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Balasubramanian K, Li B, Krakow D, Nevarez L, Ho PJ, Ainsworth JA, Nickerson DA, Bamshad MJ, Immken L, Lachman RS, Cohn DH. MED resulting from recessively inherited mutations in the gene encoding calcium-activated nucleotidase CANT1. Am J Med Genet A 2017; 173:2415-2421. [PMID: 28742282 PMCID: PMC5564418 DOI: 10.1002/ajmg.a.38349] [Citation(s) in RCA: 17] [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] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2017] [Revised: 05/05/2017] [Accepted: 06/09/2017] [Indexed: 12/20/2022]
Abstract
Multiple Epiphyseal Dysplasia (MED) is a relatively mild skeletal dysplasia characterized by mild short stature, joint pain, and early-onset osteoarthropathy. Dominantly inherited mutations in COMP, MATN3, COL9A1, COL9A2, and COL9A3, and recessively inherited mutations in SLC26A2, account for the molecular basis of disease in about 80-85% of the cases. In two families with recurrent MED of an unknown molecular basis, we used exome sequencing and candidate gene analysis to identify homozygosity for recessively inherited missense mutations in CANT1, which encodes calcium-activated nucleotidase 1. The MED phenotype is thus allelic to the more severe Desbuquois dysplasia phenotype and the results identify CANT1 as a second locus for recessively inherited MED.
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Affiliation(s)
- Karthika Balasubramanian
- Department of Molecular, Cell and Developmental Biology, University of California Los Angeles, Los Angeles, California, USA
| | - Bing Li
- Department of Molecular, Cell and Developmental Biology, University of California Los Angeles, Los Angeles, California, USA
| | - Deborah Krakow
- Department of Orthopaedic Surgery, University of California Los Angeles, Los Angeles, California, USA
- Department of Human Genetics, University of California Los Angeles, Los Angeles, California, USA
- International Skeletal Dysplasia Registry, University of California Los Angeles, Los Angeles, California, USA
| | - Lisette Nevarez
- Department of Molecular, Cell and Developmental Biology, University of California Los Angeles, Los Angeles, California, USA
| | - Patric J. Ho
- Department of Molecular, Cell and Developmental Biology, University of California Los Angeles, Los Angeles, California, USA
| | - Julia A. Ainsworth
- Department of Molecular, Cell and Developmental Biology, University of California Los Angeles, Los Angeles, California, USA
| | - Deborah A. Nickerson
- Department of Genome Sciences, University of Washington, Seattle, Washington, USA
| | - Michael J. Bamshad
- Department of Genome Sciences, University of Washington, Seattle, Washington, USA
- Department of Pediatrics, University of Washington, Seattle, Washington, USA
| | | | | | - Ralph S. Lachman
- International Skeletal Dysplasia Registry, University of California Los Angeles, Los Angeles, California, USA
| | - Daniel H. Cohn
- Department of Molecular, Cell and Developmental Biology, University of California Los Angeles, Los Angeles, California, USA
- Department of Orthopaedic Surgery, University of California Los Angeles, Los Angeles, California, USA
- International Skeletal Dysplasia Registry, University of California Los Angeles, Los Angeles, California, USA
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152
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Ng BG, Asteggiano CG, Kircher M, Buckingham KJ, Raymond K, Nickerson DA, Shendure J, Bamshad MJ, Ensslen M, Freeze HH. Encephalopathy caused by novel mutations in the CMP-sialic acid transporter, SLC35A1. Am J Med Genet A 2017; 173:2906-2911. [PMID: 28856833 DOI: 10.1002/ajmg.a.38412] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [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: 05/12/2017] [Revised: 07/21/2017] [Accepted: 07/31/2017] [Indexed: 12/16/2022]
Abstract
Transport of activated nucleotide-sugars into the Golgi is critical for proper glycosylation and mutations in these transporters cause a group of rare genetic disorders termed congenital disorders of glycosylation. We performed exome sequencing on an individual with a profound neurological presentation and identified rare compound heterozygous mutations, p.Thr156Arg and p.Glu196Lys, in the CMP-sialic acid transporter, SLC35A1. Patient primary fibroblasts and serum showed a considerable decrease in the amount of N- and O-glycans terminating in sialic acid. Direct measurement of CMP-sialic acid transport into the Golgi showed a substantial decrease in overall rate of transport. Here we report the identification of the third patient with CMP-sialic acid transporter deficiency, who presented with severe neurological phenotype, but without hematological abnormalities.
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Affiliation(s)
- Bobby G Ng
- Human Genetics Program, Sanford Burnham Prebys Medical Discovery Institute, La Jolla, California
| | - Carla G Asteggiano
- CONICET - Centro de Estudio de las Metabolopatías Congénitas, Universidad Nacional de Córdoba, Facultad de Medicina, Universidad Católica de Córdoba, Córdoba, Argentina
| | - Martin Kircher
- Department of Genome Sciences, University of Washington, Seattle, Washington
| | - Kati J Buckingham
- Department of Pediatrics, University of Washington, Seattle, Washington
| | - Kimiyo Raymond
- Biochemical Genetics Laboratory, Mayo Clinic College of Medicine, Rochester, Minnesota
| | - Deborah A Nickerson
- Department of Genome Sciences, University of Washington, Seattle, Washington
| | - Jay Shendure
- Department of Genome Sciences, University of Washington, Seattle, Washington.,Howard Hughes Medical Institute, University of Washington, Seattle, Washington
| | - Michael J Bamshad
- Department of Genome Sciences, University of Washington, Seattle, Washington.,Department of Pediatrics, University of Washington, Seattle, Washington
| | | | - Matthias Ensslen
- Department of Paediatric Neurology and Developmental Medicine, Hauner Children's Hospital, University of Munich Lindwurmstrasse 4, Munich, Germany
| | - Hudson H Freeze
- Human Genetics Program, Sanford Burnham Prebys Medical Discovery Institute, La Jolla, California
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153
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Keller RB, Tran TT, Pyott SM, Pepin MG, Savarirayan R, McGillivray G, Nickerson DA, Bamshad MJ, Byers PH. Monoallelic and biallelic CREB3L1 variant causes mild and severe osteogenesis imperfecta, respectively. Genet Med 2017; 20:411-419. [PMID: 28817112 PMCID: PMC5816725 DOI: 10.1038/gim.2017.115] [Citation(s) in RCA: 41] [Impact Index Per Article: 5.9] [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: 03/09/2017] [Accepted: 06/05/2017] [Indexed: 12/11/2022] Open
Abstract
Purpose Osteogenesis imperfecta (OI) is a heritable skeletal dysplasia. Dominant pathogenic variants in COL1A1 and COL1A2 explain the majority of OI cases. At least fifteen additional genes have been identified, but still do not account for all OI phenotypes that present. We sought the genetic cause of mild and lethal OI phenotypes in an unsolved family. Methods We performed exome sequencing on seven members of the family, both affected and unaffected. Results We identified a variant in Cyclic AMP Responsive Element Binding Protein 3-Like 1 (CREB3L1) in a consanguineous family. The variant caused a prenatal/perinatal lethal OI in homozygotes, similar to that seen in OI type II as a result of mutations in type I collagen genes, and a mild phenotype (fractures, blue sclerae) in multiple heterozygous family members. CREB3L1 encodes Old Astrocyte Specifically-Induced Substance (OASIS), an ER stress transducer. The variant disrupts a DNA-binding site and prevents OASIS from acting on its transcriptional targets including SEC24D, which encodes a component of the coat protein II (COPII) complex. Conclusion This report confirms that CREB3L1 is an OI-related gene and suggests the pathogenic mechanism of CREB3L1-associated OI involves the altered regulation of proteins involved in cellular secretion.
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Affiliation(s)
- Rachel B Keller
- Department of Pathology, University of Washington, Seattle, Washington, USA
| | - Thao T Tran
- Department of Pathology, University of Washington, Seattle, Washington, USA
| | - Shawna M Pyott
- Department of Pathology, University of Washington, Seattle, Washington, USA
| | - Melanie G Pepin
- Department of Pathology, University of Washington, Seattle, Washington, USA
| | - Ravi Savarirayan
- Victorian Clinical Genetics Services, Murdoch Children's Research Institute, Melbourne, Victoria, Australia.,Department of Paediatrics, University of Melbourne, Melbourne, Victoria, Australia
| | - George McGillivray
- Victorian Clinical Genetics Services, Murdoch Children's Research Institute, Melbourne, Victoria, Australia
| | - Deborah A Nickerson
- Center for Mendelian Genomics, University of Washington, Seattle, Washington, USA
| | - Michael J Bamshad
- Center for Mendelian Genomics, University of Washington, Seattle, Washington, USA
| | - Peter H Byers
- Department of Pathology, University of Washington, Seattle, Washington, USA.,Department of Medicine (Medical Genetics), University of Washington, Seattle, Washington, USA
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154
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Liu N, Irvin MR, Zhi D, Patki A, Beasley TM, Nickerson DA, Hill CE, Chen J, Kimmel SE, Limdi NA. Influence of common and rare genetic variation on warfarin dose among African-Americans and European-Americans using the exome array. Pharmacogenomics 2017; 18:1059-1073. [PMID: 28686080 DOI: 10.2217/pgs-2017-0046] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023] Open
Abstract
AIM We conducted a genome-wide association study using the Illumina Exome Array to identify coding SNPs that may explain additional warfarin dose variability. PATIENTS & METHODS Analysis was performed after adjustment for clinical variables and genetic factors known to influence warfarin dose among 1680 warfarin users (838 European-Americans and 842 African-Americans). Replication was performed in an independent sample. RESULTS We confirmed the influence of known genetic variants on warfarin dose variability. Our study is the first to show the association between rs12772169 and warfarin dose in African-Americans. In addition, genes COX15 and FGF5 showed significant association in European-Americans. CONCLUSION We identified some novel genes/SNPs that underpin warfarin dose response. Further replication is needed to confirm our findings.
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Affiliation(s)
- Nianjun Liu
- Department of Epidemiology & Biostatistics, School of Public Health - Bloomington, Indiana University, Bloomington, IN 47405, USA
| | - Marguerite R Irvin
- Department of Epidemiology, School of Public Health, University of Alabama at Birmingham, Birmingham, AL 35294, USA
| | - Degui Zhi
- School of Biomedical Informatics, University of Texas Health Science Center at Houston, Houston, TX 77030, USA
| | - Amit Patki
- Department of Biostatistics, School of Public Health, University of Alabama at Birmingham, Birmingham, AL 35294, USA
| | - T Mark Beasley
- Department of Biostatistics, School of Public Health, University of Alabama at Birmingham, Birmingham, AL 35294, USA
| | - Deborah A Nickerson
- Department of Genome Sciences, School of Medicine, University of Washington, Seattle, WA 98195, USA
| | - Charles E Hill
- Department of Pathology & Laboratory Medicine, Emory University School of Medicine, Atlanta, GA 30322, USA
| | - Jinbo Chen
- Department of Biostatistics & Epidemiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Stephen E Kimmel
- Department of Biostatistics & Epidemiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA.,Department of Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Nita A Limdi
- Department of Neurology, School of Medicine, University of Alabama at Birmingham, Birmingham, AL 35294, USA
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Van De Weghe JC, Rusterholz TD, Latour B, Grout ME, Aldinger KA, Shaheen R, Dempsey JC, Maddirevula S, Cheng YHH, Phelps IG, Gesemann M, Goel H, Birk OS, Alanzi T, Rawashdeh R, Khan AO, Bamshad MJ, Nickerson DA, Neuhauss SC, Dobyns WB, Alkuraya FS, Roepman R, Bachmann-Gagescu R, Doherty D, Doherty D. Mutations in ARMC9, which Encodes a Basal Body Protein, Cause Joubert Syndrome in Humans and Ciliopathy Phenotypes in Zebrafish. Am J Hum Genet 2017. [PMID: 28625504 DOI: 10.1016/j.ajhg.2017.05.010] [Citation(s) in RCA: 45] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023] Open
Abstract
Joubert syndrome (JS) is a recessive neurodevelopmental disorder characterized by hypotonia, ataxia, abnormal eye movements, and variable cognitive impairment. It is defined by a distinctive brain malformation known as the "molar tooth sign" on axial MRI. Subsets of affected individuals have malformations such as coloboma, polydactyly, and encephalocele, as well as progressive retinal dystrophy, fibrocystic kidney disease, and liver fibrosis. More than 35 genes have been associated with JS, but in a subset of families the genetic cause remains unknown. All of the gene products localize in and around the primary cilium, making JS a canonical ciliopathy. Ciliopathies are unified by their overlapping clinical features and underlying mechanisms involving ciliary dysfunction. In this work, we identify biallelic rare, predicted-deleterious ARMC9 variants (stop-gain, missense, splice-site, and single-exon deletion) in 11 individuals with JS from 8 families, accounting for approximately 1% of the disorder. The associated phenotypes range from isolated neurological involvement to JS with retinal dystrophy, additional brain abnormalities (e.g., heterotopia, Dandy-Walker malformation), pituitary insufficiency, and/or synpolydactyly. We show that ARMC9 localizes to the basal body of the cilium and is upregulated during ciliogenesis. Typical ciliopathy phenotypes (curved body shape, retinal dystrophy, coloboma, and decreased cilia) in a CRISPR/Cas9-engineered zebrafish mutant model provide additional support for ARMC9 as a ciliopathy-associated gene. Identifying ARMC9 mutations as a cause of JS takes us one step closer to a full genetic understanding of this important disorder and enables future functional work to define the central biological mechanisms underlying JS and other ciliopathies.
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Affiliation(s)
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | - Dan Doherty
- Department of Pediatrics, University of Washington, Seattle, WA 98195, USA; Center for Integrative Brain Research, Seattle Children's Research Institute, Seattle, WA 98101, USA.
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156
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Himes P, Kauffman TL, Muessig KR, Amendola LM, Berg JS, Dorschner MO, Gilmore M, Nickerson DA, Reiss JA, Richards CS, Rope AF, Simpson DK, Wilfond BS, Jarvik GP, Goddard KA. Genome sequencing and carrier testing: decisions on categorization and whether to disclose results of carrier testing. Genet Med 2017; 19:803-808. [PMID: 28079899 PMCID: PMC5509491 DOI: 10.1038/gim.2016.198] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [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] [Received: 05/18/2016] [Accepted: 10/25/2016] [Indexed: 01/01/2023] Open
Abstract
PURPOSE We investigated the use of genome sequencing for preconception carrier testing. Genome sequencing could identify one or more of thousands of X-linked or autosomal recessive conditions that could be disclosed during preconception or prenatal counseling. Therefore, a framework that helps both clinicians and patients understand the possible range of findings is needed to respect patient preferences by ensuring that information about only the desired types of genetic conditions are provided to a given patient. METHODS We categorized gene-condition pairs into groups using a previously developed taxonomy of genetic conditions. Patients could elect to receive results from these categories. A Return of Results Committee (RORC) developed inclusion and exclusion criteria for each category. RESULTS To date, the RORC has categorized 728 gene-condition pairs: 177 are categorized as life span-limiting, 406 are categorized as serious, 93 are categorized as mild, 41 are categorized as unpredictable, and 11 are categorized as adult-onset. An additional 64 gene-condition pairs were excluded from reporting to patients or put on a watch list, generally because evidence that a gene and condition were associated was limited. CONCLUSION Categorization of gene-condition pairs using our taxonomy simplifies communication regarding patient preferences for carrier information from a genomic test.Genet Med advance online publication 12 January 2017.
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Affiliation(s)
- Patricia Himes
- Department of Medical Genetics, Kaiser Permanente Northwest, Portland, Oregon, USA
| | - Tia L. Kauffman
- Center for Health Research, Kaiser Permanente Northwest, Portland, Oregon, USA
| | - Kristin R. Muessig
- Center for Health Research, Kaiser Permanente Northwest, Portland, Oregon, USA
| | - Laura M. Amendola
- Department of Medicine, Division of Medical Genetics, University of Washington, Seattle, Washington, USA
| | - Jonathan S. Berg
- Department of Genetics, University of North Carolina, Chapel Hill, North Carolina, USA
| | | | - Marian Gilmore
- Department of Medical Genetics, Kaiser Permanente Northwest, Portland, Oregon, USA
| | - Deborah A. Nickerson
- Department of Genome Sciences, University of Washington, Seattle, Washington, USA
| | - Jacob A. Reiss
- Center for Health Research, Kaiser Permanente Northwest, Portland, Oregon, USA
| | - C. Sue Richards
- Department of Molecular and Medical Genetics, Oregon Health & Science University, Portland, Oregon, USA
| | - Alan F. Rope
- Northwest Permanente, Kaiser Permanente Northwest, Portland, Oregon, USA
| | - Dana K. Simpson
- Northwest Permanente, Kaiser Permanente Northwest, Portland, Oregon, USA
| | - Benjamin S. Wilfond
- Seattle Children’s Research Institute, Treuman Katz Center for Pediatric Bioethics, Seattle, Washington, USA
| | - Gail P. Jarvik
- Department of Medicine, Division of Medical Genetics, University of Washington, Seattle, Washington, USA
- Department of Genome Sciences, University of Washington, Seattle, Washington, USA
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157
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Bien SA, Guo X, Su YR, Harrison TA, Qu C, Lu Y, Long J, Chen S, Chan AT, Conti DV, Kang HM, Hoffmeister M, Hudson TJ, Jenkins MA, Marchand LL, Newcomb PA, Slattery ML, White E, Abeçasis GR, Gruber SB, Nickerson DA, Schmit SL, Casey G, Hsu L, Zheng W, Peters U. Abstract 1300: Genetic predictors of gene expression associated with risk of colorectal cancer. Cancer Res 2017. [DOI: 10.1158/1538-7445.am2017-1300] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Abstract
To date, genome-wide association studies (GWAS) have reported common variants in over 50 loci
with weak to moderate effects on CRC risk. These genetic factors in aggregate explain only a small
fraction of familial risk of CRC. To aid in the discovery of novel CRC loci, we integrated large
transcriptome data, including those generated in the Genotype-Tissue Expression (GTEx) Project in
genetic association analyses of CRC. The computational method, PrediXcan, was used to predict
transcript levels in relevant tissues and perform gene-level association tests with CRC. Prediction
models were developed using whole blood transcriptomes (n=922) from the depression genes and
networks (DGN), as well as colon transcriptomes (transverse n=169 and sigmoid n=124) from
GTEx datasets, along with high-density genotyping data from the same subjects. Genetically
determined expression levels were tested for association with CRC in 12,186 cases and 14,718
controls from GECCO-CCFR and suggestive associations (false discovery rate = 0.2) were evaluated
in 7,481 cases and 17,796 controls from the Asia Colorectal Cancer Consortium (ACCC) and 22,974
cases and 14,392 controls from the Colorectal Transdisciplinary (CORECT) study. We attempted to
replicate novel associations for eight genes and found statistically significant associations with
CXCR1 (OR=1.21 (1.10-1.33), p-value=7.8x10-5) and CXCR2 (OR=1.24 (1.11-1.38), p-value=9.9x10-
5). We also recovered previous associations at six known GWAS loci, thereby providing additional
support for putative target genes. CXCR1 and CXCR2 are therapeutic targets for the anticancer agent
Reparixin, which is currently being investigated in a stage II clinical trial for triple negative breast
cancer. As such, these findings provide preliminary support for new molecular targets that could
potentially repurpose a putative cancer therapeutic. These findings highlight the utility integrating
transcriptome data for novel discovery and biological insight of risk loci.
Citation Format: Stephanie A. Bien, Xingyi Guo, Yu-Ru Su, Tabitha A. Harrison, Conghui Qu, Yingchang Lu, Jiron Long, Sai Chen, Andrew T. Chan, David V. Conti, Hyun M. Kang, Michael Hoffmeister, Thomas J. Hudson, Mark A. Jenkins, Loic Le Marchand, Polly A. Newcomb, Martha L. Slattery, Emily White, Goncalo R. Abeçasis, Stephen B. Gruber, Deborah A. Nickerson, Stephanie L. Schmit, Graham Casey, Li Hsu, Wei Zheng, Ulrike Peters, GECCO-CCFR-AAAC-CORECT. Genetic predictors of gene expression associated with risk of colorectal cancer [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2017; 2017 Apr 1-5; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2017;77(13 Suppl):Abstract nr 1300. doi:10.1158/1538-7445.AM2017-1300
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Affiliation(s)
| | | | - Yu-Ru Su
- 1Fred Hutchinson Cancer Research Ctr., Seattle, WA
| | | | - Conghui Qu
- 1Fred Hutchinson Cancer Research Ctr., Seattle, WA
| | | | | | | | | | | | | | | | | | | | | | | | | | - Emily White
- 1Fred Hutchinson Cancer Research Ctr., Seattle, WA
| | | | | | | | | | | | - Li Hsu
- 1Fred Hutchinson Cancer Research Ctr., Seattle, WA
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158
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Kim DS, Burt AA, Ranchalis JE, Wilmot B, Smith JD, Patterson KE, Coe BP, Li YK, Bamshad MJ, Nikolas M, Eichler EE, Swanson JM, Nigg JT, Nickerson DA, Jarvik GP. Sequencing of sporadic Attention-Deficit Hyperactivity Disorder (ADHD) identifies novel and potentially pathogenic de novo variants and excludes overlap with genes associated with autism spectrum disorder. Am J Med Genet B Neuropsychiatr Genet 2017; 174:381-389. [PMID: 28332277 PMCID: PMC5467442 DOI: 10.1002/ajmg.b.32527] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/14/2016] [Accepted: 01/03/2017] [Indexed: 02/05/2023]
Abstract
Attention-Deficit Hyperactivity Disorder (ADHD) has high heritability; however, studies of common variation account for <5% of ADHD variance. Using data from affected participants without a family history of ADHD, we sought to identify de novo variants that could account for sporadic ADHD. Considering a total of 128 families, two analyses were conducted in parallel: first, in 11 unaffected parent/affected proband trios (or quads with the addition of an unaffected sibling) we completed exome sequencing. Six de novo missense variants at highly conserved bases were identified and validated from four of the 11 families: the brain-expressed genes TBC1D9, DAGLA, QARS, CSMD2, TRPM2, and WDR83. Separately, in 117 unrelated probands with sporadic ADHD, we sequenced a panel of 26 genes implicated in intellectual disability (ID) and autism spectrum disorder (ASD) to evaluate whether variation in ASD/ID-associated genes were also present in participants with ADHD. Only one putative deleterious variant (Gln600STOP) in CHD1L was identified; this was found in a single proband. Notably, no other nonsense, splice, frameshift, or highly conserved missense variants in the 26 gene panel were identified and validated. These data suggest that de novo variant analysis in families with independently adjudicated sporadic ADHD diagnosis can identify novel genes implicated in ADHD pathogenesis. Moreover, that only one of the 128 cases (0.8%, 11 exome, and 117 MIP sequenced participants) had putative deleterious variants within our data in 26 genes related to ID and ASD suggests significant independence in the genetic pathogenesis of ADHD as compared to ASD and ID phenotypes. © 2017 Wiley Periodicals, Inc.
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Affiliation(s)
- Daniel Seung Kim
- Division of Medical Genetics, Department of Medicine, University of Washington School of Medicine, Seattle, WA
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA
- Center for Statistical Genetics, Department of Biostatistics, University of Michigan School of Public Health, Ann Arbor, MI
| | - Amber A. Burt
- Division of Medical Genetics, Department of Medicine, University of Washington School of Medicine, Seattle, WA
| | - Jane E. Ranchalis
- Division of Medical Genetics, Department of Medicine, University of Washington School of Medicine, Seattle, WA
| | - Beth Wilmot
- Division of Bioinformatics and Computational Biology, Department of Medical Informatics and Clinical Epidemiology, Oregon Health and Science University, Portland, OR
| | - Joshua D. Smith
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA
| | - Karynne E. Patterson
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA
| | - Bradley P. Coe
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA
| | - Yatong K. Li
- Center for Statistical Genetics, Department of Biostatistics, University of Michigan School of Public Health, Ann Arbor, MI
| | - Michael J. Bamshad
- Division of Medical Genetics, Department of Medicine, University of Washington School of Medicine, Seattle, WA
| | - Molly Nikolas
- Department of Psychology, University of Iowa, Iowa City, IA
| | - Evan E. Eichler
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA
| | - James M. Swanson
- Department of Psychiatry, University of California-Irvine, Irvine, CA
- Department of Epidemiology, University of California-Irvine, Irvine, CA
| | - Joel T Nigg
- Department of Psychiatry, Oregon Health and Science University, Portland, OR
| | - Deborah A. Nickerson
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA
| | - Gail P. Jarvik
- Division of Medical Genetics, Department of Medicine, University of Washington School of Medicine, Seattle, WA
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA
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159
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Maselli RA, Arredondo J, Vázquez J, Chong JX, Bamshad MJ, Nickerson DA, Lara M, Ng F, Lo VL, Pytel P, McDonald CM. Presynaptic congenital myasthenic syndrome with a homozygous sequence variant in LAMA5 combines myopia, facial tics, and failure of neuromuscular transmission. Am J Med Genet A 2017; 173:2240-2245. [PMID: 28544784 DOI: 10.1002/ajmg.a.38291] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [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: 01/12/2017] [Revised: 04/03/2017] [Accepted: 04/24/2017] [Indexed: 12/13/2022]
Abstract
Defects in genes encoding the isoforms of the laminin alpha subunit have been linked to various phenotypic manifestations, including brain malformations, muscular dystrophy, ocular defects, cardiomyopathy, and skin abnormalities. We report here a severe defect of neuromuscular transmission in a consanguineous patient with a homozygous variant in the laminin alpha-5 subunit gene (LAMA5). The variant c.8046C>T (p.Arg2659Trp) is rare and has a predicted deleterious effect. The affected individual, who also carries a rare homozygous sequence variant in LAMA1, had muscle weakness, myopia, and facial tics. Magnetic resonance imaging of brain showed mild volume loss and periventricular T2 prolongation. Repetitive nerve stimulation revealed 50% decrement of compound muscle action potential amplitudes and 250% facilitation immediately after exercise, Endplate studies identified a profound reduction of the endplate potential quantal content and endplates with normal postsynaptic folding that were denuded or partially occupied by small nerve terminals. Expression studies revealed that p.Arg2659Trp caused decreased binding of laminin alpha-5 to SV2A and impaired laminin-521 cell-adhesion and cell projection support in primary neuronal cultures. In summary, this report describing severe neuromuscular transmission failure in a patient with a LAMA5 mutation expands the list of phenotypes associated with defects in genes encoding alpha-laminins.
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Affiliation(s)
- Ricardo A Maselli
- Department of Neurology, University of California Davis, Sacramento, California
| | - Juan Arredondo
- Department of Neurology, University of California Davis, Sacramento, California
| | - Jessica Vázquez
- Department of Neurology, University of California Davis, Sacramento, California
| | - Jessica X Chong
- Department of Pediatrics, University of Washington, Seattle, Washington
| | | | - Michael J Bamshad
- Department of Pediatrics, University of Washington, Seattle, Washington.,Department of Genome Sciences, University of Washington, Seattle, Washington.,Division of Genetic Medicine, Seattle Children's Hospital, Seattle, Washington
| | - Deborah A Nickerson
- Department of Genome Sciences, University of Washington, Seattle, Washington
| | - Marian Lara
- Department of Neurology, University of California Davis, Sacramento, California
| | - Fiona Ng
- Department of Neurology, University of California Davis, Sacramento, California
| | - Victoria L Lo
- Department of Neurology, University of California Davis, Sacramento, California
| | - Peter Pytel
- Department of Pathology, University of Chicago, Chicago, Illinois
| | - Craig M McDonald
- Department of Medicine and Rehabilitation, University of California Davis, Sacramento, California
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Duran I, Taylor SP, Zhang W, Martin J, Qureshi F, Jacques SM, Wallerstein R, Lachman RS, Nickerson DA, Bamshad M, Cohn DH, Krakow D. Mutations in IFT-A satellite core component genes IFT43 and IFT121 produce short rib polydactyly syndrome with distinctive campomelia. Cilia 2017; 6:7. [PMID: 28400947 PMCID: PMC5387211 DOI: 10.1186/s13630-017-0051-y] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [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] [Received: 02/03/2017] [Accepted: 03/30/2017] [Indexed: 12/31/2022] Open
Abstract
Background Skeletal ciliopathies comprise a spectrum of ciliary malfunction disorders that have a profound effect on the skeleton. Most common among these disorders is short rib polydactyly syndrome (SRPS), a recessively inherited perinatal lethal condition characterized by a long narrow chest, markedly shortened long bones, polydactyly and, often, multi-organ system involvement. SRPS shows extensive locus heterogeneity with mutations in genes encoding proteins that participate in cilia formation and/or function. Results Herein we describe mutations in IFT43, a satellite member of the retrograde IFT-A complex, that produce a form of SRPS with unusual bending of the ribs and appendicular bones. These newly described IFT43 mutations disrupted cilia formation, produced abnormalities in cartilage growth plate architecture thus contributing to altered endochondral ossification. We further show that the IFT43 SRPS phenotype is similar to SRPS resulting from mutations in the gene encoding IFT121 (WDR35), a direct interactor with IFT43. Conclusions This study defines a new IFT43-associated phenotype, identifying an additional locus for SRPS. The data demonstrate that IFT43 is essential for ciliogenesis and that the mutations disrupted the orderly proliferation and differentiation of growth plate chondrocytes, resulting in a severe effect on endochondral ossification and mineralization. Phenotypic similarities with SRPS cases resulting from mutations in the gene encoding the IFT43 direct interacting protein IFT121 suggests that similar mechanisms may be disrupted by defects in these two IFT-A satellite interactors. Electronic supplementary material The online version of this article (doi:10.1186/s13630-017-0051-y) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Ivan Duran
- Department of Orthopaedic Surgery, David Geffen School of Medicine at the University of California at Los Angeles, Los Angeles, CA 90095 USA.,Networking Research Center on Bioengineering, Biomaterials and Nanomedicine, (CIBER-BBN), University of Malaga, Málaga, Spain
| | - S Paige Taylor
- Department of Human Genetics, David Geffen School of Medicine at the University of California at Los Angeles, Los Angeles, CA 90095 USA
| | - Wenjuan Zhang
- Department of Molecular, Cell, and Developmental Biology, University of California, Los Angeles, Los Angeles, CA 90095 USA
| | - Jorge Martin
- Department of Orthopaedic Surgery, David Geffen School of Medicine at the University of California at Los Angeles, Los Angeles, CA 90095 USA
| | - Faisal Qureshi
- Department of Pathology, Hutzel Women's Hospital/Wayne State University, Detroit, MI 48201 USA
| | - Suzanne M Jacques
- Department of Pathology, Hutzel Women's Hospital/Wayne State University, Detroit, MI 48201 USA
| | - Robert Wallerstein
- Kapi'olani Medical Center for Women and Children, Honolulu, HI 96826 USA
| | - Ralph S Lachman
- International Skeletal Dysplasia Registry, University of California, Los Angeles, Los Angeles, CA 90095 USA
| | - Deborah A Nickerson
- University of Washington Center for Mendelian Genomics, University of Washington, Seattle, WA 98195 USA
| | - Michael Bamshad
- University of Washington Center for Mendelian Genomics, University of Washington, Seattle, WA 98195 USA
| | - Daniel H Cohn
- Department of Orthopaedic Surgery, David Geffen School of Medicine at the University of California at Los Angeles, Los Angeles, CA 90095 USA.,Department of Molecular, Cell, and Developmental Biology, University of California, Los Angeles, Los Angeles, CA 90095 USA.,International Skeletal Dysplasia Registry, University of California, Los Angeles, Los Angeles, CA 90095 USA
| | - Deborah Krakow
- Department of Orthopaedic Surgery, David Geffen School of Medicine at the University of California at Los Angeles, Los Angeles, CA 90095 USA.,Department of Human Genetics, David Geffen School of Medicine at the University of California at Los Angeles, Los Angeles, CA 90095 USA.,Department of Obstetrics and Gynecology, David Geffen School of Medicine at the University of California at Los Angeles, Los Angeles, CA 90095 USA.,International Skeletal Dysplasia Registry, University of California, Los Angeles, Los Angeles, CA 90095 USA
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161
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Simon MT, Ng BG, Friederich MW, Wang RY, Boyer M, Kircher M, Collard R, Buckingham KJ, Chang R, Shendure J, Nickerson DA, Bamshad MJ, Van Hove JLK, Freeze HH, Abdenur JE. Activation of a cryptic splice site in the mitochondrial elongation factor GFM1 causes combined OXPHOS deficiency. Mitochondrion 2017; 34:84-90. [PMID: 28216230 DOI: 10.1016/j.mito.2017.02.004] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [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: 09/15/2016] [Revised: 01/11/2017] [Accepted: 02/10/2017] [Indexed: 11/17/2022]
Abstract
We report the clinical, biochemical, and molecular findings in two brothers with encephalopathy and multi-systemic disease. Abnormal transferrin glycoforms were suggestive of a type I congenital disorder of glycosylation (CDG). While exome sequencing was negative for CDG related candidate genes, the testing revealed compound heterozygous mutations in the mitochondrial elongation factor G gene (GFM1). One of the mutations had been reported previously while the second, novel variant was found deep in intron 6, activating a cryptic splice site. Functional studies demonstrated decreased GFM1 protein levels, suggested disrupted assembly of mitochondrial complexes III and V and decreased activities of mitochondrial complexes I and IV, all indicating combined OXPHOS deficiency.
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Affiliation(s)
- Mariella T Simon
- Division of Metabolic Disorders, CHOC Children's, Orange, CA, USA; Department of Developmental and Cell Biology, University of California Irvine, Irvine, CA, USA
| | - Bobby G Ng
- Human Genetics Program, Sanford Children's Health Research Center, Sanford-Burnham-Prebys Medical Discovery Institute, La Jolla, CA, USA
| | - Marisa W Friederich
- Department of Pediatrics, Section of Clinical Genetics and Metabolism, University of Colorado, Aurora, CO, USA
| | - Raymond Y Wang
- Division of Metabolic Disorders, CHOC Children's, Orange, CA, USA; Department of Pediatrics, University of California Irvine, Irvine, CA, USA
| | - Monica Boyer
- Division of Metabolic Disorders, CHOC Children's, Orange, CA, USA
| | - Martin Kircher
- Department of Genome Sciences, University of Washington, Seattle, WA, USA
| | - Renata Collard
- Department of Pediatrics, Section of Clinical Genetics and Metabolism, University of Colorado, Aurora, CO, USA
| | - Kati J Buckingham
- Department of Pediatrics, University of Washington, Seattle, WA, USA
| | - Richard Chang
- Division of Metabolic Disorders, CHOC Children's, Orange, CA, USA; Department of Pediatrics, University of California Irvine, Irvine, CA, USA
| | - Jay Shendure
- Department of Genome Sciences, University of Washington, Seattle, WA, USA; Howard Hughes Medical Institute, University of Washington, Seattle, WA, USA
| | | | - Michael J Bamshad
- Department of Genome Sciences, University of Washington, Seattle, WA, USA; Department of Pediatrics, University of Washington, Seattle, WA, USA
| | - Johan L K Van Hove
- Department of Pediatrics, Section of Clinical Genetics and Metabolism, University of Colorado, Aurora, CO, USA
| | - Hudson H Freeze
- Human Genetics Program, Sanford Children's Health Research Center, Sanford-Burnham-Prebys Medical Discovery Institute, La Jolla, CA, USA
| | - Jose E Abdenur
- Division of Metabolic Disorders, CHOC Children's, Orange, CA, USA; Department of Pediatrics, University of California Irvine, Irvine, CA, USA.
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162
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Guo DC, Duan XY, Regalado ES, Mellor-Crummey L, Kwartler CS, Kim D, Lieberman K, de Vries BB, Pfundt R, Schinzel A, Kotzot D, Shen X, Yang ML, Bamshad MJ, Nickerson DA, Gornik HL, Ganesh SK, Braverman AC, Grange DK, Milewicz DM, Milewicz DM. Loss-of-Function Mutations in YY1AP1 Lead to Grange Syndrome and a Fibromuscular Dysplasia-Like Vascular Disease. Am J Hum Genet 2017; 100:21-30. [PMID: 27939641 DOI: 10.1016/j.ajhg.2016.11.008] [Citation(s) in RCA: 69] [Impact Index Per Article: 9.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2016] [Accepted: 11/04/2016] [Indexed: 12/27/2022] Open
Abstract
Fibromuscular dysplasia (FMD) is a heterogeneous group of non-atherosclerotic and non-inflammatory arterial diseases that primarily involves the renal and cerebrovascular arteries. Grange syndrome is an autosomal-recessive condition characterized by severe and early-onset vascular disease similar to FMD and variable penetrance of brachydactyly, syndactyly, bone fragility, and learning disabilities. Exome-sequencing analysis of DNA from three affected siblings with Grange syndrome identified compound heterozygous nonsense variants in YY1AP1, and homozygous nonsense or frameshift YY1AP1 variants were subsequently identified in additional unrelated probands with Grange syndrome. YY1AP1 encodes yin yang 1 (YY1)-associated protein 1 and is an activator of the YY1 transcription factor. We determined that YY1AP1 localizes to the nucleus and is a component of the INO80 chromatin remodeling complex, which is responsible for transcriptional regulation, DNA repair, and replication. Molecular studies revealed that loss of YY1AP1 in vascular smooth muscle cells leads to cell cycle arrest with decreased proliferation and increased levels of the cell cycle regulator p21/WAF/CDKN1A and disrupts TGF-β-driven differentiation of smooth muscle cells. Identification of YY1AP1 mutations as a cause of FMD indicates that this condition can result from underlying genetic variants that significantly alter the phenotype of vascular smooth muscle cells.
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Affiliation(s)
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | - Dianna M Milewicz
- Department of Internal Medicine, The University of Texas Health Science Center at Houston McGovern Medical School, Houston, TX 77030, USA.
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163
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Abstract
Resistance to thyrotropin (TSH) (RTSH; defined by elevated TSH and a normal or hypoplastic thyroid gland) can be caused by mutations in genes encoding the TSH receptor and PAX8, and it has been linked to a locus on chromosome 15. In two nonconsanguineous families with nongoitrous euthyroid hyperthyrotropinemia, typical of the RTSH phenotype, exome analysis identified five rare DUOX2 gene variants (p.A649E, p.P1391A, p.R885L, p.G488R, and p.SF965-6SfsX29) found to be pathogenic. This form of nongoitrous dyshormonogenesis masquerades both clinically and biochemically as RTSH. Accordingly, mutations in DUOX2 should be added to those of SLC26A4 as causes of RTSH.
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Affiliation(s)
| | | | | | - Michael J. Bamshad
- Department of Genome Sciences, University of Washington, Seattle, Washington
- Department of Pediatrics, University of Washington, Seattle, Washington
| | - Jessica X. Chong
- Department of Pediatrics, University of Washington, Seattle, Washington
| | - Samuel Refetoff
- Department of Medicine, The University of Chicago, Chicago, Illinois
- Department of Pediatrics, The University of Chicago, Chicago, Illinois
- Department of Committee on Genetics, The University of Chicago, Chicago, Illinois
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164
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Postmus I, Warren HR, Trompet S, Arsenault BJ, Avery CL, Bis JC, Chasman DI, de Keyser CE, Deshmukh HA, Evans DS, Feng Q, Li X, Smit RAJ, Smith AV, Sun F, Taylor KD, Arnold AM, Barnes MR, Barratt BJ, Betteridge J, Boekholdt SM, Boerwinkle E, Buckley BM, Chen YDI, de Craen AJM, Cummings SR, Denny JC, Dubé MP, Durrington PN, Eiriksdottir G, Ford I, Guo X, Harris TB, Heckbert SR, Hofman A, Hovingh GK, Kastelein JJP, Launer LJ, Liu CT, Liu Y, Lumley T, McKeigue PM, Munroe PB, Neil A, Nickerson DA, Nyberg F, O’Brien E, O’Donnell CJ, Post W, Poulter N, Vasan RS, Rice K, Rich SS, Rivadeneira F, Sattar N, Sever P, Shaw-Hawkins S, Shields DC, Slagboom PE, Smith NL, Smith JD, Sotoodehnia N, Stanton A, Stott DJ, Stricker BH, Stürmer T, Uitterlinden AG, Wei WQ, Westendorp RGJ, Whitsel EA, Wiggins KL, Wilke RA, Ballantyne CM, Colhoun HM, Cupples LA, Franco OH, Gudnason V, Hitman G, Palmer CNA, Psaty BM, Ridker PM, Stafford JM, Stein CM, Tardif JC, Caulfield MJ, Jukema JW, Rotter JI, Krauss RM. Meta-analysis of genome-wide association studies of HDL cholesterol response to statins. J Med Genet 2016; 53:835-845. [PMID: 27587472 PMCID: PMC5309131 DOI: 10.1136/jmedgenet-2016-103966] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.9] [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: 04/18/2016] [Revised: 07/03/2016] [Accepted: 07/26/2016] [Indexed: 11/04/2022]
Abstract
BACKGROUND In addition to lowering low density lipoprotein cholesterol (LDL-C), statin therapy also raises high density lipoprotein cholesterol (HDL-C) levels. Inter-individual variation in HDL-C response to statins may be partially explained by genetic variation. METHODS AND RESULTS We performed a meta-analysis of genome-wide association studies (GWAS) to identify variants with an effect on statin-induced high density lipoprotein cholesterol (HDL-C) changes. The 123 most promising signals with p<1×10-4 from the 16 769 statin-treated participants in the first analysis stage were followed up in an independent group of 10 951 statin-treated individuals, providing a total sample size of 27 720 individuals. The only associations of genome-wide significance (p<5×10-8) were between minor alleles at the CETP locus and greater HDL-C response to statin treatment. CONCLUSIONS Based on results from this study that included a relatively large sample size, we suggest that CETP may be the only detectable locus with common genetic variants that influence HDL-C response to statins substantially in individuals of European descent. Although CETP is known to be associated with HDL-C, we provide evidence that this pharmacogenetic effect is independent of its association with baseline HDL-C levels.
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Affiliation(s)
- Iris Postmus
- Department of Gerontology and Geriatrics, Leiden University Medical Center, Leiden, the Netherlands
| | - Helen R Warren
- William Harvey Research Institute, Barts and The London School of Medicine, Queen Mary University of London, United Kingdom EC1M6BQ
- Barts NIHR Biomedical Research Unit
| | - Stella Trompet
- Department of Gerontology and Geriatrics, Leiden University Medical Center, Leiden, the Netherlands
- Department of Cardiology, Leiden University Medical Center, The Netherlands
| | | | - Christy L Avery
- Department of Epidemiology, University of North Carolina, Chapel Hill, NC, USA
| | - Joshua C Bis
- Cardiovascular Health Research Unit, Department of Medicine, University of Washington, Seattle, WA
| | - Daniel I Chasman
- Division of Preventive Medicine, Brigham and Women’s Hospital, Boston MA
- Harvard Medical School, Boston, MA
| | | | - Harshal A Deshmukh
- Medical Research Institute, University of Dundee, Ninewells Hospital and Medical School, Dundee, UK
| | - Daniel S Evans
- California Pacific Medical Center Research Institute, San Francisco, CA, USA, 94107
| | - QiPing Feng
- Department of Clinical Pharmacology, Vanderbilt University, Nashville, TN, USA
| | - Xiaohui Li
- Institute for Translational Genomics and Population Sciences, Los Angeles BioMedical Research Institute at Harbor-UCLA Medical Center, Torrance, California, United States of America
| | - Roelof AJ Smit
- Department of Cardiology, Leiden University Medical Center, The Netherlands
| | - Albert V Smith
- Icelandic Heart Association, Kopavogur, Iceland
- University of Iceland, Reykjavik, Iceland
| | - Fangui Sun
- Department of Biostatistics, Boston University School of Public Health, Boston, MA, USA
| | - Kent D Taylor
- Institute for Translational Genomics and Population Sciences, Los Angeles BioMedical Research Institute at Harbor-UCLA Medical Center, Torrance, California, United States of America
| | - Alice M Arnold
- Department of Biostatistics, University of Washington, Seattle, WA USA
| | - Michael R Barnes
- William Harvey Research Institute, Barts and The London School of Medicine, Queen Mary University of London, United Kingdom EC1M6BQ
- Barts NIHR Biomedical Research Unit
| | - Bryan J Barratt
- Personalised Healthcare and Biomarkers, AstraZeneca, Alderley Park, UK
| | | | | | - Eric Boerwinkle
- Human Genetics Center, School of Public Health, University of Texas Health Science Center at Houston, Houston, Texas, USA
| | - Brendan M Buckley
- Department of Pharmacology and Therapeutics, University College Cork, Ireland
| | - Y-D Ida Chen
- Institute for Translational Genomics and Population Sciences, Los Angeles BioMedical Research Institute at Harbor-UCLA Medical Center, Torrance, California, United States of America
| | - Anton JM de Craen
- Department of Gerontology and Geriatrics, Leiden University Medical Center, Leiden, the Netherlands
| | - Steven R Cummings
- California Pacific Medical Center Research Institute, San Francisco, CA, USA, 94107
| | - Joshua C Denny
- Department of Biomedical Informatics, Vanderbilt University, Nashville, TN, USA
- Department of Medicine, Vanderbilt University, USA
| | | | - Paul N Durrington
- Cardiovascular Research Group, School of Biosciences, University of Manchester M13 9NT, UK
| | | | - Ian Ford
- Robertson Center for Biostatistics, University of Glasgow, United Kingdom
| | - Xiuqing Guo
- Institute for Translational Genomics and Population Sciences, Los Angeles BioMedical Research Institute at Harbor-UCLA Medical Center, Torrance, California, United States of America
| | - Tamara B Harris
- Laboratory of Epidemiology, Demography, Biometry, National Institute on Aging, National Institutes of Health, 7201 Wisconsin Ave, Bethesda, MD 20892, USA
| | - Susan R Heckbert
- Department of Epidemiology, University of Washington, Seattle WA USA
- Cardiovascular Health Research Unit, University of Washington, Seattle, WA, USA
- Group Health Research Institute, Group Health Cooperative, Seattle WA USA
| | - Albert Hofman
- Department of Epidemiology, Erasmus Medical Center, Rotterdam, The Netherlands
- The Netherlands Consortium for Healthy Ageing, Leiden, the Netherlands
| | - G Kees Hovingh
- Department of Vascular Medicine, Academic Medical Center, Amsterdam, NL
| | - John JP Kastelein
- Department of Vascular Medicine, Academic Medical Center, Amsterdam, NL
| | - Leonore J Launer
- Laboratory of Epidemiology, Demography, Biometry, National Institute on Aging, National Institutes of Health, 7201 Wisconsin Ave, Bethesda, MD 20892, USA
| | - Ching-Ti Liu
- Department of Biostatistics, Boston University School of Public Health, Boston, MA, USA
| | - Yongmei Liu
- Department of Epidemiology and Prevention, Division of Public Health Sciences, Wake Forest School of Medicine, Winston-Salem, NC, USA, 27157
| | - Thomas Lumley
- Cardiovascular Health Research Unit, Department of Medicine, University of Washington, Seattle, WA
- Department of Statistic, University of Auckland, Auckland, New Zealand
| | | | - Patricia B Munroe
- William Harvey Research Institute, Barts and The London School of Medicine, Queen Mary University of London, United Kingdom EC1M6BQ
- Barts NIHR Biomedical Research Unit
| | - Andrew Neil
- Oxford Centre for Diabetes, Endocrinology and Metabolism, University of Oxford, Churchill Hospital, Old Road, Headington, Oxford, OX3 7LJ UK
| | - Deborah A Nickerson
- Department of Genome Sciences, University of Washington, Seattle, Washington, United States of America
| | - Fredrik Nyberg
- Medical Evidence and Observational Research, AstraZeneca Gothenburg, Mölndal, Sweden
- Unit of Occupational and Environmental Medicine, University of Gothenburg, Gothenburg, Sweden
| | - Eoin O’Brien
- The Conway Institute, University College Dublin, Dublin 4, Ireland
| | - Christopher J O’Donnell
- NHLBI Framingham Heart Study, Framingham, MA, USA
- Cardiology Division, Department of Medicine, Massachusetts General Hospital, Harvard Medical School, Boston, MA
- National Heart, Lung and Blood Institute, Bethesda, MD
| | - Wendy Post
- Department of Cardiology, Johns Hopkins University, Baltimore, Maryland, USA
| | - Neil Poulter
- International Centre for Circulatory Health, Imperial College, London UK
| | - Ramachandran S Vasan
- Section of Preventive Medicine and Epidemiology, Department of Medicine, Boston University School of Medicine, and the Framingham Heart Study, Framingham, MA, USA
| | - Kenneth Rice
- Department of Biostatistics, University of Washington, Seattle, WA USA
| | - Stephen S Rich
- Center for Public Health Genomics, University of Virginia, Charlottesville, VA, USA
| | - Fernando Rivadeneira
- Department of Internal Medicine, Erasmus Medical Center, Rotterdam, The Netherlands
| | - Naveed Sattar
- BHF Glasgow Cardiovascular Research Centre, Faculty of Medicine, Glasgow, United Kingdom
| | - Peter Sever
- International Centre for Circulatory Health, Imperial College, London UK
| | - Sue Shaw-Hawkins
- William Harvey Research Institute, Barts and The London School of Medicine, Queen Mary University of London, United Kingdom EC1M6BQ
- Barts NIHR Biomedical Research Unit
| | - Denis C Shields
- The Conway Institute, University College Dublin, Dublin 4, Ireland
- School of Medicine and Medical Sciences, University College Dublin
| | - P Eline Slagboom
- Department of Molecular Epidemiology, Leiden University Medical Center, Leiden, The Netherlands
| | - Nicholas L Smith
- Department of Epidemiology, University of Washington, Seattle WA USA
- Group Health Research Institute, Group Health Cooperative, Seattle WA USA
- Seattle Epidemiologic Research and Information Center, Department of Veterans Affairs Office of Research and Development, Seattle WA USA
| | - Joshua D Smith
- Department of Genome Sciences, University of Washington, Seattle, Washington, United States of America
| | - Nona Sotoodehnia
- Cardiovascular Health Research Unit, Department of Medicine, University of Washington, Seattle, WA
- Division of Cardiology, Harborview Medical Center, University of Washington, Seattle, WA USA
| | - Alice Stanton
- Molecular and Cellular Therapeutics, Royal College of Surgeons in Ireland, Dublin, Ireland
- Beaumont Hospital, Dublin, Ireland
| | - David J Stott
- Institute of Cardiovascular and Medical Sciences, Faculty of Medicine, University of Glasgow, United Kingdom
| | - Bruno H Stricker
- Department of Epidemiology, Erasmus Medical Center, Rotterdam, The Netherlands
- Department of Internal Medicine, Erasmus Medical Center, Rotterdam, The Netherlands
- Health Care Inspectorate. The Hague, The Netherlands
| | - Til Stürmer
- Department of Epidemiology, University of North Carolina, Chapel Hill, NC, USA
| | - André G Uitterlinden
- Department of Epidemiology, Erasmus Medical Center, Rotterdam, The Netherlands
- The Netherlands Consortium for Healthy Ageing, Leiden, the Netherlands
- Department of Internal Medicine, Erasmus Medical Center, Rotterdam, The Netherlands
| | - Wei-Qi Wei
- Department of Biomedical Informatics, Vanderbilt University, Nashville, TN, USA
| | - Rudi GJ Westendorp
- Department of Public Health, and Center for Healthy Ageing, University of Copenhagen, 1123 Copenhagen, Denmark
| | - Eric A Whitsel
- Department of Epidemiology, University of North Carolina, Chapel Hill, NC, USA
- Department of Medicine, University of North Carolina, Chapel Hill, NC, USA
| | - Kerri L Wiggins
- Cardiovascular Health Research Unit, Department of Medicine, University of Washington, Seattle, WA
| | - Russell A Wilke
- Department of Internal Medicine, Sanford Healthcare, Sioux Falls, SD, USA
- Department of Medicine, University of South Dakota, Sioux Falls, SD, USA
| | | | - Helen M Colhoun
- Medical Research Institute, University of Dundee, Ninewells Hospital and Medical School, Dundee, UK
- Department of Public Health, University of Dundee
| | - L Adrienne Cupples
- Department of Biostatistics, Boston University School of Public Health, Boston, MA, USA
- NHLBI Framingham Heart Study, Framingham, MA, USA
| | - Oscar H Franco
- Department of Epidemiology, Erasmus Medical Center, Rotterdam, The Netherlands
| | - Vilmundur Gudnason
- Icelandic Heart Association, Kopavogur, Iceland
- University of Iceland, Reykjavik, Iceland
| | - Graham Hitman
- Barts and the London School of Medicine and Dentistry, Queen Mary University of London, London UK
| | - Colin NA Palmer
- Medical Research Institute, University of Dundee, Ninewells Hospital and Medical School, Dundee, UK
| | - Bruce M Psaty
- Cardiovascular Health Research Unit, Department of Medicine, University of Washington, Seattle, WA
- Department of Epidemiology, University of Washington, Seattle WA USA
- Group Health Research Institute, Group Health Cooperative, Seattle WA USA
- Department of Health Services University of Washington, Seattle, WA
| | - Paul M Ridker
- Division of Preventive Medicine, Brigham and Women’s Hospital, Boston MA
| | - Jeanette M Stafford
- Department of Biostatistical Sciences, Division of Public Health Sciences, Wake Forest School of Medicine, Winston-Salem, NC, USA, 27157
| | - Charles M Stein
- Department of Medicine, Vanderbilt University, USA
- Department of Pharmacology, Vanderbilt University, Nashville, TN, USA
| | | | - Mark J Caulfield
- William Harvey Research Institute, Barts and The London School of Medicine, Queen Mary University of London, United Kingdom EC1M6BQ
- Barts NIHR Biomedical Research Unit
| | - J Wouter Jukema
- Department of Cardiology, Leiden University Medical Center, The Netherlands
- Durrer Center for Cardiogenetic Research, Amsterdam, The Netherlands
- Interuniversity Cardiology Institute of the Netherlands, Utrecht, The Netherlands
| | - Jerome I Rotter
- Institute for Translational Genomics and Population Sciences, Los Angeles BioMedical Research Institute at Harbor-UCLA Medical Center, Torrance, California, United States of America
| | - Ronald M Krauss
- Children’s Hospital Oakland Research Institute, Oakland, California, United States of America
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165
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Auer PL, Reiner AP, Wang G, Kang HM, Abecasis GR, Altshuler D, Bamshad MJ, Nickerson DA, Tracy RP, Rich SS, Leal SM, Leal SM. Guidelines for Large-Scale Sequence-Based Complex Trait Association Studies: Lessons Learned from the NHLBI Exome Sequencing Project. Am J Hum Genet 2016; 99:791-801. [PMID: 27666372 DOI: 10.1016/j.ajhg.2016.08.012] [Citation(s) in RCA: 69] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2016] [Accepted: 08/08/2016] [Indexed: 12/11/2022] Open
Abstract
Massively parallel whole-genome sequencing (WGS) data have ushered in a new era in human genetics. These data are now being used to understand the role of rare variants in complex traits and to advance the goals of precision medicine. The technological and computing advances that have enabled us to generate WGS data on thousands of individuals have also outpaced our ability to perform analyses in scientifically and statistically rigorous and thoughtful ways. The past several years have witnessed the application of whole-exome sequencing (WES) to complex traits and diseases. From our analysis of NHLBI Exome Sequencing Project (ESP) data, not only have a number of important disease and complex trait association findings emerged, but our collective experience offers some valuable lessons for WGS initiatives. These include caveats associated with generating automated pipelines for quality control and analysis of rare variants; the importance of studying minority populations; sample size requirements and efficient study designs for identifying rare-variant associations; and the significance of incidental findings in population-based genetic research. With the ESP as an example, we offer guidance and a framework on how to conduct a large-scale association study in the era of WGS.
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Affiliation(s)
| | | | | | | | | | | | | | | | | | | | | | - Suzanne M Leal
- Center for Statistical Genetics, Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA.
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166
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Turner TN, Yi Q, Krumm N, Huddleston J, Hoekzema K, F Stessman HA, Doebley AL, Bernier RA, Nickerson DA, Eichler EE. denovo-db: a compendium of human de novo variants. Nucleic Acids Res 2016; 45:D804-D811. [PMID: 27907889 PMCID: PMC5210614 DOI: 10.1093/nar/gkw865] [Citation(s) in RCA: 124] [Impact Index Per Article: 15.5] [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: 08/15/2016] [Revised: 09/19/2016] [Accepted: 10/03/2016] [Indexed: 01/01/2023] Open
Abstract
Whole-exome and whole-genome sequencing have facilitated the large-scale discovery of de novo variants in human disease. To date, most de novo discovery through next-generation sequencing focused on congenital heart disease and neurodevelopmental disorders (NDDs). Currently, de novo variants are one of the most significant risk factors for NDDs with a substantial overlap of genes involved in more than one NDD. To facilitate better usage of published data, provide standardization of annotation, and improve accessibility, we created denovo-db (http://denovo-db.gs.washington.edu), a database for human de novo variants. As of July 2016, denovo-db contained 40 different studies and 32,991 de novo variants from 23,098 trios. Database features include basic variant information (chromosome location, change, type); detailed annotation at the transcript and protein levels; severity scores; frequency; validation status; and, most importantly, the phenotype of the individual with the variant. We included a feature on our browsable website to download any query result, including a downloadable file of the full database with additional variant details. denovo-db provides necessary information for researchers to compare their data to other individuals with the same phenotype and also to controls allowing for a better understanding of the biology of de novo variants and their contribution to disease.
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Affiliation(s)
- Tychele N Turner
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA 98195, USA
| | - Qian Yi
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA 98195, USA
| | - Niklas Krumm
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA 98195, USA
| | - John Huddleston
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA 98195, USA.,Howard Hughes Medical Institute, University of Washington, Seattle, WA 98195, USA
| | - Kendra Hoekzema
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA 98195, USA
| | - Holly A F Stessman
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA 98195, USA
| | - Anna-Lisa Doebley
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA 98195, USA.,Medical Scientist Training Program, Department of Pathology, University ofWashington, Seattle, WA 98105, USA
| | - Raphael A Bernier
- Department of Psychiatry and Behavioral Sciences, University of Washington, Seattle, WA 98105, USA
| | - Deborah A Nickerson
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA 98195, USA
| | - Evan E Eichler
- Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA 98195, USA.,Howard Hughes Medical Institute, University of Washington, Seattle, WA 98195, USA
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167
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Duran I, Taylor SP, Zhang W, Martin J, Forlenza KN, Spiro RP, Nickerson DA, Bamshad M, Cohn DH, Krakow D. Destabilization of the IFT-B cilia core complex due to mutations in IFT81 causes a Spectrum of Short-Rib Polydactyly Syndrome. Sci Rep 2016; 6:34232. [PMID: 27666822 PMCID: PMC5035930 DOI: 10.1038/srep34232] [Citation(s) in RCA: 35] [Impact Index Per Article: 4.4] [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: 06/01/2016] [Accepted: 09/06/2016] [Indexed: 01/13/2023] Open
Abstract
Short-rib polydactyly syndromes (SRPS) and Asphyxiating thoracic dystrophy (ATD) or Jeune Syndrome are recessively inherited skeletal ciliopathies characterized by profound skeletal abnormalities and are frequently associated with polydactyly and multiorgan system involvement. SRPS are produced by mutations in genes that participate in the formation and function of primary cilia and usually result from disruption of retrograde intraflagellar (IFT) transport of the cilium. Herein we describe a new spectrum of SRPS caused by mutations in the gene IFT81, a key component of the IFT-B complex essential for anterograde transport. In mutant chondrocytes, the mutations led to low levels of IFT81 and mutant cells produced elongated cilia, had altered hedgehog signaling, had increased post-translation modification of tubulin, and showed evidence of destabilization of additional anterograde transport complex components. These findings demonstrate the importance of IFT81 in the skeleton, its role in the anterograde transport complex, and expand the number of loci associated with SRPS.
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Affiliation(s)
- Ivan Duran
- Department of Orthopaedic Surgery, David Geffen School of Medicine at the University of California at Los Angeles, Los Angeles, California, 90095, USA.,Networking Biomedical Research Center in Bioengineering, Biomaterials and Nanomedicine, (CIBER-BBN), University of Malaga, Malaga, 29071, Spain
| | - S Paige Taylor
- Department of Human Genetics, David Geffen School of Medicine at the University of California at Los Angeles, Los Angeles, California, 90095, USA
| | - Wenjuan Zhang
- Department of Molecular, Cell, and Developmental Biology, University of California at Los Angeles, Los Angeles, California, 90095, USA
| | - Jorge Martin
- Department of Orthopaedic Surgery, David Geffen School of Medicine at the University of California at Los Angeles, Los Angeles, California, 90095, USA
| | - Kimberly N Forlenza
- Department of Orthopaedic Surgery, David Geffen School of Medicine at the University of California at Los Angeles, Los Angeles, California, 90095, USA
| | - Rhonda P Spiro
- Children's Healthcare of Atlanta, Atlanta, GA, 30342, USA
| | - Deborah A Nickerson
- University of Washington Center for Mendelian Genomics, University of Washington, Seattle, Washington, 98195, USA
| | - Michael Bamshad
- University of Washington Center for Mendelian Genomics, University of Washington, Seattle, Washington, 98195, USA
| | - Daniel H Cohn
- Department of Orthopaedic Surgery, David Geffen School of Medicine at the University of California at Los Angeles, Los Angeles, California, 90095, USA.,Department of Molecular, Cell, and Developmental Biology, University of California at Los Angeles, Los Angeles, California, 90095, USA
| | - Deborah Krakow
- Department of Orthopaedic Surgery, David Geffen School of Medicine at the University of California at Los Angeles, Los Angeles, California, 90095, USA.,Department of Human Genetics, David Geffen School of Medicine at the University of California at Los Angeles, Los Angeles, California, 90095, USA.,Department of Obstetrics and Gynecology, David Geffen School of Medicine at the University of California at Los Angeles, Los Angeles, California, 90095, USA
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168
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Fox K, Johnsen JM, Coe BP, Frazar CD, Reiner AP, Eichler EE, Nickerson DA. Analysis of exome sequencing data sets reveals structural variation in the coding region ofABOin individuals of African ancestry. Transfusion 2016; 56:2744-2749. [DOI: 10.1111/trf.13797] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2016] [Revised: 07/06/2016] [Accepted: 07/07/2016] [Indexed: 12/26/2022]
Affiliation(s)
| | - Jill M. Johnsen
- Hematology Division; University of Washington, School of Medicine
- Bloodworks Northwest
| | | | | | - Alexander P. Reiner
- Public Health Sciences Division; Fred Hutchinson Cancer Research Center
- Department of Epidemiology; University of Washington, School of Public Health
| | - Evan E. Eichler
- Department of Genome Sciences
- Howard Hughes Medical Institute; Seattle Washington
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169
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Weinstein MM, Kang T, Lachman RS, Bamshad M, Nickerson DA, Krakow D, Cohn DH. Somatic mosaicism for a lethal TRPV4 mutation results in non-lethal metatropic dysplasia. Am J Med Genet A 2016; 170:3298-3302. [PMID: 27530454 DOI: 10.1002/ajmg.a.37942] [Citation(s) in RCA: 8] [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: 04/26/2016] [Accepted: 08/07/2016] [Indexed: 11/06/2022]
Abstract
Dominant mutations in TRPV4, which encodes the Transient Receptor Potential Cation Channel Subfamily V Member 4 calcium channel, result in a series of musculoskeletal disorders that include a set of peripheral neuropathies and a broad phenotypic spectrum of skeletal dysplasias. The skeletal phenotypes range from brachyolmia, in which there is scoliosis with mild short stature, through perinatal lethal metatropic dysplasia. We describe a case with phenotypic findings consistent with metatropic dysplasia, but in whom no TRPV4 mutation was detected by Sanger sequence analysis. Exome sequence analysis identified a known lethal metatropic dysplasia mutation, TRPV4L618P , which was present at lower frequency than would be expected for a heterozygous change. The affected individual was shown to be a somatic mosaic for the mutation, providing an explanation for the milder than expected phenotype. The data illustrate that high-throughput sequencing of genomic DNA can facilitate detection of mosaicism with higher sensitivity than Sanger sequence analysis and identify a new genetic mechanism for metatropic dysplasia. © 2016 Wiley Periodicals, Inc.
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Affiliation(s)
- Michael M Weinstein
- Department of Molecular, Cell, and Developmental Biology, University of California Los Angeles, Los Angeles
| | - Taekyu Kang
- Department of Microbiology, Immunology, and Molecular Genetics, University of California Los Angeles, Los Angeles
| | - Ralph S Lachman
- International Skeletal Dysplasia Registry, University of California Los Angeles, Los Angeles
| | - Michael Bamshad
- Department of Genome Sciences, University of Washington, Seattle.,University of Washington Center for Mendelian Genomics, University of Washington, Seattle.,Department of Pediatrics, University of Washington, Seattle.,Division of Genetic Medicine, Seattle Children's Hospital, Seattle
| | - Deborah A Nickerson
- Department of Genome Sciences, University of Washington, Seattle.,University of Washington Center for Mendelian Genomics, University of Washington, Seattle
| | - Deborah Krakow
- International Skeletal Dysplasia Registry, University of California Los Angeles, Los Angeles.,Department of Human Genetics, David Geffen School of Medicine at UCLA, Los Angeles.,Department of Orthopaedic Surgery, David Geffen School of Medicine at UCLA, Los Angeles.,Orthopaedic Hospital Research Center, David Geffen School of Medicine at UCLA, Los Angeles
| | - Daniel H Cohn
- Department of Molecular, Cell, and Developmental Biology, University of California Los Angeles, Los Angeles.,International Skeletal Dysplasia Registry, University of California Los Angeles, Los Angeles.,Department of Orthopaedic Surgery, David Geffen School of Medicine at UCLA, Los Angeles.,Orthopaedic Hospital Research Center, David Geffen School of Medicine at UCLA, Los Angeles
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170
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Wheeler PG, Ng BG, Sanford L, Sutton VR, Bartholomew DW, Pastore MT, Bamshad MJ, Kircher M, Buckingham KJ, Nickerson DA, Shendure J, Freeze HH. SRD5A3-CDG: Expanding the phenotype of a congenital disorder of glycosylation with emphasis on adult onset features. Am J Med Genet A 2016; 170:3165-3171. [PMID: 27480077 DOI: 10.1002/ajmg.a.37875] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [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: 03/21/2016] [Accepted: 07/08/2016] [Indexed: 12/15/2022]
Abstract
Increasing numbers of congenital disorders of glycosylation (CDG) have been reported recently resulting in an expansion of the phenotypes associated with this group of disorders. SRD5A3 codes for polyprenol reductase which converts polyprenol to dolichol. This is a major pathway for dolichol biosynthesis for N-glycosylation, O-mannosylation, C-mannosylation, and GPI anchor synthesis. We present the features of five individuals (three children and two adults) with mutations in SRD5A3 focusing on the variable eye and skin involvement. We compare that to 13 affected individuals from the literature including five adults allowing us to delineate the features that may develop over time with this disorder including kyphosis, retinitis pigmentosa, and cataracts. © 2016 Wiley Periodicals, Inc.
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Affiliation(s)
| | - Bobby G Ng
- Human Genetics Program, Sanford-Burnham Prebys Medical Discovery Institute, La Jolla, California
| | | | - V Reid Sutton
- Department of Molecular and Human Genetics, Baylor College of Medicine and Texas Children's Hospital, Houston, Texas
| | - Dennis W Bartholomew
- Section of Molecular and Human Genetics, Nationwide Children's Hospital, Department of Pediatrics, Ohio State University, Columbus, Ohio
| | - Matthew T Pastore
- Section of Molecular and Human Genetics, Nationwide Children's Hospital, Department of Pediatrics, Ohio State University, Columbus, Ohio
| | - Michael J Bamshad
- Department of Genome Sciences, University of Washington Center for Mendelian Genomics, University of Washington, Seattle, Washington.,Department of Pediatrics, University of Washington, Seattle, Washington
| | - Martin Kircher
- Department of Pediatrics, University of Washington, Seattle, Washington
| | - Kati J Buckingham
- Department of Pediatrics, University of Washington, Seattle, Washington
| | - Deborah A Nickerson
- Department of Genome Sciences, University of Washington Center for Mendelian Genomics, University of Washington, Seattle, Washington
| | - Jay Shendure
- Department of Genome Sciences, University of Washington Center for Mendelian Genomics, University of Washington, Seattle, Washington.,Howard Hughes Medical Institute, University of Washington, Seattle, Washington
| | - Hudson H Freeze
- Human Genetics Program, Sanford-Burnham Prebys Medical Discovery Institute, La Jolla, California
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171
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Zhang W, Taylor SP, Nevarez L, Lachman RS, Nickerson DA, Bamshad M, Krakow D, Cohn DH. IFT52 mutations destabilize anterograde complex assembly, disrupt ciliogenesis and result in short rib polydactyly syndrome. Hum Mol Genet 2016; 25:4012-4020. [PMID: 27466190 DOI: 10.1093/hmg/ddw241] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2016] [Revised: 06/25/2016] [Accepted: 07/13/2016] [Indexed: 11/14/2022] Open
Abstract
The short-rib polydactyly syndromes (SRPS) encompass a radiographically and genetically heterogeneous group of skeletal ciliopathies that are characterized by a long narrow chest, short extremities, and variable occurrence of polydactyly. Radiographic abnormalities include undermineralization of the calvarium, shortened and bowed appendicular bones, trident shaped acetabula and polydactyly. In a case of SRPS we identified compound heterozygosity for mutations in IFT52, which encodes a component of the anterograde intraflagellar transport complex. The IFT52 mutant cells synthesized a significantly reduced amount of IFT52 protein, leading to reduced synthesis of IFT74, IFT81, IFT88 and ARL13B, other key anterograde complex members. Ciliogenesis was also disrupted in the mutant cells, with a 60% reduction in the presence of cilia on mutant cells and loss of cilia length regulation for the cells with cilia. These data demonstrate that IFT52 is essential for anterograde complex integrity and for the biosynthesis and maintenance of cilia. The data identify a new locus for SRPS and show that IFT52 mutations result in a ciliopathy with primary effects on the skeleton.
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Affiliation(s)
- Wenjuan Zhang
- Department of Molecular, Cell, and Developmental Biology
| | | | | | - Ralph S Lachman
- International Skeletal Dysplasia Registry, University of California, Los Angeles, California, USA
| | - Deborah A Nickerson
- Department of Genome Sciences.,University of Washington Center for Mendelian Genomics
| | - Michael Bamshad
- Department of Genome Sciences.,University of Washington Center for Mendelian Genomics.,Department of Pediatrics, University of Washington, Seattle, Washington, USA.,Division of Genetic Medicine, Seattle Children's Hospital, Seattle, Washington, USA
| | | | - Deborah Krakow
- Department of Human Genetics.,International Skeletal Dysplasia Registry, University of California, Los Angeles, California, USA.,Department of Obstetrics and Gynecology.,Department of Orthopaedic Surgery and Orthopaedic Hospital Research Center, David Geffen School of Medicine at UCLA, Los Angeles, California, USA
| | - Daniel H Cohn
- Department of Molecular, Cell, and Developmental Biology .,International Skeletal Dysplasia Registry, University of California, Los Angeles, California, USA.,Department of Orthopaedic Surgery and Orthopaedic Hospital Research Center, David Geffen School of Medicine at UCLA, Los Angeles, California, USA.,Department of Molecular, Cell, and Developmental Biology
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172
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Peloso GM, Lange LA, Varga TV, Nickerson DA, Smith JD, Griswold ME, Musani S, Polfus LM, Mei H, Gabriel S, Quarells RC, Altshuler D, Boerwinkle E, Daly MJ, Neale B, Correa A, Reiner AP, Wilson JG, Kathiresan S. Association of Exome Sequences With Cardiovascular Traits Among Blacks in the Jackson Heart Study. ACTA ACUST UNITED AC 2016; 9:368-74. [PMID: 27422940 DOI: 10.1161/circgenetics.116.001410] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [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: 02/17/2016] [Accepted: 07/05/2016] [Indexed: 12/15/2022]
Abstract
BACKGROUND The correlation of null alleles with human phenotypes can provide insight into gene function in humans. In individuals of African ancestry, we set out to identify null and damaging missense variants, and test these variants for association with a range of cardiovascular phenotypes. METHODS AND RESULTS We performed whole-exome sequencing in 3223 black individuals from the Jackson Heart Study and found a total of 729 666 variant sites with minor allele frequency <5%, including 17 263 null variants and 49 929 missense variants predicted to be damaging by in silico algorithms. We tested null and damaging missense variants within each gene for association with 36 cardiovascular traits. We found 3 associations that met our prespecified level of significance (α=1.1×10(-7)). Null and damaging missense variants in PCSK9 were associated with 36 mg/dL lower low-density lipoprotein cholesterol (P=3×10(-21)). Three individuals in their 50s with complete PCSK9 deficiency (each compound heterozygote for PCSK9 p.Y142X and p.C679X) were identified, with one having a coronary artery calcification score in the 83rd percentile despite a low-density lipoprotein cholesterol of 32 mg/dL. A damaging missense variant in HBQ1 (p.G52A) was associated with a 2 pg/cell lower mean corpuscular hemoglobin (P=9×10(-13)) and rare damaging missense variants in VPS13A with higher red blood cell distribution width (P=9.9×10(-8)). CONCLUSIONS A limited number of null/damaging alleles with a large effect on cardiovascular traits were detectable in ≈3000 black individuals.
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Affiliation(s)
- Gina M Peloso
- From the Department of Biostatistics, Boston University School of Public Health, Boston, MA (G.M.P.); Center for Human Genetic Research (G.M.P., S.K.) and Analytic and Translational Genetics Unit, Massachusetts General Hospital, Boston, MA (M.J.D., B.N.); Program in Medical and Population Genetics, Broad Institute, Cambridge, MA (G.M.P., S.G., D.A., M.J.D., B.N., S.K.); Department of Genetics, University of North Carolina, Chapel Hill, NC (L.A.L.); Genetic and Molecular Epidemiology Unit, Department of Clinical Sciences, Lund University, Malmö, Sweden (T.V.V.); Department of Genome Sciences, University of Washington, Seattle, WA (D.A.N., J.D.S.); Center of Biostatistics & Bioinformatics (M.E.G., H.M.), Department of Medicine (S.M.), Department of Pediatrics & Medicine (A.C.), and Department of Physiology & Biophysics (J.G.W.), University of Mississippi Medical Center, Jackson, MS; Human Genetics Center, University of Texas Health Science Center, Houston, TX (L.M.P., E.B.); Cardiovascular Research Institute, Morehouse School of Medicine, Atlanta, GA (R.C.Q.); Department of Medicine, Harvard Medical School, Boston, MA (D.A., S.K.); and Department of Epidemiology, University of Washington School of Public Health, Seattle, WA (A.P.R.).
| | - Leslie A Lange
- From the Department of Biostatistics, Boston University School of Public Health, Boston, MA (G.M.P.); Center for Human Genetic Research (G.M.P., S.K.) and Analytic and Translational Genetics Unit, Massachusetts General Hospital, Boston, MA (M.J.D., B.N.); Program in Medical and Population Genetics, Broad Institute, Cambridge, MA (G.M.P., S.G., D.A., M.J.D., B.N., S.K.); Department of Genetics, University of North Carolina, Chapel Hill, NC (L.A.L.); Genetic and Molecular Epidemiology Unit, Department of Clinical Sciences, Lund University, Malmö, Sweden (T.V.V.); Department of Genome Sciences, University of Washington, Seattle, WA (D.A.N., J.D.S.); Center of Biostatistics & Bioinformatics (M.E.G., H.M.), Department of Medicine (S.M.), Department of Pediatrics & Medicine (A.C.), and Department of Physiology & Biophysics (J.G.W.), University of Mississippi Medical Center, Jackson, MS; Human Genetics Center, University of Texas Health Science Center, Houston, TX (L.M.P., E.B.); Cardiovascular Research Institute, Morehouse School of Medicine, Atlanta, GA (R.C.Q.); Department of Medicine, Harvard Medical School, Boston, MA (D.A., S.K.); and Department of Epidemiology, University of Washington School of Public Health, Seattle, WA (A.P.R.)
| | - Tibor V Varga
- From the Department of Biostatistics, Boston University School of Public Health, Boston, MA (G.M.P.); Center for Human Genetic Research (G.M.P., S.K.) and Analytic and Translational Genetics Unit, Massachusetts General Hospital, Boston, MA (M.J.D., B.N.); Program in Medical and Population Genetics, Broad Institute, Cambridge, MA (G.M.P., S.G., D.A., M.J.D., B.N., S.K.); Department of Genetics, University of North Carolina, Chapel Hill, NC (L.A.L.); Genetic and Molecular Epidemiology Unit, Department of Clinical Sciences, Lund University, Malmö, Sweden (T.V.V.); Department of Genome Sciences, University of Washington, Seattle, WA (D.A.N., J.D.S.); Center of Biostatistics & Bioinformatics (M.E.G., H.M.), Department of Medicine (S.M.), Department of Pediatrics & Medicine (A.C.), and Department of Physiology & Biophysics (J.G.W.), University of Mississippi Medical Center, Jackson, MS; Human Genetics Center, University of Texas Health Science Center, Houston, TX (L.M.P., E.B.); Cardiovascular Research Institute, Morehouse School of Medicine, Atlanta, GA (R.C.Q.); Department of Medicine, Harvard Medical School, Boston, MA (D.A., S.K.); and Department of Epidemiology, University of Washington School of Public Health, Seattle, WA (A.P.R.)
| | - Deborah A Nickerson
- From the Department of Biostatistics, Boston University School of Public Health, Boston, MA (G.M.P.); Center for Human Genetic Research (G.M.P., S.K.) and Analytic and Translational Genetics Unit, Massachusetts General Hospital, Boston, MA (M.J.D., B.N.); Program in Medical and Population Genetics, Broad Institute, Cambridge, MA (G.M.P., S.G., D.A., M.J.D., B.N., S.K.); Department of Genetics, University of North Carolina, Chapel Hill, NC (L.A.L.); Genetic and Molecular Epidemiology Unit, Department of Clinical Sciences, Lund University, Malmö, Sweden (T.V.V.); Department of Genome Sciences, University of Washington, Seattle, WA (D.A.N., J.D.S.); Center of Biostatistics & Bioinformatics (M.E.G., H.M.), Department of Medicine (S.M.), Department of Pediatrics & Medicine (A.C.), and Department of Physiology & Biophysics (J.G.W.), University of Mississippi Medical Center, Jackson, MS; Human Genetics Center, University of Texas Health Science Center, Houston, TX (L.M.P., E.B.); Cardiovascular Research Institute, Morehouse School of Medicine, Atlanta, GA (R.C.Q.); Department of Medicine, Harvard Medical School, Boston, MA (D.A., S.K.); and Department of Epidemiology, University of Washington School of Public Health, Seattle, WA (A.P.R.)
| | - Joshua D Smith
- From the Department of Biostatistics, Boston University School of Public Health, Boston, MA (G.M.P.); Center for Human Genetic Research (G.M.P., S.K.) and Analytic and Translational Genetics Unit, Massachusetts General Hospital, Boston, MA (M.J.D., B.N.); Program in Medical and Population Genetics, Broad Institute, Cambridge, MA (G.M.P., S.G., D.A., M.J.D., B.N., S.K.); Department of Genetics, University of North Carolina, Chapel Hill, NC (L.A.L.); Genetic and Molecular Epidemiology Unit, Department of Clinical Sciences, Lund University, Malmö, Sweden (T.V.V.); Department of Genome Sciences, University of Washington, Seattle, WA (D.A.N., J.D.S.); Center of Biostatistics & Bioinformatics (M.E.G., H.M.), Department of Medicine (S.M.), Department of Pediatrics & Medicine (A.C.), and Department of Physiology & Biophysics (J.G.W.), University of Mississippi Medical Center, Jackson, MS; Human Genetics Center, University of Texas Health Science Center, Houston, TX (L.M.P., E.B.); Cardiovascular Research Institute, Morehouse School of Medicine, Atlanta, GA (R.C.Q.); Department of Medicine, Harvard Medical School, Boston, MA (D.A., S.K.); and Department of Epidemiology, University of Washington School of Public Health, Seattle, WA (A.P.R.)
| | - Michael E Griswold
- From the Department of Biostatistics, Boston University School of Public Health, Boston, MA (G.M.P.); Center for Human Genetic Research (G.M.P., S.K.) and Analytic and Translational Genetics Unit, Massachusetts General Hospital, Boston, MA (M.J.D., B.N.); Program in Medical and Population Genetics, Broad Institute, Cambridge, MA (G.M.P., S.G., D.A., M.J.D., B.N., S.K.); Department of Genetics, University of North Carolina, Chapel Hill, NC (L.A.L.); Genetic and Molecular Epidemiology Unit, Department of Clinical Sciences, Lund University, Malmö, Sweden (T.V.V.); Department of Genome Sciences, University of Washington, Seattle, WA (D.A.N., J.D.S.); Center of Biostatistics & Bioinformatics (M.E.G., H.M.), Department of Medicine (S.M.), Department of Pediatrics & Medicine (A.C.), and Department of Physiology & Biophysics (J.G.W.), University of Mississippi Medical Center, Jackson, MS; Human Genetics Center, University of Texas Health Science Center, Houston, TX (L.M.P., E.B.); Cardiovascular Research Institute, Morehouse School of Medicine, Atlanta, GA (R.C.Q.); Department of Medicine, Harvard Medical School, Boston, MA (D.A., S.K.); and Department of Epidemiology, University of Washington School of Public Health, Seattle, WA (A.P.R.)
| | - Solomon Musani
- From the Department of Biostatistics, Boston University School of Public Health, Boston, MA (G.M.P.); Center for Human Genetic Research (G.M.P., S.K.) and Analytic and Translational Genetics Unit, Massachusetts General Hospital, Boston, MA (M.J.D., B.N.); Program in Medical and Population Genetics, Broad Institute, Cambridge, MA (G.M.P., S.G., D.A., M.J.D., B.N., S.K.); Department of Genetics, University of North Carolina, Chapel Hill, NC (L.A.L.); Genetic and Molecular Epidemiology Unit, Department of Clinical Sciences, Lund University, Malmö, Sweden (T.V.V.); Department of Genome Sciences, University of Washington, Seattle, WA (D.A.N., J.D.S.); Center of Biostatistics & Bioinformatics (M.E.G., H.M.), Department of Medicine (S.M.), Department of Pediatrics & Medicine (A.C.), and Department of Physiology & Biophysics (J.G.W.), University of Mississippi Medical Center, Jackson, MS; Human Genetics Center, University of Texas Health Science Center, Houston, TX (L.M.P., E.B.); Cardiovascular Research Institute, Morehouse School of Medicine, Atlanta, GA (R.C.Q.); Department of Medicine, Harvard Medical School, Boston, MA (D.A., S.K.); and Department of Epidemiology, University of Washington School of Public Health, Seattle, WA (A.P.R.)
| | - Linda M Polfus
- From the Department of Biostatistics, Boston University School of Public Health, Boston, MA (G.M.P.); Center for Human Genetic Research (G.M.P., S.K.) and Analytic and Translational Genetics Unit, Massachusetts General Hospital, Boston, MA (M.J.D., B.N.); Program in Medical and Population Genetics, Broad Institute, Cambridge, MA (G.M.P., S.G., D.A., M.J.D., B.N., S.K.); Department of Genetics, University of North Carolina, Chapel Hill, NC (L.A.L.); Genetic and Molecular Epidemiology Unit, Department of Clinical Sciences, Lund University, Malmö, Sweden (T.V.V.); Department of Genome Sciences, University of Washington, Seattle, WA (D.A.N., J.D.S.); Center of Biostatistics & Bioinformatics (M.E.G., H.M.), Department of Medicine (S.M.), Department of Pediatrics & Medicine (A.C.), and Department of Physiology & Biophysics (J.G.W.), University of Mississippi Medical Center, Jackson, MS; Human Genetics Center, University of Texas Health Science Center, Houston, TX (L.M.P., E.B.); Cardiovascular Research Institute, Morehouse School of Medicine, Atlanta, GA (R.C.Q.); Department of Medicine, Harvard Medical School, Boston, MA (D.A., S.K.); and Department of Epidemiology, University of Washington School of Public Health, Seattle, WA (A.P.R.)
| | - Hao Mei
- From the Department of Biostatistics, Boston University School of Public Health, Boston, MA (G.M.P.); Center for Human Genetic Research (G.M.P., S.K.) and Analytic and Translational Genetics Unit, Massachusetts General Hospital, Boston, MA (M.J.D., B.N.); Program in Medical and Population Genetics, Broad Institute, Cambridge, MA (G.M.P., S.G., D.A., M.J.D., B.N., S.K.); Department of Genetics, University of North Carolina, Chapel Hill, NC (L.A.L.); Genetic and Molecular Epidemiology Unit, Department of Clinical Sciences, Lund University, Malmö, Sweden (T.V.V.); Department of Genome Sciences, University of Washington, Seattle, WA (D.A.N., J.D.S.); Center of Biostatistics & Bioinformatics (M.E.G., H.M.), Department of Medicine (S.M.), Department of Pediatrics & Medicine (A.C.), and Department of Physiology & Biophysics (J.G.W.), University of Mississippi Medical Center, Jackson, MS; Human Genetics Center, University of Texas Health Science Center, Houston, TX (L.M.P., E.B.); Cardiovascular Research Institute, Morehouse School of Medicine, Atlanta, GA (R.C.Q.); Department of Medicine, Harvard Medical School, Boston, MA (D.A., S.K.); and Department of Epidemiology, University of Washington School of Public Health, Seattle, WA (A.P.R.)
| | - Stacey Gabriel
- From the Department of Biostatistics, Boston University School of Public Health, Boston, MA (G.M.P.); Center for Human Genetic Research (G.M.P., S.K.) and Analytic and Translational Genetics Unit, Massachusetts General Hospital, Boston, MA (M.J.D., B.N.); Program in Medical and Population Genetics, Broad Institute, Cambridge, MA (G.M.P., S.G., D.A., M.J.D., B.N., S.K.); Department of Genetics, University of North Carolina, Chapel Hill, NC (L.A.L.); Genetic and Molecular Epidemiology Unit, Department of Clinical Sciences, Lund University, Malmö, Sweden (T.V.V.); Department of Genome Sciences, University of Washington, Seattle, WA (D.A.N., J.D.S.); Center of Biostatistics & Bioinformatics (M.E.G., H.M.), Department of Medicine (S.M.), Department of Pediatrics & Medicine (A.C.), and Department of Physiology & Biophysics (J.G.W.), University of Mississippi Medical Center, Jackson, MS; Human Genetics Center, University of Texas Health Science Center, Houston, TX (L.M.P., E.B.); Cardiovascular Research Institute, Morehouse School of Medicine, Atlanta, GA (R.C.Q.); Department of Medicine, Harvard Medical School, Boston, MA (D.A., S.K.); and Department of Epidemiology, University of Washington School of Public Health, Seattle, WA (A.P.R.)
| | - Rakale Collins Quarells
- From the Department of Biostatistics, Boston University School of Public Health, Boston, MA (G.M.P.); Center for Human Genetic Research (G.M.P., S.K.) and Analytic and Translational Genetics Unit, Massachusetts General Hospital, Boston, MA (M.J.D., B.N.); Program in Medical and Population Genetics, Broad Institute, Cambridge, MA (G.M.P., S.G., D.A., M.J.D., B.N., S.K.); Department of Genetics, University of North Carolina, Chapel Hill, NC (L.A.L.); Genetic and Molecular Epidemiology Unit, Department of Clinical Sciences, Lund University, Malmö, Sweden (T.V.V.); Department of Genome Sciences, University of Washington, Seattle, WA (D.A.N., J.D.S.); Center of Biostatistics & Bioinformatics (M.E.G., H.M.), Department of Medicine (S.M.), Department of Pediatrics & Medicine (A.C.), and Department of Physiology & Biophysics (J.G.W.), University of Mississippi Medical Center, Jackson, MS; Human Genetics Center, University of Texas Health Science Center, Houston, TX (L.M.P., E.B.); Cardiovascular Research Institute, Morehouse School of Medicine, Atlanta, GA (R.C.Q.); Department of Medicine, Harvard Medical School, Boston, MA (D.A., S.K.); and Department of Epidemiology, University of Washington School of Public Health, Seattle, WA (A.P.R.)
| | - David Altshuler
- From the Department of Biostatistics, Boston University School of Public Health, Boston, MA (G.M.P.); Center for Human Genetic Research (G.M.P., S.K.) and Analytic and Translational Genetics Unit, Massachusetts General Hospital, Boston, MA (M.J.D., B.N.); Program in Medical and Population Genetics, Broad Institute, Cambridge, MA (G.M.P., S.G., D.A., M.J.D., B.N., S.K.); Department of Genetics, University of North Carolina, Chapel Hill, NC (L.A.L.); Genetic and Molecular Epidemiology Unit, Department of Clinical Sciences, Lund University, Malmö, Sweden (T.V.V.); Department of Genome Sciences, University of Washington, Seattle, WA (D.A.N., J.D.S.); Center of Biostatistics & Bioinformatics (M.E.G., H.M.), Department of Medicine (S.M.), Department of Pediatrics & Medicine (A.C.), and Department of Physiology & Biophysics (J.G.W.), University of Mississippi Medical Center, Jackson, MS; Human Genetics Center, University of Texas Health Science Center, Houston, TX (L.M.P., E.B.); Cardiovascular Research Institute, Morehouse School of Medicine, Atlanta, GA (R.C.Q.); Department of Medicine, Harvard Medical School, Boston, MA (D.A., S.K.); and Department of Epidemiology, University of Washington School of Public Health, Seattle, WA (A.P.R.)
| | - Eric Boerwinkle
- From the Department of Biostatistics, Boston University School of Public Health, Boston, MA (G.M.P.); Center for Human Genetic Research (G.M.P., S.K.) and Analytic and Translational Genetics Unit, Massachusetts General Hospital, Boston, MA (M.J.D., B.N.); Program in Medical and Population Genetics, Broad Institute, Cambridge, MA (G.M.P., S.G., D.A., M.J.D., B.N., S.K.); Department of Genetics, University of North Carolina, Chapel Hill, NC (L.A.L.); Genetic and Molecular Epidemiology Unit, Department of Clinical Sciences, Lund University, Malmö, Sweden (T.V.V.); Department of Genome Sciences, University of Washington, Seattle, WA (D.A.N., J.D.S.); Center of Biostatistics & Bioinformatics (M.E.G., H.M.), Department of Medicine (S.M.), Department of Pediatrics & Medicine (A.C.), and Department of Physiology & Biophysics (J.G.W.), University of Mississippi Medical Center, Jackson, MS; Human Genetics Center, University of Texas Health Science Center, Houston, TX (L.M.P., E.B.); Cardiovascular Research Institute, Morehouse School of Medicine, Atlanta, GA (R.C.Q.); Department of Medicine, Harvard Medical School, Boston, MA (D.A., S.K.); and Department of Epidemiology, University of Washington School of Public Health, Seattle, WA (A.P.R.)
| | - Mark J Daly
- From the Department of Biostatistics, Boston University School of Public Health, Boston, MA (G.M.P.); Center for Human Genetic Research (G.M.P., S.K.) and Analytic and Translational Genetics Unit, Massachusetts General Hospital, Boston, MA (M.J.D., B.N.); Program in Medical and Population Genetics, Broad Institute, Cambridge, MA (G.M.P., S.G., D.A., M.J.D., B.N., S.K.); Department of Genetics, University of North Carolina, Chapel Hill, NC (L.A.L.); Genetic and Molecular Epidemiology Unit, Department of Clinical Sciences, Lund University, Malmö, Sweden (T.V.V.); Department of Genome Sciences, University of Washington, Seattle, WA (D.A.N., J.D.S.); Center of Biostatistics & Bioinformatics (M.E.G., H.M.), Department of Medicine (S.M.), Department of Pediatrics & Medicine (A.C.), and Department of Physiology & Biophysics (J.G.W.), University of Mississippi Medical Center, Jackson, MS; Human Genetics Center, University of Texas Health Science Center, Houston, TX (L.M.P., E.B.); Cardiovascular Research Institute, Morehouse School of Medicine, Atlanta, GA (R.C.Q.); Department of Medicine, Harvard Medical School, Boston, MA (D.A., S.K.); and Department of Epidemiology, University of Washington School of Public Health, Seattle, WA (A.P.R.)
| | - Benjamin Neale
- From the Department of Biostatistics, Boston University School of Public Health, Boston, MA (G.M.P.); Center for Human Genetic Research (G.M.P., S.K.) and Analytic and Translational Genetics Unit, Massachusetts General Hospital, Boston, MA (M.J.D., B.N.); Program in Medical and Population Genetics, Broad Institute, Cambridge, MA (G.M.P., S.G., D.A., M.J.D., B.N., S.K.); Department of Genetics, University of North Carolina, Chapel Hill, NC (L.A.L.); Genetic and Molecular Epidemiology Unit, Department of Clinical Sciences, Lund University, Malmö, Sweden (T.V.V.); Department of Genome Sciences, University of Washington, Seattle, WA (D.A.N., J.D.S.); Center of Biostatistics & Bioinformatics (M.E.G., H.M.), Department of Medicine (S.M.), Department of Pediatrics & Medicine (A.C.), and Department of Physiology & Biophysics (J.G.W.), University of Mississippi Medical Center, Jackson, MS; Human Genetics Center, University of Texas Health Science Center, Houston, TX (L.M.P., E.B.); Cardiovascular Research Institute, Morehouse School of Medicine, Atlanta, GA (R.C.Q.); Department of Medicine, Harvard Medical School, Boston, MA (D.A., S.K.); and Department of Epidemiology, University of Washington School of Public Health, Seattle, WA (A.P.R.)
| | - Adolfo Correa
- From the Department of Biostatistics, Boston University School of Public Health, Boston, MA (G.M.P.); Center for Human Genetic Research (G.M.P., S.K.) and Analytic and Translational Genetics Unit, Massachusetts General Hospital, Boston, MA (M.J.D., B.N.); Program in Medical and Population Genetics, Broad Institute, Cambridge, MA (G.M.P., S.G., D.A., M.J.D., B.N., S.K.); Department of Genetics, University of North Carolina, Chapel Hill, NC (L.A.L.); Genetic and Molecular Epidemiology Unit, Department of Clinical Sciences, Lund University, Malmö, Sweden (T.V.V.); Department of Genome Sciences, University of Washington, Seattle, WA (D.A.N., J.D.S.); Center of Biostatistics & Bioinformatics (M.E.G., H.M.), Department of Medicine (S.M.), Department of Pediatrics & Medicine (A.C.), and Department of Physiology & Biophysics (J.G.W.), University of Mississippi Medical Center, Jackson, MS; Human Genetics Center, University of Texas Health Science Center, Houston, TX (L.M.P., E.B.); Cardiovascular Research Institute, Morehouse School of Medicine, Atlanta, GA (R.C.Q.); Department of Medicine, Harvard Medical School, Boston, MA (D.A., S.K.); and Department of Epidemiology, University of Washington School of Public Health, Seattle, WA (A.P.R.)
| | - Alex P Reiner
- From the Department of Biostatistics, Boston University School of Public Health, Boston, MA (G.M.P.); Center for Human Genetic Research (G.M.P., S.K.) and Analytic and Translational Genetics Unit, Massachusetts General Hospital, Boston, MA (M.J.D., B.N.); Program in Medical and Population Genetics, Broad Institute, Cambridge, MA (G.M.P., S.G., D.A., M.J.D., B.N., S.K.); Department of Genetics, University of North Carolina, Chapel Hill, NC (L.A.L.); Genetic and Molecular Epidemiology Unit, Department of Clinical Sciences, Lund University, Malmö, Sweden (T.V.V.); Department of Genome Sciences, University of Washington, Seattle, WA (D.A.N., J.D.S.); Center of Biostatistics & Bioinformatics (M.E.G., H.M.), Department of Medicine (S.M.), Department of Pediatrics & Medicine (A.C.), and Department of Physiology & Biophysics (J.G.W.), University of Mississippi Medical Center, Jackson, MS; Human Genetics Center, University of Texas Health Science Center, Houston, TX (L.M.P., E.B.); Cardiovascular Research Institute, Morehouse School of Medicine, Atlanta, GA (R.C.Q.); Department of Medicine, Harvard Medical School, Boston, MA (D.A., S.K.); and Department of Epidemiology, University of Washington School of Public Health, Seattle, WA (A.P.R.)
| | - James G Wilson
- From the Department of Biostatistics, Boston University School of Public Health, Boston, MA (G.M.P.); Center for Human Genetic Research (G.M.P., S.K.) and Analytic and Translational Genetics Unit, Massachusetts General Hospital, Boston, MA (M.J.D., B.N.); Program in Medical and Population Genetics, Broad Institute, Cambridge, MA (G.M.P., S.G., D.A., M.J.D., B.N., S.K.); Department of Genetics, University of North Carolina, Chapel Hill, NC (L.A.L.); Genetic and Molecular Epidemiology Unit, Department of Clinical Sciences, Lund University, Malmö, Sweden (T.V.V.); Department of Genome Sciences, University of Washington, Seattle, WA (D.A.N., J.D.S.); Center of Biostatistics & Bioinformatics (M.E.G., H.M.), Department of Medicine (S.M.), Department of Pediatrics & Medicine (A.C.), and Department of Physiology & Biophysics (J.G.W.), University of Mississippi Medical Center, Jackson, MS; Human Genetics Center, University of Texas Health Science Center, Houston, TX (L.M.P., E.B.); Cardiovascular Research Institute, Morehouse School of Medicine, Atlanta, GA (R.C.Q.); Department of Medicine, Harvard Medical School, Boston, MA (D.A., S.K.); and Department of Epidemiology, University of Washington School of Public Health, Seattle, WA (A.P.R.)
| | - Sekar Kathiresan
- From the Department of Biostatistics, Boston University School of Public Health, Boston, MA (G.M.P.); Center for Human Genetic Research (G.M.P., S.K.) and Analytic and Translational Genetics Unit, Massachusetts General Hospital, Boston, MA (M.J.D., B.N.); Program in Medical and Population Genetics, Broad Institute, Cambridge, MA (G.M.P., S.G., D.A., M.J.D., B.N., S.K.); Department of Genetics, University of North Carolina, Chapel Hill, NC (L.A.L.); Genetic and Molecular Epidemiology Unit, Department of Clinical Sciences, Lund University, Malmö, Sweden (T.V.V.); Department of Genome Sciences, University of Washington, Seattle, WA (D.A.N., J.D.S.); Center of Biostatistics & Bioinformatics (M.E.G., H.M.), Department of Medicine (S.M.), Department of Pediatrics & Medicine (A.C.), and Department of Physiology & Biophysics (J.G.W.), University of Mississippi Medical Center, Jackson, MS; Human Genetics Center, University of Texas Health Science Center, Houston, TX (L.M.P., E.B.); Cardiovascular Research Institute, Morehouse School of Medicine, Atlanta, GA (R.C.Q.); Department of Medicine, Harvard Medical School, Boston, MA (D.A., S.K.); and Department of Epidemiology, University of Washington School of Public Health, Seattle, WA (A.P.R.).
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Huyghe J, Chen S, Kang HM, Harrison TA, Berndt SI, Bézieau S, Brenner H, Casey G, Chan AT, Chang-Claude J, Steven GJ, Gruber SB, Gsur A, Hoffmeister M, Hudson TJ, Le Marchand L, Newcomb PA, Potter JD, Qu C, Slattery ML, Smith JD, White E, Hsu L, Abecasis GR, Nickerson DA, Peters U. Abstract 5230: Large scale whole genome sequencing with imputation into GWAS improves our understanding of the genetic architecture of colorectal cancer. Cancer Res 2016. [DOI: 10.1158/1538-7445.am2016-5230] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Abstract
Whole-genome sequencing (WGS) has started a new era in human genetics in which data can be used to more fully understand the role of genetic variation in common complex diseases, including the role of less frequent and rare variants and structural variation. To explore the impact of these variants on colorectal cancer risk we conducted the first large scale WGS study for colorectal cancer (CRC) including 1,961 CRC cases and 981 controls. These WGS data as well as those from the Haplotype Reference Consortium were imputed in 13,104 CRC cases and 15,521 controls with genome-wide association study (GWAS) data that are part of the Colorectal Cancer Family Registry (CCFR) and the Genetics and Epidemiology of Colorectal Cancer Consortium (GECCO). Focusing on rare and less frequent variants, insertions and deletions we observed potentially novel variants: a less frequent variant (MAF = 0.026) on chromosome 5 located in NREP/STARD4-AS1 (p = value 4E-08); and a novel rare multi-allelic variant (MAF = 0.003) on chromosome 9 near KLF9 and TRPM3 (p-value 2E-09; the other allele of this multi-allelic variant had a MAF of 0.0003 and p-value of 0.55). Furthermore, we observed an independent locus close to the known region 8q24 that was located upstream of GSDMC (MAF = 0.16, p-value 5E-08). Within the known region 8q23/EIF3H we identified several low frequency variants with similar MAF (0.0181 to 0.0204) including a 6bp deletion with p-values between 4E-08 and 1E-09 that were independent of the common variant signal in this region. In addition, we identified statistically significant (p<5E-08) deletions, insertions, and an essential splice site within known GWAS loci that present interesting candidates for functional studies. We will follow up these findings in independent samples from the Colorectal Cancer Transdisciplinary Study (CORECT) and CCFR, as well as additional samples currently genotyped in GECCO. In conclusion, next generation sequencing combined with imputation in large GWAS data sets has the potential to identify novel low frequency and rare genetic variants, aid fine-mapping of known CRC susceptibility loci and point to interesting functional candidates.
Citation Format: Jeroen Huyghe, Sai Chen, Hyun M. Kang, Tabitha A. Harrison, Sonja I. Berndt, Stephane Bézieau, Hermann Brenner, Graham Casey, Andrew T. Chan, Jenny Chang-Claude, Gallinger J. Steven, Stephen B. Gruber, Andrea Gsur, Michael Hoffmeister, Thomas J. Hudson, Loic Le Marchand, Polly A. Newcomb, John D. Potter, Conghui Qu, Martha L. Slattery, Joshua D. Smith, Emily White, Li Hsu, Goncalo R. Abecasis, Deborah A. Nickerson, Ulrike Peters. Large scale whole genome sequencing with imputation into GWAS improves our understanding of the genetic architecture of colorectal cancer. [abstract]. In: Proceedings of the 107th Annual Meeting of the American Association for Cancer Research; 2016 Apr 16-20; New Orleans, LA. Philadelphia (PA): AACR; Cancer Res 2016;76(14 Suppl):Abstract nr 5230.
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Affiliation(s)
- Jeroen Huyghe
- 1Fred Hutchinson Cancer Research Center, Seattle, WA
| | - Sai Chen
- 2University of Michigan, Ann Arbors, MI
| | | | | | | | | | | | - Graham Casey
- 6University of Southern California, Los Angeles, CA
| | | | | | | | | | - Andrea Gsur
- 9Medical University of Vienna, Vienna, Australia
| | | | - Thomas J. Hudson
- 10Ontario Institute for Cancer Research, Toronto, Ontario, Canada
| | | | | | | | - Conghui Qu
- 1Fred Hutchinson Cancer Research Center, Seattle, WA
| | | | | | - Emily White
- 1Fred Hutchinson Cancer Research Center, Seattle, WA
| | - Li Hsu
- 1Fred Hutchinson Cancer Research Center, Seattle, WA
| | | | | | - Ulrike Peters
- 1Fred Hutchinson Cancer Research Center, Seattle, WA
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174
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Bien SA, Harrison TA, Auer PL, Qu F, Huyghe J, Banbury B, Greenside P, Abecasis GR, Berndt SI, Bézieau S, Brenner H, Casey G, Chan AT, Chang-Claude J, Chen S, Smith JD, Le Marchand L, Carlson C, Newcomb PA, Fuchsberger C, Slattery ML, Kang HM, White E, Potter J, Gallinger SJ, Hoffmeister M, Gruber SB, Nickerson DA, Peters U, Kundaje A, Hsu L. Abstract 4489: Using functional data from Roadmap Epigenomics to inform analysis of rare variants linked to gene expression in a large colorectal cancer study. Cancer Res 2016. [DOI: 10.1158/1538-7445.am2016-4489] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Abstract
To investigate the role of low frequency and rare genetic variation in colorectal cancer (CRC) susceptibility, the Genetics and Epidemiology of Colorectal Cancer Consortium (GECCO) and the Colorectal Cancer Family Registry (CCFR) conducted whole genome sequencing and imputed into genome-wide association studies (GWAS) of 14,718 CRC cases and 12,186 controls. These data provide a unique opportunity to investigate rare variants, which contribute to the majority of the variation in the genome. To improve power for discovering rare CRC susceptibility variants (<1% MAF), Roadmap Epigenomics data were used to construct biologically relevant testing sets of enhancers, promoters and exons for gene-based association testing across the genome. Since enhancers exert their effects by impacting expression of target genes, we defined enhancer-gene networks by linking enhancer(s) to target gene expression using Roadmap chromatin state maps and gene expression. Variants in linked enhancers from digestive and immune tissues were aggregated together with variants in the promoter and non-synonymous coding variants in the target gene. We tested 9,884 variant sets for association with CRC risk using the Mixed effects Score Test (MiST). Our most significant findings are for acyl-Coenzyme A dehydrogenase, C-2 to C-3 short chain precursor-ACADS (p = 1×10−4), AlkB homologs, including AlkB homolog 1-ALKBH1 (p = 2×10−4), and SRA stem-loop interacting RNA binding protein-SLIRP (p = 2×10−4). We will replicate these findings within the Colorectal Cancer Transdisciplinary Study (CORECT), as well as additional samples currently genotyped in CCFR and GECCO (over 25,000 CRC cases and controls). Although the top findings are statistically non-significant in this initial dataset, each of these genes linked to molecular pathways implicated in CRC carcinogenesis (fatty acid metabolism, DNA/RNA repair, and Nuclear Receptor signaling pathway, which interacts with the Wnt, beta-catenin pathways to result in a diverse array of cellular effects including altered cellular adhesion, tissue morphogenesis, and oncogenesis). Our current findings suggest that although functional insight can improve power for novel discovery, even larger sample sizes and/or pathway-based analyses are necessary to understand the role of rare variants in CRC carcinogenesis.
Citation Format: Stephanie A. Bien, Tabitha A. Harrison, Paul L. Auer, Flora Qu, Jeroen Huyghe, Barbara Banbury, Peyton Greenside, Goncalo R. Abecasis, Sonja I. Berndt, Stephane Bézieau, Hermann Brenner, Graham Casey, Andrew T. Chan, Jenny Chang-Claude, Sai Chen, Joshua D. Smith, Loic Le Marchand, Christopher Carlson, Polly A. Newcomb, Christian Fuchsberger, Marty L. Slattery, Hyun M. Kang, Emily White, John Potter, Steven J. Gallinger, Michael Hoffmeister, Stephen B. Gruber, Deborah A. Nickerson, Ulrike Peters, Anshul Kundaje, Li Hsu. Using functional data from Roadmap Epigenomics to inform analysis of rare variants linked to gene expression in a large colorectal cancer study. [abstract]. In: Proceedings of the 107th Annual Meeting of the American Association for Cancer Research; 2016 Apr 16-20; New Orleans, LA. Philadelphia (PA): AACR; Cancer Res 2016;76(14 Suppl):Abstract nr 4489.
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Affiliation(s)
| | | | | | - Flora Qu
- 1Fred Hutchinson Cancer Research Center, Seattle, WA
| | - Jeroen Huyghe
- 1Fred Hutchinson Cancer Research Center, Seattle, WA
| | | | | | | | - Sonja I. Berndt
- 5National Cancer Institute, National Institutes of Health, Bethesda, MD
| | | | | | - Graham Casey
- 8University of Southern California, Los Angeles, CA
| | | | | | - Sai Chen
- 4University of Michigan, Ann Arbor, MI
| | | | | | | | | | | | | | | | - Emily White
- 1Fred Hutchinson Cancer Research Center, Seattle, WA
| | - John Potter
- 1Fred Hutchinson Cancer Research Center, Seattle, WA
| | | | | | | | | | - Ulrike Peters
- 1Fred Hutchinson Cancer Research Center, Seattle, WA
| | | | - Li Hsu
- 1Fred Hutchinson Cancer Research Center, Seattle, WA
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175
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Tajuddin SM, Schick UM, Eicher JD, Chami N, Giri A, Brody JA, Hill WD, Kacprowski T, Li J, Lyytikäinen LP, Manichaikul A, Mihailov E, O'Donoghue ML, Pankratz N, Pazoki R, Polfus LM, Smith AV, Schurmann C, Vacchi-Suzzi C, Waterworth DM, Evangelou E, Yanek LR, Burt A, Chen MH, van Rooij FJA, Floyd JS, Greinacher A, Harris TB, Highland HM, Lange LA, Liu Y, Mägi R, Nalls MA, Mathias RA, Nickerson DA, Nikus K, Starr JM, Tardif JC, Tzoulaki I, Velez Edwards DR, Wallentin L, Bartz TM, Becker LC, Denny JC, Raffield LM, Rioux JD, Friedrich N, Fornage M, Gao H, Hirschhorn JN, Liewald DCM, Rich SS, Uitterlinden A, Bastarache L, Becker DM, Boerwinkle E, de Denus S, Bottinger EP, Hayward C, Hofman A, Homuth G, Lange E, Launer LJ, Lehtimäki T, Lu Y, Metspalu A, O'Donnell CJ, Quarells RC, Richard M, Torstenson ES, Taylor KD, Vergnaud AC, Zonderman AB, Crosslin DR, Deary IJ, Dörr M, Elliott P, Evans MK, Gudnason V, Kähönen M, Psaty BM, Rotter JI, Slater AJ, Dehghan A, White HD, Ganesh SK, Loos RJF, Esko T, Faraday N, Wilson JG, Cushman M, Johnson AD, Edwards TL, Zakai NA, Lettre G, Reiner AP, Auer PL. Large-Scale Exome-wide Association Analysis Identifies Loci for White Blood Cell Traits and Pleiotropy with Immune-Mediated Diseases. Am J Hum Genet 2016; 99:22-39. [PMID: 27346689 DOI: 10.1016/j.ajhg.2016.05.003] [Citation(s) in RCA: 47] [Impact Index Per Article: 5.9] [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: 02/17/2016] [Accepted: 05/03/2016] [Indexed: 12/11/2022] Open
Abstract
White blood cells play diverse roles in innate and adaptive immunity. Genetic association analyses of phenotypic variation in circulating white blood cell (WBC) counts from large samples of otherwise healthy individuals can provide insights into genes and biologic pathways involved in production, differentiation, or clearance of particular WBC lineages (myeloid, lymphoid) and also potentially inform the genetic basis of autoimmune, allergic, and blood diseases. We performed an exome array-based meta-analysis of total WBC and subtype counts (neutrophils, monocytes, lymphocytes, basophils, and eosinophils) in a multi-ancestry discovery and replication sample of ∼157,622 individuals from 25 studies. We identified 16 common variants (8 of which were coding variants) associated with one or more WBC traits, the majority of which are pleiotropically associated with autoimmune diseases. Based on functional annotation, these loci included genes encoding surface markers of myeloid, lymphoid, or hematopoietic stem cell differentiation (CD69, CD33, CD87), transcription factors regulating lineage specification during hematopoiesis (ASXL1, IRF8, IKZF1, JMJD1C, ETS2-PSMG1), and molecules involved in neutrophil clearance/apoptosis (C10orf54, LTA), adhesion (TNXB), or centrosome and microtubule structure/function (KIF9, TUBD1). Together with recent reports of somatic ASXL1 mutations among individuals with idiopathic cytopenias or clonal hematopoiesis of undetermined significance, the identification of a common regulatory 3' UTR variant of ASXL1 suggests that both germline and somatic ASXL1 mutations contribute to lower blood counts in otherwise asymptomatic individuals. These association results shed light on genetic mechanisms that regulate circulating WBC counts and suggest a prominent shared genetic architecture with inflammatory and autoimmune diseases.
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Affiliation(s)
- Salman M Tajuddin
- Laboratory of Epidemiology and Population Sciences, National Institute on Aging, NIH, Baltimore, MD 21224, USA
| | - Ursula M Schick
- The Charles Bronfman Institute for Personalized Medicine, The Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; The Genetics of Obesity and Related Metabolic Traits Program, The Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - John D Eicher
- Population Sciences Branch, National Heart Lung and Blood Institute, The Framingham Heart Study, Framingham, MA 01702, USA
| | - Nathalie Chami
- Department of Medicine, Université de Montréal, Montréal, QC H3T 1J4, Canada; Montreal Heart Institute, Montréal, QC H1T 1C8, Canada
| | - Ayush Giri
- Division of Epidemiology, Institute for Medicine and Public Health, Vanderbilt University, Nashville, TN 37235, USA
| | - Jennifer A Brody
- Department of Medicine, University of Washington, Seattle, WA 98101, USA
| | - W David Hill
- Centre for Cognitive Ageing and Cognitive Epidemiology, University of Edinburgh, Edinburgh EH8 9JZ, UK; Department of Psychology, University of Edinburgh, Edinburgh EH8 9JZ, UK
| | - Tim Kacprowski
- Department of Functional Genomics, Interfaculty Institute for Genetics and Functional Genomics, University Medicine Greifswald and Ernst-Mortiz-Arndt University Greifswald, Greifswald 17475, Germany; DZHK (German Centre for Cardiovascular Research), partner site Greifswald, Greifswald, Germany
| | - Jin Li
- Department of Medicine, Division of Cardiovascular Medicine, Stanford University School of Medicine, Palo Alto, CA 94305, USA
| | - Leo-Pekka Lyytikäinen
- Department of Clinical Chemistry, Fimlab Laboratories, Tampere 33520, Finland; Department of Clinical Chemistry, University of Tampere School of Medicine, Tampere 33014, Finland
| | - Ani Manichaikul
- Center for Public Health Genomics, University of Virginia, Charlottesville, VA 22908, USA
| | - Evelin Mihailov
- Estonian Genome Center, University of Tartu, Tartu 51010, Estonia
| | - Michelle L O'Donoghue
- TIMI Study Group, Cardiovascular Division, Brigham and Women's Hospital, Boston, MA 02115, USA
| | - Nathan Pankratz
- Department of Laboratory Medicine and Pathology, University of Minnesota, Minneapolis, MN 55454, USA
| | - Raha Pazoki
- Department of Epidemiology, Erasmus University Medical Center, Rotterdam 3000, the Netherlands
| | - Linda M Polfus
- Human Genetics Center, School of Public Health, University of Texas Health Science Center at Houston, Houston, TX 77030, USA
| | - Albert Vernon Smith
- Icelandic Heart Association, 201 Kopavogur, Iceland; Faculty of Medicine, University of Iceland, 101 Reykjavik, Iceland
| | - Claudia Schurmann
- The Charles Bronfman Institute for Personalized Medicine, The Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; The Genetics of Obesity and Related Metabolic Traits Program, The Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Caterina Vacchi-Suzzi
- Department of Family, Population and Preventive Medicine, Stony Brook University, Stony Brook, NY 11794, USA
| | - Dawn M Waterworth
- Genetics, Target Sciences, GlaxoSmithKline, King of Prussia, PA 19406, USA
| | - Evangelos Evangelou
- Department of Epidemiology and Biostatistics, MRC-PHE Centre for Environment and Health, School of Public Health, Imperial College London, London W2 1PG, UK; Department of Hygiene and Epidemiology, University of Ioannina Medical School, Ioannina 45110, Greece
| | - Lisa R Yanek
- Department of Medicine, Division of General Internal Medicine, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Amber Burt
- Division of Medical Genetics, Department of Medicine, University of Washington, Seattle, WA 98195, USA
| | - Ming-Huei Chen
- Population Sciences Branch, National Heart Lung and Blood Institute, The Framingham Heart Study, Framingham, MA 01702, USA
| | - Frank J A van Rooij
- Department of Epidemiology, Erasmus University Medical Center, Rotterdam 3000, the Netherlands
| | - James S Floyd
- Department of Medicine, University of Washington, Seattle, WA 98101, USA
| | - Andreas Greinacher
- Institute for Immunology and Transfusion Medicine, University Medicine Greifswald, Greifswald 17475, Germany
| | - Tamara B Harris
- Laboratory of Epidemiology, Demography, and Biometry, National Institute on Aging, Intramural Research Program, NIH, Bethesda, MD 20892, USA
| | - Heather M Highland
- Human Genetics Center, School of Public Health, University of Texas Health Science Center at Houston, Houston, TX 77030, USA; Department of Epidemiology, University of North Carolina at Chapel Hill, Chapel Hill, NC 27514, USA
| | - Leslie A Lange
- Department of Genetics, University of North Carolina, Chapel Hill, NC 27514, USA
| | - Yongmei Liu
- Center for Human Genetics, Division of Public Health Sciences, Wake Forest School of Medicine, Winston-Salem, NC 27157, USA
| | - Reedik Mägi
- Estonian Genome Center, University of Tartu, Tartu 51010, Estonia
| | - Mike A Nalls
- Laboratory of Neurogenetics, National Institute on Aging, NIH, Bethesda, MD 20892, USA
| | - Rasika A Mathias
- Department of Medicine, Divisions of Allergy and Clinical Immunology and General Internal Medicine, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Deborah A Nickerson
- Department of Genome Sciences, School of Medicine, University of Washington, Seattle, WA 98105, USA
| | - Kjell Nikus
- Department of Cardiology, Heart Center, Tampere University Hospital, Tampere 33521, Finland; University of Tampere School of Medicine, Tampere 33014, Finland
| | - John M Starr
- Centre for Cognitive Ageing and Cognitive Epidemiology, University of Edinburgh, Edinburgh EH8 9JZ, UK; Alzheimer Scotland Dementia Research Centre, Edinburgh EH8 9JZ, UK
| | - Jean-Claude Tardif
- Department of Medicine, Université de Montréal, Montréal, QC H3T 1J4, Canada; Montreal Heart Institute, Montréal, QC H1T 1C8, Canada
| | - Ioanna Tzoulaki
- Department of Epidemiology and Biostatistics, MRC-PHE Centre for Environment and Health, School of Public Health, Imperial College London, London W2 1PG, UK; Department of Hygiene and Epidemiology, University of Ioannina Medical School, Ioannina 45110, Greece
| | - Digna R Velez Edwards
- Vanderbilt Epidemiology Center, Department of Obstetrics and Gynecology, Institute for Medicine and Public Health, Vanderbilt Genetics Institute, Vanderbilt University, Nashville, TN 37203, USA
| | - Lars Wallentin
- Department of Medical Sciences, Cardiology, and Uppsala Clinical Research Center, Uppsala University, 751 85 Uppsala, Sweden
| | - Traci M Bartz
- Department of Biostatistics, University of Washington, Seattle, WA 98195, USA
| | - Lewis C Becker
- Department of Medicine, Divisions of Cardiology and General Internal Medicine, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Joshua C Denny
- Department of Biomedical Informatics, School of Medicine, Vanderbilt University, Nashville, TN 37203, USA
| | - Laura M Raffield
- Department of Genetics, University of North Carolina, Chapel Hill, NC 27514, USA
| | - John D Rioux
- Department of Medicine, Université de Montréal, Montréal, QC H3T 1J4, Canada; Montreal Heart Institute, Montréal, QC H1T 1C8, Canada
| | - Nele Friedrich
- DZHK (German Centre for Cardiovascular Research), partner site Greifswald, Greifswald, Germany; Institute of Clinical Chemistry and Laboratory Medicine, University Medicine Greifswald, Greifswald 13347, Germany
| | - Myriam Fornage
- Institute of Molecular Medicine, The University of Texas Health Science Center at Houston, Houston, TX 77030, USA
| | - He Gao
- Department of Epidemiology and Biostatistics, MRC-PHE Centre for Environment and Health, School of Public Health, Imperial College London, London W2 1PG, UK
| | - Joel N Hirschhorn
- Program in Medical and Population Genetics, Broad Institute, Cambridge, MA 02142, USA; Department of Endocrinology, Boston Children's Hospital, Boston, MA 02115, USA
| | - David C M Liewald
- Centre for Cognitive Ageing and Cognitive Epidemiology, University of Edinburgh, Edinburgh EH8 9JZ, UK; Department of Psychology, University of Edinburgh, Edinburgh EH8 9JZ, UK
| | - Stephen S Rich
- Center for Public Health Genomics, University of Virginia, Charlottesville, VA 22908, USA
| | - Andre Uitterlinden
- Department of Epidemiology, Erasmus University Medical Center, Rotterdam 3000, the Netherlands; Department of Internal Medicine, Erasmus University Medical Center, Rotterdam 3000, the Netherlands; Netherlands Consortium for Healthy Ageing (NCHA), Rotterdam 3015, the Netherlands
| | - Lisa Bastarache
- Department of Biomedical Informatics, School of Medicine, Vanderbilt University, Nashville, TN 37203, USA
| | - Diane M Becker
- Department of Medicine, Division of General Internal Medicine, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - 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
| | - Simon de Denus
- Montreal Heart Institute, Montréal, QC H1T 1C8, Canada; Faculty of Pharmacy, Université de Montréal, Montréal, QC H3T 1J4, Canada
| | - Erwin P Bottinger
- The Charles Bronfman Institute for Personalized Medicine, The Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Caroline Hayward
- MRC Human Genetics Unit, Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh EH4 2XU, UK
| | - Albert Hofman
- Department of Epidemiology, Erasmus University Medical Center, Rotterdam 3000, the Netherlands; Department of Epidemiology, Harvard TH Chan School of Public Health, Boston, MA 02115, USA
| | - Georg Homuth
- Department of Functional Genomics, Interfaculty Institute for Genetics and Functional Genomics, University Medicine Greifswald and Ernst-Mortiz-Arndt University Greifswald, Greifswald 17475, Germany
| | - Ethan Lange
- Departments of Genetics and Biostatistics, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Lenore J Launer
- Laboratory of Epidemiology, Demography, and Biometry, National Institute on Aging, Intramural Research Program, NIH, Bethesda, MD 20892, USA
| | - Terho Lehtimäki
- Department of Clinical Chemistry, Fimlab Laboratories, Tampere 33520, Finland; Department of Clinical Chemistry, University of Tampere School of Medicine, Tampere 33014, Finland
| | - Yingchang Lu
- The Charles Bronfman Institute for Personalized Medicine, The Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; The Genetics of Obesity and Related Metabolic Traits Program, The Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Andres Metspalu
- Estonian Genome Center, University of Tartu, Tartu 51010, Estonia
| | - Chris J O'Donnell
- National Heart, Lung, and Blood Institute, The Framingham Heart Study, Framingham, MA 01702, USA; Cardiology Section and Center for Population Genomics, Boston Veteran's Administration (VA) Healthcare, Boston, MA 02118, USA
| | - Rakale C Quarells
- Morehouse School of Medicine, Social Epidemiology Research Center, Cardiovascular Research Institute, Atlanta, GA 30310, USA
| | - Melissa Richard
- Institute of Molecular Medicine, The University of Texas Health Science Center at Houston, Houston, TX 77030, USA
| | - Eric S Torstenson
- Division of Epidemiology, Institute for Medicine and Public Health, Vanderbilt University, Nashville, TN 37235, USA
| | - Kent D Taylor
- Institute for Translational Genomics and Population Sciences, Los Angeles Biomedical Research Institute, Torrance, CA 90502, USA; Department of Pediatrics, Harbor-UCLA Medical Center, Torrance, CA 90502, USA
| | - Anne-Claire Vergnaud
- Department of Epidemiology and Biostatistics, MRC-PHE Centre for Environment and Health, School of Public Health, Imperial College London, London W2 1PG, UK
| | - Alan B Zonderman
- Laboratory of Epidemiology and Population Sciences, National Institute on Aging, NIH, Baltimore, MD 21224, USA
| | - David R Crosslin
- Department of Biomedical Informatics and Medical Education, University of Washington, Seattle, WA 98195, 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
| | - Marcus Dörr
- DZHK (German Centre for Cardiovascular Research), partner site Greifswald, Greifswald, Germany; Department of Cardiology, University Medicine Greifswald, Greifswald 17475, Germany
| | - Paul Elliott
- Department of Epidemiology and Biostatistics, MRC-PHE Centre for Environment and Health, School of Public Health, Imperial College London, London W2 1PG, UK
| | - Michele K Evans
- Laboratory of Epidemiology and Population Sciences, National Institute on Aging, NIH, Baltimore, MD 21224, USA
| | - Vilmundur Gudnason
- Icelandic Heart Association, 201 Kopavogur, Iceland; Faculty of Medicine, University of Iceland, 101 Reykjavik, Iceland
| | - Mika Kähönen
- Department of Clinical Physiology, Tampere University Hospital, Tampere 33521, Finland; Department of Clinical Physiology, University of Tampere School of Medicine, Tampere 33014, Finland
| | - Bruce M Psaty
- Cardiovascular Health Research Unit, Departments of Epidemiology, Health Services, and Medicine, University of Washington, Seattle, WA 98101, USA; Group Health Research Institute, Group Health Cooperative, Seattle, WA 98101, USA
| | - Jerome I Rotter
- Institute for Translational Genomics and Population Sciences, Los Angeles Biomedical Research Institute, Torrance, CA 90502, USA; Department of Pediatrics, Harbor-UCLA Medical Center, Torrance, CA 90502, USA
| | - Andrew J Slater
- OmicSoft Corporation, Cary, NC 27513, USA; Genetics, Target Sciences, GlaxoSmithKline, Research Triangle Park, NC 27709, USA
| | - Abbas Dehghan
- Department of Epidemiology, Erasmus University Medical Center, Rotterdam 3000, the Netherlands
| | - Harvey D White
- Green Lane Cardiovascular Service, Auckland City Hospital and University of Auckland, Auckland 1142, New Zealand
| | - Santhi K Ganesh
- Departments of Internal Medicine and Human Genetics, University of Michigan, Ann Arbor, MI 48108, USA
| | - Ruth J F Loos
- The Charles Bronfman Institute for Personalized Medicine, The Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; The Genetics of Obesity and Related Metabolic Traits Program, The Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; The Mindich Child Health and Development Institute, The Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Tõnu Esko
- Estonian Genome Center, University of Tartu, Tartu 51010, Estonia; Program in Medical and Population Genetics, Broad Institute, Cambridge, MA 02142, USA
| | - Nauder Faraday
- Department of Anesthesiology and Critical Care Medicine, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - James G Wilson
- Department of Physiology and Biophysics, University of Mississippi Medical Center, Jackson, MS 39216, USA
| | - Mary Cushman
- Division of Hematology Oncology, Department of Medicine, The University of Vermont, Colchester, VT 05446, USA
| | - Andrew D Johnson
- Population Sciences Branch, National Heart Lung and Blood Institute, The Framingham Heart Study, Framingham, MA 01702, USA
| | - Todd L Edwards
- Division of Epidemiology, Department of Medicine, Institute for Medicine and Public Health, Vanderbilt Genetics Institute, Vanderbilt University, Nashville, TN 37203, USA
| | - Neil A Zakai
- Division of Hematology Oncology, Department of Medicine, The University of Vermont, Colchester, VT 05446, USA
| | - Guillaume Lettre
- Department of Medicine, Université de Montréal, Montréal, QC H3T 1J4, Canada; Montreal Heart Institute, Montréal, QC H1T 1C8, Canada
| | - Alex P Reiner
- Department of Epidemiology, University of Washington, Seattle, WA 98195, USA; Division of Public Health Sciences, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA.
| | - Paul L Auer
- Zilber School of Public Health, University of Wisconsin-Milwaukee, Milwaukee, WI 53205, USA.
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Eicher JD, Chami N, Kacprowski T, Nomura A, Chen MH, Yanek LR, Tajuddin SM, Schick UM, Slater AJ, Pankratz N, Polfus L, Schurmann C, Giri A, Brody JA, Lange LA, Manichaikul A, Hill WD, Pazoki R, Elliot P, Evangelou E, Tzoulaki I, Gao H, Vergnaud AC, Mathias RA, Becker DM, Becker LC, Burt A, Crosslin DR, Lyytikäinen LP, Nikus K, Hernesniemi J, Kähönen M, Raitoharju E, Mononen N, Raitakari OT, Lehtimäki T, Cushman M, Zakai NA, Nickerson DA, Raffield LM, Quarells R, Willer CJ, Peloso GM, Abecasis GR, Liu DJ, Deloukas P, Samani NJ, Schunkert H, Erdmann J, Fornage M, Richard M, Tardif JC, Rioux JD, Dube MP, de Denus S, Lu Y, Bottinger EP, Loos RJF, Smith AV, Harris TB, Launer LJ, Gudnason V, Velez Edwards DR, Torstenson ES, Liu Y, Tracy RP, Rotter JI, Rich SS, Highland HM, Boerwinkle E, Li J, Lange E, Wilson JG, Mihailov E, Mägi R, Hirschhorn J, Metspalu A, Esko T, Vacchi-Suzzi C, Nalls MA, Zonderman AB, Evans MK, Engström G, Orho-Melander M, Melander O, O'Donoghue ML, Waterworth DM, Wallentin L, White HD, Floyd JS, Bartz TM, Rice KM, Psaty BM, Starr JM, Liewald DCM, Hayward C, Deary IJ, Greinacher A, Völker U, Thiele T, Völzke H, van Rooij FJA, Uitterlinden AG, Franco OH, Dehghan A, Edwards TL, Ganesh SK, Kathiresan S, Faraday N, Auer PL, Reiner AP, Lettre G, Johnson AD. Platelet-Related Variants Identified by Exomechip Meta-analysis in 157,293 Individuals. Am J Hum Genet 2016; 99:40-55. [PMID: 27346686 PMCID: PMC5005441 DOI: 10.1016/j.ajhg.2016.05.005] [Citation(s) in RCA: 67] [Impact Index Per Article: 8.4] [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: 02/18/2016] [Accepted: 05/03/2016] [Indexed: 12/13/2022] Open
Abstract
Platelet production, maintenance, and clearance are tightly controlled processes indicative of platelets' important roles in hemostasis and thrombosis. Platelets are common targets for primary and secondary prevention of several conditions. They are monitored clinically by complete blood counts, specifically with measurements of platelet count (PLT) and mean platelet volume (MPV). Identifying genetic effects on PLT and MPV can provide mechanistic insights into platelet biology and their role in disease. Therefore, we formed the Blood Cell Consortium (BCX) to perform a large-scale meta-analysis of Exomechip association results for PLT and MPV in 157,293 and 57,617 individuals, respectively. Using the low-frequency/rare coding variant-enriched Exomechip genotyping array, we sought to identify genetic variants associated with PLT and MPV. In addition to confirming 47 known PLT and 20 known MPV associations, we identified 32 PLT and 18 MPV associations not previously observed in the literature across the allele frequency spectrum, including rare large effect (FCER1A), low-frequency (IQGAP2, MAP1A, LY75), and common (ZMIZ2, SMG6, PEAR1, ARFGAP3/PACSIN2) variants. Several variants associated with PLT/MPV (PEAR1, MRVI1, PTGES3) were also associated with platelet reactivity. In concurrent BCX analyses, there was overlap of platelet-associated variants with red (MAP1A, TMPRSS6, ZMIZ2) and white (PEAR1, ZMIZ2, LY75) blood cell traits, suggesting common regulatory pathways with shared genetic architecture among these hematopoietic lineages. Our large-scale Exomechip analyses identified previously undocumented associations with platelet traits and further indicate that several complex quantitative hematological, lipid, and cardiovascular traits share genetic factors.
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Affiliation(s)
- John D Eicher
- Population Sciences Branch, National Heart Lung and Blood Institute, The Framingham Heart Study, Framingham, MA 01702, USA
| | - Nathalie Chami
- Department of Medicine, Université de Montréal, Montréal, QC H3T 1J4, Canada; Montreal Heart Institute, Montréal, QC H1T 1C8, Canada
| | - Tim Kacprowski
- Department of Functional Genomics, Interfaculty Institute for Genetics and Functional Genomics, University Medicine Greifswald and Ernst-Mortiz-Arndt University Greifswald, Greifswald 17475, Germany; DZHK (German Centre for Cardiovascular Research), partner site Greifswald, Greifswald, Germany
| | - Akihiro Nomura
- Center for Human Genetic Research, Massachusetts General Hospital, Boston, MA 02114, USA; Program in Medical and Population Genetics, Broad Institute, Cambridge, MA 02142, USA; Cardiovascular Research Center, Massachusetts General Hospital, Boston, MA 02114, USA; Department of Medicine, Harvard Medical School, Boston, MA 02115, USA; Division of Cardiovascular Medicine, Kanazawa University Graduate School of Medical Science, Kanazawa, Ishikawa 9200942, Japan
| | - Ming-Huei Chen
- Population Sciences Branch, National Heart Lung and Blood Institute, The Framingham Heart Study, Framingham, MA 01702, USA
| | - Lisa R Yanek
- Department of Medicine, Division of General Internal Medicine, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Salman M Tajuddin
- Laboratory of Epidemiology and Population Sciences, National Institute on Aging, NIH, Baltimore, MD 21224, USA
| | - Ursula M Schick
- The Charles Bronfman Institute for Personalized Medicine, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; The Genetics of Obesity and Related Metabolic Traits Program, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Andrew J Slater
- Genetics, Target Sciences, GlaxoSmithKline, Research Triangle Park, NC 27709, USA; OmicSoft Corporation, Cary, NC 27513, USA
| | - Nathan Pankratz
- Department of Laboratory Medicine and Pathology, University of Minnesota, Minneapolis, MN 55454, USA
| | - Linda Polfus
- Human Genetics Center, School of Public Health, University of Texas Health Science Center at Houston, Houston, TX 77030, USA
| | - Claudia Schurmann
- The Charles Bronfman Institute for Personalized Medicine, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA; The Genetics of Obesity and Related Metabolic Traits Program, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Ayush Giri
- Division of Epidemiology, Institute for Medicine and Public Health, Vanderbilt University, Nashville, TN 37235, USA
| | - Jennifer A Brody
- Department of Medicine, University of Washington, Seattle, WA 98101, USA
| | - Leslie A Lange
- Department of Genetics, University of North Carolina, Chapel Hill, NC 27514, USA
| | - Ani Manichaikul
- Center for Public Health Genomics, University of Virginia, Charlottesville, VA 22908, USA
| | - W David Hill
- Centre for Cognitive Ageing and Cognitive Epidemiology, University of Edinburgh, Edinburgh EH8 9JZ, UK; Department of Psychology, University of Edinburgh, Edinburgh EH8 9JZ, UK
| | - Raha Pazoki
- Department of Epidemiology, Erasmus MC, Rotterdam 3000, the Netherlands
| | - Paul Elliot
- Department of Epidemiology and Biostatistics, MRC-PHE Centre for Environment and Health, School of Public Health, Imperial College London, London W2 1PG, UK
| | - Evangelos Evangelou
- Department of Epidemiology and Biostatistics, MRC-PHE Centre for Environment and Health, School of Public Health, Imperial College London, London W2 1PG, UK; Department of Hygiene and Epidemiology, University of Ioannina Medical School, Ioannina 45110, Greece
| | - Ioanna Tzoulaki
- Department of Epidemiology and Biostatistics, MRC-PHE Centre for Environment and Health, School of Public Health, Imperial College London, London W2 1PG, UK; Department of Hygiene and Epidemiology, University of Ioannina Medical School, Ioannina 45110, Greece
| | - He Gao
- Department of Epidemiology and Biostatistics, MRC-PHE Centre for Environment and Health, School of Public Health, Imperial College London, London W2 1PG, UK
| | - Anne-Claire Vergnaud
- Department of Epidemiology and Biostatistics, MRC-PHE Centre for Environment and Health, School of Public Health, Imperial College London, London W2 1PG, UK
| | - Rasika A Mathias
- Department of Medicine, Division of General Internal Medicine, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA; Divisions of Allergy and Clinical Immunology, Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Diane M Becker
- Department of Medicine, Division of General Internal Medicine, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Lewis C Becker
- Department of Medicine, Division of General Internal Medicine, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA; Divisions of Cardiology, Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Amber Burt
- Division of Medical Genetics, Department of Medicine, University of Washington, Seattle, WA 98195, USA
| | - David R Crosslin
- Department of Biomedical Informatics and Medical Education, University of Washington, Seattle, WA 98105, USA
| | - Leo-Pekka Lyytikäinen
- Department of Clinical Chemistry, Fimlab Laboratories, Tampere 33520, Finland; Department of Clinical Chemistry, University of Tampere School of Medicine, Tampere 33514, Finland
| | - Kjell Nikus
- Department of Cardiology, Heart Center, Tampere University Hospital, Tampere 33521, Finland; University of Tampere, School of Medicine, Tampere 33514, Finland
| | - Jussi Hernesniemi
- Department of Clinical Chemistry, Fimlab Laboratories, Tampere 33520, Finland; Department of Clinical Chemistry, University of Tampere School of Medicine, Tampere 33514, Finland; Department of Cardiology, Heart Center, Tampere University Hospital, Tampere 33521, Finland
| | - Mika Kähönen
- Department of Clinical Physiology, Tampere University Hospital, Tampere 33521, Finland; Department of Clinical Physiology, University of Tampere, Tampere 33514, Finland
| | - Emma Raitoharju
- Department of Clinical Chemistry, Fimlab Laboratories, Tampere 33520, Finland; Department of Clinical Chemistry, University of Tampere School of Medicine, Tampere 33514, Finland
| | - Nina Mononen
- Department of Clinical Chemistry, Fimlab Laboratories, Tampere 33520, Finland; Department of Clinical Chemistry, University of Tampere School of Medicine, Tampere 33514, Finland
| | - Olli T Raitakari
- Department of Clinical Physiology and Nuclear Medicine, Turku University Hospital, Turku 20521, Finland; Research Centre of Applied and Preventive Cardiovascular Medicine, University of Turku, Turku 20520, Finland
| | - Terho Lehtimäki
- Department of Clinical Chemistry, Fimlab Laboratories, Tampere 33520, Finland; Department of Clinical Chemistry, University of Tampere School of Medicine, Tampere 33514, Finland
| | - Mary Cushman
- Departments of Medicine and Pathology, University of Vermont College of Medicine, Burlington, VT 05405, USA
| | - Neil A Zakai
- Departments of Medicine and Pathology, University of Vermont College of Medicine, Burlington, VT 05405, USA
| | - Deborah A Nickerson
- Department of Genome Sciences, University of Washington, Seattle, WA 98105, USA
| | - Laura M Raffield
- Department of Genetics, University of North Carolina, Chapel Hill, NC 27514, USA
| | - Rakale Quarells
- Morehouse School of Medicine, Social Epidemiology Research Center, Cardiovascular Research Institute, Atlanta, GA 30310, USA
| | - Cristen J Willer
- Department of Internal Medicine, Division of Cardiovascular Medicine, University of Michigan, Ann Arbor, MI 48108, USA; Department of Computational Medicine and Bioinformatics, Department of Human Genetics, University of Michigan, Ann Arbor, MI 48108, USA; Department of Biostatistics, University of Michigan, Ann Arbor, MI 48108, USA
| | - Gina M Peloso
- Center for Human Genetic Research, Massachusetts General Hospital, Boston, MA 02114, USA; Program in Medical and Population Genetics, Broad Institute, Cambridge, MA 02142, USA; Department of Biostatistics, Boston University School of Public Health, Boston, MA 02118, USA
| | - Goncalo R Abecasis
- Center for Statistical Genetics, Department of Biostatistics, University of Michigan, Ann Arbor, MI 48108, USA
| | - Dajiang J Liu
- Department of Public Health Sciences, College of Medicine, Pennsylvania State University, Hershey, PA 17033, USA
| | - Panos Deloukas
- William Harvey Research Institute, Queen Mary University London, London E1 4NS, UK; Princess Al-Jawhara Al-Brahim Centre of Excellence in Research of Hereditary Disorders (PACER-HD), King Abdulaziz University, Jeddah 21589, Saudi Arabia
| | - Nilesh J Samani
- Department of Cardiovascular Sciences, University of Leicester, Leicester LE1 7RH, UK; NIHR Leicester Cardiovascular Biomedical Research Unit, Glenfield Hospital, Leicester LE3 9QP, UK
| | - Heribert Schunkert
- DZHK (German Centre for Cardiovascular Research), partner site Munich Heart Alliance, Munich 80333, Germany; Deutsches Herzzentrum München, Technische Universität München, Munich 80333, Germany
| | - Jeanette Erdmann
- Institute for Integrative and Experimental Genomics, University of Lübeck, Lübeck 23562, Germany; DZHK (German Research Centre for Cardiovascular Research), partner site Hamburg/Lübeck/Kiel, Lübeck 23562, Germany
| | - Myriam Fornage
- Institute of Molecular Medicine, The University of Texas Health Science Center at Houston, Houston, TX 77030, USA
| | - Melissa Richard
- Institute of Molecular Medicine, The University of Texas Health Science Center at Houston, Houston, TX 77030, USA
| | - Jean-Claude Tardif
- Department of Medicine, Université de Montréal, Montréal, QC H3T 1J4, Canada; Montreal Heart Institute, Montréal, QC H1T 1C8, Canada
| | - John D Rioux
- Department of Medicine, Université de Montréal, Montréal, QC H3T 1J4, Canada; Montreal Heart Institute, Montréal, QC H1T 1C8, Canada
| | - Marie-Pierre Dube
- Department of Medicine, Université de Montréal, Montréal, QC H3T 1J4, Canada; Montreal Heart Institute, Montréal, QC H1T 1C8, Canada
| | - Simon de Denus
- Montreal Heart Institute, Montréal, QC H1T 1C8, Canada; Faculty of Pharmacy, Université de Montréal, Montréal, QC H3T 1J4, Canada
| | - Yingchang Lu
- The Charles Bronfman Institute for Personalized Medicine, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Erwin P Bottinger
- The Charles Bronfman Institute for Personalized Medicine, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Ruth J F Loos
- The Charles Bronfman Institute for Personalized Medicine, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Albert Vernon Smith
- Icelandic Heart Association, Kopavogur 201, Iceland; Faculty of Medicine, University of Iceland, Reykjavik 101, Iceland
| | - Tamara B Harris
- Laboratory of Epidemiology, Demography, and Biometry, National Institute on Aging, Intramural Research Program, NIH, Bethesda, MD 21224, USA
| | - Lenore J Launer
- Laboratory of Epidemiology, Demography, and Biometry, National Institute on Aging, Intramural Research Program, NIH, Bethesda, MD 21224, USA
| | - Vilmundur Gudnason
- Icelandic Heart Association, Kopavogur 201, Iceland; Faculty of Medicine, University of Iceland, Reykjavik 101, Iceland
| | - Digna R Velez Edwards
- Vanderbilt Epidemiology Center, Department of Obstetrics & Gynecology, Institute for Medicine and Public Health, Vanderbilt Genetics Institute, Vanderbilt University, Nashville, TN 37203, USA
| | - Eric S Torstenson
- Division of Epidemiology, Institute for Medicine and Public Health, Vanderbilt University, Nashville, TN 37235, USA
| | - Yongmei Liu
- Center for Human Genetics, Division of Public Health Sciences, Wake Forest School of Medicine, Winston-Salem, NC 27157, USA
| | - Russell P Tracy
- Departments of Pathology and Laboratory Medicine and Biochemistry, University of Vermont College of Medicine, Colchester, VT 05446, USA
| | - Jerome I Rotter
- Institute for Translational Genomics and Population Sciences, Los Angeles Biomedical Research Institute, Torrance, CA 90502, USA; Department of Pediatrics, Harbor-UCLA Medical Center, Torrance, CA 90502, USA
| | - Stephen S Rich
- Center for Public Health Genomics, University of Virginia, Charlottesville, VA 22908, USA
| | - Heather M Highland
- The University of Texas School of Public Health, The University of Texas Graduate School of Biomedical Sciences at Houston, The University of Texas Health Science Center at Houston, Houston, TX 77030, USA; Department of Epidemiology, University of North Carolina, Chapel Hill, NC 27514, USA
| | - 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
| | - Jin Li
- Department of Medicine, Division of Cardiovascular Medicine, Stanford University School of Medicine, Palo Alto, CA 94305, USA
| | - Ethan Lange
- Department of Genetics, University of North Carolina, Chapel Hill, NC 27514, USA; Department of Biostatistics, University of North Carolina, Chapel Hill, NC 27514, USA
| | - James G Wilson
- Department of Physiology and Biophysics, University of Mississippi Medical Center, Jackson, MS 39216, USA
| | - Evelin Mihailov
- Estonian Genome Center, University of Tartu, Tartu 51010, Estonia
| | - Reedik Mägi
- Estonian Genome Center, University of Tartu, Tartu 51010, Estonia
| | - Joel Hirschhorn
- Program in Medical and Population Genetics, Broad Institute, Cambridge, MA 02142, USA; Department of Endocrinology, Boston Children's Hospital, Boston, MA 02115, USA
| | - Andres Metspalu
- Estonian Genome Center, University of Tartu, Tartu 51010, Estonia
| | - Tõnu Esko
- Program in Medical and Population Genetics, Broad Institute, Cambridge, MA 02142, USA; Estonian Genome Center, University of Tartu, Tartu 51010, Estonia
| | - Caterina Vacchi-Suzzi
- Department of Family, Population and Preventive Medicine, Stony Brook University, Stony Brook, NY 11794, USA
| | - Mike A Nalls
- Laboratory of Neurogenetics, National Institute on Aging, NIH, Bethesda, MD 21224, USA
| | - Alan B Zonderman
- Laboratory of Epidemiology and Population Sciences, National Institute on Aging, NIH, Baltimore, MD 21224, USA
| | - Michele K Evans
- Laboratory of Epidemiology and Population Sciences, National Institute on Aging, NIH, Baltimore, MD 21224, USA
| | - Gunnar Engström
- Department of Clinical Sciences Malmö, Lund University, Malmö 221 00, Sweden; Skåne University Hospital, Malmö 222 41, Sweden
| | - Marju Orho-Melander
- Department of Clinical Sciences Malmö, Lund University, Malmö 221 00, Sweden; Skåne University Hospital, Malmö 222 41, Sweden
| | - Olle Melander
- Department of Clinical Sciences Malmö, Lund University, Malmö 221 00, Sweden; Skåne University Hospital, Malmö 222 41, Sweden
| | - Michelle L O'Donoghue
- TIMI Study Group, Cardiovascular Division, Brigham and Women's Hospital, Boston, MA 02115, USA
| | - Dawn M Waterworth
- Genetics, Target Sciences, GlaxoSmithKline, King of Prussia, PA 19406, USA
| | - Lars Wallentin
- Department of Medical Sciences, Cardiology, and Uppsala Clinical Research Center, Uppsala University, Uppsala 751 85, Sweden
| | - Harvey D White
- Green Lane Cardiovascular Service, Auckland City Hospital and University of Auckland, Auckland 1142, New Zealand
| | - James S Floyd
- Department of Medicine, University of Washington, Seattle, WA 98101, USA
| | - Traci M Bartz
- Department of Biostatistics, University of Washington, Seattle, WA 98195, USA
| | - Kenneth M Rice
- Department of Biostatistics, University of Washington, Seattle, WA 98195, USA
| | - Bruce M Psaty
- Cardiovascular Health Research Unit, Departments of Medicine, Epidemiology and Health Services, University of Washington, Seattle, WA 98101, USA; Group Health Research Institute, Group Health Cooperative, Seattle, WA 98101, USA
| | - J M Starr
- Centre for Cognitive Ageing and Cognitive Epidemiology, University of Edinburgh, Edinburgh EH8 9JZ, UK; Alzheimer Scotland Research Centre, Edinburgh EH8 9JZ, UK
| | - David C M Liewald
- Centre for Cognitive Ageing and Cognitive Epidemiology, University of Edinburgh, Edinburgh EH8 9JZ, UK; Department of Psychology, University of Edinburgh, Edinburgh EH8 9JZ, UK
| | - Caroline Hayward
- MRC Human Genetics Unit, Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh EH4 2XU, UK
| | - 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
| | - Andreas Greinacher
- Institute for Immunology and Transfusion Medicine, University Medicine Greifswald, Greifswald 17475, Germany
| | - Uwe Völker
- Department of Functional Genomics, Interfaculty Institute for Genetics and Functional Genomics, University Medicine Greifswald and Ernst-Mortiz-Arndt University Greifswald, Greifswald 17475, Germany; DZHK (German Centre for Cardiovascular Research), partner site Greifswald, Greifswald, Germany
| | - Thomas Thiele
- Institute for Immunology and Transfusion Medicine, University Medicine Greifswald, Greifswald 17475, Germany
| | - Henry Völzke
- DZHK (German Centre for Cardiovascular Research), partner site Greifswald, Greifswald, Germany; Institute for Community Medicine, University Medicine Greifswald, Greifswald 13347, Germany
| | | | - André G Uitterlinden
- Department of Epidemiology, Erasmus MC, Rotterdam 3000, the Netherlands; Department of Internal Medicine, Erasmus MC, Rotterdam 3000, the Netherlands; Netherlands Consortium for Healthy Ageing (NCHA), Rotterdam 3015, the Netherlands
| | - Oscar H Franco
- Department of Epidemiology, Erasmus MC, Rotterdam 3000, the Netherlands
| | - Abbas Dehghan
- Department of Epidemiology, Erasmus MC, Rotterdam 3000, the Netherlands
| | - Todd L Edwards
- Division of Epidemiology, Institute for Medicine and Public Health, Vanderbilt University, Nashville, TN 37235, USA
| | - Santhi K Ganesh
- Departments of Internal and Human Genetics, University of Michigan, Ann Arbor, MI 48108, USA
| | - Sekar Kathiresan
- Center for Human Genetic Research, Massachusetts General Hospital, Boston, MA 02114, USA; Program in Medical and Population Genetics, Broad Institute, Cambridge, MA 02142, USA; Cardiovascular Research Center, Massachusetts General Hospital, Boston, MA 02114, USA; Department of Medicine, Harvard Medical School, Boston, MA 02115, USA
| | - Nauder Faraday
- Department of Anesthesiology & Critical Care Medicine, Johns Hopkins University School of Medicine, Baltimore, MD 21205, USA
| | - Paul L Auer
- Zilber School of Public Health, University of Wisconsin-Milwaukee, Milwaukee, WI 53205, USA
| | - Alex P Reiner
- Department of Epidemiology, University of Washington, Seattle, WA 98105, USA; Division of Public Health Sciences, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA
| | - Guillaume Lettre
- Department of Medicine, Université de Montréal, Montréal, QC H3T 1J4, Canada; Montreal Heart Institute, Montréal, QC H1T 1C8, Canada
| | - Andrew D Johnson
- Population Sciences Branch, National Heart Lung and Blood Institute, The Framingham Heart Study, Framingham, MA 01702, USA.
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Du M, Jiao S, Bien SA, Gala M, Abecasis G, Bezieau S, Brenner H, Butterbach K, Caan BJ, Carlson CS, Casey G, Chang-Claude J, Conti DV, Curtis KR, Duggan D, Gallinger S, Haile RW, Harrison TA, Hayes RB, Hoffmeister M, Hopper JL, Hudson TJ, Jenkins MA, Küry S, Le Marchand L, Leal SM, Newcomb PA, Nickerson DA, Potter JD, Schoen RE, Schumacher FR, Seminara D, Slattery ML, Hsu L, Chan AT, White E, Berndt SI, Peters U. Fine-Mapping of Common Genetic Variants Associated with Colorectal Tumor Risk Identified Potential Functional Variants. PLoS One 2016; 11:e0157521. [PMID: 27379672 PMCID: PMC4933364 DOI: 10.1371/journal.pone.0157521] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [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: 10/08/2015] [Accepted: 06/01/2016] [Indexed: 01/27/2023] Open
Abstract
Genome-wide association studies (GWAS) have identified many common single nucleotide polymorphisms (SNPs) associated with colorectal cancer risk. These SNPs may tag correlated variants with biological importance. Fine-mapping around GWAS loci can facilitate detection of functional candidates and additional independent risk variants. We analyzed 11,900 cases and 14,311 controls in the Genetics and Epidemiology of Colorectal Cancer Consortium and the Colon Cancer Family Registry. To fine-map genomic regions containing all known common risk variants, we imputed high-density genetic data from the 1000 Genomes Project. We tested single-variant associations with colorectal tumor risk for all variants spanning genomic regions 250-kb upstream or downstream of 31 GWAS-identified SNPs (index SNPs). We queried the University of California, Santa Cruz Genome Browser to examine evidence for biological function. Index SNPs did not show the strongest association signals with colorectal tumor risk in their respective genomic regions. Bioinformatics analysis of SNPs showing smaller P-values in each region revealed 21 functional candidates in 12 loci (5q31.1, 8q24, 11q13.4, 11q23, 12p13.32, 12q24.21, 14q22.2, 15q13, 18q21, 19q13.1, 20p12.3, and 20q13.33). We did not observe evidence of additional independent association signals in GWAS-identified regions. Our results support the utility of integrating data from comprehensive fine-mapping with expanding publicly available genomic databases to help clarify GWAS associations and identify functional candidates that warrant more onerous laboratory follow-up. Such efforts may aid the eventual discovery of disease-causing variant(s).
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Affiliation(s)
- Mengmeng Du
- Department of Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, New York, NY, United States of America
- Public Health Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, WA, United States of America
- * E-mail: (MD); (UP)
| | - Shuo Jiao
- Public Health Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, WA, United States of America
| | - Stephanie A. Bien
- Public Health Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, WA, United States of America
- School of Public Health, University of Washington, Seattle, WA, United States of America
| | - Manish Gala
- Division of Gastroenterology, Massachusetts General Hospital and Harvard Medical School, Boston, MA, United States of America
| | - Goncalo Abecasis
- Department of Biostatistics, University of Michigan School of Public Health, Ann Arbor, MI, United States of America
| | | | - Hermann Brenner
- Division of Clinical Epidemiology and Aging Research, German Cancer Research Center (DKFZ), Heidelberg, Germany
- German Cancer Consortium (DKTK), Heidelberg, Germany
| | - Katja Butterbach
- Division of Clinical Epidemiology and Aging Research, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Bette J. Caan
- Division of Research, Kaiser Permanente Medical Care Program of Northern California, Oakland, CA, United States of America
| | - Christopher S. Carlson
- Public Health Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, WA, United States of America
| | - Graham Casey
- Keck School of Medicine, University of Southern California, Los Angeles, CA, United States of America
| | - Jenny Chang-Claude
- Division of Cancer Epidemiology, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - David V. Conti
- Keck School of Medicine, University of Southern California, Los Angeles, CA, United States of America
| | - Keith R. Curtis
- Public Health Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, WA, United States of America
| | - David Duggan
- Translational Genomics Research Institute, Phoenix, Arizona, United States of America
| | - Steven Gallinger
- Department of Surgery, Mount Sinai Hospital, Toronto, ON, Canada
| | - Robert W. Haile
- Keck School of Medicine, University of Southern California, Los Angeles, CA, United States of America
| | - Tabitha A. Harrison
- Public Health Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, WA, United States of America
| | - Richard B. Hayes
- Division of Epidemiology, Department of Population Health, New York University School of Medicine, New York, NY, United States of America
| | - Michael Hoffmeister
- Division of Clinical Epidemiology and Aging Research, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - John L. Hopper
- Melbourne School of Population and Global Health, The University of Melbourne, Melbourne, Victoria, Australia
| | - Thomas J. Hudson
- Ontario Institute for Cancer Research, Toronto, ON, Canada
- Departments of Medical Biophysics and Molecular Genetics, University of Toronto, Toronto, ON, Canada
| | - Mark A. Jenkins
- Melbourne School of Population and Global Health, The University of Melbourne, Melbourne, Victoria, Australia
| | - Sébastien Küry
- Service de Génétique Médicale, CHU Nantes, Nantes, France
| | - Loic Le Marchand
- Epidemiology Program, University of Hawaii Cancer Center, Honolulu, HI, United States of America
| | - Suzanne M. Leal
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, United States of America
| | - Polly A. Newcomb
- Public Health Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, WA, United States of America
- School of Public Health, University of Washington, Seattle, WA, United States of America
| | - Deborah A. Nickerson
- Genome Sciences, University of Washington, Seattle, WA, United States of America
| | - John D. Potter
- Public Health Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, WA, United States of America
- School of Public Health, University of Washington, Seattle, WA, United States of America
- Centre for Public Health Research, Massey University, Wellington, New Zealand
| | - Robert E. Schoen
- Department of Medicine and Epidemiology, University of Pittsburgh Medical Center, Pittsburgh, PA, United States of America
| | - Fredrick R. Schumacher
- Keck School of Medicine, University of Southern California, Los Angeles, CA, United States of America
| | - Daniela Seminara
- Division of Cancer Control and Population Sciences, National Cancer Institute, Bethesda, MD, United States of America
| | - Martha L. Slattery
- Department of Internal Medicine, University of Utah Health Sciences Center, Salt Lake City, UT, United States of America
| | - Li Hsu
- Public Health Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, WA, United States of America
| | - Andrew T. Chan
- Division of Gastroenterology, Massachusetts General Hospital and Harvard Medical School, Boston, MA, United States of America
- Channing Division of Network Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, United States of America
| | - Emily White
- Public Health Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, WA, United States of America
- School of Public Health, University of Washington, Seattle, WA, United States of America
| | - Sonja I. Berndt
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Bethesda, MD, United States of America
| | - Ulrike Peters
- Public Health Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, WA, United States of America
- School of Public Health, University of Washington, Seattle, WA, United States of America
- * E-mail: (MD); (UP)
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178
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Green RC, Goddard KAB, Jarvik GP, Amendola LM, Appelbaum PS, Berg JS, Bernhardt BA, Biesecker LG, Biswas S, Blout CL, Bowling KM, Brothers KB, Burke W, Caga-Anan CF, Chinnaiyan AM, Chung WK, Clayton EW, Cooper GM, East K, Evans JP, Fullerton SM, Garraway LA, Garrett JR, Gray SW, Henderson GE, Hindorff LA, Holm IA, Lewis MH, Hutter CM, Janne PA, Joffe S, Kaufman D, Knoppers BM, Koenig BA, Krantz ID, Manolio TA, McCullough L, McEwen J, McGuire A, Muzny D, Myers RM, Nickerson DA, Ou J, Parsons DW, Petersen GM, Plon SE, Rehm HL, Roberts JS, Robinson D, Salama JS, Scollon S, Sharp RR, Shirts B, Spinner NB, Tabor HK, Tarczy-Hornoch P, Veenstra DL, Wagle N, Weck K, Wilfond BS, Wilhelmsen K, Wolf SM, Wynn J, Yu JH. Clinical Sequencing Exploratory Research Consortium: Accelerating Evidence-Based Practice of Genomic Medicine. Am J Hum Genet 2016; 98:1051-1066. [PMID: 27181682 DOI: 10.1016/j.ajhg.2016.04.011] [Citation(s) in RCA: 109] [Impact Index Per Article: 13.6] [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: 12/24/2015] [Accepted: 04/14/2016] [Indexed: 12/11/2022] Open
Abstract
Despite rapid technical progress and demonstrable effectiveness for some types of diagnosis and therapy, much remains to be learned about clinical genome and exome sequencing (CGES) and its role within the practice of medicine. The Clinical Sequencing Exploratory Research (CSER) consortium includes 18 extramural research projects, one National Human Genome Research Institute (NHGRI) intramural project, and a coordinating center funded by the NHGRI and National Cancer Institute. The consortium is exploring analytic and clinical validity and utility, as well as the ethical, legal, and social implications of sequencing via multidisciplinary approaches; it has thus far recruited 5,577 participants across a spectrum of symptomatic and healthy children and adults by utilizing both germline and cancer sequencing. The CSER consortium is analyzing data and creating publically available procedures and tools related to participant preferences and consent, variant classification, disclosure and management of primary and secondary findings, health outcomes, and integration with electronic health records. Future research directions will refine measures of clinical utility of CGES in both germline and somatic testing, evaluate the use of CGES for screening in healthy individuals, explore the penetrance of pathogenic variants through extensive phenotyping, reduce discordances in public databases of genes and variants, examine social and ethnic disparities in the provision of genomics services, explore regulatory issues, and estimate the value and downstream costs of sequencing. The CSER consortium has established a shared community of research sites by using diverse approaches to pursue the evidence-based development of best practices in genomic medicine.
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Affiliation(s)
- Robert C Green
- Division of Genetics, Department of Medicine, Brigham and Women's Hospital, Boston, MA 02115, USA; Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Harvard Medical School, Boston, MA 02115, USA; Partners Personalized Medicine, Boston, MA 02139, USA.
| | - Katrina A B Goddard
- Center for Health Research, Kaiser Permanente Northwest, Portland, OR 97227, USA
| | - Gail P Jarvik
- Department of Genome Sciences, University of Washington, Seattle, WA 98195, USA; Division of Medical Genetics, Department of Medicine, University of Washington, Seattle, WA 98195, USA; Clinical Sequencing Exploratory Research Coordinating Center, University of Washington, Seattle, WA 98195, USA
| | - Laura M Amendola
- Division of Medical Genetics, Department of Medicine, University of Washington, Seattle, WA 98195, USA; Clinical Sequencing Exploratory Research Coordinating Center, University of Washington, Seattle, WA 98195, USA
| | - Paul S Appelbaum
- Department of Psychiatry, Columbia University Medical Center and New York State Psychiatric Institute, New York, NY 10032, USA
| | - Jonathan S Berg
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Barbara A Bernhardt
- Division of Translational Medicine and Human Genetics, Department of Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Leslie G Biesecker
- Medical Genomics and Metabolic Genetics Branch, National Human Genome Research Institute, NIH, Bethesda, MD 20892, USA
| | - Sawona Biswas
- Division of Translational Medicine and Human Genetics, Department of Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA; Department of Pediatrics, Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA
| | - Carrie L Blout
- Division of Genetics, Department of Medicine, Brigham and Women's Hospital, Boston, MA 02115, USA
| | - Kevin M Bowling
- HudsonAlpha Institute for Biotechnology, Huntsville, AL 35806, USA
| | - Kyle B Brothers
- Department of Pediatrics, University of Louisville, Louisville, KY 40202, USA
| | - Wylie Burke
- Division of Medical Genetics, Department of Medicine, University of Washington, Seattle, WA 98195, USA; Clinical Sequencing Exploratory Research Coordinating Center, University of Washington, Seattle, WA 98195, USA; Department of Bioethics and Humanities, Department of Medicine, University of Washington, Seattle, WA 98195, USA
| | | | - Arul M Chinnaiyan
- Michigan Center for Translational Pathology, Ann Arbor, MI 48109, USA; Comprehensive Cancer Center, University of Michigan, Ann Arbor, MI 48109, USA; Departments of Pathology and Urology, University of Michigan, Ann Arbor, MI 48109, USA; Howard Hughes Medical Institute, Ann Arbor, MI 48109, USA
| | - Wendy K Chung
- Department of Pediatrics, Columbia University, New York, NY 10029, USA; Department of Medicine, Columbia University Medical Center, New York, NY 10032, USA
| | - Ellen W Clayton
- Center for Biomedical Ethics and Society, Vanderbilt University, Nashville, TN 37203, USA
| | - Gregory M Cooper
- HudsonAlpha Institute for Biotechnology, Huntsville, AL 35806, USA
| | - Kelly East
- HudsonAlpha Institute for Biotechnology, Huntsville, AL 35806, USA
| | - James P Evans
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Stephanie M Fullerton
- Department of Bioethics and Humanities, Department of Medicine, University of Washington, Seattle, WA 98195, USA
| | - Levi A Garraway
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Department of Medical Oncology and Center for Cancer Precision Medicine, Dana-Farber Cancer Institute, Boston, MA 02115, USA; Department of Medicine, Brigham and Women's Hospital, Boston, MA 02115, USA
| | - Jeremy R Garrett
- Children's Mercy Bioethics Center, Children's Mercy Hospital, Kansas City, MO 64108, USA; Departments of Pediatrics and Philosophy, University of Missouri - Kansas City, Kansas City, MO 64110, USA
| | - Stacy W Gray
- Harvard Medical School, Boston, MA 02115, USA; Dana-Farber Cancer Institute, Boston, MA 02115, USA
| | - Gail E Henderson
- Department of Social Medicine, School of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Lucia A Hindorff
- Division of Genomic Medicine, National Human Genome Research Institute, NIH, Bethesda, MD 20892, USA
| | - Ingrid A Holm
- Harvard Medical School, Boston, MA 02115, USA; Division of Genetics and Genomics and the Manton Center for Orphan Diseases Research, Boston Children's Hospital, Boston, MA 02115, USA
| | | | - Carolyn M Hutter
- Division of Genomic Medicine, National Human Genome Research Institute, NIH, Bethesda, MD 20892, USA
| | - Pasi A Janne
- Harvard Medical School, Boston, MA 02115, USA; Dana-Farber Cancer Institute, Boston, MA 02115, USA
| | - Steven Joffe
- Department of Medical Ethics & Health Policy, University of Pennsylvania School of Medicine, Philadelphia, PA 19104, USA
| | - David Kaufman
- Division of Genomics and Society, National Human Genome Research Institute, NIH, Bethesda, MD 20892, USA
| | - Bartha M Knoppers
- Centre of Genomics and Policy, Faculty of Medicine, Department of Human Genetics, McGill University, Montreal, QC H3A 1B1, Canada
| | - Barbara A Koenig
- Institute for Health and Aging, University of California, San Francisco, San Francisco, CA 94118, USA
| | - Ian D Krantz
- Division of Translational Medicine and Human Genetics, Department of Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA; Department of Pediatrics, Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA
| | - Teri A Manolio
- Division of Genomic Medicine, National Human Genome Research Institute, NIH, Bethesda, MD 20892, USA
| | - Laurence McCullough
- Center for Medical Ethics and Health Policy, Baylor College of Medicine, Houston, TX 77030, USA
| | - Jean McEwen
- Division of Genomics and Society, National Human Genome Research Institute, NIH, Bethesda, MD 20892, USA
| | - Amy McGuire
- Center for Medical Ethics and Health Policy, Baylor College of Medicine, Houston, TX 77030, USA
| | - Donna Muzny
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX 77030, USA
| | - Richard M Myers
- HudsonAlpha Institute for Biotechnology, Huntsville, AL 35806, USA
| | - Deborah A Nickerson
- Department of Genome Sciences, University of Washington, Seattle, WA 98195, USA; Clinical Sequencing Exploratory Research Coordinating Center, University of Washington, Seattle, WA 98195, USA
| | - Jeffrey Ou
- Division of Medical Genetics, Department of Medicine, University of Washington, Seattle, WA 98195, USA; Clinical Sequencing Exploratory Research Coordinating Center, University of Washington, Seattle, WA 98195, USA
| | - Donald W Parsons
- Baylor College of Medicine and Texas Children's Cancer Center, Houston, TX 77030, USA
| | - Gloria M Petersen
- Department of Health Sciences Research, Mayo Clinic College of Medicine, Rochester, MN 55905, USA
| | - Sharon E Plon
- Baylor College of Medicine and Texas Children's Cancer Center, Houston, TX 77030, USA
| | - Heidi L Rehm
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Harvard Medical School, Boston, MA 02115, USA; Partners Personalized Medicine, Boston, MA 02139, USA; Laboratory for Molecular Medicine, Partners HealthCare, Cambridge, MA 02139, USA
| | - J Scott Roberts
- Department of Health Behavior & Health Education, University of Michigan School of Public Health, Ann Arbor, MI 48109, USA
| | - Dan Robinson
- Michigan Center for Translational Pathology, Ann Arbor, MI 48109, USA
| | - Joseph S Salama
- Division of Medical Genetics, Department of Medicine, University of Washington, Seattle, WA 98195, USA; Clinical Sequencing Exploratory Research Coordinating Center, University of Washington, Seattle, WA 98195, USA
| | - Sarah Scollon
- Department of Pediatrics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Richard R Sharp
- Biomedical Ethics Research Program, Mayo Clinic College of Medicine, Rochester, MN 55905, USA
| | - Brian Shirts
- Department of Laboratory Medicine, University of Washington, Seattle, WA 98195, USA
| | - Nancy B Spinner
- Division of Translational Medicine and Human Genetics, Department of Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA 19104, USA; Department of Pathology and Laboratory Medicine, Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA
| | - Holly K Tabor
- Department of Pediatrics and Seattle Children's Research Institute, University of Washington, Seattle, WA, USA
| | - Peter Tarczy-Hornoch
- Division of Medical Genetics, Department of Medicine, University of Washington, Seattle, WA 98195, USA; University of Washington, Seattle, WA 98105, USA
| | - David L Veenstra
- Department of Pharmacy, University of Washington, Seattle, WA 98195, USA
| | - Nikhil Wagle
- Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Department of Medical Oncology and Center for Cancer Precision Medicine, Dana-Farber Cancer Institute, Boston, MA 02115, USA; Department of Medicine, Brigham and Women's Hospital, Boston, MA 02115, USA
| | - Karen Weck
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA; Department of Pathology and Laboratory Medicine, University of North Carolina at Chapel Hill, NC 27599, USA
| | - Benjamin S Wilfond
- Department of Pediatrics and Seattle Children's Research Institute, University of Washington, Seattle, WA, USA
| | - Kirk Wilhelmsen
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Susan M Wolf
- Law School, Medical School, and Consortium on Law and Values in Health, Environment, & the Life Sciences, Minneapolis, University of Minnesota, MN 55455, USA
| | - Julia Wynn
- Department of Pediatrics, Columbia University, New York, NY 10029, USA
| | - Joon-Ho Yu
- Department of Pediatrics, University of Washington, Seattle, WA 98195, USA
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Rosenthal EA, Makaryan V, Burt AA, Crosslin DR, Kim DS, Smith JD, Nickerson DA, Reiner AP, Rich SS, Jackson RD, Ganesh SK, Polfus LM, Qi L, Dale DC, Jarvik GP. Association Between Absolute Neutrophil Count and Variation at TCIRG1: The NHLBI Exome Sequencing Project. Genet Epidemiol 2016; 40:470-4. [PMID: 27229898 DOI: 10.1002/gepi.21976] [Citation(s) in RCA: 10] [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: 11/25/2015] [Revised: 02/22/2016] [Accepted: 04/05/2016] [Indexed: 11/11/2022]
Abstract
Neutrophils are a key component of innate immunity. Individuals with low neutrophil count are susceptible to frequent infections. Linkage and association between congenital neutropenia and a single rare missense variant in TCIRG1 have been reported in a single family. Here, we report on nine rare missense variants at evolutionarily conserved sites in TCIRG1 that are associated with lower absolute neutrophil count (ANC; p = 0.005) in 1,058 participants from three cohorts: Atherosclerosis Risk in Communities (ARIC), Coronary Artery Risk Development in Young Adults (CARDIA), and Jackson Heart Study (JHS) of the NHLBI Grand Opportunity Exome Sequencing Project (GO ESP). These results validate the effects of TCIRG1 coding variation on ANC and suggest that this gene may be associated with a spectrum of mild to severe effects on ANC.
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Affiliation(s)
- Elisabeth A Rosenthal
- Division of Medical Genetics, School of Medicine, University of Washington, Seattle, Washington, United States of America
| | - Vahagn Makaryan
- Division of General Internal Medicine, School of Medicine, University of Washington, Seattle, Washington, United States of America
| | - Amber A Burt
- Division of Medical Genetics, School of Medicine, University of Washington, Seattle, Washington, United States of America
| | - David R Crosslin
- Department of Genome Sciences, University of Washington, Seattle, Washington, United States of America
| | - Daniel Seung Kim
- Department of Genome Sciences, University of Washington, Seattle, Washington, United States of America
| | - Joshua D Smith
- Department of Genome Sciences, University of Washington, Seattle, Washington, United States of America
| | - Deborah A Nickerson
- Department of Genome Sciences, University of Washington, Seattle, Washington, United States of America
| | - Alex P Reiner
- Department of Epidemiology, School of Public Health, University of Washington, Seattle, Washington, United States of America
| | - Stephen S Rich
- Center for Public Health Genomics, School of Medicine, University of Virginia, Charlottesville, Virginia, United States of America
| | - Rebecca D Jackson
- Division of Endocrinology, Diabetes and Metabolism, Department of Internal Medicine, The Ohio State University, Columbus, Ohio, United States of America
| | - Santhi K Ganesh
- Department of Human Genetics, University of Michigan Medical School, Ann Arbor, Michigan, United States of America.,Department of Internal Medicine, University of Michigan Medical School, Ann Arbor, Michigan, United States of America
| | - Linda M Polfus
- Human Genetics Center, University of Texas Health Science Center, Houston, Texas, United States of America
| | - Lihong Qi
- Division of Biostatistics, Department of Public Health Sciences, School of Medicine, University of California, Davis, California, United States of America
| | - David C Dale
- Division of General Internal Medicine, School of Medicine, University of Washington, Seattle, Washington, United States of America
| | | | - Gail P Jarvik
- Division of Medical Genetics, School of Medicine, University of Washington, Seattle, Washington, United States of America.,Department of Genome Sciences, University of Washington, Seattle, Washington, United States of America
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180
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Gao L, Emond MJ, Louie T, Cheadle C, Berger AE, Rafaels N, Vergara C, Kim Y, Taub MA, Ruczinski I, Mathai SC, Rich SS, Nickerson DA, Hummers LK, Bamshad MJ, Hassoun PM, Mathias RA, Barnes KC. Identification of Rare Variants in ATP8B4 as a Risk Factor for Systemic Sclerosis by Whole-Exome Sequencing. Arthritis Rheumatol 2016; 68:191-200. [PMID: 26473621 DOI: 10.1002/art.39449] [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] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2014] [Accepted: 09/24/2015] [Indexed: 01/02/2023]
Abstract
OBJECTIVE To determine the contribution of rare variants as genetic modifiers of the expressivity, penetrance, and severity of systemic sclerosis (SSc). METHODS We performed whole-exome sequencing of 78 European American patients with SSc, including 35 patients without pulmonary arterial hypertension (PAH) and 43 patients with PAH. Association testing of case-control probability for rare variants was performed using the unified sequence kernel association test with optimal kernel weighting and small sample adjustment by comparing all SSc patients with a reference population of 3,179 controls from the Exome Sequencing Project 5,500 exome data set. Replication genotyping was performed in an independent sample of 3,263 patients (415 patients with SSc and 2,848 controls). We conducted expression profiling of messenger RNA from 61 SSc patients (19 without PAH and 42 with PAH) and 41 corresponding controls. RESULTS The ATP8B4 gene was associated with a significant increase in the risk of SSc (P = 2.77 × 10(-7)). Among the 64 ATP8B4 variants tested, a single missense variant, c.1308C>G (F436L, rs55687265), provided the most compelling evidence of association (P = 9.35 × 10(-10), odds ratio [OR] 6.11), which was confirmed in the replication cohort (P = 0.012, OR 1.86) and meta-analysis (P = 1.92 × 10(-7), OR 2.5). Genes involved in E3 ubiquitin-protein ligase complex (ASB10) and cyclic nucleotide gated channelopathies (CNGB3) as well as HLA-DRB5 and HSPB2 (heat-shock protein 27) provided additional evidence of association (P < 10(-5)). Differential ATP8B4 expression was observed among the SSc patients compared to the controls (P = 0.0005). CONCLUSION ATP8B4 may represent a putative genetic risk factor for SSc and pulmonary vascular complications.
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Affiliation(s)
- Li Gao
- Johns Hopkins University, Baltimore, Maryland
| | | | | | | | | | | | | | - Yoonhee Kim
- National Human Genome Research Institute, NIH, Baltimore, Maryland
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181
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Ng BG, Shiryaev SA, Rymen D, Eklund EA, Raymond K, Kircher M, Abdenur JE, Alehan F, Midro AT, Bamshad MJ, Barone R, Berry GT, Brumbaugh JE, Buckingham KJ, Clarkson K, Cole FS, O'Connor S, Cooper GM, Van Coster R, Demmer LA, Diogo L, Fay AJ, Ficicioglu C, Fiumara A, Gahl WA, Ganetzky R, Goel H, Harshman LA, He M, Jaeken J, James PM, Katz D, Keldermans L, Kibaek M, Kornberg AJ, Lachlan K, Lam C, Yaplito-Lee J, Nickerson DA, Peters HL, Race V, Régal L, Rush JS, Rutledge SL, Shendure J, Souche E, Sparks SE, Trapane P, Sanchez-Valle A, Vilain E, Vøllo A, Waechter CJ, Wang RY, Wolfe LA, Wong DA, Wood T, Yang AC, Matthijs G, Freeze HH. ALG1-CDG: Clinical and Molecular Characterization of 39 Unreported Patients. Hum Mutat 2016; 37:653-60. [PMID: 26931382 DOI: 10.1002/humu.22983] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.9] [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: 12/17/2015] [Accepted: 02/17/2016] [Indexed: 12/16/2022]
Abstract
Congenital disorders of glycosylation (CDG) arise from pathogenic mutations in over 100 genes leading to impaired protein or lipid glycosylation. ALG1 encodes a β1,4 mannosyltransferase that catalyzes the addition of the first of nine mannose moieties to form a dolichol-lipid linked oligosaccharide intermediate required for proper N-linked glycosylation. ALG1 mutations cause a rare autosomal recessive disorder termed ALG1-CDG. To date 13 mutations in 18 patients from 14 families have been described with varying degrees of clinical severity. We identified and characterized 39 previously unreported cases of ALG1-CDG from 32 families and add 26 new mutations. Pathogenicity of each mutation was confirmed based on its inability to rescue impaired growth or hypoglycosylation of a standard biomarker in an alg1-deficient yeast strain. Using this approach we could not establish a rank order comparison of biomarker glycosylation and patient phenotype, but we identified mutations with a lethal outcome in the first two years of life. The recently identified protein-linked xeno-tetrasaccharide biomarker, NeuAc-Gal-GlcNAc2 , was seen in all 27 patients tested. Our study triples the number of known patients and expands the molecular and clinical correlates of this disorder.
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Affiliation(s)
- Bobby G Ng
- Human Genetics Program, Sanford Burnham Prebys Medical Discovery Institute, La Jolla, California
| | - Sergey A Shiryaev
- Human Genetics Program, Sanford Burnham Prebys Medical Discovery Institute, La Jolla, California
| | - Daisy Rymen
- Center for Human Genetics, University of Leuven, Leuven, Belgium.,Center for Metabolic Diseases, University Hospital of Leuven, Leuven, Belgium
| | - Erik A Eklund
- Section of Experimental Pediatrics, Department of Clinical Sciences, Lund University, Lund, Sweden
| | - Kimiyo Raymond
- Biochemical Genetics Laboratory, Mayo Clinic College of Medicine, Rochester, Minnesota
| | - Martin Kircher
- Department of Genome Sciences, University of Washington, Seattle, Washington
| | - Jose E Abdenur
- Division of Metabolic Disorders, Children's Hospital of Orange County, Orange, California.,Department of Pediatrics, University of California-Irvine School of Medicine, Orange, California
| | - Fusun Alehan
- Division of Pediatric Neurology, Baskent University School of Medicine, Ankara, Turkey
| | - Alina T Midro
- Department of Clinical Genetics, Medical University, Bialystok, Poland
| | - Michael J Bamshad
- Department of Genome Sciences, University of Washington, Seattle, Washington.,Department of Pediatrics, University of Washington, Seattle, Washington
| | - Rita Barone
- Pediatric Neurology Policlinico, University of Catania, Catania, Italy
| | - Gerard T Berry
- Department of Pediatrics, Harvard Medical School, Boston, Massachusetts
| | - Jane E Brumbaugh
- Stead Family Department of Pediatrics, University of Iowa Children's Hospital, Iowa City, Iowa
| | - Kati J Buckingham
- Department of Pediatrics, University of Washington, Seattle, Washington
| | | | - F Sessions Cole
- Division of Newborn Medicine, Department of Pediatrics, Washington University School of Medicine, St. Louis, Missouri
| | - Shawn O'Connor
- Division of Newborn Medicine, Department of Pediatrics, Washington University School of Medicine, St. Louis, Missouri
| | | | - Rudy Van Coster
- Department of Pediatrics, Division of Pediatric Neurology and Metabolism, University Hospital Gent, Gent, Belgium
| | - Laurie A Demmer
- Clinical Genetics Program, Carolinas Health Care, Levine Childrens Hospital, Charlotte, North Carolina
| | - Luisa Diogo
- Centro de Desenvolvimento da Criança- Pediatric Hospital - CHUC, Coimbra, Portugal
| | - Alexander J Fay
- Division of Pediatric Neurology, Washington University, St. Louis, Missouri
| | - Can Ficicioglu
- Department of Pediatrics, Section of Metabolic Disease, The Children's Hospital of Philadelphia, Perelman School of Medicine at the University of Pennsylvania Philadelphia, Pennsylvania
| | - Agata Fiumara
- Centre for Inherited Metabolic Diseases, Department of Clinical and Experimental Medicine, University of Catania, Catania, Italy
| | - William A Gahl
- NIH Undiagnosed Diseases Program, Common Fund, Office of the Director, NIH and National Human Genome Research Institute, NIH, Bethesda, Maryland
| | - Rebecca Ganetzky
- Department of Pediatrics, Section of Metabolic Disease, The Children's Hospital of Philadelphia, Perelman School of Medicine at the University of Pennsylvania Philadelphia, Pennsylvania
| | - Himanshu Goel
- Hunter Genetics, Waratah, New South Wales, School of Medicine and Public Health, University of Newcastle, Callaghan, New South Wales, Australia
| | - Lyndsay A Harshman
- Stead Family Department of Pediatrics, University of Iowa Children's Hospital, Iowa City, Iowa
| | - Miao He
- Department of Pathology and Laboratory Medicine, The Children's Hospital of Philadelphia, Philadelphia, Pennsylvania
| | - Jaak Jaeken
- Center for Metabolic Diseases, University Hospital of Leuven, Leuven, Belgium
| | - Philip M James
- Division of Genetics & Metabolism, Phoenix Children's Hospital, Phoenix, Arizona
| | - Daniel Katz
- Pediatric Neurology, Stormont-Vail Health Care, Topeka, Kansas
| | | | - Maria Kibaek
- Department of Pediatrics, Odense University Hospital, Odense, Denmark
| | - Andrew J Kornberg
- Department of Neurology, Royal Children's Hospital, Parkville, Victoria, Australia
| | - Katherine Lachlan
- Human Genetics and Genomic Medicine, University of Southampton and Wessex Clinical Genetics Service, Southampton, United Kingdom
| | - Christina Lam
- National Human Genome Research Institute, NIH, Bethesda, Maryland
| | - Joy Yaplito-Lee
- Department of Metabolic Medicine, Royal Children's Hospital, Murdoch Childrens Research Institute, Parkville, Victoria, Australia
| | - Deborah A Nickerson
- Department of Genome Sciences, University of Washington, Seattle, Washington
| | - Heidi L Peters
- Department of Metabolic Medicine, Royal Children's Hospital, Murdoch Childrens Research Institute, Parkville, Victoria, Australia
| | - Valerie Race
- Center for Human Genetics, University of Leuven, Leuven, Belgium
| | - Luc Régal
- Department of Pediatric Neurology and Metabolism, University Hospital of Brussels, Brussels, Belgium
| | - Jeffrey S Rush
- Department of Molecular and Cellular Biochemistry, College of Medicine, University of Kentucky, Lexington, Kentucky
| | - S Lane Rutledge
- Department of Genetics, University of Alabama at Birmingham, Birmingham, Alabama
| | - Jay Shendure
- Department of Genome Sciences, University of Washington, Seattle, Washington.,Howard Hughes Medical Institute, University of Washington, Seattle, Washington
| | - Erika Souche
- Center for Human Genetics, University of Leuven, Leuven, Belgium
| | | | - Pamela Trapane
- Stead Family Department of Pediatrics, University of Iowa Children's Hospital, Iowa City, Iowa
| | | | - Eric Vilain
- Department of Human Genetics, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, California.,Department of Pediatrics, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, California
| | - Arve Vøllo
- Department of Pediatrics, Hospital of Ostfold N-1603 Fredrikstad, Norway
| | - Charles J Waechter
- Department of Molecular and Cellular Biochemistry, College of Medicine, University of Kentucky, Lexington, Kentucky
| | - Raymond Y Wang
- Division of Metabolic Disorders, Children's Hospital of Orange County, Orange, California.,Department of Pediatrics, University of California-Irvine School of Medicine, Orange, California
| | - Lynne A Wolfe
- NIH Undiagnosed Diseases Program, Common Fund, Office of the Director, NIH and National Human Genome Research Institute, NIH, Bethesda, Maryland
| | - Derek A Wong
- Department of Pediatrics, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, California
| | - Tim Wood
- Greenwood Genetic Center, Greenwood, South Carolina
| | - Amy C Yang
- Department of Genetics and Genomic Sciences Icahn School of Medicine at Mount Sinai, New York, New York
| | | | - Gert Matthijs
- Center for Human Genetics, University of Leuven, Leuven, Belgium
| | - Hudson H Freeze
- Human Genetics Program, Sanford Burnham Prebys Medical Discovery Institute, La Jolla, California
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182
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Shendre A, Brown TM, Liu N, Hill CE, Beasley TM, Nickerson DA, Limdi NA. Race-Specific Influence of CYP4F2 on Dose and Risk of Hemorrhage Among Warfarin Users. Pharmacotherapy 2016; 36:263-72. [PMID: 26877068 DOI: 10.1002/phar.1717] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
Abstract
OBJECTIVE The p.V433M in cytochrome P450 4F2 (rs2108622, CYP4F2*3) is associated with a higher warfarin dose and lower risk of hemorrhage among European Americans. We evaluate the influence of CYP4F2*3 on warfarin dose, time to target international normalized ratio (INR), and stable dose, proportion of time spent in target range (PTTR), as well as the risk of overanticoagulation and hemorrhage among European and African Americans. DESIGN CYP4F2*3 was genotyped in 1238 patients initiated on warfarin in a prospective inception cohort. Multivariable linear regression was used to assess warfarin dose and PTTR; proportional hazards analysis was performed to evaluate time to target INR and stable dose, overanticoagulation, and hemorrhage. SETTING Two outpatient anticoagulation clinics. PARTICIPANTS A total of 1238 anticoagulated patients. OUTCOMES Warfarin dose (mg/day), time to target INR and stable dose, PTTR, overanticoagulation (INR more than 4), and major hemorrhage. RESULTS Minor allele frequency for the CYP4F2*3 variant was 30.3% among European Americans and 8.4% among African Americans. CYP4F2*3 was associated with higher dose among European Americans but not African Americans. Compared to CYP4F2*1/*1, *1/*3 was associated with a statistically nonsignificant increase in dose (4.5%, p=0.22) and *3/*3 was associated with a statistically significant increase in dose (13.2%, p=0.02). CYP4F2 genotype did not influence time to target INR, time to stable dose, or PTTR in either race group. CYP4F2*3/*3 was associated with a 31% lower risk of over anticoagulation (p=0.06). Incidence of hemorrhage was lower among participants with CYP4F2 *3/*3 compared with *1/*3 or *1/*1 (incidence rate ratio = 0.45, 95% confidence interval 0.14-1.11, p=0.09). After controlling for covariates, CYP4F2 *3/*3 was associated with a 52% lower risk of hemorrhage, although this was not statistically significant (p=0.24). CONCLUSION Possession of CYP4F2*3 variant influences warfarin dose among European Americans but not African Americans. The CYP4F2-dose, CYP4F2-overanticoagulation, and CYP4F2-hemorrhage association follows a recessive pattern with possession of CYP4F2*3/*3 genotype likely demonstrating a protective effect. These findings need further confirmation.
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Affiliation(s)
- Aditi Shendre
- Department of Epidemiology, University of Alabama at Birmingham, Birmingham, Alabama
| | - Todd M Brown
- Department of Medicine, University of Alabama at Birmingham, Birmingham, Alabama
| | - Nianjun Liu
- Biostatistics, Section on Statistical Genetics, University of Alabama at Birmingham, Birmingham, Alabama
| | - Charles E Hill
- Department of Pathology and Laboratory Medicine, Emory University School of Medicine, Atlanta, Georgia
| | - T Mark Beasley
- Biostatistics, Section on Statistical Genetics, University of Alabama at Birmingham, Birmingham, Alabama
| | - Deborah A Nickerson
- Genome Sciences, School of Medicine, University of Washington, Seattle, Washington
| | - Nita A Limdi
- Department of Neurology, University of Alabama at Birmingham, Birmingham, Alabama
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183
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Theusch E, Kim K, Stevens K, Smith JD, Chen YDI, Rotter JI, Nickerson DA, Medina MW. Statin-induced expression change of INSIG1 in lymphoblastoid cell lines correlates with plasma triglyceride statin response in a sex-specific manner. Pharmacogenomics J 2016; 17:222-229. [PMID: 26927283 PMCID: PMC5008997 DOI: 10.1038/tpj.2016.12] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/16/2015] [Revised: 01/21/2016] [Accepted: 01/27/2016] [Indexed: 02/06/2023]
Abstract
Statins are widely prescribed to lower plasma low-density lipoprotein (LDL) cholesterol levels. They also modestly reduce plasma triglyceride (TG), an independent cardiovascular disease risk factor, in most people. The mechanism and inter-individual variability of TG statin response is poorly understood. We measured statin-induced gene expression changes in lymphoblastoid cell lines derived from 150 participants of a simvastatin clinical trial and identified 23 genes (false discovery rate, FDR=15%) with expression changes correlated with plasma TG response. The correlation of insulin-induced gene 1 (INSIG1) expression changes with TG response (rho=0.32, q=0.11) was driven by men (interaction P=0.0055). rs73161338 was associated with INSIG1 expression changes (P=5.4 × 10−5) and TG response in two statin clinical trials (P=0.0048), predominantly in men. A combined model including INSIG1 expression level and splicing changes accounted for 29.5% of plasma TG statin response variance in men (P=5.6 × 10−6). Our results suggest that INSIG1 variation may contribute to statin-induced changes in plasma TG in a sex-specific manner.
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Affiliation(s)
- E Theusch
- Children's Hospital Oakland Research Institute, Oakland, CA, USA
| | - K Kim
- Children's Hospital Oakland Research Institute, Oakland, CA, USA
| | - K Stevens
- Children's Hospital Oakland Research Institute, Oakland, CA, USA
| | - J D Smith
- Department of Genome Sciences, University of Washington, Seattle, WA, USA
| | - Y-D I Chen
- Departments of Pediatrics and Medicine, Los Angeles Biomedical Research Institute at Harbor-UCLA, Torrance, CA, USA
| | - J I Rotter
- Departments of Pediatrics and Medicine, Los Angeles Biomedical Research Institute at Harbor-UCLA, Torrance, CA, USA
| | - D A Nickerson
- Department of Genome Sciences, University of Washington, Seattle, WA, USA
| | - M W Medina
- Children's Hospital Oakland Research Institute, Oakland, CA, USA
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184
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Wallace S, Guo DC, Regalado E, Mellor-Crummey L, Bamshad M, Nickerson DA, Dauser R, Hanchard N, Marom R, Martin E, Berka V, Sharina I, Ganesan V, Saunders D, Morris SA, Milewicz DM. Disrupted nitric oxide signaling due to GUCY1A3 mutations increases risk for moyamoya disease, achalasia and hypertension. Clin Genet 2016; 90:351-60. [PMID: 26777256 DOI: 10.1111/cge.12739] [Citation(s) in RCA: 49] [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] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2015] [Revised: 01/11/2016] [Accepted: 01/13/2016] [Indexed: 12/23/2022]
Abstract
Moyamoya disease (MMD) is a progressive vasculopathy characterized by occlusion of the terminal portion of the internal carotid arteries and its branches, and the formation of compensatory moyamoya collateral vessels. Homozygous mutations in GUCY1A3 have been reported as a cause of MMD and achalasia. Probands (n = 96) from unrelated families underwent sequencing of GUCY1A3. Functional studies were performed to confirm the pathogenicity of identified GUCY1A3 variants. Two affected individuals from the unrelated families were found to have compound heterozygous mutations in GUCY1A3. MM041 was diagnosed with achalasia at 4 years of age, hypertension and MMD at 18 years of age. MM149 was diagnosed with MMD and hypertension at the age of 20 months. Both individuals carry one allele that is predicted to lead to haploinsufficiency and a second allele that is predicted to produce a mutated protein. Biochemical studies of one of these alleles, GUCY1A3 Cys517Tyr, showed that the mutant protein (a subunit of soluble guanylate cyclase) has a significantly blunted signaling response with exposure to nitric oxide (NO). GUCY1A3 missense and haploinsufficiency mutations disrupt NO signaling leading to MMD and hypertension, with or without achalasia.
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Affiliation(s)
- S Wallace
- Division of Medical Genetics, Cardiology, and Hematology, Department of Internal Medicine, University of Texas Health Science Center, Houston, TX, USA
| | - D-C Guo
- Division of Medical Genetics, Cardiology, and Hematology, Department of Internal Medicine, University of Texas Health Science Center, Houston, TX, USA
| | - E Regalado
- Division of Medical Genetics, Cardiology, and Hematology, Department of Internal Medicine, University of Texas Health Science Center, Houston, TX, USA
| | - L Mellor-Crummey
- Division of Medical Genetics, Cardiology, and Hematology, Department of Internal Medicine, University of Texas Health Science Center, Houston, TX, USA
| | - M Bamshad
- Department of Genome Sciences, University of Washington, Seattle, WA, USA
| | - D A Nickerson
- Department of Genome Sciences, University of Washington, Seattle, WA, USA
| | - R Dauser
- Department of Neurosurgery, Texas Children's Hospital, Houston, TX, USA
| | - N Hanchard
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
| | - R Marom
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
| | - E Martin
- Division of Medical Genetics, Cardiology, and Hematology, Department of Internal Medicine, University of Texas Health Science Center, Houston, TX, USA
| | - V Berka
- Division of Medical Genetics, Cardiology, and Hematology, Department of Internal Medicine, University of Texas Health Science Center, Houston, TX, USA
| | - I Sharina
- Division of Medical Genetics, Cardiology, and Hematology, Department of Internal Medicine, University of Texas Health Science Center, Houston, TX, USA
| | - V Ganesan
- Neuroscience Unit, University College of London Institute of Child Health, London, UK
| | - D Saunders
- Department of Radiology, Great Ormond Street Hospital, London, UK
| | - S A Morris
- Department of Pediatrics - Cardiology, Texas Children's Hospital and Baylor College of Medicine, Houston, TX, USA
| | - D M Milewicz
- Division of Medical Genetics, Cardiology, and Hematology, Department of Internal Medicine, University of Texas Health Science Center, Houston, TX, USA.
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185
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Shah K, Ali RH, Ansar M, Lee K, Chishti MS, Abbe I, Li B, Smith JD, Nickerson DA, Shendure J, Coucke PJ, Steyaert W, Bamshad MJ, Santos-Cortez RLP, Leal SM, Ahmad W. Mitral regurgitation as a phenotypic manifestation of nonphotosensitive trichothiodystrophy due to a splice variant in MPLKIP. BMC Med Genet 2016; 17:13. [PMID: 26880286 PMCID: PMC4754937 DOI: 10.1186/s12881-016-0275-5] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/28/2015] [Accepted: 02/03/2016] [Indexed: 12/22/2022]
Abstract
Background Nonphotosensitive trichothiodystrophy (TTDN) is a rare autosomal recessive disorder of neuroectodermal origin. The condition is marked by hair abnormalities, intellectual impairment, nail dystrophies and susceptibility to infections but with no UV sensitivity. Methods We identified three consanguineous Pakistani families with varied TTDN features and used homozygosity mapping, linkage analysis, and Sanger and exome sequencing in order to identify pathogenic variants. Haplotype analysis was performed and haplotype age estimated. A splicing assay was used to validate the effect of the MPLKIP splice variant on expression. Results Affected individuals from all families exhibit several TTDN features along with a heart-specific feature, i.e. mitral regurgitation. Exome sequencing in the probands from families ED168 and ED241 identified a homozygous splice mutation c.339 + 1G > A within MPLKIP. The same splice variant co-segregates with TTDN in a third family ED210. The MPLKIP splice variant was not found in public databases, e.g. the Exome Aggregation Consortium, and in unrelated Pakistani controls. Functional analysis of the splice variant confirmed intron retention, which leads to protein truncation and loss of a phosphorylation site. Haplotype analysis identified a 585.1-kb haplotype which includes the MPLKIP variant, supporting the existence of a founder haplotype that is estimated to be 25,900 years old. Conclusion This study extends the allelic and phenotypic spectra of MPLKIP-related TTDN, to include a splice variant that causes cardiomyopathy as part of the TTDN phenotype.
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Affiliation(s)
- Khadim Shah
- Department of Biochemistry, Faculty of Biological Sciences, Quaid-i-Azam University, Islamabad, 45320, Pakistan
| | - Raja Hussain Ali
- Department of Biochemistry, Faculty of Biological Sciences, Quaid-i-Azam University, Islamabad, 45320, Pakistan.,Center for Medical Genetics, Ghent University Hospital, 9000, Ghent, Belgium
| | - Muhammad Ansar
- Department of Biochemistry, Faculty of Biological Sciences, Quaid-i-Azam University, Islamabad, 45320, Pakistan.,Center for Statistical Genetics, Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Kwanghyuk Lee
- Center for Statistical Genetics, Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Muhammad Salman Chishti
- Department of Biochemistry, Hazara University, Mansehra, Khyber Pakhtunkhwa, 21300, Pakistan
| | - Izoduwa Abbe
- Center for Statistical Genetics, Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Biao Li
- Center for Statistical Genetics, Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, 77030, USA
| | | | - Joshua D Smith
- Department of Genome Sciences, University of Washington, Seattle, Washington, 98195, USA
| | - Deborah A Nickerson
- Department of Genome Sciences, University of Washington, Seattle, Washington, 98195, USA
| | - Jay Shendure
- Department of Genome Sciences, University of Washington, Seattle, Washington, 98195, USA
| | - Paul J Coucke
- Center for Medical Genetics, Ghent University Hospital, 9000, Ghent, Belgium
| | - Wouter Steyaert
- Center for Medical Genetics, Ghent University Hospital, 9000, Ghent, Belgium
| | - Michael J Bamshad
- Department of Genome Sciences, University of Washington, Seattle, Washington, 98195, USA
| | - Regie Lyn P Santos-Cortez
- Center for Statistical Genetics, Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Suzanne M Leal
- Center for Statistical Genetics, Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, 77030, USA.
| | - Wasim Ahmad
- Department of Biochemistry, Faculty of Biological Sciences, Quaid-i-Azam University, Islamabad, 45320, Pakistan.
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186
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Santos-Cortez RLP, Faridi R, Rehman AU, Lee K, Ansar M, Wang X, Morell RJ, Isaacson R, Belyantseva IA, Dai H, Acharya A, Qaiser TA, Muhammad D, Ali RA, Shams S, Hassan MJ, Shahzad S, Raza SI, Bashir ZEH, Smith JD, Nickerson DA, Bamshad MJ, Riazuddin S, Ahmad W, Friedman TB, Leal SM. Autosomal-Recessive Hearing Impairment Due to Rare Missense Variants within S1PR2. Am J Hum Genet 2016; 98:331-8. [PMID: 26805784 DOI: 10.1016/j.ajhg.2015.12.004] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.5] [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: 10/14/2015] [Accepted: 12/07/2015] [Indexed: 11/17/2022] Open
Abstract
The sphingosine-1-phosphate receptors (S1PRs) are a well-studied class of transmembrane G protein-coupled sphingolipid receptors that mediate multiple cellular processes. However, S1PRs have not been previously reported to be involved in the genetic etiology of human traits. S1PR2 lies within the autosomal-recessive nonsyndromic hearing impairment (ARNSHI) locus DFNB68 on 19p13.2. From exome sequence data we identified two pathogenic S1PR2 variants, c.323G>C (p.Arg108Pro) and c.419A>G (p.Tyr140Cys). Each of these variants co-segregates with congenital profound hearing impairment in consanguineous Pakistani families with maximum LOD scores of 6.4 for family DEM4154 and 3.3 for family PKDF1400. Neither S1PR2 missense variant was reported among ∼120,000 chromosomes in the Exome Aggregation Consortium database, in 76 unrelated Pakistani exomes, or in 720 Pakistani control chromosomes. Both DNA variants affect highly conserved residues of S1PR2 and are predicted to be damaging by multiple bioinformatics tools. Molecular modeling predicts that these variants affect binding of sphingosine-1-phosphate (p.Arg108Pro) and G protein docking (p.Tyr140Cys). In the previously reported S1pr2(-/-) mice, stria vascularis abnormalities, organ of Corti degeneration, and profound hearing loss were observed. Additionally, hair cell defects were seen in both knockout mice and morphant zebrafish. Family PKDF1400 presents with ARNSHI, which is consistent with the lack of gross malformations in S1pr2(-/-) mice, whereas family DEM4154 has lower limb malformations in addition to hearing loss. Our findings suggest the possibility of developing therapies against hair cell damage (e.g., from ototoxic drugs) through targeted stimulation of S1PR2.
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Affiliation(s)
- Regie Lyn P Santos-Cortez
- Center for Statistical Genetics, Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Rabia Faridi
- Laboratory of Molecular Genetics, National Institute on Deafness and Other Communication Disorders, NIH, Bethesda, MD 20892, USA; Centre of Excellence in Molecular Biology, University of the Punjab, Lahore 54550, Pakistan
| | - Atteeq U Rehman
- Laboratory of Molecular Genetics, National Institute on Deafness and Other Communication Disorders, NIH, Bethesda, MD 20892, USA
| | - Kwanghyuk Lee
- Center for Statistical Genetics, Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Muhammad Ansar
- Center for Statistical Genetics, Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA; Department of Biochemistry, Faculty of Biological Sciences, Quaid-i-Azam University, Islamabad 45320, Pakistan
| | - Xin Wang
- Center for Statistical Genetics, Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Robert J Morell
- Laboratory of Molecular Genetics, National Institute on Deafness and Other Communication Disorders, NIH, Bethesda, MD 20892, USA
| | - Rivka Isaacson
- Department of Chemistry, Faculty of Natural and Mathematical Sciences, King's College London, London WC2R 2LS, UK
| | - Inna A Belyantseva
- Laboratory of Molecular Genetics, National Institute on Deafness and Other Communication Disorders, NIH, Bethesda, MD 20892, USA
| | - Hang Dai
- Center for Statistical Genetics, Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Anushree Acharya
- Center for Statistical Genetics, Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Tanveer A Qaiser
- Centre of Excellence in Molecular Biology, University of the Punjab, Lahore 54550, Pakistan
| | - Dost Muhammad
- Chandka Medical College, Larkana, Sindh 77150, Pakistan
| | | | - Sulaiman Shams
- Department of Biochemistry, Abdul Wali Khan University, Mardan, 23200 Khyber Pakhtunkhwa, Pakistan
| | - Muhammad Jawad Hassan
- Department of Healthcare Biotechnology, Atta-ur-Rahman School of Applied Biosciences (ASAB), National University of Science & Technology (NUST), Islamabad 44000, Pakistan
| | - Shaheen Shahzad
- Department of Biotechnology and Bioinformatics, International Islamic University, Islamabad 44000, Pakistan
| | - Syed Irfan Raza
- Department of Biochemistry, Faculty of Biological Sciences, Quaid-i-Azam University, Islamabad 45320, Pakistan
| | - Zil-E-Huma Bashir
- Centre of Excellence in Molecular Biology, University of the Punjab, Lahore 54550, Pakistan
| | - Joshua D Smith
- Department of Genome Sciences, University of Washington, Seattle, WA 98195, USA
| | - Deborah A Nickerson
- Department of Genome Sciences, University of Washington, Seattle, WA 98195, USA
| | - Michael J Bamshad
- Department of Genome Sciences, University of Washington, Seattle, WA 98195, USA
| | - Sheikh Riazuddin
- University of Lahore, Lahore 54550, Pakistan; Allama Iqbal Medical Research Centre, Jinnah Hospital Complex, Lahore 54550, Pakistan; Shaheed Zulfiqar Ali Bhutto Medical University, Islamabad 44000, Pakistan
| | - Wasim Ahmad
- Department of Biochemistry, Faculty of Biological Sciences, Quaid-i-Azam University, Islamabad 45320, Pakistan
| | - Thomas B Friedman
- Laboratory of Molecular Genetics, National Institute on Deafness and Other Communication Disorders, NIH, Bethesda, MD 20892, USA
| | - Suzanne M Leal
- Center for Statistical Genetics, Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA.
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187
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Kalman LV, Agúndez JA, Appell ML, Black JL, Bell GC, Boukouvala S, Bruckner C, Bruford E, Bruckner C, Caudle K, Coulthard S, Daly AK, Del Tredici AL, den Dunnen JT, Drozda K, Everts R, Flockhart D, Freimuth R, Gaedigk A, Hachad H, Hartshorne T, Ingelman-Sundberg M, Klein TE, Lauschke VM, Maglott DR, McLeod HL, McMillin GA, Meyer UA, Müller DJ, Nickerson DA, Oetting WS, Pacanowski M, Pratt VM, Relling MV, Roberts A, Rubinstein WS, Sangkuhl K, Schwab M, Scott SA, Sim SC, Thirumaran RK, Toji LH, Tyndale R, van Schaik RHN, Whirl-Carrillo M, Yeo KTJ, Zanger UM. Pharmacogenetic allele nomenclature: International workgroup recommendations for test result reporting. Clin Pharmacol Ther 2016; 99:172-85. [PMID: 26479518 PMCID: PMC4724253 DOI: 10.1002/cpt.280] [Citation(s) in RCA: 118] [Impact Index Per Article: 14.8] [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: 09/03/2015] [Revised: 10/13/2015] [Accepted: 10/14/2015] [Indexed: 12/21/2022]
Abstract
This article provides nomenclature recommendations developed by an international workgroup to increase transparency and standardization of pharmacogenetic (PGx) result reporting. Presently, sequence variants identified by PGx tests are described using different nomenclature systems. In addition, PGx analysis may detect different sets of variants for each gene, which can affect interpretation of results. This practice has caused confusion and may thereby impede the adoption of clinical PGx testing. Standardization is critical to move PGx forward.
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Affiliation(s)
- Lisa V. Kalman
- Centers for Disease, Control and Prevention, 1600 Clifton Rd, MSG23, Atlanta GA 30333, 404 498-2707, 404 498-2231
| | - José A.G. Agúndez
- Dept. Pharmacology, University of Extremadura, Avda de la, Universidad s/n., 10071 Cáceres, SPAIN, +34924289458, +34927257000
| | - Malin Lindqvist Appell
- Department of Medical and Health sciences, Faculty of Medicine and Health Sciences, Linköping University, Division of Drug Research, Linköping University, SE-581 83, LINKÖPING, +4613286880
| | | | - Gillian C. Bell
- Moffitt Cancer Center, 12902 Magnolia Dr Tampa, FL 33612, 813-745-6525, 813-745-3882
| | - Sotiria Boukouvala
- Democritus University of Thrace, Department of Molecular Biology and Genetics, Building 10, University Campus, Alexandroupolis 68100, Greece, +30-25510-30613, +30-25510-30632
| | - Carsten Bruckner
- Affymetrix, 3420 Central Expy, Santa Clara, CA 95051, USA, 1-408-731-5879
| | - Elspeth Bruford
- HUGO Gene, Nomenclature, Committee (HGNC), EMBL-EBI, European Molecular Biology Laboratory, Wellcome Genome Campus, Hinxton, CB10 1SD, UK, +44-1223-494468, +44-1223-492624
| | - Carsten Bruckner
- Affymetrix, 3420 Central Expy, Santa Clara, CA 95051, USA, 1-408-731-5879
| | - Kelly Caudle
- St. Jude Children’s Research Hospital, 262 Danny Thomas Place, MS 313 Memphis, TN 38105, 901-595-3125, 901-595-3994
| | - Sally Coulthard
- Newcastle University, Institute for Cellular Medicine, William Leech Building, Newcastle Medical School, Framlington Place, Newcastle University NE2 4HH UK, +44 1912080723, +44 1912085232
| | - Ann K. Daly
- Newcastle University, Institute of Cellular Medicine, Framlington Place, Newcastle upon Tyne, NE2 4HH, UK, None, 44-191-208-7031
| | - Andria L. Del Tredici
- Millennium Health, LLC, 16981 Via Tazon, San Diego, CA 92127, none, (858) 451-3535 x1682
| | - Johan T den Dunnen
- Leiden University Medical Center, Human Genetics and Clinical Genetics, PO Box 9600, 2300RC Leiden, Nederland, none, +31-71-5269501
| | - Katarzyna Drozda
- Food and Drug Administration, 10903 New Hampshire Ave. Silver Spring, MD 20993, 240 402-0422
| | - Robin Everts
- Agena Bioscience, 3565 General Atomics Court, San Diego, CA 92121, None, +1 858-882-2655
| | - David Flockhart
- Indiana University, 950 W. Walnut St., room 402, Indianaplis, IN 46202, 317-274-2810
| | - Robert Freimuth
- Mayo Clinic, 200 First Street SW Rochester, MN 55905, 507-284-0753
| | - Andrea Gaedigk
- Division of Clinical Pharmacology & Therapeutic Innovation, Children’s Mercy Kansas City and School of Medicine, University of Missouri-Kansas City, 2401 Gillham Road, Kansas City, MO 64108, 816-234-1958, 816-234-3941
| | - Houda Hachad
- Translational Software, 12410 SE 32 Street Suite 150, Bellevue, WA 98005, 206-777-4132
| | - Toinette Hartshorne
- Genetic Analysis, Thermo Fisher Scientific, 180 Oyster Point Blvd. South San Francisco, CA 94080, 650-244-1669, 650-246-4080
| | - Magnus Ingelman-Sundberg
- Karolinska Institutet, Department of Physiology and Pharmacology, Nanna Svartz väg 2, 17177 Stockholm, SwedenSE, +468337327, +46852487735+
| | - Teri E. Klein
- Department of Genetics, Stanford University, 443 Via Ortega Avenue, Stanford, CA 94305, 650-725-3863, 650-736-0156
| | - Volker M. Lauschke
- Karolinska Institutet, Department of Physiology and Pharmacology, Nanna Svartz väg 2, 17177 Stockholm, Sweden, +46 8-337327, +46 8-5248-7711
| | - Donna R. Maglott
- National Institutes of Health / National Library of Medicine / National Center for Biotechnology Information, 45 Center Drive, Bethesda, MD 20894, 301 435-4895
| | - Howard L. McLeod
- Moffitt Cancer Center, 12902 Magnolia Drive, Tampa FL 33612, 813-745-3347
| | - Gwendolyn A. McMillin
- University of Utah and ARUP Laboratories, 500 Chipeta Way, Salt Lake City UT 84108, 801-584-5207, 801-583-2787
| | - Urs A. Meyer
- University of Basel, Biozentrum, Klingelbergstrasse 50/70, CH 4056, Basel, Switzerland, +41612672208, +41 61 267 2220
| | - Daniel J. Müller
- Dept. of Psychiatry, University of Toronto, CAMH, 250 College ST., R132, 416 979 4666, 416 535 8501 (x. 36851)
| | - Deborah A. Nickerson
- University of Washington, Department of Genome Sciences, Box 355065, Seattle, WA, 98195-5065, 206-221-6498, 206-685-7387
| | - William S. Oetting
- Experimental and Clinical Pharmacology, University of Minnesota, 7-115 Weaver-Densford Hall, 308 Harvard Street SE, Minneapolis, MN 55455, 612-624-6645, 612-624-1139
| | - Michael Pacanowski
- U.S. Food and Drug Administration, 10903 New Hampshire Ave., WO Building 51, Rm 2132, HFD870, Silver Spring, MD 20993, 301-847-8720, 301-796-3919
| | - Victoria M. Pratt
- Indiana University School of Medicine, 975 W. Walnut St., IB-130, Indianapolis IN 46202, 317-274-2293, 317-274-8322
| | - Mary V. Relling
- Chair, Pharmaceutical Dept., St. Jude Children’s Research Hospital, 262 Danny Thomas Place, Room I-5112 Memphis, TN 38105, ph 901 595 2348, fax 901 595 8869
| | - Ali Roberts
- Aegis Science Corporation, 515 Great Circle Road, Nashville, TN 37228, 615-255-3030, 615-477-9429
| | - Wendy S. Rubinstein
- National Institutes of Health / National Library of Medicine / National Center for Biotechnology Information, 45 Center Drive, Bethesda, MD 20894, 301.480.4023, 301.435.5991
| | - Katrin Sangkuhl
- Stanford University, 443 Via Ortega, Room 213, MC4245, Stanford CA 94305, 650-725-3863, 650-725-0659
| | - Matthias Schwab
- Dr Margarete Fischer-Bosch- Institute of Clinical Pharmacology, Stuttgart and Department of Clinical Pharmacology, University Hospital, Tuebingen, Germany, Auerbachstrasse 112, 70378 Stuttgart, +49 711 859295, +49 711 8101 3700
| | - Stuart A. Scott
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, One Gustave L. Levy Place, Box 1487, 212-241-0139, 212-241-3780
| | - Sarah C Sim
- Karolinska Institutet, Department of Physiology and Pharmacology, Nanna Svartz Väg 2, 171 77 Stockholm, Sweden, +468337327, +46852487735
| | - Ranjit K Thirumaran
- Genelex Corporation, 3101 Western Ave., Suite 100, Seattle, WA 98121., 206 219-4000, 206 826-1926
| | - Lorraine H. Toji
- Coriell Institute for Medical Research, 403 Haddon Avenue, Camden, NJ 08103, 856 757-9719
| | - Rachel Tyndale
- CAMH and Departments of Psychiatry, Pharmacology and Toxicology, University of Toronto, Rm 4326, Department of Pharmacology, 1 King’s College Circle, Toronto, Canada, M5S 1A8., 416 978-6395, 416 978-6374
| | - Ron HN van Schaik
- 1Dept Clinical Chemistry, Erasmus MC Rotterdam; 2IFCC Task Force Pharmacogenetics, Room Na-415; Wytemaweg 80, 3015CN Rotterdam, The Netherlands, +31-10-7033119
| | - Michelle Whirl-Carrillo
- Department of Genetics, Stanford University, 443 Via Ortega, Rm 213 Stanford, CA 94305, 650-725-3863, 650-725-0659
| | - Kiang-Teck J Yeo
- Department of Pathology, The University of Chicago, 5841 S Maryland Ave, MC 0004, TW010, Chicago, IL 60637, 773-702-6268, 773-702-1318
| | - Ulrich M. Zanger
- Dr. Margarete Fischer-Bosch Institute of Clinical Pharmacology, Auerbachstrasse 112, Stuttgart, 70376, Germany, +49-711-859295, +49-711-81013704
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188
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Regalado ES, Guo DC, Santos-Cortez RLP, Hostetler E, Bensend TA, Pannu H, Estrera A, Safi H, Mitchell AL, Evans JP, Leal SM, Bamshad M, Shendure J, Nickerson DA, Milewicz DM. Pathogenic FBN1 variants in familial thoracic aortic aneurysms and dissections. Clin Genet 2016; 89:719-23. [PMID: 26621581 DOI: 10.1111/cge.12702] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [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: 10/15/2015] [Revised: 11/24/2015] [Accepted: 11/26/2015] [Indexed: 11/26/2022]
Abstract
Marfan syndrome (MFS) due to mutations in FBN1 is a known cause of thoracic aortic aneurysms and acute aortic dissections (TAAD) associated with pleiotropic manifestations. Genetic predisposition to TAAD can also be inherited in families in the absence of syndromic features, termed familial TAAD (FTAAD), and several causative genes have been identified to date. FBN1 mutations can also be identified in FTAAD families, but the frequency of these mutations has not been established. We performed exome sequencing of 183 FTAAD families and identified pathogenic FBN1 variants in five (2.7%) of these families. We also identified eight additional FBN1 rare variants that could not be unequivocally classified as disease-causing in six families. FBN1 sequencing should be considered in individuals with FTAAD even without significant systemic features of MFS.
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Affiliation(s)
- E S Regalado
- Division of Medical Genetics, Department of Internal Medicine, University of Texas Health Science Center at Houston (UTHealth), Houston, TX, USA
| | - D C Guo
- Division of Medical Genetics, Department of Internal Medicine, University of Texas Health Science Center at Houston (UTHealth), Houston, TX, USA
| | - R L P Santos-Cortez
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
| | - E Hostetler
- Division of Medical Genetics, Department of Internal Medicine, University of Texas Health Science Center at Houston (UTHealth), Houston, TX, USA
| | - T A Bensend
- Division of Medical Genetics, Department of Internal Medicine, University of Texas Health Science Center at Houston (UTHealth), Houston, TX, USA
| | - H Pannu
- Division of Medical Genetics, Department of Internal Medicine, University of Texas Health Science Center at Houston (UTHealth), Houston, TX, USA
| | - A Estrera
- Department of Cardiothoracic and Vascular Surgery, University of Texas Health Science Center at Houston, Houston, TX, USA
| | - H Safi
- Department of Cardiothoracic and Vascular Surgery, University of Texas Health Science Center at Houston, Houston, TX, USA
| | - A L Mitchell
- Department of Genetics and Genome Sciences, University Hospitals of Cleveland, Cleveland, OH, USA
| | - J P Evans
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - S M Leal
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
| | - M Bamshad
- Department of Genome Sciences, University of Washington, Seattle, WA, USA
| | - J Shendure
- Department of Genome Sciences, University of Washington, Seattle, WA, USA
| | - D A Nickerson
- Department of Genome Sciences, University of Washington, Seattle, WA, USA
| | | | - D M Milewicz
- Division of Medical Genetics, Department of Internal Medicine, University of Texas Health Science Center at Houston (UTHealth), Houston, TX, USA
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189
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Guo DC, Regalado ES, Gong L, Duan X, Santos-Cortez RLP, Arnaud P, Ren Z, Cai B, Hostetler EM, Moran R, Liang D, Estrera A, Safi HJ, Leal SM, Bamshad MJ, Shendure J, Nickerson DA, Jondeau G, Boileau C, Milewicz DM. LOX Mutations Predispose to Thoracic Aortic Aneurysms and Dissections. Circ Res 2016; 118:928-34. [PMID: 26838787 DOI: 10.1161/circresaha.115.307130] [Citation(s) in RCA: 152] [Impact Index Per Article: 19.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/13/2015] [Accepted: 01/11/2016] [Indexed: 01/08/2023]
Abstract
RATIONALE Mutations in several genes have been identified that are responsible for 25% of families with familial thoracic aortic aneurysms and dissections. However, the causative gene remains unknown in 75% of families. OBJECTIVES To identify the causative mutation in families with autosomal dominant inheritance of thoracic aortic aneurysms and dissections. METHODS AND RESULTS Exome sequencing was used to identify the mutation responsible for a large family with thoracic aortic aneurysms and dissections. A heterozygous rare variant, c.839G>T (p.Ser280Arg), was identified in LOX, encoding a lysyl oxidase, that segregated with disease in the family. Sanger and exome sequencing was used to investigate mutations in LOX in an additional 410 probands from unrelated families. Additional LOX rare variants that segregated with disease in families were identified, including c.125G>A (p.Trp42*), c.604G>T (p.Gly202*), c.743C>T (p.Thr248Ile), c.800A>C (p.Gln267Pro), and c.1044T>A (p.Ser348Arg). The altered amino acids cause haploinsufficiency for LOX or are located at a highly conserved LOX catalytic domain, which is relatively invariant in the population. Expression of the LOX variants p.Ser280Arg and p.Ser348Arg resulted in significantly lower lysyl oxidase activity when compared with the wild-type protein. Individuals with LOX variants had fusiform enlargement of the root and ascending thoracic aorta, leading to ascending aortic dissections. CONCLUSIONS These data, along with previous studies showing that the deficiency of LOX in mice or inhibition of lysyl oxidases in turkeys and rats causes aortic dissections, support the conclusion that rare genetic variants in LOX predispose to thoracic aortic disease.
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Affiliation(s)
- Dong-chuan Guo
- From the Departments of Internal Medicine (D.G., E.S.R., L.G., X.D., Z.R., B.C., E.M.H., D.M.M.) and Cardiothoracic and Vascular Surgery (A.E., H.J.S.), University of Texas Health Science Center, Houston; Department of Molecular and Human Genetics, Center for Statistical Genetics, Baylor College of Medicine, Houston, TX (R.L.P.S.-C., S.M.L.); Laboratory for Vascular Translational Science, INSERM U1148, Hôpital Bichat, Paris, France (P.A., G.J., C.B.); Centre National de Référence pour le syndrome de Marfan et apparentés, Département de Génétique Moléculaire, AP-HP, Hôpital Bichat, Paris, France (P.A., C.B.); Department of Pediatrics, MetroHealth Medical Center, Cleveland, OH (R.M.); Department of Medicine, Stanford University Medical Center, CA (D.L.); and Department of Genome Sciences, University of Washington, Seattle (M.J.B., J.S., D.A.N.)
| | - Ellen S Regalado
- From the Departments of Internal Medicine (D.G., E.S.R., L.G., X.D., Z.R., B.C., E.M.H., D.M.M.) and Cardiothoracic and Vascular Surgery (A.E., H.J.S.), University of Texas Health Science Center, Houston; Department of Molecular and Human Genetics, Center for Statistical Genetics, Baylor College of Medicine, Houston, TX (R.L.P.S.-C., S.M.L.); Laboratory for Vascular Translational Science, INSERM U1148, Hôpital Bichat, Paris, France (P.A., G.J., C.B.); Centre National de Référence pour le syndrome de Marfan et apparentés, Département de Génétique Moléculaire, AP-HP, Hôpital Bichat, Paris, France (P.A., C.B.); Department of Pediatrics, MetroHealth Medical Center, Cleveland, OH (R.M.); Department of Medicine, Stanford University Medical Center, CA (D.L.); and Department of Genome Sciences, University of Washington, Seattle (M.J.B., J.S., D.A.N.)
| | - Limin Gong
- From the Departments of Internal Medicine (D.G., E.S.R., L.G., X.D., Z.R., B.C., E.M.H., D.M.M.) and Cardiothoracic and Vascular Surgery (A.E., H.J.S.), University of Texas Health Science Center, Houston; Department of Molecular and Human Genetics, Center for Statistical Genetics, Baylor College of Medicine, Houston, TX (R.L.P.S.-C., S.M.L.); Laboratory for Vascular Translational Science, INSERM U1148, Hôpital Bichat, Paris, France (P.A., G.J., C.B.); Centre National de Référence pour le syndrome de Marfan et apparentés, Département de Génétique Moléculaire, AP-HP, Hôpital Bichat, Paris, France (P.A., C.B.); Department of Pediatrics, MetroHealth Medical Center, Cleveland, OH (R.M.); Department of Medicine, Stanford University Medical Center, CA (D.L.); and Department of Genome Sciences, University of Washington, Seattle (M.J.B., J.S., D.A.N.)
| | - Xueyan Duan
- From the Departments of Internal Medicine (D.G., E.S.R., L.G., X.D., Z.R., B.C., E.M.H., D.M.M.) and Cardiothoracic and Vascular Surgery (A.E., H.J.S.), University of Texas Health Science Center, Houston; Department of Molecular and Human Genetics, Center for Statistical Genetics, Baylor College of Medicine, Houston, TX (R.L.P.S.-C., S.M.L.); Laboratory for Vascular Translational Science, INSERM U1148, Hôpital Bichat, Paris, France (P.A., G.J., C.B.); Centre National de Référence pour le syndrome de Marfan et apparentés, Département de Génétique Moléculaire, AP-HP, Hôpital Bichat, Paris, France (P.A., C.B.); Department of Pediatrics, MetroHealth Medical Center, Cleveland, OH (R.M.); Department of Medicine, Stanford University Medical Center, CA (D.L.); and Department of Genome Sciences, University of Washington, Seattle (M.J.B., J.S., D.A.N.)
| | - Regie Lyn P Santos-Cortez
- From the Departments of Internal Medicine (D.G., E.S.R., L.G., X.D., Z.R., B.C., E.M.H., D.M.M.) and Cardiothoracic and Vascular Surgery (A.E., H.J.S.), University of Texas Health Science Center, Houston; Department of Molecular and Human Genetics, Center for Statistical Genetics, Baylor College of Medicine, Houston, TX (R.L.P.S.-C., S.M.L.); Laboratory for Vascular Translational Science, INSERM U1148, Hôpital Bichat, Paris, France (P.A., G.J., C.B.); Centre National de Référence pour le syndrome de Marfan et apparentés, Département de Génétique Moléculaire, AP-HP, Hôpital Bichat, Paris, France (P.A., C.B.); Department of Pediatrics, MetroHealth Medical Center, Cleveland, OH (R.M.); Department of Medicine, Stanford University Medical Center, CA (D.L.); and Department of Genome Sciences, University of Washington, Seattle (M.J.B., J.S., D.A.N.)
| | - Pauline Arnaud
- From the Departments of Internal Medicine (D.G., E.S.R., L.G., X.D., Z.R., B.C., E.M.H., D.M.M.) and Cardiothoracic and Vascular Surgery (A.E., H.J.S.), University of Texas Health Science Center, Houston; Department of Molecular and Human Genetics, Center for Statistical Genetics, Baylor College of Medicine, Houston, TX (R.L.P.S.-C., S.M.L.); Laboratory for Vascular Translational Science, INSERM U1148, Hôpital Bichat, Paris, France (P.A., G.J., C.B.); Centre National de Référence pour le syndrome de Marfan et apparentés, Département de Génétique Moléculaire, AP-HP, Hôpital Bichat, Paris, France (P.A., C.B.); Department of Pediatrics, MetroHealth Medical Center, Cleveland, OH (R.M.); Department of Medicine, Stanford University Medical Center, CA (D.L.); and Department of Genome Sciences, University of Washington, Seattle (M.J.B., J.S., D.A.N.)
| | - Zhao Ren
- From the Departments of Internal Medicine (D.G., E.S.R., L.G., X.D., Z.R., B.C., E.M.H., D.M.M.) and Cardiothoracic and Vascular Surgery (A.E., H.J.S.), University of Texas Health Science Center, Houston; Department of Molecular and Human Genetics, Center for Statistical Genetics, Baylor College of Medicine, Houston, TX (R.L.P.S.-C., S.M.L.); Laboratory for Vascular Translational Science, INSERM U1148, Hôpital Bichat, Paris, France (P.A., G.J., C.B.); Centre National de Référence pour le syndrome de Marfan et apparentés, Département de Génétique Moléculaire, AP-HP, Hôpital Bichat, Paris, France (P.A., C.B.); Department of Pediatrics, MetroHealth Medical Center, Cleveland, OH (R.M.); Department of Medicine, Stanford University Medical Center, CA (D.L.); and Department of Genome Sciences, University of Washington, Seattle (M.J.B., J.S., D.A.N.)
| | - Bo Cai
- From the Departments of Internal Medicine (D.G., E.S.R., L.G., X.D., Z.R., B.C., E.M.H., D.M.M.) and Cardiothoracic and Vascular Surgery (A.E., H.J.S.), University of Texas Health Science Center, Houston; Department of Molecular and Human Genetics, Center for Statistical Genetics, Baylor College of Medicine, Houston, TX (R.L.P.S.-C., S.M.L.); Laboratory for Vascular Translational Science, INSERM U1148, Hôpital Bichat, Paris, France (P.A., G.J., C.B.); Centre National de Référence pour le syndrome de Marfan et apparentés, Département de Génétique Moléculaire, AP-HP, Hôpital Bichat, Paris, France (P.A., C.B.); Department of Pediatrics, MetroHealth Medical Center, Cleveland, OH (R.M.); Department of Medicine, Stanford University Medical Center, CA (D.L.); and Department of Genome Sciences, University of Washington, Seattle (M.J.B., J.S., D.A.N.)
| | - Ellen M Hostetler
- From the Departments of Internal Medicine (D.G., E.S.R., L.G., X.D., Z.R., B.C., E.M.H., D.M.M.) and Cardiothoracic and Vascular Surgery (A.E., H.J.S.), University of Texas Health Science Center, Houston; Department of Molecular and Human Genetics, Center for Statistical Genetics, Baylor College of Medicine, Houston, TX (R.L.P.S.-C., S.M.L.); Laboratory for Vascular Translational Science, INSERM U1148, Hôpital Bichat, Paris, France (P.A., G.J., C.B.); Centre National de Référence pour le syndrome de Marfan et apparentés, Département de Génétique Moléculaire, AP-HP, Hôpital Bichat, Paris, France (P.A., C.B.); Department of Pediatrics, MetroHealth Medical Center, Cleveland, OH (R.M.); Department of Medicine, Stanford University Medical Center, CA (D.L.); and Department of Genome Sciences, University of Washington, Seattle (M.J.B., J.S., D.A.N.)
| | - Rocio Moran
- From the Departments of Internal Medicine (D.G., E.S.R., L.G., X.D., Z.R., B.C., E.M.H., D.M.M.) and Cardiothoracic and Vascular Surgery (A.E., H.J.S.), University of Texas Health Science Center, Houston; Department of Molecular and Human Genetics, Center for Statistical Genetics, Baylor College of Medicine, Houston, TX (R.L.P.S.-C., S.M.L.); Laboratory for Vascular Translational Science, INSERM U1148, Hôpital Bichat, Paris, France (P.A., G.J., C.B.); Centre National de Référence pour le syndrome de Marfan et apparentés, Département de Génétique Moléculaire, AP-HP, Hôpital Bichat, Paris, France (P.A., C.B.); Department of Pediatrics, MetroHealth Medical Center, Cleveland, OH (R.M.); Department of Medicine, Stanford University Medical Center, CA (D.L.); and Department of Genome Sciences, University of Washington, Seattle (M.J.B., J.S., D.A.N.)
| | - David Liang
- From the Departments of Internal Medicine (D.G., E.S.R., L.G., X.D., Z.R., B.C., E.M.H., D.M.M.) and Cardiothoracic and Vascular Surgery (A.E., H.J.S.), University of Texas Health Science Center, Houston; Department of Molecular and Human Genetics, Center for Statistical Genetics, Baylor College of Medicine, Houston, TX (R.L.P.S.-C., S.M.L.); Laboratory for Vascular Translational Science, INSERM U1148, Hôpital Bichat, Paris, France (P.A., G.J., C.B.); Centre National de Référence pour le syndrome de Marfan et apparentés, Département de Génétique Moléculaire, AP-HP, Hôpital Bichat, Paris, France (P.A., C.B.); Department of Pediatrics, MetroHealth Medical Center, Cleveland, OH (R.M.); Department of Medicine, Stanford University Medical Center, CA (D.L.); and Department of Genome Sciences, University of Washington, Seattle (M.J.B., J.S., D.A.N.)
| | - Anthony Estrera
- From the Departments of Internal Medicine (D.G., E.S.R., L.G., X.D., Z.R., B.C., E.M.H., D.M.M.) and Cardiothoracic and Vascular Surgery (A.E., H.J.S.), University of Texas Health Science Center, Houston; Department of Molecular and Human Genetics, Center for Statistical Genetics, Baylor College of Medicine, Houston, TX (R.L.P.S.-C., S.M.L.); Laboratory for Vascular Translational Science, INSERM U1148, Hôpital Bichat, Paris, France (P.A., G.J., C.B.); Centre National de Référence pour le syndrome de Marfan et apparentés, Département de Génétique Moléculaire, AP-HP, Hôpital Bichat, Paris, France (P.A., C.B.); Department of Pediatrics, MetroHealth Medical Center, Cleveland, OH (R.M.); Department of Medicine, Stanford University Medical Center, CA (D.L.); and Department of Genome Sciences, University of Washington, Seattle (M.J.B., J.S., D.A.N.)
| | - Hazim J Safi
- From the Departments of Internal Medicine (D.G., E.S.R., L.G., X.D., Z.R., B.C., E.M.H., D.M.M.) and Cardiothoracic and Vascular Surgery (A.E., H.J.S.), University of Texas Health Science Center, Houston; Department of Molecular and Human Genetics, Center for Statistical Genetics, Baylor College of Medicine, Houston, TX (R.L.P.S.-C., S.M.L.); Laboratory for Vascular Translational Science, INSERM U1148, Hôpital Bichat, Paris, France (P.A., G.J., C.B.); Centre National de Référence pour le syndrome de Marfan et apparentés, Département de Génétique Moléculaire, AP-HP, Hôpital Bichat, Paris, France (P.A., C.B.); Department of Pediatrics, MetroHealth Medical Center, Cleveland, OH (R.M.); Department of Medicine, Stanford University Medical Center, CA (D.L.); and Department of Genome Sciences, University of Washington, Seattle (M.J.B., J.S., D.A.N.)
| | | | - Suzanne M Leal
- From the Departments of Internal Medicine (D.G., E.S.R., L.G., X.D., Z.R., B.C., E.M.H., D.M.M.) and Cardiothoracic and Vascular Surgery (A.E., H.J.S.), University of Texas Health Science Center, Houston; Department of Molecular and Human Genetics, Center for Statistical Genetics, Baylor College of Medicine, Houston, TX (R.L.P.S.-C., S.M.L.); Laboratory for Vascular Translational Science, INSERM U1148, Hôpital Bichat, Paris, France (P.A., G.J., C.B.); Centre National de Référence pour le syndrome de Marfan et apparentés, Département de Génétique Moléculaire, AP-HP, Hôpital Bichat, Paris, France (P.A., C.B.); Department of Pediatrics, MetroHealth Medical Center, Cleveland, OH (R.M.); Department of Medicine, Stanford University Medical Center, CA (D.L.); and Department of Genome Sciences, University of Washington, Seattle (M.J.B., J.S., D.A.N.)
| | - Michael J Bamshad
- From the Departments of Internal Medicine (D.G., E.S.R., L.G., X.D., Z.R., B.C., E.M.H., D.M.M.) and Cardiothoracic and Vascular Surgery (A.E., H.J.S.), University of Texas Health Science Center, Houston; Department of Molecular and Human Genetics, Center for Statistical Genetics, Baylor College of Medicine, Houston, TX (R.L.P.S.-C., S.M.L.); Laboratory for Vascular Translational Science, INSERM U1148, Hôpital Bichat, Paris, France (P.A., G.J., C.B.); Centre National de Référence pour le syndrome de Marfan et apparentés, Département de Génétique Moléculaire, AP-HP, Hôpital Bichat, Paris, France (P.A., C.B.); Department of Pediatrics, MetroHealth Medical Center, Cleveland, OH (R.M.); Department of Medicine, Stanford University Medical Center, CA (D.L.); and Department of Genome Sciences, University of Washington, Seattle (M.J.B., J.S., D.A.N.)
| | - Jay Shendure
- From the Departments of Internal Medicine (D.G., E.S.R., L.G., X.D., Z.R., B.C., E.M.H., D.M.M.) and Cardiothoracic and Vascular Surgery (A.E., H.J.S.), University of Texas Health Science Center, Houston; Department of Molecular and Human Genetics, Center for Statistical Genetics, Baylor College of Medicine, Houston, TX (R.L.P.S.-C., S.M.L.); Laboratory for Vascular Translational Science, INSERM U1148, Hôpital Bichat, Paris, France (P.A., G.J., C.B.); Centre National de Référence pour le syndrome de Marfan et apparentés, Département de Génétique Moléculaire, AP-HP, Hôpital Bichat, Paris, France (P.A., C.B.); Department of Pediatrics, MetroHealth Medical Center, Cleveland, OH (R.M.); Department of Medicine, Stanford University Medical Center, CA (D.L.); and Department of Genome Sciences, University of Washington, Seattle (M.J.B., J.S., D.A.N.)
| | - Deborah A Nickerson
- From the Departments of Internal Medicine (D.G., E.S.R., L.G., X.D., Z.R., B.C., E.M.H., D.M.M.) and Cardiothoracic and Vascular Surgery (A.E., H.J.S.), University of Texas Health Science Center, Houston; Department of Molecular and Human Genetics, Center for Statistical Genetics, Baylor College of Medicine, Houston, TX (R.L.P.S.-C., S.M.L.); Laboratory for Vascular Translational Science, INSERM U1148, Hôpital Bichat, Paris, France (P.A., G.J., C.B.); Centre National de Référence pour le syndrome de Marfan et apparentés, Département de Génétique Moléculaire, AP-HP, Hôpital Bichat, Paris, France (P.A., C.B.); Department of Pediatrics, MetroHealth Medical Center, Cleveland, OH (R.M.); Department of Medicine, Stanford University Medical Center, CA (D.L.); and Department of Genome Sciences, University of Washington, Seattle (M.J.B., J.S., D.A.N.)
| | - Guillaume Jondeau
- From the Departments of Internal Medicine (D.G., E.S.R., L.G., X.D., Z.R., B.C., E.M.H., D.M.M.) and Cardiothoracic and Vascular Surgery (A.E., H.J.S.), University of Texas Health Science Center, Houston; Department of Molecular and Human Genetics, Center for Statistical Genetics, Baylor College of Medicine, Houston, TX (R.L.P.S.-C., S.M.L.); Laboratory for Vascular Translational Science, INSERM U1148, Hôpital Bichat, Paris, France (P.A., G.J., C.B.); Centre National de Référence pour le syndrome de Marfan et apparentés, Département de Génétique Moléculaire, AP-HP, Hôpital Bichat, Paris, France (P.A., C.B.); Department of Pediatrics, MetroHealth Medical Center, Cleveland, OH (R.M.); Department of Medicine, Stanford University Medical Center, CA (D.L.); and Department of Genome Sciences, University of Washington, Seattle (M.J.B., J.S., D.A.N.)
| | - Catherine Boileau
- From the Departments of Internal Medicine (D.G., E.S.R., L.G., X.D., Z.R., B.C., E.M.H., D.M.M.) and Cardiothoracic and Vascular Surgery (A.E., H.J.S.), University of Texas Health Science Center, Houston; Department of Molecular and Human Genetics, Center for Statistical Genetics, Baylor College of Medicine, Houston, TX (R.L.P.S.-C., S.M.L.); Laboratory for Vascular Translational Science, INSERM U1148, Hôpital Bichat, Paris, France (P.A., G.J., C.B.); Centre National de Référence pour le syndrome de Marfan et apparentés, Département de Génétique Moléculaire, AP-HP, Hôpital Bichat, Paris, France (P.A., C.B.); Department of Pediatrics, MetroHealth Medical Center, Cleveland, OH (R.M.); Department of Medicine, Stanford University Medical Center, CA (D.L.); and Department of Genome Sciences, University of Washington, Seattle (M.J.B., J.S., D.A.N.)
| | - Dianna M Milewicz
- From the Departments of Internal Medicine (D.G., E.S.R., L.G., X.D., Z.R., B.C., E.M.H., D.M.M.) and Cardiothoracic and Vascular Surgery (A.E., H.J.S.), University of Texas Health Science Center, Houston; Department of Molecular and Human Genetics, Center for Statistical Genetics, Baylor College of Medicine, Houston, TX (R.L.P.S.-C., S.M.L.); Laboratory for Vascular Translational Science, INSERM U1148, Hôpital Bichat, Paris, France (P.A., G.J., C.B.); Centre National de Référence pour le syndrome de Marfan et apparentés, Département de Génétique Moléculaire, AP-HP, Hôpital Bichat, Paris, France (P.A., C.B.); Department of Pediatrics, MetroHealth Medical Center, Cleveland, OH (R.M.); Department of Medicine, Stanford University Medical Center, CA (D.L.); and Department of Genome Sciences, University of Washington, Seattle (M.J.B., J.S., D.A.N.).
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Van Driest SL, Wells QS, Stallings S, Bush WS, Gordon A, Nickerson DA, Kim JH, Crosslin DR, Jarvik GP, Carrell DS, Ralston JD, Larson EB, Bielinski SJ, Olson JE, Ye Z, Kullo IJ, Abul-Husn NS, Scott SA, Bottinger E, Almoguera B, Connolly J, Chiavacci R, Hakonarson H, Rasmussen-Torvik LJ, Pan V, Persell SD, Smith M, Chisholm RL, Kitchner TE, He MM, Brilliant MH, Wallace JR, Doheny KF, Shoemaker MB, Li R, Manolio TA, Callis TE, Macaya D, Williams MS, Carey D, Kapplinger JD, Ackerman MJ, Ritchie MD, Denny JC, Roden DM. Association of Arrhythmia-Related Genetic Variants With Phenotypes Documented in Electronic Medical Records. JAMA 2016; 315:47-57. [PMID: 26746457 PMCID: PMC4758131 DOI: 10.1001/jama.2015.17701] [Citation(s) in RCA: 131] [Impact Index Per Article: 16.4] [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: 12/14/2022]
Abstract
IMPORTANCE Large-scale DNA sequencing identifies incidental rare variants in established Mendelian disease genes, but the frequency of related clinical phenotypes in unselected patient populations is not well established. Phenotype data from electronic medical records (EMRs) may provide a resource to assess the clinical relevance of rare variants. OBJECTIVE To determine the clinical phenotypes from EMRs for individuals with variants designated as pathogenic by expert review in arrhythmia susceptibility genes. DESIGN, SETTING, AND PARTICIPANTS This prospective cohort study included 2022 individuals recruited for nonantiarrhythmic drug exposure phenotypes from October 5, 2012, to September 30, 2013, for the Electronic Medical Records and Genomics Network Pharmacogenomics project from 7 US academic medical centers. Variants in SCN5A and KCNH2, disease genes for long QT and Brugada syndromes, were assessed for potential pathogenicity by 3 laboratories with ion channel expertise and by comparison with the ClinVar database. Relevant phenotypes were determined from EMRs, with data available from 2002 (or earlier for some sites) through September 10, 2014. EXPOSURES One or more variants designated as pathogenic in SCN5A or KCNH2. MAIN OUTCOMES AND MEASURES Arrhythmia or electrocardiographic (ECG) phenotypes defined by International Classification of Diseases, Ninth Revision (ICD-9) codes, ECG data, and manual EMR review. RESULTS Among 2022 study participants (median age, 61 years [interquartile range, 56-65 years]; 1118 [55%] female; 1491 [74%] white), a total of 122 rare (minor allele frequency <0.5%) nonsynonymous and splice-site variants in 2 arrhythmia susceptibility genes were identified in 223 individuals (11% of the study cohort). Forty-two variants in 63 participants were designated potentially pathogenic by at least 1 laboratory or ClinVar, with low concordance across laboratories (Cohen κ = 0.26). An ICD-9 code for arrhythmia was found in 11 of 63 (17%) variant carriers vs 264 of 1959 (13%) of those without variants (difference, +4%; 95% CI, -5% to +13%; P = .35). In the 1270 (63%) with ECGs, corrected QT intervals were not different in variant carriers vs those without (median, 429 vs 439 milliseconds; difference, -10 milliseconds; 95% CI, -16 to +3 milliseconds; P = .17). After manual review, 22 of 63 participants (35%) with designated variants had any ECG or arrhythmia phenotype, and only 2 had corrected QT interval longer than 500 milliseconds. CONCLUSIONS AND RELEVANCE Among laboratories experienced in genetic testing for cardiac arrhythmia disorders, there was low concordance in designating SCN5A and KCNH2 variants as pathogenic. In an unselected population, the putatively pathogenic genetic variants were not associated with an abnormal phenotype. These findings raise questions about the implications of notifying patients of incidental genetic findings.
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Affiliation(s)
| | - Quinn S Wells
- Vanderbilt University Medical Center, Nashville, Tennessee
| | | | - William S Bush
- Vanderbilt University Medical Center, Nashville, Tennessee2Case Western Reserve University, Cleveland, Ohio
| | | | | | | | | | | | | | | | - Eric B Larson
- Group Health Research Institute, Seattle, Washington
| | | | | | - Zi Ye
- Mayo Clinic, Rochester, Minnesota
| | | | | | - Stuart A Scott
- Icahn School of Medicine at Mount Sinai, New York, New York
| | | | - Berta Almoguera
- The Children's Hospital of Philadelphia, Philadelphia, Pennsylvania
| | - John Connolly
- The Children's Hospital of Philadelphia, Philadelphia, Pennsylvania
| | | | - Hakon Hakonarson
- The Children's Hospital of Philadelphia, Philadelphia, Pennsylvania8Perelman School of Medicine, University of Pennsylvania, Philadelphia
| | | | - Vivian Pan
- Northwestern University Feinberg School of Medicine, Chicago, Illinois
| | - Stephen D Persell
- Northwestern University Feinberg School of Medicine, Chicago, Illinois
| | - Maureen Smith
- Northwestern University Feinberg School of Medicine, Chicago, Illinois
| | - Rex L Chisholm
- Northwestern University Feinberg School of Medicine, Chicago, Illinois
| | | | - Max M He
- Marshfield Clinic Research Foundation, Marshfield, Wisconsin
| | | | | | | | | | - Rongling Li
- National Human Genome Research Institute, National Institutes of Health, Bethesda, Maryland
| | - Teri A Manolio
- National Human Genome Research Institute, National Institutes of Health, Bethesda, Maryland
| | | | | | | | - David Carey
- Geisinger Health System, Danville, Pennsylvania
| | | | | | - Marylyn D Ritchie
- Pennsylvania State University, University Park16Geisinger Health System, Danville, Pennsylvania
| | - Joshua C Denny
- Vanderbilt University Medical Center, Nashville, Tennessee
| | - Dan M Roden
- Vanderbilt University Medical Center, Nashville, Tennessee
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191
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Ullah R, Ansar M, Durrani ZU, Lee K, Santos-Cortez RLP, Muhammad D, Ali M, Zia M, Ayub M, Khan S, Smith JD, Nickerson DA, Shendure J, Bamshad M, Leal SM, Ahmad W. Novel mutations in the genes TGM1 and ALOXE3 underlying autosomal recessive congenital ichthyosis. Int J Dermatol 2015; 55:524-30. [PMID: 26578203 DOI: 10.1111/ijd.12950] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [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] [Received: 09/02/2014] [Revised: 12/06/2014] [Accepted: 12/10/2014] [Indexed: 11/29/2022]
Abstract
BACKGROUND Ichthyoses are clinically characterized by scaling or hyperkeratosis of the skin or both. It can be an isolated condition limited to the skin or appear secondarily with involvement of other cutaneous or systemic abnormalities. METHODS The present study investigated clinical and molecular characterization of three consanguineous families (A, B, C) segregating two different forms of autosomal recessive congenital ichthyosis (ARCI). Linkage in three consanguineous families (A, B, C) segregating two different forms of ARCI was searched by typing microsatellite and single nucleotide polymorphism marker analysis. Sequencing of the two genes TGM1 and ALOXE3 was performed by the dideoxy chain termination method. RESULTS Genome-wide linkage analysis established linkage in family A to TGM1 gene on chromosome 14q11 and in families B and C to ALOXE3 gene on chromosome 17p13. Subsequently, sequencing of these genes using samples from affected family members led to the identification of three novel mutations: a missense variant p.Trp455Arg in TGM1 (family A); a nonsense variant p.Arg140* in ALOXE3 (family B); and a complex rearrangement in ALOXE3 (family C). CONCLUSION The present study further extends the spectrum of mutations in the two genes involved in causing ARCI. Characterizing the clinical spectrum resulting from mutations in the TGM1 and ALOXE3 genes will improve diagnosis and may direct clinical care of the family members.
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Affiliation(s)
- Rahim Ullah
- Department of Biotechnology, Faculty of Biological Sciences, Quaid-i-Azam University, Islamabad, Pakistan
| | - Muhammad Ansar
- Department of Biochemistry, Faculty of Biological Sciences, Quaid-i-Azam University, Islamabad, Pakistan.,Center for Statistical Genetics, Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
| | - Zaka Ullah Durrani
- Department of Biochemistry, Faculty of Biological Sciences, Quaid-i-Azam University, Islamabad, Pakistan
| | - Kwanghyuk Lee
- Center for Statistical Genetics, Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
| | - Regie Lyn P Santos-Cortez
- Center for Statistical Genetics, Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
| | - Dost Muhammad
- Department of Biochemistry, Faculty of Biological Sciences, Quaid-i-Azam University, Islamabad, Pakistan
| | - Mahboob Ali
- Department of Biochemistry, Faculty of Biological Sciences, Quaid-i-Azam University, Islamabad, Pakistan
| | - Muhammad Zia
- Department of Biotechnology, Faculty of Biological Sciences, Quaid-i-Azam University, Islamabad, Pakistan
| | - Muhammad Ayub
- Institute of Biochemistry, University of Baluchistan, Quetta, Pakistan
| | - Suliman Khan
- Department of Biotechnology, Faculty of Biological Sciences, Quaid-i-Azam University, Islamabad, Pakistan
| | - Josh D Smith
- Department of Genome Sciences, University of Washington, Seattle, WA, USA
| | | | - Jay Shendure
- Department of Genome Sciences, University of Washington, Seattle, WA, USA
| | - Michael Bamshad
- Department of Genome Sciences, University of Washington, Seattle, WA, USA
| | - Suzanne M Leal
- Center for Statistical Genetics, Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
| | - Wasim Ahmad
- Department of Biochemistry, Faculty of Biological Sciences, Quaid-i-Azam University, Islamabad, Pakistan
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192
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Kim DS, Kim JH, Burt AA, Crosslin DR, Burnham N, Kim CE, McDonald-McGinn DM, Zackai EH, Nicolson SC, Spray TL, Stanaway IB, Nickerson DA, Heagerty PJ, Hakonarson H, Gaynor JW, Jarvik GP. Burden of potentially pathologic copy number variants is higher in children with isolated congenital heart disease and significantly impairs covariate-adjusted transplant-free survival. J Thorac Cardiovasc Surg 2015; 151:1147-51.e4. [PMID: 26704054 DOI: 10.1016/j.jtcvs.2015.09.136] [Citation(s) in RCA: 49] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/20/2015] [Revised: 08/14/2015] [Accepted: 09/14/2015] [Indexed: 12/23/2022]
Abstract
OBJECTIVES Copy number variants (CNVs) are duplications or deletions of genomic regions. Large CNVs are potentially pathogenic and are overrepresented in children with congenital heart disease (CHD). We sought to determine the frequency of large CNVs in children with isolated CHD, and to evaluate the relationship of these potentially pathogenic CNVs with transplant-free survival. METHODS These cases are derived from a prospective cohort of patients with nonsyndromic CHD (n = 422) identified before first surgery. Healthy pediatric controls (n = 500) were obtained from the electronic Medical Records and Genetic Epidemiology Network, and CNV frequency was contrasted for CHD cases and controls. CNVs were determined algorithmically; subsequently screened for >95% overlap between 2 methods, size (>300 kb), quality score, overlap with a gene, and novelty (absent from databases of known, benign CNVs); and separately validated by quantitative polymerase chain reaction. Survival likelihoods for cases were calculated using Cox proportional hazards modeling to evaluate the joint effect of CNV burden and known confounders on transplant-free survival. RESULTS Children with nonsyndromic CHD had a higher burden of potentially pathogenic CNVs compared with pediatric controls (12.1% vs 5.0%; P = .00016). Presence of a CNV was associated with significantly decreased transplant-free survival after surgery (hazard ratio, 3.42; 95% confidence interval, 1.66-7.09; P = .00090) with confounder adjustment. CONCLUSIONS We confirm that children with isolated CHD have a greater burden of rare/large CNVs. We report a novel finding that these CNVs are associated with an adjusted 2.55-fold increased risk of death or transplant. These data suggest that CNV burden is an important modifier of survival after surgery for CHD.
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Affiliation(s)
- Daniel Seung Kim
- Division of Medical Genetics, Department of Medicine, University of Washington, Seattle, Wash; Department of Genome Sciences, University of Washington, Seattle, Wash; Department of Biostatistics, University of Washington, Seattle, Wash
| | - Jerry H Kim
- Department of Anesthesiology and Pain Medicine, University of Washington, Seattle, Wash
| | - Amber A Burt
- Division of Medical Genetics, Department of Medicine, University of Washington, Seattle, Wash
| | - David R Crosslin
- Division of Medical Genetics, Department of Medicine, University of Washington, Seattle, Wash; Department of Genome Sciences, University of Washington, Seattle, Wash
| | - Nancy Burnham
- Division of Cardiothoracic Surgery, The Children's Hospital of Philadelphia, Philadelphia, Pa
| | - Cecilia E Kim
- Center for Applied Genomics, The Children's Hospital of Philadelphia, Philadelphia, Pa
| | | | - Elaine H Zackai
- Division of Genetics, The Children's Hospital of Philadelphia, Philadelphia, Pa
| | - Susan C Nicolson
- Division of Cardiothoracic Anesthesiology, The Children's Hospital of Philadelphia, Philadelphia, Pa
| | - Thomas L Spray
- Division of Cardiothoracic Surgery, The Children's Hospital of Philadelphia, Philadelphia, Pa
| | - Ian B Stanaway
- Department of Genome Sciences, University of Washington, Seattle, Wash
| | | | | | - Hakon Hakonarson
- Center for Applied Genomics, The Children's Hospital of Philadelphia, Philadelphia, Pa
| | - J William Gaynor
- Division of Cardiothoracic Surgery, The Children's Hospital of Philadelphia, Philadelphia, Pa
| | - Gail P Jarvik
- Division of Medical Genetics, Department of Medicine, University of Washington, Seattle, Wash; Department of Genome Sciences, University of Washington, Seattle, Wash.
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Reinier F, Zoledziewska M, Hanna D, Smith JD, Valentini M, Zara I, Berutti R, Sanna S, Oppo M, Cusano R, Satta R, Montesu MA, Jones C, Cerimele D, Nickerson DA, Angius A, Cucca F, Cottoni F, Crisponi L. Mandibular hypoplasia, deafness, progeroid features and lipodystrophy (MDPL) syndrome in the context of inherited lipodystrophies. Metabolism 2015; 64:1530-40. [PMID: 26350127 DOI: 10.1016/j.metabol.2015.07.022] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [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: 12/23/2014] [Revised: 07/10/2015] [Accepted: 07/23/2015] [Indexed: 12/12/2022]
Abstract
BACKGROUND Lipodystrophies are a large heterogeneous group of genetic or acquired disorders characterized by generalized or partial fat loss, usually associated with metabolic complications such as diabetes mellitus, hypertriglyceridemia and hepatic steatosis. Many efforts have been made in the last years in identifying the genetic etiologies of several lipodystrophy forms, although some remain to be elucidated. METHODS We report here the clinical description of a woman with a rare severe lipodystrophic and progeroid syndrome associated with hypertriglyceridemia and diabetes whose genetic bases have been clarified through whole-exome sequencing (WES) analysis. RESULTS This article reports the 5th MDPL (Mandibular hypoplasia, deafness, progeroid features, and lipodystrophy syndrome) patient with the same de novo p.S605del mutation in POLD1. We provided further genetic evidence that this is a disease-causing mutation along with a plausible molecular mechanism responsible for this recurring event. Moreover we overviewed the current classification of the inherited forms of lipodystrophy, along with their underlying molecular basis. CONCLUSIONS Progress in the identification of lipodystrophy genes will help in better understanding the role of the pathways involved in the complex physiology of fat. This will lead to new targets towards develop innovative therapeutic strategies for treating the disorder and its metabolic complications, as well as more common forms of adipose tissue redistribution as observed in the metabolic syndrome and type 2 diabetes.
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Affiliation(s)
- Frederic Reinier
- Centre for Advanced Studies, Research and Development in Sardinia (CRS4), Pula, Italy; Department of Genome Sciences, University of Washington, Seattle, WA, USA
| | - Magdalena Zoledziewska
- Istituto di Ricerca Genetica e Biomedica (IRGB), Consiglio Nazionale delle Ricerche (CNR), Monserrato, Italy
| | - David Hanna
- Department of Genome Sciences, University of Washington, Seattle, WA, USA
| | - Josh D Smith
- Department of Genome Sciences, University of Washington, Seattle, WA, USA
| | - Maria Valentini
- Centre for Advanced Studies, Research and Development in Sardinia (CRS4), Pula, Italy
| | - Ilenia Zara
- Centre for Advanced Studies, Research and Development in Sardinia (CRS4), Pula, Italy
| | - Riccardo Berutti
- Centre for Advanced Studies, Research and Development in Sardinia (CRS4), Pula, Italy
| | - Serena Sanna
- Istituto di Ricerca Genetica e Biomedica (IRGB), Consiglio Nazionale delle Ricerche (CNR), Monserrato, Italy
| | - Manuela Oppo
- Centre for Advanced Studies, Research and Development in Sardinia (CRS4), Pula, Italy; Dipartimento di Scienze Biomediche, Università di Sassari, Sassari, Italy
| | - Roberto Cusano
- Centre for Advanced Studies, Research and Development in Sardinia (CRS4), Pula, Italy
| | - Rosanna Satta
- Dipartimento di Scienze Chirurgiche, Microchirurgiche e Mediche-Dermatologia-Università di Sassari, Italy
| | - Maria Antonietta Montesu
- Dipartimento di Scienze Chirurgiche, Microchirurgiche e Mediche-Dermatologia-Università di Sassari, Italy
| | - Chris Jones
- Centre for Advanced Studies, Research and Development in Sardinia (CRS4), Pula, Italy
| | - Decio Cerimele
- Dipartimento di Scienze Chirurgiche, Microchirurgiche e Mediche-Dermatologia-Università di Sassari, Italy
| | | | - Andrea Angius
- Centre for Advanced Studies, Research and Development in Sardinia (CRS4), Pula, Italy; Istituto di Ricerca Genetica e Biomedica (IRGB), Consiglio Nazionale delle Ricerche (CNR), Monserrato, Italy
| | - Francesco Cucca
- Istituto di Ricerca Genetica e Biomedica (IRGB), Consiglio Nazionale delle Ricerche (CNR), Monserrato, Italy; Dipartimento di Scienze Biomediche, Università di Sassari, Sassari, Italy
| | - Francesca Cottoni
- Dipartimento di Scienze Chirurgiche, Microchirurgiche e Mediche-Dermatologia-Università di Sassari, Italy
| | - Laura Crisponi
- Istituto di Ricerca Genetica e Biomedica (IRGB), Consiglio Nazionale delle Ricerche (CNR), Monserrato, Italy.
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194
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Staples J, Ekunwe L, Lange E, Wilson JG, Nickerson DA, Below JE. PRIMUS: improving pedigree reconstruction using mitochondrial and Y haplotypes. Bioinformatics 2015; 32:596-8. [PMID: 26515822 DOI: 10.1093/bioinformatics/btv618] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2015] [Accepted: 10/12/2015] [Indexed: 11/14/2022] Open
Abstract
UNLABELLED PRIMUS is a pedigree reconstruction algorithm that uses estimates of genome-wide identity by descent to reconstruct pedigrees consistent with observed genetic data. However, when genetic data for individuals within a pedigree are missing, often multiple pedigrees can be reconstructed that fit the data. We report a major expansion of PRIMUS that uses mitochondrial (mtDNA) and non-recombining Y chromosome (NRY) haplotypes to eliminate many pedigree structures that are inconsistent with the genetic data. We demonstrate that discordances in mtDNA and NRY haplotypes substantially reduce the number of potential pedigrees, and often lead to the identification of the correct pedigree. AVAILABILITY AND IMPLEMENTATION We have implemented PRIMUS updates in PERL and it is available at primus.gs.washington.edu.
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Affiliation(s)
- Jeffrey Staples
- Department of Genome Sciences, University of Washington, Seattle, WA 98195, USA
| | - Lynette Ekunwe
- College of Public Service, Jackson State University, Jackson Heart Study, Jackson, MS 39213, USA
| | - Ethan Lange
- Department of Genetics, University of North Carolina, Chapel Hill, NC 27599, USA
| | - James G Wilson
- Department of Physiology and Biophysics, University of Mississippi Medical Center, Jackson, MS 39216, USA and
| | - Deborah A Nickerson
- Department of Genome Sciences, University of Washington, Seattle, WA 98195, USA
| | - Jennifer E Below
- Department of Epidemiology, University of Texas Health Science Center, Houston, TX 77225, USA
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195
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Auer PL, Nalls M, Meschia JF, Worrall BB, Longstreth WT, Seshadri S, Kooperberg C, Burger KM, Carlson CS, Carty CL, Chen WM, Cupples LA, DeStefano AL, Fornage M, Hardy J, Hsu L, Jackson RD, Jarvik GP, Kim DS, Lakshminarayan K, Lange LA, Manichaikul A, Quinlan AR, Singleton AB, Thornton TA, Nickerson DA, Peters U, Rich SS. Rare and Coding Region Genetic Variants Associated With Risk of Ischemic Stroke: The NHLBI Exome Sequence Project. JAMA Neurol 2015; 72:781-8. [PMID: 25961151 DOI: 10.1001/jamaneurol.2015.0582] [Citation(s) in RCA: 39] [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] [Indexed: 02/02/2023]
Abstract
IMPORTANCE Stroke is the second leading cause of death and the third leading cause of years of life lost. Genetic factors contribute to stroke prevalence, and candidate gene and genome-wide association studies (GWAS) have identified variants associated with ischemic stroke risk. These variants often have small effects without obvious biological significance. Exome sequencing may discover predicted protein-altering variants with a potentially large effect on ischemic stroke risk. OBJECTIVE To investigate the contribution of rare and common genetic variants to ischemic stroke risk by targeting the protein-coding regions of the human genome. DESIGN, SETTING, AND PARTICIPANTS The National Heart, Lung, and Blood Institute (NHLBI) Exome Sequencing Project (ESP) analyzed approximately 6000 participants from numerous cohorts of European and African ancestry. For discovery, 365 cases of ischemic stroke (small-vessel and large-vessel subtypes) and 809 European ancestry controls were sequenced; for replication, 47 affected sibpairs concordant for stroke subtype and an African American case-control series were sequenced, with 1672 cases and 4509 European ancestry controls genotyped. The ESP's exome sequencing and genotyping started on January 1, 2010, and continued through June 30, 2012. Analyses were conducted on the full data set between July 12, 2012, and July 13, 2013. MAIN OUTCOMES AND MEASURES Discovery of new variants or genes contributing to ischemic stroke risk and subtype (primary analysis) and determination of support for protein-coding variants contributing to risk in previously published candidate genes (secondary analysis). RESULTS We identified 2 novel genes associated with an increased risk of ischemic stroke: a protein-coding variant in PDE4DIP (rs1778155; odds ratio, 2.15; P = 2.63 × 10(-8)) with an intracellular signal transduction mechanism and in ACOT4 (rs35724886; odds ratio, 2.04; P = 1.24 × 10(-7)) with a fatty acid metabolism; confirmation of PDE4DIP was observed in affected sibpair families with large-vessel stroke subtype and in African Americans. Replication of protein-coding variants in candidate genes was observed for 2 previously reported GWAS associations: ZFHX3 (cardioembolic stroke) and ABCA1 (large-vessel stroke). CONCLUSIONS AND RELEVANCE Exome sequencing discovered 2 novel genes and mechanisms, PDE4DIP and ACOT4, associated with increased risk for ischemic stroke. In addition, ZFHX3 and ABCA1 were discovered to have protein-coding variants associated with ischemic stroke. These results suggest that genetic variation in novel pathways contributes to ischemic stroke risk and serves as a target for prediction, prevention, and therapy.
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Affiliation(s)
- Paul L Auer
- Joseph J. Zilber School of Public Health, University of Wisconsin, Milwaukee2Division of Public Health Sciences, Fred Hutchinson Cancer Research Center, Seattle, Washington
| | - Mike Nalls
- Laboratory of Neurogenetics, National Institute on Aging, National Institutes of Health, Bethesda, Maryland
| | | | | | - W T Longstreth
- Department of Neurology, University of Washington, Seattle
| | - Sudha Seshadri
- Department of Neurology, Boston University School of Medicine, Boston, Massachusetts
| | - Charles Kooperberg
- Division of Public Health Sciences, Fred Hutchinson Cancer Research Center, Seattle, Washington
| | - Kathleen M Burger
- Department of Neurology, George Washington University Hospital, Washington, DC
| | - Christopher S Carlson
- Division of Public Health Sciences, Fred Hutchinson Cancer Research Center, Seattle, Washington
| | - Cara L Carty
- Division of Public Health Sciences, Fred Hutchinson Cancer Research Center, Seattle, Washington
| | - Wei-Min Chen
- Center for Public Health Genomics, University of Virginia, Charlottesville
| | - L Adrienne Cupples
- Department of Biostatistics, Boston University School of Public Health, Boston, Massachusetts
| | - Anita L DeStefano
- Department of Biostatistics, Boston University School of Public Health, Boston, Massachusetts
| | - Myriam Fornage
- Institute for Molecular Medicine, University of Texas Health Science Center, Houston
| | - John Hardy
- Department of Neuroscience, Reta Lila Weston Institute, University College London, London, England
| | - Li Hsu
- Division of Public Health Sciences, Fred Hutchinson Cancer Research Center, Seattle, Washington
| | - Rebecca D Jackson
- Department of Internal Medicine, The Ohio State University, Columbus
| | - Gail P Jarvik
- Department of Medicine, University of Washington, Seattle
| | - Daniel S Kim
- Department of Genome Sciences, University of Washington, Seattle
| | | | - Leslie A Lange
- Department of Genetics, University of North Carolina, Chapel Hill
| | - Ani Manichaikul
- Center for Public Health Genomics, University of Virginia, Charlottesville
| | - Aaron R Quinlan
- Center for Public Health Genomics, University of Virginia, Charlottesville
| | - Andrew B Singleton
- Laboratory of Neurogenetics, National Institute on Aging, National Institutes of Health, Bethesda, Maryland
| | | | | | - Ulrike Peters
- Division of Public Health Sciences, Fred Hutchinson Cancer Research Center, Seattle, Washington
| | - Stephen S Rich
- Center for Public Health Genomics, University of Virginia, Charlottesville
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196
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Ng BG, Raymond K, Kircher M, Buckingham KJ, Wood T, Shendure J, Nickerson DA, Bamshad MJ, Wong JTS, Monteiro FP, Graham BH, Jackson S, Sparkes R, Scheuerle AE, Cathey S, Kok F, Gibson JB, Freeze HH. Expanding the Molecular and Clinical Phenotype of SSR4-CDG. Hum Mutat 2015; 36:1048-51. [PMID: 26264460 DOI: 10.1002/humu.22856] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [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: 06/19/2015] [Accepted: 08/02/2015] [Indexed: 01/16/2023]
Abstract
Congenital disorders of glycosylation (CDG) are a group of mostly autosomal recessive disorders primarily characterized by neurological abnormalities. Recently, we described a single CDG patient with a de novo mutation in the X-linked gene, Signal Sequence Receptor 4 (SSR4). We performed whole-exome sequencing to identify causal variants in several affected individuals who had either an undifferentiated neurological disorder or unsolved CDG of unknown etiology based on abnormal transferrin glycosylation. We now report eight affected males with either de novo (4) or inherited (4) loss of function mutations in SSR4. Western blot analysis revealed that the mutations caused a complete loss of SSR4 protein. In nearly all cases, the abnormal glycosylation of serum transferrin was only slightly above the accepted normal cutoff range.
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Affiliation(s)
- Bobby G Ng
- Human Genetics Program, Sanford - Burnham - Prebys Medical Discovery Institute, La Jolla, California
| | - Kimiyo Raymond
- Biochemical Genetics Laboratory, Mayo Clinic College of Medicine, Rochester, Minnesota
| | - Martin Kircher
- Department of Genome Sciences, University of Washington, Seattle, Washington
| | - Kati J Buckingham
- Department of Pediatrics, University of Washington, Seattle, Washington
| | - Tim Wood
- Department of Clinical Genetics, Greenwood Genetic Center, Charleston Office, North Charleston, South Caroline
| | - Jay Shendure
- Department of Genome Sciences, University of Washington, Seattle, Washington
| | - Deborah A Nickerson
- Department of Genome Sciences, University of Washington, Seattle, Washington
| | - Michael J Bamshad
- Department of Genome Sciences, University of Washington, Seattle, Washington.,Department of Pediatrics, University of Washington, Seattle, Washington
| | | | - Jonathan T S Wong
- Human Genetics Program, Sanford - Burnham - Prebys Medical Discovery Institute, La Jolla, California
| | - Fabiola Paoli Monteiro
- Department of Medical Genetics, University of Campinas (UNICAMP), São Paulo, Brazil.,Mendelics Genomic Analysis, São Paulo, São Paulo, Brazil
| | - Brett H Graham
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas
| | - Sheryl Jackson
- Department of Medical Genetics, University of Calgary, Calgary, AB, Canada
| | - Rebecca Sparkes
- Department of Medical Genetics, University of Calgary, Calgary, AB, Canada
| | - Angela E Scheuerle
- Department of Pediatrics, University of Texas Southwestern Medical Center, Dallas, Texas
| | - Sara Cathey
- Department of Clinical Genetics, Greenwood Genetic Center, Charleston Office, North Charleston, South Caroline
| | - Fernando Kok
- Mendelics Genomic Analysis, São Paulo, São Paulo, Brazil.,Department of Neurology, University of São Paulo, São Paulo, Brazil
| | - James B Gibson
- Clinical and Metabolic Genetics, Specially for Children, Austin, Texas
| | - Hudson H Freeze
- Human Genetics Program, Sanford - Burnham - Prebys Medical Discovery Institute, La Jolla, California
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197
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Santos-Cortez RLP, Chiong CM, Reyes-Quintos MRT, Tantoco MLC, Wang X, Acharya A, Abbe I, Giese AP, Smith JD, Allen EK, Li B, Cutiongco-de la Paz EM, Garcia MC, Llanes EGD, Labra PJ, Gloria-Cruz TLI, Chan AL, Wang GT, Daly KA, Shendure J, Bamshad MJ, Nickerson DA, Patel JA, Riazuddin S, Sale MM, Chonmaitree T, Ahmed ZM, Abes GT, Leal SM. Rare A2ML1 variants confer susceptibility to otitis media. Nat Genet 2015; 47:917-20. [PMID: 26121085 PMCID: PMC4528370 DOI: 10.1038/ng.3347] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.3] [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] [Received: 02/15/2015] [Accepted: 06/03/2015] [Indexed: 11/15/2022]
Abstract
A duplication variant within the middle ear-specific gene A2ML1 cosegregates with otitis media in an indigenous Filipino pedigree (LOD score = 7.5 at reduced penetrance) and lies within a founder haplotype that is also shared by 3 otitis-prone European-American and Hispanic-American children but is absent in non-otitis-prone children and >62,000 next-generation sequences. We identified seven additional A2ML1 variants in six otitis-prone children. Collectively, our studies support a role for A2ML1 in the pathophysiology of otitis media.
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Affiliation(s)
- Regie Lyn P. Santos-Cortez
- Center for Statistical Genetics, Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, USA
| | - Charlotte M. Chiong
- Philippine National Ear Institute, University of the Philippines Manila – National Institutes of Health, Manila, Philippines
- Department of Otorhinolaryngology, University of the Philippines College of Medicine – Philippine General Hospital, Manila, Philippines
| | - Ma. Rina T. Reyes-Quintos
- Philippine National Ear Institute, University of the Philippines Manila – National Institutes of Health, Manila, Philippines
- Department of Otorhinolaryngology, University of the Philippines College of Medicine – Philippine General Hospital, Manila, Philippines
| | - Ma. Leah C. Tantoco
- Philippine National Ear Institute, University of the Philippines Manila – National Institutes of Health, Manila, Philippines
| | - Xin Wang
- Center for Statistical Genetics, Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, USA
| | - Anushree Acharya
- Center for Statistical Genetics, Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, USA
| | - Izoduwa Abbe
- Center for Statistical Genetics, Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, USA
| | - Arnaud P. Giese
- Department of Otorhinolaryngology Head & Neck Surgery, School of Medicine, University of Maryland, Baltimore, Maryland, USA
| | - Joshua D. Smith
- Department of Genome Sciences, University of Washington, Seattle, Washington, USA
| | - E. Kaitlynn Allen
- Center for Public Health Genomics, University of Virginia School of Medicine, Charlottesville, Virginia, USA
- Department of Biochemistry and Molecular Genetics, University of Virginia, Charlottesville, Virginia, USA
| | - Biao Li
- Center for Statistical Genetics, Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, USA
| | - Eva Maria Cutiongco-de la Paz
- Institute of Human Genetics, University of the Philippines Manila – National Institutes of Health, Manila, Philippines
- Department of Pediatrics, University of the Philippines College of Medicine – Philippine General Hospital, Manila, Philippines
| | - Marieflor Cristy Garcia
- Department of Otorhinolaryngology, University of the Philippines College of Medicine – Philippine General Hospital, Manila, Philippines
| | - Erasmo Gonzalo D.V. Llanes
- Philippine National Ear Institute, University of the Philippines Manila – National Institutes of Health, Manila, Philippines
- Department of Otorhinolaryngology, University of the Philippines College of Medicine – Philippine General Hospital, Manila, Philippines
| | - Patrick John Labra
- Department of Otorhinolaryngology, University of the Philippines College of Medicine – Philippine General Hospital, Manila, Philippines
| | - Teresa Luisa I. Gloria-Cruz
- Philippine National Ear Institute, University of the Philippines Manila – National Institutes of Health, Manila, Philippines
- Department of Otorhinolaryngology, University of the Philippines College of Medicine – Philippine General Hospital, Manila, Philippines
| | - Abner L. Chan
- Philippine National Ear Institute, University of the Philippines Manila – National Institutes of Health, Manila, Philippines
- Department of Otorhinolaryngology, University of the Philippines College of Medicine – Philippine General Hospital, Manila, Philippines
| | - Gao T. Wang
- Center for Statistical Genetics, Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, USA
| | - Kathleen A. Daly
- Department of Otolaryngology, Head and Neck Surgery, University of Minnesota, Minneapolis, Minnesota, USA
| | - Jay Shendure
- Department of Genome Sciences, University of Washington, Seattle, Washington, USA
| | - Michael J. Bamshad
- Department of Genome Sciences, University of Washington, Seattle, Washington, USA
| | - Deborah A. Nickerson
- Department of Genome Sciences, University of Washington, Seattle, Washington, USA
| | - Janak A. Patel
- Division of Pediatric Infectious Disease and Immunology, Department of Pediatrics, University of Texas Medical Branch, Galveston, Texas, USA
| | - Saima Riazuddin
- Department of Otorhinolaryngology Head & Neck Surgery, School of Medicine, University of Maryland, Baltimore, Maryland, USA
| | - Michele M. Sale
- Center for Public Health Genomics, University of Virginia School of Medicine, Charlottesville, Virginia, USA
- Department of Biochemistry and Molecular Genetics, University of Virginia, Charlottesville, Virginia, USA
- Department of Public Health Sciences, University of Virginia, Charlottesville, Virginia, USA
| | | | - Tasnee Chonmaitree
- Division of Pediatric Infectious Disease and Immunology, Department of Pediatrics, University of Texas Medical Branch, Galveston, Texas, USA
| | - Zubair M. Ahmed
- Department of Otorhinolaryngology Head & Neck Surgery, School of Medicine, University of Maryland, Baltimore, Maryland, USA
| | - Generoso T. Abes
- Philippine National Ear Institute, University of the Philippines Manila – National Institutes of Health, Manila, Philippines
- Department of Otorhinolaryngology, University of the Philippines College of Medicine – Philippine General Hospital, Manila, Philippines
| | - Suzanne M. Leal
- Center for Statistical Genetics, Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, USA
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198
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McLaren CE, Emond MJ, Subramaniam VN, Phatak PD, Barton JC, Adams PC, Goh JB, McDonald CJ, Powell LW, Gurrin LC, Allen KJ, Nickerson DA, Louie T, Ramm GA, Anderson GJ, McLaren GD. Exome sequencing in HFE C282Y homozygous men with extreme phenotypes identifies a GNPAT variant associated with severe iron overload. Hepatology 2015; 62:429-39. [PMID: 25605615 PMCID: PMC4508230 DOI: 10.1002/hep.27711] [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] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/07/2014] [Accepted: 01/13/2015] [Indexed: 12/12/2022]
Abstract
UNLABELLED To identify polymorphisms associated with variability of iron overload severity in HFE-associated hemochromatosis, we performed exome sequencing of DNA from 35 male HFE C282Y homozygotes with either markedly increased iron stores (n = 22; cases) or with normal or mildly increased iron stores (n = 13; controls). The 35 participants, residents of the United States, Canada, and Australia, reported no or light alcohol consumption. Sequencing data included 82,068 single-nucleotide variants, and 10,337 genes were tested for a difference between cases and controls. A variant in the GNPAT gene showed the most significant association with severe iron overload (P = 3 × 10(-6) ; P = 0.033 by the likelihood ratio test after correction for multiple comparisons). Sixteen of twenty-two participants with severe iron overload had glyceronephosphate O-acyltransferase (GNPAT) polymorphism p.D519G (rs11558492; 15 heterozygotes, one homozygote). No control participant had this polymorphism. To examine functional consequences of GNPAT deficiency, we performed small interfering RNA-based knockdown of GNPAT in the human liver-derived cell line, HepG2/C3A. This knockdown resulted in a >17-fold decrease in expression of the messenger RNA encoding the iron-regulatory hormone, hepcidin. CONCLUSION GNPAT p.D519G is associated with a high-iron phenotype in HFE C282Y homozygotes and may participate in hepcidin regulation.
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Affiliation(s)
| | - Mary J. Emond
- Department of Biostatistics, University of Washington, Seattle, WA
| | - V. Nathan Subramaniam
- QIMR Berghofer Medical Research Institute, Brisbane, Australia,Faculty of Medicine and Biomedical Sciences, The University of Queensland, Brisbane, Australia
| | | | | | - Paul C. Adams
- Department of Medicine, London Health Sciences Centre, London, ON, Canada
| | - Justin B. Goh
- QIMR Berghofer Medical Research Institute, Brisbane, Australia,Faculty of Medicine and Biomedical Sciences, The University of Queensland, Brisbane, Australia
| | | | - Lawrie W. Powell
- QIMR Berghofer Medical Research Institute, Brisbane, Australia,Faculty of Medicine and Biomedical Sciences, The University of Queensland, Brisbane, Australia,Royal Brisbane & Women’s Hospital, Brisbane, Australia
| | - Lyle C. Gurrin
- Centre for MEGA Epidemiology, The University of Melbourne, Melbourne, Australia
| | | | | | - Tin Louie
- Department of Biostatistics, University of Washington, Seattle, WA
| | - Grant A. Ramm
- QIMR Berghofer Medical Research Institute, Brisbane, Australia,Faculty of Medicine and Biomedical Sciences, The University of Queensland, Brisbane, Australia
| | - Gregory J. Anderson
- QIMR Berghofer Medical Research Institute, Brisbane, Australia,School of Medicine and School of Chemistry and Molecular Bioscience, University of Queensland
| | - Gordon D. McLaren
- Department of Veterans Affairs Long Beach Healthcare System, Long Beach, CA,Division of Hematology/Oncology, Department of Medicine, University of California, Irvine, CA
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199
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Ansar M, Raza SI, Lee K, Irfanullah, Shahi S, Acharya A, Dai H, Smith JD, Shendure J, Bamshad MJ, Nickerson DA, Santos-Cortez RLP, Ahmad W, Leal SM. A homozygous missense variant in type I keratin KRT25 causes autosomal recessive woolly hair. J Med Genet 2015; 52:676-80. [PMID: 26160856 DOI: 10.1136/jmedgenet-2015-103255] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [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: 05/08/2015] [Accepted: 06/20/2015] [Indexed: 11/04/2022]
Abstract
BACKGROUND Woolly hair (WH) is a hair abnormality that is primarily characterised by tightly curled hair with abnormal growth. METHODS In two unrelated consanguineous Pakistani families with non-syndromic autosomal recessive (AR) WH, homozygosity mapping and linkage analysis identified a locus within 17q21.1-q22, which contains the type I keratin gene cluster. A DNA sample from an affected individual from each family underwent exome sequencing. RESULTS A homozygous missense variant c.950T>C (p.(Leu317Pro)) within KRT25 segregated with ARWH in both families, and has a combined maximum two-point LOD score of 7.9 at ϴ=0. The KRT25 variant is predicted to result in disruption of the second α-helical rod domain and the entire protein structure, thus possibly interfering with heterodimerisation of K25 with type II keratins within the inner root sheath (IRS) of the hair follicle and the medulla of the hair shaft. CONCLUSIONS Our findings implicate a novel gene involved in human hair abnormality, and are consistent with the curled, fragile hair found in mice with Krt25 mutations, and further support the role of IRS-specific type I keratins in hair follicle development and maintenance of hair texture.
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Affiliation(s)
- Muhammad Ansar
- Department of Biochemistry, Faculty of Biological Sciences, Quaid-i-Azam University, Islamabad, Pakistan Department of Molecular and Human Genetics, Center for Statistical Genetics, Baylor College of Medicine, Houston, Texas, USA
| | - Syed Irfan Raza
- Department of Biochemistry, Faculty of Biological Sciences, Quaid-i-Azam University, Islamabad, Pakistan Department of Biochemistry & Molecular Biology, National University of Science & Technology (NUST), Islamabad, Pakistan
| | - Kwanghyuk Lee
- Department of Molecular and Human Genetics, Center for Statistical Genetics, Baylor College of Medicine, Houston, Texas, USA
| | - Irfanullah
- Department of Biochemistry, Faculty of Biological Sciences, Quaid-i-Azam University, Islamabad, Pakistan
| | - Shamim Shahi
- Department of Biochemistry, Faculty of Biological Sciences, Quaid-i-Azam University, Islamabad, Pakistan
| | - Anushree Acharya
- Department of Molecular and Human Genetics, Center for Statistical Genetics, Baylor College of Medicine, Houston, Texas, USA
| | - Hang Dai
- Department of Molecular and Human Genetics, Center for Statistical Genetics, Baylor College of Medicine, Houston, Texas, USA
| | - Joshua D Smith
- Department of Genome Sciences, University of Washington, Seattle, Washington, USA
| | - Jay Shendure
- Department of Genome Sciences, University of Washington, Seattle, Washington, USA
| | - Michael J Bamshad
- Department of Genome Sciences, University of Washington, Seattle, Washington, USA
| | - Deborah A Nickerson
- Department of Genome Sciences, University of Washington, Seattle, Washington, USA
| | - Regie Lyn P Santos-Cortez
- Department of Molecular and Human Genetics, Center for Statistical Genetics, Baylor College of Medicine, Houston, Texas, USA
| | - Wasim Ahmad
- Department of Biochemistry, Faculty of Biological Sciences, Quaid-i-Azam University, Islamabad, Pakistan
| | - Suzanne M Leal
- Department of Molecular and Human Genetics, Center for Statistical Genetics, Baylor College of Medicine, Houston, Texas, USA
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Crosslin DR, Robertson PD, Carrell DS, Gordon AS, Hanna DS, Burt A, Fullerton SM, Scrol A, Ralston J, Leppig K, Hartzler A, Baldwin E, Andrade MD, Kullo IJ, Tromp G, Doheny KF, Ritchie MD, Crane PK, Nickerson DA, Larson EB, Jarvik GP. Prospective participant selection and ranking to maximize actionable pharmacogenetic variants and discovery in the eMERGE Network. Genome Med 2015. [PMID: 26221186 PMCID: PMC4517371 DOI: 10.1186/s13073-015-0181-z] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [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] [Indexed: 12/30/2022] Open
Abstract
Background In an effort to return actionable results from variant data to electronic health records (EHRs), participants in the Electronic Medical Records and Genomics (eMERGE) Network are being sequenced with the targeted Pharmacogenomics Research Network sequence platform (PGRNseq). This cost-effective, highly-scalable, and highly-accurate platform was created to explore rare variation in 84 key pharmacogenetic genes with strong drug phenotype associations. Methods To return Clinical Laboratory Improvement Amendments (CLIA) results to our participants at the Group Health Cooperative, we sequenced the DNA of 900 participants (61 % female) with non-CLIA biobanked samples. We then selected 450 of those to be re-consented, to redraw blood, and ultimately to validate CLIA variants in anticipation of returning the results to the participant and EHR. These 450 were selected using an algorithm we designed to harness data from self-reported race, diagnosis and procedure codes, medical notes, laboratory results, and variant-level bioinformatics to ensure selection of an informative sample. We annotated the multi-sample variant call format by a combination of SeattleSeq and SnpEff tools, with additional custom variables including evidence from ClinVar, OMIM, HGMD, and prior clinical associations. Results We focused our analyses on 27 actionable genes, largely driven by the Clinical Pharmacogenetics Implementation Consortium. We derived a ranking system based on the total number of coding variants per participant (75.2±14.7), and the number of coding variants with high or moderate impact (11.5±3.9). Notably, we identified 11 stop-gained (1 %) and 519 missense (20 %) variants out of a total of 1785 in these 27 genes. Finally, we prioritized variants to be returned to the EHR with prior clinical evidence of pathogenicity or annotated as stop-gain for the following genes: CACNA1S and RYR1 (malignant hyperthermia); SCN5A, KCNH2, and RYR2 (arrhythmia); and LDLR (high cholesterol). Conclusions The incorporation of genetics into the EHR for clinical decision support is a complex undertaking for many reasons including lack of prior consent for return of results, lack of biospecimens collected in a CLIA environment, and EHR integration. Our study design accounts for these hurdles and is an example of a pilot system that can be utilized before expanding to an entire health system. Electronic supplementary material The online version of this article (doi:10.1186/s13073-015-0181-z) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- David R Crosslin
- Department of Medicine, Division of Medical Genetics, University of Washington, 1705 NE Pacific Street, Seattle, 98195 WA USA ; Department of Genome Sciences, University of Washington, 3720 15th Avenue NE, Seattle, 98195 WA USA
| | - Peggy D Robertson
- Department of Genome Sciences, University of Washington, 3720 15th Avenue NE, Seattle, 98195 WA USA
| | - David S Carrell
- Group Health Research Institute, Group Health Cooperative, 1730 Minor Avenue, Seattle, 98101 WA USA
| | - Adam S Gordon
- Department of Genome Sciences, University of Washington, 3720 15th Avenue NE, Seattle, 98195 WA USA
| | - David S Hanna
- Department of Pathology, University of Washington, 1959 NE Pacific Street, Seattle, 98195 WA USA
| | - Amber Burt
- Department of Medicine, Division of Medical Genetics, University of Washington, 1705 NE Pacific Street, Seattle, 98195 WA USA
| | - Stephanie M Fullerton
- Department of Bioethics and Humanities, University of Washington, 1959 NE Pacific Street, Seattle, 98195 WA USA
| | - Aaron Scrol
- Group Health Research Institute, Group Health Cooperative, 1730 Minor Avenue, Seattle, 98101 WA USA
| | - James Ralston
- Department of Pathology, University of Washington, 1959 NE Pacific Street, Seattle, 98195 WA USA
| | - Kathleen Leppig
- Department of Pathology, University of Washington, 1959 NE Pacific Street, Seattle, 98195 WA USA
| | - Andrea Hartzler
- Department of Pathology, University of Washington, 1959 NE Pacific Street, Seattle, 98195 WA USA
| | - Eric Baldwin
- Department of Pathology, University of Washington, 1959 NE Pacific Street, Seattle, 98195 WA USA
| | - Mariza de Andrade
- Division of Biomedical Statistics and Informatics, Mayo Clinic, 200 First Street SW, Rochester, 55905 MN USA
| | - Iftikhar J Kullo
- Division of Cardiovascular Diseases, Mayo Clinic, 200 First Street SW, Rochester, 55905 MN USA
| | - Gerard Tromp
- The Sigfried and Janet Weis Center for Research, Geisinger Health System, 100 North Academy Avenue, Danville, 17882 PA USA
| | - Kimberly F Doheny
- Center for Inherited Disease Research, Johns Hopkins University School of Medicine, 333 Cassell Drive, Baltimore, 21224 MD USA
| | - Marylyn D Ritchie
- Center for Systems Genomics, Department of Biochemistry and Molecular Biology, Pennsylvania State University, 512A Wartik Laboratory, University Park, 16802 PA USA ; Biomedical and Translational Informatics, Geisinger Health System, 100 North Academy Avenue, Danville, 17882 PA USA
| | - Paul K Crane
- Division of General Internal Medicine, University of Washington, 325 Ninth Avenue, Seattle, 981014 WA USA
| | - Deborah A Nickerson
- Department of Genome Sciences, University of Washington, 3720 15th Avenue NE, Seattle, 98195 WA USA
| | - Eric B Larson
- Group Health Research Institute, Group Health Cooperative, 1730 Minor Avenue, Seattle, 98101 WA USA
| | - Gail P Jarvik
- Department of Medicine, Division of Medical Genetics, University of Washington, 1705 NE Pacific Street, Seattle, 98195 WA USA ; Department of Genome Sciences, University of Washington, 3720 15th Avenue NE, Seattle, 98195 WA USA
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