiovascular disease (CVD). To investigate genetic associations with systolic BP (SBP), diastolic BP (DBP), mean arterial pressure (MAP) and pulse pressure (PP), we genotyped ∼50 000 single-nucleotide polymorphisms (SNPs) that capture variation in ∼2100 candidate genes for cardiovascular phenotypes in 61 619 individuals of European ancestry from cohort studies in the USA and Europe. We identified novel associations between rs347591 and SBP (chromosome 3p25.3, in an intron of HRH1) and between rs2169137 and DBP (chromosome1q32.1 in an intron of MDM4) and between rs2014408 and SBP (chromosome 11p15 in an intron of SOX6), previously reported to be associated with MAP. We also confirmed 10 previously known loci associated with SBP, DBP, MAP or PP (ADRB1, ATP2B1, SH2B3/ATXN2, CSK, CYP17A1, FURIN, HFE, LSP1, MTHFR, SOX6) at array-wide significance (P < 2.4 × 10(-6)). We then replicated these associations in an independent set of 65 886 individuals of European ancestry. The findings from expression QTL (eQTL) analysis showed associations of SNPs in the MDM4 region with MDM4 expression. We did not find any evidence of association of the two novel SNPs in MDM4 and HRH1 with sequelae of high BP including coronary artery disease (CAD), left ventricular hypertrophy (LVH) or stroke. In summary, we identified two novel loci associated with BP and confirmed multiple previously reported associations. Our findings extend our understanding of genes involved in BP regulation, some of which may eventually provide new targets for therapeutic intervention.
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Affiliation(s)
- Santhi K. Ganesh
- Division of Cardiovascular Medicine, University of Michigan Health System, Ann Arbor, MI, USA
| | - Vinicius Tragante
- Department of Cardiology, Division Heart and Lungs
- Department of Medical Genetics and
| | - Wei Guo
- Department of Epidemiology and Biostatistics, School of Medicine and
| | - Yiran Guo
- Center for Applied Genomics, Abramson Research Center, The Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA
| | - Matthew B. Lanktree
- Departments of Medicine and Biochemistry, Schulich School of Medicine and Dentistry, University of Western Ontario, London, ON, Canada
| | - Erin N. Smith
- Department of Pediatrics and Rady's Children's Hospital, School of Medicine, University of California at San Diego, La Jolla, CA 92093, USA
| | - Toby Johnson
- Clinical Pharmacology and Barts and The London Genome Centre, William Harvey Research Institute, Barts and
- The London School of Medicine and Dentistry, Queen Mary University of London, Charterhouse Square, London EC1M 6BQ, UK
| | - Berta Almoguera Castillo
- Center for Applied Genomics, Abramson Research Center, The Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA
| | - John Barnard
- Department of Quantitative Health Sciences, Lerner Research Institute, Cleveland Clinic, Cleveland, OH, USA
| | | | - Yen-Pei Christy Chang
- Department of Medicine and
- Division of Endocrinology, Diabetes and Nutrition, University of Maryland School of Medicine, Baltimore, MD, USA
| | - Clara C. Elbers
- Department of Medical Genetics and
- Julius Center for Health Sciences and Primary Care, University Medical Center Utrecht, Utrecht, The Netherlands
| | - Martin Farrall
- Department of Cardiovascular Medicine, The Wellcome Trust Centre for Human Genetics, University of Oxford, OxfordOX3 7BN, UK
| | - Mary E. Fischer
- Department of Ophthalmology and Visual Sciences, University of Wisconsin, Madison, WI, USA
| | - Nora Franceschini
- Department of Epidemiology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Tom R. Gaunt
- MRC Centre for Causal Analyses in Translational Epidemiology, School of Social and Community Medicine, University of Bristol, Oakfield House, Oakfield Grove, Bristol BS8 2BN, UK
| | | | | | - Yan Gong
- Department of Pharmacotherapy and Translational Research and Center for Pharmacogenomics and
| | - Aaron Isaacs
- Genetic Epidemiology Unit, Department of Epidemiology and
| | - Marcus E. Kleber
- LURIC Study nonprofit LLC, Freiburg, Germany
- Mannheim Institute of Public Health, Social and Preventive Medicine, Mannheim Medical Faculty, University of Heidelberg, Mannheim, Germany
| | | | - Caitrin W. McDonough
- Department of Pharmacotherapy and Translational Research and Center for Pharmacogenomics and
| | | | - Olle Mellander
- Hypertension and Cardiovascular Disease, Department of Clinical Sciences, Lund University, Malmö, Sweden
- Centre of Emergency Medicine, Skåne University Hospital, Malmö, Sweden
| | | | | | - Sandosh Padmanabhan
- BHF Glasgow Cardiovascular Research Centre, University of Glasgow, 126 University Place, Glasgow G12 8TA, UK
| | - Tom S. Price
- MRC SGDP Centre, Institute of Psychiatry, London, UK
| | - Ramakrishnan Rajagopalan
- Department of Medicine, Division of Medical Genetics, University of Washington, Seattle, WA, USA
| | | | - Sonia Shah
- UCL Genetics Institute, Department of Genetics, Evolution and Environment, University College London, Kathleen Lonsdale Building, Gower Place, London WC1E 6BT, UK
| | | | | | | | - Erik P.A. Van Iperen
- Durrer Center for Cardiogenetic Research
- Department of Clinical Epidemiology, Biostatistics and Bioinformatics
| | | | | | - Li Zhang
- Department of Quantitative Health Sciences, Lerner Research Institute, Cleveland Clinic, Cleveland, OH, USA
| | - Amber L. Beitelshees
- Department of Quantitative Health Sciences, Lerner Research Institute, Cleveland Clinic, Cleveland, OH, USA
| | - Gerald S. Berenson
- Department of Epidemiology, Tulane University, 1440 Canal Street, Suite 1829, New Orleans, LA, USA
| | - Deepak L. Bhatt
- VA Boston Healthcare System, Brigham and Women's Hospital, and Harvard Medical School, Boston, MA, USA
| | - Jolanda M.A. Boer
- National Institute for Public Health and the Environment (RIVM), Bilthoven, The Netherlands
| | - Eric Boerwinkle
- Human Genetics Center and Institute of Molecular Medicine and Division of Epidemiology, University of Texas Health Science Center, Houston, TX, USA
| | - Ben Burkley
- Department of Pharmacotherapy and Translational Research and Center for Pharmacogenomics and
| | - Amber Burt
- Department of Medicine, Division of Medical Genetics, University of Washington, Seattle, WA, USA
| | - Aravinda Chakravarti
- Center for Complex Disease Genomics, McKusick-Nathans Institute of Genetic Medicine and
| | - Wei Chen
- Department of Epidemiology, Tulane University, 1440 Canal Street, Suite 1829, New Orleans, LA, USA
| | - Rhonda M. Cooper-DeHoff
- Department of Pharmacotherapy and Translational Research and Center for Pharmacogenomics and
| | - Sean P. Curtis
- Merck Research Laboratories, PO Box 2000, Rahway, NJ 07065, USA
| | | | - David Duggan
- Translational Genomics Research Institute, Phoenix, AZ, USA
| | - Georg B. Ehret
- Center for Complex Disease Genomics, McKusick-Nathans Institute of Genetic Medicine and
| | - Richard R. Fabsitz
- Division of Cardiovascular Sciences, National Heart, Lung, and Blood Institute, Bethesda, MD, USA
| | - Myriam Fornage
- Human Genetics Center and Institute of Molecular Medicine and Division of Epidemiology, University of Texas Health Science Center, Houston, TX, USA
| | | | - Clement E. Furlong
- Department of Medicine, Division of Medical Genetics, University of Washington, Seattle, WA, USA
| | | | - Marten H. Hofker
- Molecular Genetics, Medical Biology Section, Department of Pathology and Medical Biology
| | | | - Susan A. Kirkland
- Department of Community Health and Epidemiology, Dalhousie University, Canada
| | | | | | - Andrea Z. LaCroix
- Division of Public Health Sciences, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - Taimour Y. Langaee
- Department of Pharmacotherapy and Translational Research and Center for Pharmacogenomics and
| | - Yun R. Li
- Center for Applied Genomics, Abramson Research Center, The Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA
| | - Honghuang Lin
- Department of Medicine, Boston University School of Medicine, Boston, MA, USA
| | - Kiang Liu
- Department of Preventive Medicine, Northwestern University Feinberg School of Medicine, Chicago, IL, USA
| | - Steffi Maiwald
- Department of Vascular Medicine, University of Amsterdam, Amsterdam, The Netherlands
| | - Rainer Malik
- Institute for Stroke and Dementia Research and
- Neurologische Klinik, Klinikum Grosshadern, Ludwig-Maximilians-Universität, München, Germany
| | | | - Gurunathan Murugesan
- Pathology and Laboratory Medicine Institute, Cleveland Clinic, Cleveland, OH, USA
| | - Christopher Newton-Cheh
- Broad Institute of Harvard and MIT, Cambridge, MA, USA
- Center for Human Genetic Research, Massachusetts General Hospital, Boston, MA, USA
| | - Jeffery R. O'Connell
- Division of Endocrinology, Diabetes and Nutrition, University of Maryland School of Medicine, Baltimore, MD, USA
| | - N. Charlotte Onland-Moret
- Department of Medical Genetics and
- Julius Center for Health Sciences and Primary Care, University Medical Center Utrecht, Utrecht, The Netherlands
| | - Willem H. Ouwehand
- Department of Haematology, University of Cambridge and NHS Blood and Transplant, Cambridge and Human Genetics, Wellcome Trust Sanger Institute, Hinxton, UK
| | - Walter Palmas
- Department of Medicine, Columbia University, New York, NY, USA
| | - Brenda W. Penninx
- Department of Psychiatry/EMGO Institute, VU University Medical Centre, Amsterdam, The Netherlands
| | - Carl J. Pepine
- Division of Cardiovascular Medicine, University of Florida College of Medicine, Gainesville, FL, USA
| | - Mary Pettinger
- Division of Cardiovascular Sciences, National Heart, Lung, and Blood Institute, Bethesda, MD, USA
| | | | - Vasan S. Ramachandran
- Department of Medicine, Boston University School of Medicine, Boston, MA, USA
- National Heart, Lung and Blood Institute's Framingham Heart Study, 73 Mt.Wayte Avenue Suite #2, Framingham, MA, USA
| | - Jane Ranchalis
- Department of Medicine, Division of Medical Genetics, University of Washington, Seattle, WA, USA
| | - Susan Redline
- Department of Medicine, Brigham and Women's Hospital, Harvard Medical School and
| | - Paul M. Ridker
- Department of Medicine, Brigham and Women's Hospital, Harvard Medical School and
| | - Lynda M. Rose
- Department of Medicine, Brigham and Women's Hospital, Harvard Medical School and
| | - Hubert Scharnag
- Division of Cardiovascular Medicine, University of Michigan Health System, Ann Arbor, MI, USA
- Clinical Institute of Medical and Chemical Laboratory Diagnostics, Medical University of Graz, Austria
| | - Nicholas J. Schork
- The Scripps Translational Science Institute and The Scripps Research Institute, 3344 N. Torrey Pines Ct. Ste 300, La Jolla, CA, USA
| | - Daichi Shimbo
- Department of Medicine, Columbia University, New York, NY, USA
| | - Alan R. Shuldiner
- Division of Endocrinology, Diabetes and Nutrition, University of Maryland School of Medicine, Baltimore, MD, USA
- Geriatric Research and Education Clinical Center, Veterans Administration Medical Center, Baltimore, MD, USA
| | - Sathanur R. Srinivasan
- Department of Epidemiology, Tulane University, 1440 Canal Street, Suite 1829, New Orleans, LA, USA
| | | | | | | | - Mieke D. Trip
- Department of Cardiology, AMC, Amsterdam, The Netherlands
| | | | - W. Monique Verschuren
- National Institute for Public Health and the Environment (RIVM), Bilthoven, The Netherlands
| | | | | | - Sharon Wyatt
- School of Nursing, University of Mississippi Medical Center, Jackson, MS, USA
| | - J. Hunter Young
- Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, MD, USA
| | | | - Mark J. Caulfield
- Clinical Pharmacology and Barts and The London Genome Centre, William Harvey Research Institute, Barts and
| | - Daniel I. Chasman
- Department of Medicine, Brigham and Women's Hospital, Harvard Medical School and
| | - Karina W. Davidson
- Departments of Medicine & Psychiatry, Columbia University, New York, NY, USA
| | | | - Garret A. FitzGerald
- The Institute for Translational Medicine and Therapeutics, School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - John G. Gums
- Departments of Pharmacotherapy and Translational Research and Community Health and Family Medicine, University of Florida, Gainesville, FL, USA
| | - Hakon Hakonarson
- Center for Applied Genomics, Abramson Research Center, The Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA
| | | | - Thomas Illig
- Research Unit of Molecular Epidemiology, Helmholtz Zentrum München, German Research Center for Environmental Health, Neuherberg, Germany
- Hannover Unified Biobank, Hannover Medical School, Hannover, Germany
| | - Gail P. Jarvik
- Department of Medicine, Division of Medical Genetics, University of Washington, Seattle, WA, USA
| | - Julie A. Johnson
- Department of Pharmacotherapy and Translational Research and Center for Pharmacogenomics and
| | | | - Wolfgang Koenig
- Department of Internal Medicine I—Cardiology, University of Ulm Medical Centre, Ulm, Germany
| | | | - Winfried März
- Mannheim Institute of Public Health, Social and Preventive Medicine, Mannheim Medical Faculty, University of Heidelberg, Mannheim, Germany
- Synlab Academy, Mannheim, Germany
| | - Braxton D. Mitchell
- Division of Endocrinology, Diabetes and Nutrition, University of Maryland School of Medicine, Baltimore, MD, USA
| | - Sarah S. Murray
- Scripps Translational Science Institute and Scripps Health, 3344 N. Torrey Pines Ct. Ste 300, La Jolla, CA, USA
| | - Albertine J. Oldehinkel
- Interdisciplinary Center Psychopathology and Emotion Regulation, Groningen University, University Medical Center Groningen, Groningen, The Netherlands
| | - Daniel J. Rader
- Cardiovascular Institute, The Perelman School of Medicine at the University of Pennsylvania, PA, USA
| | - Muredach P. Reilly
- Cardiovascular Institute, The Perelman School of Medicine at the University of Pennsylvania, PA, USA
| | - Alex P. Reiner
- Division of Public Health Sciences, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - Eric E. Schadt
- Department of Genetics and Genomic Sciences, Mount Sinai School of Medicine, New York, NY, USA
| | - Roy L. Silverstein
- Department of Molecular Medicine, Cleveland Clinic Lerner College of Medicine, Case Western Reserve University, Cleveland, OH, USA
- Department of Cell Biology, Lerner Research Institute, Cleveland Clinic
| | | | - Alice V. Stanton
- Molecular & Cellular Therapeutics, Royal College of Surgeons in Ireland, 123 St Stephens Green, Dublin 2, Ireland
| | - André G. Uitterlinden
- Departments of Epidemiology and Internal Medicine, Erasmus Medical Center, Rotterdam, The Netherlands
| | | | - Yvonne T. van der Schouw
- Julius Center for Health Sciences and Primary Care, University Medical Center Utrecht, Utrecht, The Netherlands
| | - Nilesh J. Samani
- Department of Cardiovascular Sciences, University of Leicester and
- Leicester NIHR Biomedical Research Unit in Cardiovascular Disease, Glenfield Hospital, Leicester LE3 9QP, UK
| | - Andrew D. Johnson
- National Heart, Lung and Blood Institute's Framingham Heart Study, 73 Mt.Wayte Avenue Suite #2, Framingham, MA, USA
| | - Patricia B. Munroe
- Clinical Pharmacology and Barts and The London Genome Centre, William Harvey Research Institute, Barts and
- The London School of Medicine and Dentistry, Queen Mary University of London, Charterhouse Square, London EC1M 6BQ, UK
| | - Paul I.W. de Bakker
- Department of Medical Genetics and
- Julius Center for Health Sciences and Primary Care, University Medical Center Utrecht, Utrecht, The Netherlands
- Broad Institute of Harvard and MIT, Cambridge, MA, USA
- Division of Genetics, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | - Xiaofeng Zhu
- Department of Epidemiology and Biostatistics, School of Medicine and
| | - Daniel Levy
- Center for Population Studies, National Heart, Lung, and Blood Institute, Framingham, MA, USA
| | - Brendan J. Keating
- Center for Applied Genomics, Abramson Research Center, The Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA
| | - Folkert W. Asselbergs
- Department of Cardiology, Division Heart and Lungs
- Department of Medical Genetics and
- Julius Center for Health Sciences and Primary Care, University Medical Center Utrecht, Utrecht, The Netherlands
- Durrer Center for Cardiogenetic Research
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Kripke DF, Nievergelt CM, Tranah GJ, Murray SS, Rex KM, Grizas AP, Hahn EK, Lee HJ, Kelsoe JR, Kline LE. FMR1, circadian genes and depression: suggestive associations or false discovery? J Circadian Rhythms 2013; 11:3. [PMID: 23521777 PMCID: PMC3627611 DOI: 10.1186/1740-3391-11-3] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2013] [Accepted: 03/21/2013] [Indexed: 11/11/2022] Open
Abstract
Background There are several indications that malfunctions of the circadian clock contribute to depression. To search for particular circadian gene polymorphisms associated with depression, diverse polymorphisms were genotyped in two samples covering a range of depressed volunteers and participants with normal mood. Methods Depression mood self-ratings and DNA were collected independently from a sample of patients presenting to a sleep disorders center (1086 of European origin) and from a separate sample consisting of 399 participants claiming delayed sleep phase symptoms and 406 partly-matched controls. A custom Illumina Golden Gate array of 768 selected single nucleotide polymorphisms (SNPs) was assayed in both samples, supplemented by additional SNPlex and Taqman assays, including assay of 41 ancestry-associated markers (AIMs) to control stratification. Results In the Sleep Clinic sample, these assays yielded Bonferroni-significant association with depressed mood in three linked SNPs of the gene FMR1: rs25702 (nominal P=1.77E-05), rs25714 (P=1.83E-05), and rs28900 (P=5.24E-05). This FMR1 association was supported by 8 SNPs with nominal significance and a nominally-significant gene-wise set test. There was no association of depressed mood with FMR1 in the delayed sleep phase case–control sample or in downloaded GWAS data from the GenRED 2 sample contrasting an early-onset recurrent depression sample with controls. No replication was located in other GWAS studies of depression. Our data did weakly replicate a previously-reported association of depression with PPARGC1B rs7732671 (P=0.0235). Suggestive associations not meeting strict criteria for multiple testing and replication were found with GSK3B, NPAS2, RORA, PER3, CRY1, MTNR1A and NR1D1. Notably, 16 SNPs nominally associated with depressed mood (14 in GSK3B) were also nominally associated with delayed sleep phase syndrome (P=3E10-6). Conclusions Considering the inconsistencies between samples and the likelihood that the significant three FMR1 SNPs might be linked to complex polymorphisms more functionally related to depression, large gene resequencing studies may be needed to clarify the import for depression of these circadian genes.
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Affiliation(s)
- Daniel F Kripke
- Department of Psychiatry, University of California, San Diego, La Jolla, CA 92093-0603, USA.
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Deo R, Nalls MA, Avery CL, Smith JG, Evans DS, Keller MF, Butler AM, Buxbaum SG, Li G, Miguel Quibrera P, Smith EN, Tanaka T, Akylbekova EL, Alonso A, Arking DE, Benjamin EJ, Berenson GS, Bis JC, Chen LY, Chen W, Cummings SR, Ellinor PT, Evans MK, Ferrucci L, Fox ER, Heckbert SR, Heiss G, Hsueh WC, Kerr KF, Limacher MC, Liu Y, Lubitz SA, Magnani JW, Mehra R, Marcus GM, Murray SS, Newman AB, Njajou O, North KE, Paltoo DN, Psaty BM, Redline SS, Reiner AP, Robinson JG, Rotter JI, Samdarshi TE, Schnabel RB, Schork NJ, Singleton AB, Siscovick D, Soliman EZ, Sotoodehnia N, Srinivasan SR, Taylor HA, Trevisan M, Zhang Z, Zonderman AB, Newton-Cheh C, Whitsel EA. Common genetic variation near the connexin-43 gene is associated with resting heart rate in African Americans: a genome-wide association study of 13,372 participants. Heart Rhythm 2012. [PMID: 23183192 DOI: 10.1016/j.hrthm.2012.11.014] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
BACKGROUND Genome-wide association studies have identified several genetic loci associated with variation in resting heart rate in European and Asian populations. No study has evaluated genetic variants associated with heart rate in African Americans. OBJECTIVE To identify novel genetic variants associated with resting heart rate in African Americans. METHODS Ten cohort studies participating in the Candidate-gene Association Resource and Continental Origins and Genetic Epidemiology Network consortia performed genome-wide genotyping of single nucleotide polymorphisms (SNPs) and imputed 2,954,965 SNPs using HapMap YRI and CEU panels in 13,372 participants of African ancestry. Each study measured the RR interval (ms) from 10-second resting 12-lead electrocardiograms and estimated RR-SNP associations using covariate-adjusted linear regression. Random-effects meta-analysis was used to combine cohort-specific measures of association and identify genome-wide significant loci (P≤2.5×10(-8)). RESULTS Fourteen SNPs on chromosome 6q22 exceeded the genome-wide significance threshold. The most significant association was for rs9320841 (+13 ms per minor allele; P = 4.98×10(-15)). This SNP was approximately 350 kb downstream of GJA1, a locus previously identified as harboring SNPs associated with heart rate in Europeans. Adjustment for rs9320841 also attenuated the association between the remaining 13 SNPs in this region and heart rate. In addition, SNPs in MYH6, which have been identified in European genome-wide association study, were associated with similar changes in the resting heart rate as this population of African Americans. CONCLUSIONS An intergenic region downstream of GJA1 (the gene encoding connexin 43, the major protein of the human myocardial gap junction) and an intragenic region within MYH6 are associated with variation in resting heart rate in African Americans as well as in populations of European and Asian origin.
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Affiliation(s)
- R Deo
- Division of Cardiology, Electrophysiology Section, University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA.
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Smith JG, Avery CL, Evans DS, Nalls MA, Meng YA, Smith EN, Palmer C, Tanaka T, Mehra R, Butler AM, Young T, Buxbaum SG, Kerr KF, Berenson GS, Schnabel RB, Li G, Ellinor PT, Magnani JW, Chen W, Bis JC, Curb JD, Hsueh WC, Rotter JI, Liu Y, Newman AB, Limacher MC, North KE, Reiner AP, Quibrera PM, Schork NJ, Singleton AB, Psaty BM, Soliman EZ, Solomon AJ, Srinivasan SR, Alonso A, Wallace R, Redline S, Zhang ZM, Post WS, Zonderman AB, Taylor HA, Murray SS, Ferrucci L, Arking DE, Evans MK, Fox ER, Sotoodehnia N, Heckbert SR, Whitsel EA, Newton-Cheh C. Impact of ancestry and common genetic variants on QT interval in African Americans. ACTA ACUST UNITED AC 2012; 5:647-55. [PMID: 23166209 DOI: 10.1161/circgenetics.112.962787] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
BACKGROUND Ethnic differences in cardiac arrhythmia incidence have been reported, with a particularly high incidence of sudden cardiac death and low incidence of atrial fibrillation in individuals of African ancestry. We tested the hypotheses that African ancestry and common genetic variants are associated with prolonged duration of cardiac repolarization, a central pathophysiological determinant of arrhythmia, as measured by the electrocardiographic QT interval. METHODS AND RESULTS First, individual estimates of African and European ancestry were inferred from genome-wide single-nucleotide polymorphism (SNP) data in 7 population-based cohorts of African Americans (n=12,097) and regressed on measured QT interval from ECGs. Second, imputation was performed for 2.8 million SNPs, and a genome-wide association study of QT interval was performed in 10 cohorts (n=13,105). There was no evidence of association between genetic ancestry and QT interval (P=0.94). Genome-wide significant associations (P<2.5 × 10(-8)) were identified with SNPs at 2 loci, upstream of the genes NOS1AP (rs12143842, P=2 × 10(-15)) and ATP1B1 (rs1320976, P=2 × 10(-10)). The most significant SNP in NOS1AP was the same as the strongest SNP previously associated with QT interval in individuals of European ancestry. Low probability values (P<10(-5)) were observed for SNPs at several other loci previously identified in genome-wide association studies in individuals of European ancestry, including KCNQ1, KCNH2, LITAF, and PLN. CONCLUSIONS We observed no difference in duration of cardiac repolarization with global genetic indices of African American ancestry. In addition, our genome-wide association study extends the association of polymorphisms at several loci associated with repolarization in individuals of European ancestry to include individuals of African ancestry.
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Affiliation(s)
- J Gustav Smith
- Department of Cardiology, Lund University, Skåne University Hospital, Sweden.
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Butler AM, Yin X, Evans DS, Nalls MA, Smith EN, Tanaka T, Li G, Buxbaum SG, Whitsel EA, Alonso A, Arking DE, Benjamin EJ, Berenson GS, Bis JC, Chen W, Deo R, Ellinor PT, Heckbert SR, Heiss G, Hsueh WC, Keating BJ, Kerr KF, Li Y, Limacher MC, Liu Y, Lubitz SA, Marciante KD, Mehra R, Meng YA, Newman AB, Newton-Cheh C, North KE, Palmer CD, Psaty BM, Quibrera PM, Redline S, Reiner AP, Rotter JI, Schnabel RB, Schork NJ, Singleton AB, Smith JG, Soliman EZ, Srinivasan SR, Zhang ZM, Zonderman AB, Ferrucci L, Murray SS, Evans MK, Sotoodehnia N, Magnani JW, Avery CL. Novel loci associated with PR interval in a genome-wide association study of 10 African American cohorts. ACTA ACUST UNITED AC 2012; 5:639-46. [PMID: 23139255 DOI: 10.1161/circgenetics.112.963991] [Citation(s) in RCA: 43] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
BACKGROUND The PR interval, as measured by the resting, standard 12-lead ECG, reflects the duration of atrial/atrioventricular nodal depolarization. Substantial evidence exists for a genetic contribution to PR, including genome-wide association studies that have identified common genetic variants at 9 loci influencing PR in populations of European and Asian descent. However, few studies have examined loci associated with PR in African Americans. METHODS AND RESULTS We present results from the largest genome-wide association study to date of PR in 13 415 adults of African descent from 10 cohorts. We tested for association between PR (ms) and ≈2.8 million genotyped and imputed single-nucleotide polymorphisms. Imputation was performed using HapMap 2 YRI and CEU panels. Study-specific results, adjusted for global ancestry and clinical correlates of PR, were meta-analyzed using the inverse variance method. Variation in genome-wide test statistic distributions was noted within studies (λ range: 0.9-1.1), although not after genomic control correction was applied to the overall meta-analysis (λ: 1.008). In addition to generalizing previously reported associations with MEIS1, SCN5A, ARHGAP24, CAV1, and TBX5 to African American populations at the genome-wide significance level (P<5.0 × 10(-8)), we also identified a novel locus: ITGA9, located in a region previously implicated in SCN5A expression. The 3p21 region harboring SCN5A also contained 2 additional independent secondary signals influencing PR (P<5.0 × 10(-8)). CONCLUSIONS This study demonstrates the ability to map novel loci in African Americans as well as the generalizability of loci associated with PR across populations of African, European, and Asian descent.
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Affiliation(s)
- Anne M Butler
- Department of Epidemiology, University of North Carolina, Chapel Hill, 27514, USA.
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Brown TT, Kuperman JM, Chung Y, Erhart M, McCabe C, Hagler DJ, Venkatraman VK, Akshoomoff N, Amaral DG, Bloss CS, Casey BJ, Chang L, Ernst TM, Frazier JA, Gruen JR, Kaufmann WE, Kenet T, Kennedy DN, Murray SS, Sowell ER, Jernigan TL, Dale AM. Neuroanatomical assessment of biological maturity. Curr Biol 2012; 22:1693-8. [PMID: 22902750 DOI: 10.1016/j.cub.2012.07.002] [Citation(s) in RCA: 250] [Impact Index Per Article: 20.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2012] [Revised: 06/20/2012] [Accepted: 07/02/2012] [Indexed: 11/25/2022]
Abstract
Structural MRI allows unparalleled in vivo study of the anatomy of the developing human brain. For more than two decades, MRI research has revealed many new aspects of this multifaceted maturation process, significantly augmenting scientific knowledge gathered from postmortem studies. Postnatal brain development is notably protracted and involves considerable changes in cerebral cortical, subcortical, and cerebellar structures, as well as significant architectural changes in white matter fiber tracts (see [12]). Although much work has described isolated features of neuroanatomical development, it remains a critical challenge to characterize the multidimensional nature of brain anatomy, capturing different phases of development among individuals. Capitalizing on key advances in multisite, multimodal MRI, and using cross-validated nonlinear modeling, we demonstrate that developmental brain phase can be assessed with much greater precision than has been possible using other biological measures, accounting for more than 92% of the variance in age. Further, our composite metric of morphology, diffusivity, and signal intensity shows that the average difference in phase among children of the same age is only about 1 year, revealing for the first time a latent phenotype in the human brain for which maturation timing is tightly controlled.
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Affiliation(s)
- Timothy T Brown
- Multimodal Imaging Laboratory, University of California, San Diego, School of Medicine, La Jolla, CA 92037, USA.
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Price MJ, Murray SS, Angiolillo DJ, Lillie E, Smith EN, Tisch RL, Schork NJ, Teirstein PS, Topol EJ. Influence of Genetic Polymorphisms on the Effect of High- and Standard-Dose Clopidogrel After Percutaneous Coronary Intervention. J Am Coll Cardiol 2012; 59:1928-37. [DOI: 10.1016/j.jacc.2011.11.068] [Citation(s) in RCA: 112] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/14/2011] [Revised: 11/17/2011] [Accepted: 11/29/2011] [Indexed: 11/29/2022]
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Oikonen M, Tikkanen E, Juhola J, Tuovinen T, Seppälä I, Juonala M, Taittonen L, Mikkilä V, Kähönen M, Ripatti S, Viikari J, Lehtimäki T, Havulinna AS, Kee F, Newton-Cheh C, Peltonen L, Schork NJ, Murray SS, Berenson GS, Chen W, Srinivasan SR, Salomaa V, Raitakari OT. Genetic variants and blood pressure in a population-based cohort: the Cardiovascular Risk in Young Finns study. Hypertension 2011; 58:1079-85. [PMID: 22025373 DOI: 10.1161/hypertensionaha.111.179291] [Citation(s) in RCA: 41] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
Abstract
Clinical relevance of a genetic predisposition to elevated blood pressure was quantified during the transition from childhood to adulthood in a population-based Finnish cohort (N=2357). Blood pressure was measured at baseline in 1980 (age 3-18 years) and in follow-ups in 1983, 1986, 2001, and 2007. Thirteen single nucleotide polymorphisms associated with blood pressure were genotyped, and 3 genetic risk scores associated with systolic and diastolic blood pressures and their combination were derived for all of the participants. Effects of the genetic risk score were 0.47 mm Hg for systolic and 0.53 mm Hg for diastolic blood pressures (both P<0.01). The combination genetic risk score was associated with diastolic blood pressure from age 9 years onward (β=0.68 mm Hg; P=0.015). Replications in 1194 participants of the Bogalusa Heart Study showed essentially similar results. The participants in the highest quintile of the combination genetic risk score had a 1.82-fold risk of hypertension in adulthood (P<0.0001) compared with the lowest quintile, independent of a family history of premature hypertension. These findings show that genetic variants are associated with preclinical blood pressure traits in childhood; individuals with several susceptibility alleles have, on average, a 0.5-mm Hg higher blood pressure, and this trajectory continues from childhood to adulthood.
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Affiliation(s)
- Mervi Oikonen
- Research Centre of Applied and Preventive Cardiovascular Medicine, University of Turku, PO Box 52, FI-20521 Turku, Finland.
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Greenwood TA, Lazzeroni LC, Murray SS, Cadenhead KS, Calkins ME, Dobie DJ, Green MF, Gur RE, Gur RC, Hardiman G, Kelsoe JR, Leonard S, Light GA, Nuechterlein KH, Olincy A, Radant AD, Schork NJ, Seidman LJ, Siever LJ, Silverman JM, Stone WS, Swerdlow NR, Tsuang DW, Tsuang MT, Turetsky BI, Freedman R, Braff DL. Analysis of 94 candidate genes and 12 endophenotypes for schizophrenia from the Consortium on the Genetics of Schizophrenia. Am J Psychiatry 2011; 168:930-46. [PMID: 21498463 PMCID: PMC3751972 DOI: 10.1176/appi.ajp.2011.10050723] [Citation(s) in RCA: 208] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
Abstract
OBJECTIVE The authors used a custom array of 1,536 single-nucleotide polymorphisms (SNPs) to interrogate 94 functionally relevant candidate genes for schizophrenia and identify associations with 12 heritable neurophysiological and neurocognitive endophenotypes in data collected by the Consortium on the Genetics of Schizophrenia. METHOD Variance-component association analyses of 534 genotyped subjects from 130 families were conducted by using Merlin software. A novel bootstrap total significance test was also developed to overcome the limitations of existing genomic multiple testing methods and robustly demonstrate significant associations in the context of complex family data and possible population stratification effects. RESULTS Associations with endophenotypes were observed for 46 genes of potential functional significance, with three SNPs at p<10(-4), 27 SNPs at p<10(-3), and 147 SNPs at p<0.01. The bootstrap analyses confirmed that the 47 SNP-endophenotype combinations with the strongest evidence of association significantly exceeded that expected by chance alone, with 93% of these findings expected to be true. Many of the genes interact on a molecular level, and eight genes (e.g., NRG1 and ERBB4) displayed evidence for pleiotropy, revealing associations with four or more endophenotypes. The results collectively support a strong role for genes related to glutamate signaling in mediating schizophrenia susceptibility. CONCLUSIONS This study supports use of relevant endophenotypes and the bootstrap total significance test for identifying genetic variation underlying the etiology of schizophrenia. In addition, the observation of extensive pleiotropy for some genes and singular associations for others suggests alternative, independent pathways mediating pathogenesis in the "group of schizophrenias."
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Affiliation(s)
| | - Laura C. Lazzeroni
- Departments of Psychiatry and Behavioral Sciences and of Pediatrics, Stanford University, Stanford, CA
| | | | | | - Monica E. Calkins
- Department of Psychiatry, University of Pennsylvania, Philadelphia, PA
| | - Dorcas J. Dobie
- Department of Psychiatry and Behavioral Sciences, University of Washington, Seattle, WA
,VA Puget Sound Health Care System, Seattle, WA
| | - Michael F. Green
- Department of Psychiatry and Biobehavioral Sciences, Geffen School of Medicine at University of California Los Angeles, Los Angeles, CA
| | - Raquel E. Gur
- Department of Psychiatry, University of Pennsylvania, Philadelphia, PA
| | - Reuben C. Gur
- Department of Psychiatry, University of Pennsylvania, Philadelphia, PA
| | - Gary Hardiman
- Biomedical Genomics Laboratory, University of California San Diego, La Jolla, CA
,Department of Medicine, University of California San Diego, La Jolla, CA
| | - John R. Kelsoe
- Department of Psychiatry, University of California San Diego, La Jolla, CA
,San Diego VA Healthcare System, San Diego, CA
| | - Sherry Leonard
- Department of Psychiatry, University of Colorado Health Sciences Center, Denver, CO
| | - Gregory A. Light
- Department of Psychiatry, University of California San Diego, La Jolla, CA
| | - Keith H. Nuechterlein
- Department of Psychiatry and Biobehavioral Sciences, Geffen School of Medicine at University of California Los Angeles, Los Angeles, CA
| | - Ann Olincy
- Department of Psychiatry, University of Colorado Health Sciences Center, Denver, CO
| | - Allen D. Radant
- Department of Psychiatry and Behavioral Sciences, University of Washington, Seattle, WA
,VA Puget Sound Health Care System, Seattle, WA
| | - Nicholas J. Schork
- Scripps Genomic Medicine, La Jolla, CA
,Department of Molecular and Experimental Medicine, The Scripps Research Institute, La Jolla, CA
| | - Larry J. Seidman
- Department of Psychiatry, Harvard Medical School, Massachusetts Mental Health Center Public Psychiatry Division of the Beth Israel Deaconess Medical Center, Boston, MA
,Harvard Institute of Psychiatric Epidemiology and Genetics, Boston, MA
| | - Larry J. Siever
- Department of Psychiatry, The Mount Sinai School of Medicine, New York, NY
,James J. Peters VA Medical Center, VISN 3 MIRECC, New York, NY
| | - Jeremy M. Silverman
- Department of Psychiatry, The Mount Sinai School of Medicine, New York, NY
,James J. Peters VA Medical Center, VISN 3 MIRECC, New York, NY
| | - William S. Stone
- Department of Psychiatry, Harvard Medical School, Massachusetts Mental Health Center Public Psychiatry Division of the Beth Israel Deaconess Medical Center, Boston, MA
,Harvard Institute of Psychiatric Epidemiology and Genetics, Boston, MA
| | - Neal R. Swerdlow
- Department of Psychiatry, University of California San Diego, La Jolla, CA
| | - Debby W. Tsuang
- Department of Psychiatry and Behavioral Sciences, University of Washington, Seattle, WA
,VA Puget Sound Health Care System, Seattle, WA
| | - Ming T. Tsuang
- Department of Psychiatry, University of California San Diego, La Jolla, CA
,Department of Psychiatry, Harvard Medical School, Massachusetts Mental Health Center Public Psychiatry Division of the Beth Israel Deaconess Medical Center, Boston, MA
,Harvard Institute of Psychiatric Epidemiology and Genetics, Boston, MA
| | - Bruce I. Turetsky
- Department of Psychiatry, University of Pennsylvania, Philadelphia, PA
| | - Robert Freedman
- Department of Psychiatry, University of Colorado Health Sciences Center, Denver, CO
| | - David L. Braff
- Department of Psychiatry, University of California San Diego, La Jolla, CA
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Winn ME, Shaw M, April C, Klotzle B, Fan JB, Murray SS, Schork NJ. Gene expression profiling of human whole blood samples with the Illumina WG-DASL assay. BMC Genomics 2011; 12:412. [PMID: 21843359 PMCID: PMC3175478 DOI: 10.1186/1471-2164-12-412] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2011] [Accepted: 08/15/2011] [Indexed: 12/23/2022] Open
Abstract
Background Microarray-based gene expression analysis of peripheral whole blood is a common strategy in the development of clinically relevant biomarker panels for a variety of human diseases. However, the results of such an analysis are often plagued by decreased sensitivity and reliability due to the effects of relatively high levels of globin mRNA in whole blood. Globin reduction assays have been shown to overcome such effects, but they require large amounts of total RNA and may induce distinct gene expression profiles. The Illumina whole genome DASL assay can detect gene expression levels using partially degraded RNA samples and has the potential to detect rare transcripts present in highly heterogeneous whole blood samples without the need for globin reduction. We assessed the utility of the whole genome DASL assay in an analysis of peripheral whole blood gene expression profiles. Results We find that gene expression detection is significantly increased with the use of whole genome DASL compared to the standard IVT-based direct hybridization. Additionally, globin-probe negative whole genome DASL did not exhibit significant improvements over globin-probe positive whole genome DASL. Globin reduction further increases the detection sensitivity and reliability of both whole genome DASL and IVT-based direct hybridization with little effect on raw intensity correlations. Raw intensity correlations between total RNA and globin reduced RNA were 0.955 for IVT-based direct hybridization and 0.979 for whole genome DASL. Conclusions Overall, the detection sensitivity of the whole genome DASL assay is higher than the IVT-based direct hybridization assay, with or without globin reduction, and should be considered in conjunction with globin reduction methods for future blood-based gene expression studies.
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Affiliation(s)
- Mary E Winn
- Scripps Genomic Medicine and Scripps Translational Science Institute, The Scripps Research Institute, La Jolla, CA 92037, USA.
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Kripke DF, Nievergelt CM, Tranah GJ, Murray SS, McCarthy MJ, Rex KM, Parimi N, Kelsoe JR. Polymorphisms in melatonin synthesis pathways: possible influences on depression. J Circadian Rhythms 2011; 9:8. [PMID: 21827647 PMCID: PMC3177871 DOI: 10.1186/1740-3391-9-8] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2011] [Accepted: 08/09/2011] [Indexed: 11/14/2022] Open
Abstract
Background It has been reported that rs4446909, a single nucleotide polymorphism (SNP) in the promoter of acetylserotonin methyltransferase (ASMT), influences the expression of the ASMT enzyme. The common G allele is associated with lower ASMT activity, and therefore, diminishes conversion of N-acetylserotonin to melatonin. The G allele was associated with recurrent depressive disorder in a Polish group. ASMT might also affect bipolar relapse, given evidence that N-acetylserotonin might stimulate TRKB receptors, and TRKB may influence mood relapse in bipolar disorder. Additionally, arylalkylamine N-acetyltransferase (AANAT) polymorphisms have been reported associated with depression, perhaps through their influence upon N-acetylserotonin or melatonin synthesis. Results To replicate and further explore these ideas, rs4446909 was genotyped in four research groups, as part of a panel of 610 SNPs surveyed by an Illumina Golden Gate assay. In 768 cases with delayed sleep phase disorder or matched controls, rs4446909 was indeed associated with the depressive symptoms on a self-report scale (P = 0.01, R2 = 0.007). However, there was no significant association of rs4446909 with self-reported depression in a sleep clinic patient group or with two groups of elderly men and women from multicenter studies, nor was the response to lithium treatment associated with rs4446909 in bipolar patients. No associations of two AANAT SNPs with depression were found. Conclusions The evidence did not support a strong influence of rs4446909 upon mood, but the partial replication may be consistent with a modest effect. It is possible that larger or younger subject groups with improved phenotype ascertainment might demonstrate more persuasive replication.
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Affiliation(s)
- Daniel F Kripke
- Department of Psychiatry, University of California, San Diego, 9500 Gilman Drive, La Jolla, California 92093, USA.
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Harismendy O, Bhatia G, Rahim NG, Bansal V, Nakano M, Scott M, Wang X, Dib C, Turlotte E, Heintzman N, Murray SS, Deleuze JF, Sipe JC, Ren B, Bafna V, Topol EJ, Frazer KA. Deciphering the genetic basis of common diseases by integrated functional annotation of common and rare variants. Genome Biol 2010. [PMCID: PMC3026222 DOI: 10.1186/gb-2010-11-s1-i8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
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Smith EN, Chen W, Kähönen M, Kettunen J, Lehtimäki T, Peltonen L, Raitakari OT, Salem RM, Schork NJ, Shaw M, Srinivasan SR, Topol EJ, Viikari JS, Berenson GS, Murray SS. Longitudinal genome-wide association of cardiovascular disease risk factors in the Bogalusa heart study. PLoS Genet 2010; 6:e1001094. [PMID: 20838585 PMCID: PMC2936521 DOI: 10.1371/journal.pgen.1001094] [Citation(s) in RCA: 111] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2010] [Accepted: 07/27/2010] [Indexed: 01/11/2023] Open
Abstract
Cardiovascular disease (CVD) is the leading cause of death worldwide. Recent genome-wide association (GWA) studies have pinpointed many loci associated with CVD risk factors in adults. It is unclear, however, if these loci predict trait levels at all ages, if they are associated with how a trait develops over time, or if they could be used to screen individuals who are pre-symptomatic to provide the opportunity for preventive measures before disease onset. We completed a genome-wide association study on participants in the longitudinal Bogalusa Heart Study (BHS) and have characterized the association between genetic factors and the development of CVD risk factors from childhood to adulthood. We report 7 genome-wide significant associations involving CVD risk factors, two of which have been previously reported. Top regions were tested for replication in the Young Finns Study (YF) and two associations strongly replicated: rs247616 in CETP with HDL levels (combined P = 9.7×10−24), and rs445925 at APOE with LDL levels (combined P = 8.7×10−19). We show that SNPs previously identified in adult cross-sectional studies tend to show age-independent effects in the BHS with effect sizes consistent with previous reports. Previously identified variants were associated with adult trait levels above and beyond those seen in childhood; however, variants with time-dependent effects were also promising predictors. This is the first GWA study to evaluate the role of common genetic variants in the development of CVD risk factors in children as they advance through adulthood and highlights the utility of using longitudinal studies to identify genetic predictors of adult traits in children. We have studied the association between genetic factors on a whole genome level and cardiovascular disease (CVD) risk factors in a population of individuals studied from childhood through adulthood. The longitudinal study design has enabled the investigation of genetic variation influencing trait values over time. We have identified DNA variants that are associated with CVD trait values consistently over time, and a second set of variants that are associated with CVD trait values in a time-dependent manner. We also show that variants previously identified in adult populations have consistent effects within our population and that these effects are usually similar across childhood through adulthood. The discovery of time-dependent variants that influence CVD trait values over time can potentially be used to screen young individuals who are pre-symptomatic and provide the opportunity for preventive measures decades before disease onset.
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Affiliation(s)
- Erin N. Smith
- Scripps Genomic Medicine and Scripps Translational Science Institute, La Jolla, California, United States of America
| | - Wei Chen
- Department of Epidemiology, Tulane University, New Orleans, Louisiana, United States of America
| | - Mika Kähönen
- Department of Clinical Physiology, University Hospital of Tampere and University of Tampere Medical School, Tampere, Finland
| | - Johannes Kettunen
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, United Kingdom
- FIMM, Institute for Molecular Medicine Finland, Helsinki, Finland
| | - Terho Lehtimäki
- Department of Clinical Chemistry, University Hospital of Tampere and University of Tampere Medical School, Tampere, Finland
| | - Leena Peltonen
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, United Kingdom
- FIMM, Institute for Molecular Medicine Finland, Helsinki, Finland
- The Broad Institute of MIT and Harvard, Boston, Massachusetts, United States of America
| | - Olli T. Raitakari
- Department of Clinical Physiology, Turku University Hospital and Centre of Applied and Preventive Cardiovascular Medicine, University of Turku, Turku, Finland
| | - Rany M. Salem
- The Broad Institute of MIT and Harvard, Boston, Massachusetts, United States of America
| | - Nicholas J. Schork
- Scripps Genomic Medicine and Scripps Translational Science Institute, La Jolla, California, United States of America
| | - Marian Shaw
- Scripps Genomic Medicine and Scripps Translational Science Institute, La Jolla, California, United States of America
| | - Sathanur R. Srinivasan
- Department of Epidemiology, Tulane University, New Orleans, Louisiana, United States of America
| | - Eric J. Topol
- Scripps Genomic Medicine and Scripps Translational Science Institute, La Jolla, California, United States of America
| | - Jorma S. Viikari
- Department of Medicine, University of Turku and Turku University Hospital, Turku, Finland
| | - Gerald S. Berenson
- Department of Epidemiology, Tulane University, New Orleans, Louisiana, United States of America
| | - Sarah S. Murray
- Scripps Genomic Medicine and Scripps Translational Science Institute, La Jolla, California, United States of America
- * E-mail:
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Levy D, Neuhausen SL, Hunt SC, Kimura M, Hwang SJ, Chen W, Bis JC, Fitzpatrick AL, Smith E, Johnson AD, Gardner JP, Srinivasan SR, Schork N, Rotter JI, Herbig U, Psaty BM, Sastrasinh M, Murray SS, Vasan RS, Province MA, Glazer NL, Lu X, Cao X, Kronmal R, Mangino M, Soranzo N, Spector TD, Berenson GS, Aviv A. Genome-wide association identifies OBFC1 as a locus involved in human leukocyte telomere biology. Proc Natl Acad Sci U S A 2010; 107:9293-8. [PMID: 20421499 PMCID: PMC2889047 DOI: 10.1073/pnas.0911494107] [Citation(s) in RCA: 217] [Impact Index Per Article: 15.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Telomeres are engaged in a host of cellular functions, and their length is regulated by multiple genes. Telomere shortening, in the course of somatic cell replication, ultimately leads to replicative senescence. In humans, rare mutations in genes that regulate telomere length have been identified in monogenic diseases such as dyskeratosis congenita and idiopathic pulmonary fibrosis, which are associated with shortened leukocyte telomere length (LTL) and increased risk for aplastic anemia. Shortened LTL is observed in a host of aging-related complex genetic diseases and is associated with diminished survival in the elderly. We report results of a genome-wide association study of LTL in a consortium of four observational studies (n = 3,417 participants with LTL and genome-wide genotyping). SNPs in the regions of the oligonucleotide/oligosaccharide-binding folds containing one gene (OBFC1; rs4387287; P = 3.9 x 10(-9)) and chemokine (C-X-C motif) receptor 4 gene (CXCR4; rs4452212; P = 2.9 x 10(-8)) were associated with LTL at a genome-wide significance level (P < 5 x 10(-8)). We attempted replication of the top SNPs at these loci through de novo genotyping of 1,893 additional individuals and in silico lookup in another observational study (n = 2,876), and we confirmed the association findings for OBFC1 but not CXCR4. In addition, we confirmed the telomerase RNA component (TERC) as a gene associated with LTL (P = 1.1 x 10(-5)). The identification of OBFC1 through genome-wide association as a locus for interindividual variation in LTL in the general population advances the understanding of telomere biology in humans and may provide insights into aging-related disorders linked to altered LTL dynamics.
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Affiliation(s)
- Daniel Levy
- National Heart, Lung, and Blood Institute's Framingham Heart Study, Framingham, MA
- Center for Population Studies, National Heart, Lung, and Blood Institute, Bethesda, MD
- Divisions of Cardiology and Epidemiology, Boston University School of Medicine, Boston, MA 02118
| | - Susan L. Neuhausen
- Department Population Sciences, The Beckman Research Institute of the City of Hope, Duarte, CA 91010
| | - Steven C. Hunt
- Cardiovascular Genetics Division, University of Utah School of Medicine, Salt Lake City, UT 84112
| | - Masayuki Kimura
- Center of Human Development and Aging, New Jersey Medical School, Newark, NJ 07101
| | - Shih-Jen Hwang
- National Heart, Lung, and Blood Institute's Framingham Heart Study, Framingham, MA
- Center for Population Studies, National Heart, Lung, and Blood Institute, Bethesda, MD
- Divisions of Cardiology and Epidemiology, Boston University School of Medicine, Boston, MA 02118
| | - Wei Chen
- Bogalusa Heart Study, Tulane University School of Public Health and Tropical Medicine, New Orleans, LA 70112
| | - Joshua C. Bis
- Cardiovascular Health Research Unit and Department of Medicine, University of Washington, Seattle, WA 98105
- Group Health Research Institute, Group Health, Seattle, WA 98105
| | - Annette L. Fitzpatrick
- Departments of Epidemiology and Global Health, University of Washington, Seattle, WA 98105
| | - Erin Smith
- The Scripps Translational Science Institute and The Scripps Research Institute, San Diego, CA 92037
| | - Andrew D. Johnson
- National Heart, Lung, and Blood Institute's Framingham Heart Study, Framingham, MA
- Center for Population Studies, National Heart, Lung, and Blood Institute, Bethesda, MD
- Divisions of Cardiology and Epidemiology, Boston University School of Medicine, Boston, MA 02118
| | - Jeffrey P. Gardner
- Center of Human Development and Aging, New Jersey Medical School, Newark, NJ 07101
| | - Sathanur R. Srinivasan
- Bogalusa Heart Study, Tulane University School of Public Health and Tropical Medicine, New Orleans, LA 70112
| | - Nicholas Schork
- The Scripps Translational Science Institute and The Scripps Research Institute, San Diego, CA 92037
| | - Jerome I. Rotter
- Medical Genetics Institute, Cedars-Sinai Medical Center, Los Angeles, CA 90048
| | - Utz Herbig
- Center of Human Development and Aging, New Jersey Medical School, Newark, NJ 07101
| | - Bruce M. Psaty
- Cardiovascular Health Research Unit and Department of Medicine, University of Washington, Seattle, WA 98105
- Group Health Research Institute, Group Health, Seattle, WA 98105
- Departments of Epidemiology and Health Services, University of Washington, Seattle, WA 98105
| | - Malinee Sastrasinh
- Center of Human Development and Aging, New Jersey Medical School, Newark, NJ 07101
| | - Sarah S. Murray
- The Scripps Translational Science Institute and The Scripps Research Institute, San Diego, CA 92037
| | - Ramachandran S. Vasan
- National Heart, Lung, and Blood Institute's Framingham Heart Study, Framingham, MA
- Center for Population Studies, National Heart, Lung, and Blood Institute, Bethesda, MD
- Divisions of Cardiology and Epidemiology, Boston University School of Medicine, Boston, MA 02118
| | - Michael A. Province
- Division of Statistical Genomics, Washington University School of Medicine, St. Louis, MO 63108
| | - Nicole L. Glazer
- Cardiovascular Health Research Unit and Department of Medicine, University of Washington, Seattle, WA 98105
- Group Health Research Institute, Group Health, Seattle, WA 98105
| | - Xiaobin Lu
- Center of Human Development and Aging, New Jersey Medical School, Newark, NJ 07101
| | - Xiaojian Cao
- Center of Human Development and Aging, New Jersey Medical School, Newark, NJ 07101
| | - Richard Kronmal
- Department of Biostatistics, University of Washington, Seattle, WA 98105
| | - Massimo Mangino
- Department of Twin Research and Genetic Epidemiology, King's College, London SE1 7EH, United Kingdom; and
| | - Nicole Soranzo
- Department of Twin Research and Genetic Epidemiology, King's College, London SE1 7EH, United Kingdom; and
- Wellcome Trust Sanger Institute, Hinxton CB10 1HH, United Kingdom
| | - Tim D. Spector
- Department of Twin Research and Genetic Epidemiology, King's College, London SE1 7EH, United Kingdom; and
| | - Gerald S. Berenson
- Bogalusa Heart Study, Tulane University School of Public Health and Tropical Medicine, New Orleans, LA 70112
| | - Abraham Aviv
- Center of Human Development and Aging, New Jersey Medical School, Newark, NJ 07101
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Bansal V, Harismendy O, Tewhey R, Murray SS, Schork NJ, Topol EJ, Frazer KA. Accurate detection and genotyping of SNPs utilizing population sequencing data. Genome Res 2010; 20:537-45. [PMID: 20150320 DOI: 10.1101/gr.100040.109] [Citation(s) in RCA: 80] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Next-generation sequencing technologies have made it possible to sequence targeted regions of the human genome in hundreds of individuals. Deep sequencing represents a powerful approach for the discovery of the complete spectrum of DNA sequence variants in functionally important genomic intervals. Current methods for single nucleotide polymorphism (SNP) detection are designed to detect SNPs from single individual sequence data sets. Here, we describe a novel method SNIP-Seq (single nucleotide polymorphism identification from population sequence data) that leverages sequence data from a population of individuals to detect SNPs and assign genotypes to individuals. To evaluate our method, we utilized sequence data from a 200-kilobase (kb) region on chromosome 9p21 of the human genome. This region was sequenced in 48 individuals (five sequenced in duplicate) using the Illumina GA platform. Using this data set, we demonstrate that our method is highly accurate for detecting variants and can filter out false SNPs that are attributable to sequencing errors. The concordance of sequencing-based genotype assignments between duplicate samples was 98.8%. The 200-kb region was independently sequenced to a high depth of coverage using two sequence pools containing the 48 individuals. Many of the novel SNPs identified by SNIP-Seq from the individual sequencing were validated by the pooled sequencing data and were subsequently confirmed by Sanger sequencing. We estimate that SNIP-Seq achieves a low false-positive rate of approximately 2%, improving upon the higher false-positive rate for existing methods that do not utilize population sequence data. Collectively, these results suggest that analysis of population sequencing data is a powerful approach for the accurate detection of SNPs and the assignment of genotypes to individual samples.
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Affiliation(s)
- Vikas Bansal
- Scripps Translational Science Institute, The Scripps Research Institute, La Jolla, CA 92037, USA.
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Schork NJ, Murray SS, Frazer KA, Topol EJ. Common vs. rare allele hypotheses for complex diseases. Curr Opin Genet Dev 2009; 19:212-9. [PMID: 19481926 PMCID: PMC2914559 DOI: 10.1016/j.gde.2009.04.010] [Citation(s) in RCA: 403] [Impact Index Per Article: 26.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2009] [Revised: 04/27/2009] [Accepted: 04/28/2009] [Indexed: 01/08/2023]
Abstract
There has been growing debate over the nature of the genetic contribution to individual susceptibility to common complex diseases such as diabetes, osteoporosis, and cancer. The 'Common Disease, Common Variant (CDCV)' hypothesis argues that genetic variations with appreciable frequency in the population at large, but relatively low 'penetrance' (or the probability that a carrier of the relevant variants will express the disease), are the major contributors to genetic susceptibility to common diseases. The 'Common Disease, Rare Variant (CDRV)' hypothesis, on the contrary, argues that multiple rare DNA sequence variations, each with relatively high penetrance, are the major contributors to genetic susceptibility to common diseases. Both hypotheses have their place in current research efforts.
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Affiliation(s)
- Nicholas J Schork
- Scripps Genomic Medicine, and Department of Molecular and Experimental Medicine, The Scripps Research Institute, La Jolla, CA 92037, United States.
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Abstract
The last few years have seen extensive efforts to catalogue human genetic variation and correlate it with phenotypic differences. Most common SNPs have now been assessed in genome-wide studies for statistical associations with many complex traits, including many important common diseases. Although these studies have provided new biological insights, only a limited amount of the heritable component of any complex trait has been identified and it remains a challenge to elucidate the functional link between associated variants and phenotypic traits. Technological advances, such as the ability to detect rare and structural variants, and a clear understanding of the challenges in linking different types of variation with phenotype, will be essential for future progress.
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Affiliation(s)
- Kelly A Frazer
- Scripps Genomic Medicine, Scripps Translational Science Institute and The Scripps Research Institute, La Jolla, California 92037, USA.
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50
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Harismendy O, Ng PC, Strausberg RL, Wang X, Stockwell TB, Beeson KY, Schork NJ, Murray SS, Topol EJ, Levy S, Frazer KA. Evaluation of next generation sequencing platforms for population targeted sequencing studies. Genome Biol 2009; 10:R32. [PMID: 19327155 PMCID: PMC2691003 DOI: 10.1186/gb-2009-10-3-r32] [Citation(s) in RCA: 399] [Impact Index Per Article: 26.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2008] [Revised: 02/23/2009] [Accepted: 03/27/2009] [Indexed: 12/03/2022] Open
Abstract
Human sequence generated from three next-generation sequencing platforms reveals systematic variability in sequence coverage due to local sequence characteristics. Background Next generation sequencing (NGS) platforms are currently being utilized for targeted sequencing of candidate genes or genomic intervals to perform sequence-based association studies. To evaluate these platforms for this application, we analyzed human sequence generated by the Roche 454, Illumina GA, and the ABI SOLiD technologies for the same 260 kb in four individuals. Results Local sequence characteristics contribute to systematic variability in sequence coverage (>100-fold difference in per-base coverage), resulting in patterns for each NGS technology that are highly correlated between samples. A comparison of the base calls to 88 kb of overlapping ABI 3730xL Sanger sequence generated for the same samples showed that the NGS platforms all have high sensitivity, identifying >95% of variant sites. At high coverage, depth base calling errors are systematic, resulting from local sequence contexts; as the coverage is lowered additional 'random sampling' errors in base calling occur. Conclusions Our study provides important insights into systematic biases and data variability that need to be considered when utilizing NGS platforms for population targeted sequencing studies.
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Affiliation(s)
- Olivier Harismendy
- Scripps Genomic Medicine, Scripps Translational Science Institute, The Scripps Research Institute, La Jolla, CA 92037, USA.
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