1
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Zhou Y, Li L, Zhou D, Yu Z, Ren Y, Liao Y, Yuan C, Yin Y, Gu X, Cui Y. One panel with four single nucleotide polymorphisms for Chinese children with asthma: Integrating public data and whole exome sequencing. Pediatr Allergy Immunol 2024; 35:e14182. [PMID: 38899630 DOI: 10.1111/pai.14182] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/28/2024] [Revised: 06/04/2024] [Indexed: 06/21/2024]
Abstract
BACKGROUND Polymorphisms in susceptibility genes are a major risk factor for the development of asthma. Understanding these genetic variants helps elucidate asthma's pathogenesis, predict its onset, expedite antiasthma medication development, and achieve precise targeted individualized treatment. This study developed a test kit based on susceptibility genes for predicting asthma in Chinese children. METHODS The present study constructed a VariantPro Targeted Library Preparation System with 72 single nucleotide polymorphism (SNP) loci associated with asthma from the ClinVar, OMIM, and SNPedia databases. These SNP loci were detected in the peripheral blood of 499 children with asthma and 500 healthy children. Significant differences were discovered for seven SNP loci. Simultaneously, whole exome sequencing of 46 children with asthma and 50 healthy children identified eight SNP loci with significant differences. The 15 SNP loci identified from Chinese children with asthma were validated in an independent population of 97 children with asthma and 93 healthy children by conducting multiplex polymerase chain reaction (PCR)-next-generation sequencing genotyping. RESULTS Four loci (rs12422149, rs7216389, rs4065275, and rs41453444) were identified, and a single-tube multifluorescent qPCR (real-time quantitative PCR) test kit was developed using these four SNP loci. The kit was tested on 269 children with asthma and 724 children with bronchopneumonia. CONCLUSIONS We identified four loci as susceptibility genes and developed a quantitative PCR test kit for predicting asthma development in Chinese children.
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Affiliation(s)
- Ying Zhou
- Department of Pediatrics Laboratory, The Affiliated Children's Hospital of Jiangnan University, Wuxi, China
| | - Lin Li
- Oxford Suzhou Centre for Advanced Research, Suzhou, China
| | - Dongmei Zhou
- Clinical Research Center, The Affiliated Wuxi People's Hospital of Nanjing Medical University, Wuxi, China
| | - Zhiwei Yu
- Department of Respiratory, The Affiliated Children's Hospital of Jiangnan University, Wuxi, China
| | - Yaning Ren
- Clinical Research Center, The Affiliated Wuxi People's Hospital of Nanjing Medical University, Wuxi, China
| | - Yuanfen Liao
- Clinical Research Center, The Affiliated Wuxi People's Hospital of Nanjing Medical University, Wuxi, China
| | - Cunyin Yuan
- Clinical Research Center, The Affiliated Wuxi People's Hospital of Nanjing Medical University, Wuxi, China
| | - Yong Yin
- Department of Respiratory, Shanghai Children's Medical Center, Affiliated with Shanghai Jiaotong University School of Medicine, Shanghai, China
| | - Xiaohong Gu
- Department of Respiratory, The Affiliated Children's Hospital of Jiangnan University, Wuxi, China
| | - Yubao Cui
- Clinical Research Center, The Affiliated Wuxi People's Hospital of Nanjing Medical University, Wuxi, China
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2
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Voorhies K, Mohammed A, Chinthala L, Kong SW, Lee IH, Kho AT, McGeachie M, Mandl KD, Raby B, Hayes M, Davis RL, Wu AC, Lutz SM. GSDMB/ORMDL3 Rare/Common Variants Are Associated with Inhaled Corticosteroid Response among Children with Asthma. Genes (Basel) 2024; 15:420. [PMID: 38674355 PMCID: PMC11049905 DOI: 10.3390/genes15040420] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2024] [Revised: 03/12/2024] [Accepted: 03/26/2024] [Indexed: 04/28/2024] Open
Abstract
Inhaled corticosteroids (ICS) are efficacious in the treatment of asthma, which affects more than 300 million people in the world. While genome-wide association studies have identified genes involved in differential treatment responses to ICS in asthma, few studies have evaluated the effects of combined rare and common variants on ICS response among children with asthma. Among children with asthma treated with ICS with whole exome sequencing (WES) data in the PrecisionLink Biobank (91 White and 20 Black children), we examined the effect and contribution of rare and common variants with hospitalizations or emergency department visits. For 12 regions previously associated with asthma and ICS response (DPP10, FBXL7, NDFIP1, TBXT, GLCCI1, HDAC9, TBXAS1, STAT6, GSDMB/ORMDL3, CRHR1, GNGT2, FCER2), we used the combined sum test for the sequence kernel association test (SKAT) adjusting for age, sex, and BMI and stratified by race. Validation was conducted in the Biorepository and Integrative Genomics (BIG) Initiative (83 White and 134 Black children). Using a Bonferroni threshold for the 12 regions tested (i.e., 0.05/12 = 0.004), GSDMB/ORMDL3 was significantly associated with ICS response for the combined effect of rare and common variants (p-value = 0.003) among White children in the PrecisionLink Biobank and replicated in the BIG Initiative (p-value = 0.02). Using WES data, the combined effect of rare and common variants for GSDMB/ORMDL3 was associated with ICS response among asthmatic children in the PrecisionLink Biobank and replicated in the BIG Initiative. This proof-of-concept study demonstrates the power of biobanks of pediatric real-life populations in asthma genomic investigations.
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Affiliation(s)
- Kirsten Voorhies
- Department of Population Medicine, Harvard Pilgrim Health Care Institute, Boston, MA 02215, USA
| | - Akram Mohammed
- Center in Biomedical Informatics, University of Tennessee Health Science Center, Memphis, TN 38163, USA
| | - Lokesh Chinthala
- Center in Biomedical Informatics, University of Tennessee Health Science Center, Memphis, TN 38163, USA
| | - Sek Won Kong
- Computational Health Informatics Program, Boston Children’s Hospital, Boston, MA 02115, USA
| | - In-Hee Lee
- Computational Health Informatics Program, Boston Children’s Hospital, Boston, MA 02115, USA
| | - Alvin T. Kho
- Computational Health Informatics Program, Boston Children’s Hospital, Boston, MA 02115, USA
| | - Michael McGeachie
- Channing Division for Network Medicine, Brigham and Women’s Hospital, Boston, MA 02115, USA
| | - Kenneth D. Mandl
- Computational Health Informatics Program, Boston Children’s Hospital, Boston, MA 02115, USA
| | - Benjamin Raby
- Division of Pulmonary Medicine, Boston Children’s Hospital, Boston, MA 02115, USA
| | - Melanie Hayes
- Center in Biomedical Informatics, University of Tennessee Health Science Center, Memphis, TN 38163, USA
| | - Robert L. Davis
- Center in Biomedical Informatics, University of Tennessee Health Science Center, Memphis, TN 38163, USA
| | - Ann Chen Wu
- Department of Population Medicine, Harvard Pilgrim Health Care Institute, Boston, MA 02215, USA
| | - Sharon M. Lutz
- Department of Population Medicine, Harvard Pilgrim Health Care Institute, Boston, MA 02215, USA
- Department of Biostatistics, Harvard T.H. Chan School of Public Health, Boston, MA 02115, USA
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3
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Clay S, Alladina J, Smith NP, Visness CM, Wood RA, O'Connor GT, Cohen RT, Khurana Hershey GK, Kercsmar CM, Gruchalla RS, Gill MA, Liu AH, Kim H, Kattan M, Bacharier LB, Rastogi D, Rivera-Spoljaric K, Robison RG, Gergen PJ, Busse WW, Villani AC, Cho JL, Medoff BD, Gern JE, Jackson DJ, Ober C, Dapas M. Gene-based association study of rare variants in children of diverse ancestries implicates TNFRSF21 in the development of allergic asthma. J Allergy Clin Immunol 2024; 153:809-820. [PMID: 37944567 PMCID: PMC10939893 DOI: 10.1016/j.jaci.2023.10.023] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2023] [Revised: 09/25/2023] [Accepted: 10/12/2023] [Indexed: 11/12/2023]
Abstract
BACKGROUND Most genetic studies of asthma and allergy have focused on common variation in individuals primarily of European ancestry. Studying the role of rare variation in quantitative phenotypes and in asthma phenotypes in populations of diverse ancestries can provide additional, important insights into the development of these traits. OBJECTIVE We sought to examine the contribution of rare variants to different asthma- or allergy-associated quantitative traits in children with diverse ancestries and explore their role in asthma phenotypes. METHODS We examined whole-genome sequencing data from children participants in longitudinal studies of asthma (n = 1035; parent-identified as 67% Black and 25% Hispanic) to identify rare variants (minor allele frequency < 0.01). We assigned variants to genes and tested for associations using an omnibus variant-set test between each of 24,902 genes and 8 asthma-associated quantitative traits. On combining our results with external data on predicted gene expression in humans and mouse knockout studies, we identified 3 candidate genes. A burden of rare variants in each gene and in a combined 3-gene score was tested for its associations with clinical phenotypes of asthma. Finally, published single-cell gene expression data in lower airway mucosal cells after allergen challenge were used to assess transcriptional responses to allergen. RESULTS Rare variants in USF1 were significantly associated with blood neutrophil count (P = 2.18 × 10-7); rare variants in TNFRSF21 with total IgE (P = 6.47 × 10-6) and PIK3R6 with eosinophil count (P = 4.10 × 10-5) reached suggestive significance. These 3 findings were supported by independent data from human and mouse studies. A burden of rare variants in TNFRSF21 and in a 3-gene score was associated with allergy-related phenotypes in cohorts of children with mild and severe asthma. Furthermore, TNFRSF21 was significantly upregulated in bronchial basal epithelial cells from adults with allergic asthma but not in adults with allergies (but not asthma) after allergen challenge. CONCLUSIONS We report novel associations between rare variants in genes and allergic and inflammatory phenotypes in children with diverse ancestries, highlighting TNFRSF21 as contributing to the development of allergic asthma.
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Affiliation(s)
- Selene Clay
- Department of Human Genetics, University of Chicago, Chicago, Ill.
| | - Jehan Alladina
- Division of Pulmonary and Critical Care Medicine, Massachusetts General Hospital and Harvard Medical School, Boston, Mass; Center for Immunology and Inflammatory Diseases, Massachusetts General Hospital and Harvard Medical School, Boston, Mass
| | - Neal P Smith
- Center for Immunology and Inflammatory Diseases, Massachusetts General Hospital and Harvard Medical School, Boston, Mass; Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, Mass; Massachusetts General Hospital Cancer Center, Boston, Mass
| | | | - Robert A Wood
- Pediatric Allergy and Immunology Department, Johns Hopkins Bloomberg School of Public Health, Baltimore, Md
| | - George T O'Connor
- Department of Pediatrics, Boston University School of Medicine, Boston, Mass
| | - Robyn T Cohen
- Department of Pediatrics, Boston University School of Medicine, Boston, Mass
| | | | - Carolyn M Kercsmar
- Division of Pulmonary Medicine, Cincinnati Children's Hospital Medical Center, Cincinnati, Ohio
| | - Rebecca S Gruchalla
- Internal Medicine and Pediatrics, University of Texas Southwestern Medical Center, Dallas, Tex
| | - Michelle A Gill
- Pediatric Infectious Diseases, St. Louis Children's Hospital, St Louis, Mo
| | - Andrew H Liu
- Breathing Institute, Children's Hospital Colorado, Aurora, Colo
| | - Haejin Kim
- Allergy and Immunology, Henry Ford Health, Detroit, Mich
| | - Meyer Kattan
- Department of Pediatrics, Columbia University Medical Center, New York, NY
| | - Leonard B Bacharier
- Department of Pediatrics, Monroe Carell Jr Children's Hospital at Vanderbilt University Medical Center, Nashville, Tenn
| | - Deepa Rastogi
- Division of Pulmonology and Sleep Medicine, Children's National Hospital, Washington, DC
| | - Katherine Rivera-Spoljaric
- Department of Pediatric Allergy, Immunology, and Pulmonary Medicine, Washington University School of Medicine, St Louis, Mo
| | - Rachel G Robison
- Department of Pediatrics, Monroe Carell Jr Children's Hospital at Vanderbilt University Medical Center, Nashville, Tenn; Ann & Robert H. Lurie Children's Hospital, Chicago, Ill
| | - Peter J Gergen
- National Institute of Allergy and Infectious Diseases, Rockville, Md
| | - William W Busse
- Department of Medicine, University of Wisconsin School of Medicine and Public Health, Madison, Wis
| | - Alexandra-Chloe Villani
- Center for Immunology and Inflammatory Diseases, Massachusetts General Hospital and Harvard Medical School, Boston, Mass; Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, Mass; Massachusetts General Hospital Cancer Center, Boston, Mass
| | - Josalyn L Cho
- Division of Pulmonary, Critical Care and Occupational Medicine, University of Iowa Carver College of Medicine, Iowa City, Iowa
| | - Benjamin D Medoff
- Division of Pulmonary and Critical Care Medicine, Massachusetts General Hospital and Harvard Medical School, Boston, Mass; Center for Immunology and Inflammatory Diseases, Massachusetts General Hospital and Harvard Medical School, Boston, Mass
| | - James E Gern
- Department of Pediatrics, University of Wisconsin School of Medicine and Public Health, Madison, Wis
| | - Daniel J Jackson
- Department of Pediatrics, University of Wisconsin School of Medicine and Public Health, Madison, Wis
| | - Carole Ober
- Department of Human Genetics, University of Chicago, Chicago, Ill
| | - Matthew Dapas
- Department of Human Genetics, University of Chicago, Chicago, Ill
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4
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Cha J, Choi S. Gene-Smoking Interaction Analysis for the Identification of Novel Asthma-Associated Genetic Factors. Int J Mol Sci 2023; 24:12266. [PMID: 37569643 PMCID: PMC10419280 DOI: 10.3390/ijms241512266] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2023] [Revised: 07/26/2023] [Accepted: 07/30/2023] [Indexed: 08/13/2023] Open
Abstract
Asthma is a complex heterogeneous disease caused by gene-environment interactions. Although numerous genome-wide association studies have been conducted, these interactions have not been systemically investigated. We sought to identify genetic factors associated with the asthma phenotype in 66,857 subjects from the Health Examination Study, Cardiovascular Disease Association Study, and Korea Association Resource Study cohorts. We investigated asthma-associated gene-environment (smoking status) interactions at the level of single nucleotide polymorphisms, genes, and gene sets. We identified two potentially novel (SETDB1 and ZNF8) and five previously reported (DM4C, DOCK8, MMP20, MYL7, and ADCY9) genes associated with increased asthma risk. Numerous gene ontology processes, including regulation of T cell differentiation in the thymus (GO:0033081), were significantly enriched for asthma risk. Functional annotation analysis confirmed the causal relationship between five genes (two potentially novel and three previously reported genes) and asthma through genome-wide functional prediction scores (combined annotation-dependent depletion, deleterious annotation of genetic variants using neural networks, and RegulomeDB). Our findings elucidate the genetic architecture of asthma and improve the understanding of its biological mechanisms. However, further studies are necessary for developing preventive treatments based on environmental factors and understanding the immune system mechanisms that contribute to the etiology of asthma.
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Affiliation(s)
- Junho Cha
- Department of Applied Artificial Intelligence, College of Computing, Hanyang University, 55 Hanyang-daehak-ro, Sangnok-gu, Ansan 15588, Republic of Korea;
| | - Sungkyoung Choi
- Department of Applied Artificial Intelligence, College of Computing, Hanyang University, 55 Hanyang-daehak-ro, Sangnok-gu, Ansan 15588, Republic of Korea;
- Department of Mathematical Data Science, College of Science and Convergence Technology, Hanyang University, 55 Hanyang-daehak-ro, Sangnok-gu, Ansan 15588, Republic of Korea
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5
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Shamsi BH, Chen H, Yang X, Liu M, Liu Y. Association between polymorphisms of the GSDMB gene and allergic rhinitis risk in the Chinese population: a case-control study. J Asthma 2023:1-10. [PMID: 36847643 DOI: 10.1080/02770903.2023.2185893] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/01/2023]
Abstract
BACKGROUND Allergic rhinitis (AR) is a great risk factor for developing asthma, and its pathogenesis is affected by various factors, such as gene and environment. GSDMB is related to allergic diseases. Our purpose is to explore the correlation of single nucleotide polymorphisms (SNPs) in GSDMB and AR risk in the Chinese population. METHODS We performed a case-control study including 1005 cases and 1004 controls. Rs2305479, rs4795400, and rs12450091 in GSDMB were geneotyped using Agena MassARRAY. The relationships between GSDMB SNPs and AR risk were assessed by logistic regression analysis in PLINK1.9. RESULTS Our study showed that rs4795400 was a protective factor for AR in overall (TT vs. CC: OR = 0.66, p = 0.009; TT vs. CC/TC: OR = 0.67, p = 0.008; additive: OR = 0.87, p = 0.042 males, people with BMI ≤ 24, and living in wind-blown sand area. Rs2305479 was associated with a reduced AR risk in males (TT vs. CC: OR = 0.47, p = 0.014; TT vs. CC/TC: OR = 0.43, p = 0.004). However, rs12450091 was a risk factor for AR in people living in the loess hilly region (CC: OR = 4.75, p = 0.047). The levels of EO and EO_per in the case group were significantly higher than those in the control group (p < 0.05). CONCLUSION This study indicated that GSDMB polymorphisms (rs4795400, rs2305479, and rs12450091) were associated with AR susceptibility. Further studies are required to confirm our findings and to clarify the functional relationship.
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Affiliation(s)
- Bilal Haider Shamsi
- Department of Science and Education, Shenmu Hospital, The Affiliated Shenmu Hospital of Northwest University, Shenmu, China
| | - Haiyuan Chen
- Department of Information, Shenmu Hospital, The Affiliated Shenmu Hospital of Northwest University, Shenmu, China
| | - Xiong Yang
- Department of Nephrology, Shenmu Hospital, The Affiliated Shenmu Hospital of Northwest University, Shenmu, China
| | - Mingxia Liu
- Department of Prevention and Protection, Shenmu Hospital, The Affiliated Shenmu Hospital of Northwest University, Shenmu, China
| | - Yonglin Liu
- Department of Science and Education, Shenmu Hospital, The Affiliated Shenmu Hospital of Northwest University, Shenmu, China
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6
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Gao Y, Felsky D, Reyes-Dumeyer D, Sariya S, Rentería MA, Ma Y, Klein HU, Cosentino S, De Jager PL, Bennett DA, Brickman AM, Schellenberg GD, Mayeux R, Barral S. Integration of GWAS and brain transcriptomic analyses in a multiethnic sample of 35,245 older adults identifies DCDC2 gene as predictor of episodic memory maintenance. Alzheimers Dement 2022; 18:1797-1811. [PMID: 34873813 PMCID: PMC9170841 DOI: 10.1002/alz.12524] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2021] [Revised: 10/03/2021] [Accepted: 10/12/2021] [Indexed: 01/28/2023]
Abstract
Identifying genes underlying memory function will help characterize cognitively resilient and high-risk declining subpopulations contributing to precision medicine strategies. We estimated episodic memory trajectories in 35,245 ethnically diverse older adults representing eight independent cohorts. We conducted apolipoprotein E (APOE)-stratified genome-wide association study (GWAS) analyses and combined individual cohorts' results via meta-analysis. Three independent transcriptomics datasets were used to further interpret GWAS signals. We identified DCDC2 gene significantly associated with episodic memory (Pmeta = 3.3 x 10-8 ) among non-carriers of APOE ε4 (N = 24,941). Brain transcriptomics revealed an association between episodic memory maintenance and (1) increased dorsolateral prefrontal cortex DCDC2 expression (P = 3.8 x 10-4 ) and (2) lower burden of pathological Alzheimer's disease (AD) hallmarks (paired helical fragment tau P = .003, and amyloid beta load P = .008). Additional transcriptomics results comparing AD and cognitively healthy brain samples showed a downregulation of DCDC2 levels in superior temporal gyrus (P = .007) and inferior frontal gyrus (P = .013). Our work identified DCDC2 gene as a novel predictor of memory maintenance.
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Affiliation(s)
- Yizhe Gao
- Taub Institute for Research on Alzheimer’s Disease
and the Aging Brain, Vagelos College of Physicians and Surgeons, Columbia
University, New York, NY, USA
| | - Daniel Felsky
- Krembil Centre for Neuroinformatics, Centre for Addiction
and Mental Health, Toronto, ON, Canada.,Department of Psychiatry & Institute of Medical
Science, University of Toronto, Toronto, ON, Canada
| | - Dolly Reyes-Dumeyer
- Taub Institute for Research on Alzheimer’s Disease
and the Aging Brain, Vagelos College of Physicians and Surgeons, Columbia
University, New York, NY, USA.,G.H. Sergievsky Center, Vagelos College of Physicians and
Surgeons, Columbia University, New York, NY, USA.,Department of Neurology, Vagelos College of Physicians and
Surgeons, New York-Presbyterian Hospital, Columbia University Medical Center, New
York, NY, USA
| | - Sanjeev Sariya
- Taub Institute for Research on Alzheimer’s Disease
and the Aging Brain, Vagelos College of Physicians and Surgeons, Columbia
University, New York, NY, USA
| | - Miguel Arce Rentería
- Taub Institute for Research on Alzheimer’s Disease
and the Aging Brain, Vagelos College of Physicians and Surgeons, Columbia
University, New York, NY, USA.,Department of Neurology, Vagelos College of Physicians and
Surgeons, New York-Presbyterian Hospital, Columbia University Medical Center, New
York, NY, USA
| | - Yiyi Ma
- Center for Translational & Computational
Neuroimmunology, Department of Neurology, Columbia University Irving Medical Center,
New York, NY, 10032, USA
| | - Hans-Ulrich Klein
- Taub Institute for Research on Alzheimer’s Disease
and the Aging Brain, Vagelos College of Physicians and Surgeons, Columbia
University, New York, NY, USA.,Center for Translational & Computational
Neuroimmunology, Department of Neurology, Columbia University Irving Medical Center,
New York, NY, 10032, USA
| | - Stephanie Cosentino
- Taub Institute for Research on Alzheimer’s Disease
and the Aging Brain, Vagelos College of Physicians and Surgeons, Columbia
University, New York, NY, USA.,G.H. Sergievsky Center, Vagelos College of Physicians and
Surgeons, Columbia University, New York, NY, USA.,Department of Neurology, Vagelos College of Physicians and
Surgeons, New York-Presbyterian Hospital, Columbia University Medical Center, New
York, NY, USA
| | - Philip L. De Jager
- Taub Institute for Research on Alzheimer’s Disease
and the Aging Brain, Vagelos College of Physicians and Surgeons, Columbia
University, New York, NY, USA.,Center for Translational & Computational
Neuroimmunology, Department of Neurology, Columbia University Irving Medical Center,
New York, NY, 10032, USA.,Cell Circuits Program, Broad Institute, Cambridge, MA,
USA
| | - David A. Bennett
- Rush University Medical Center, Rush Alzheimer’s
Disease Center, Chicago, IL, USA.,Rush University Medical Center, Department of Neurological
Sciences, Chicago, IL, USA
| | - Adam M. Brickman
- Taub Institute for Research on Alzheimer’s Disease
and the Aging Brain, Vagelos College of Physicians and Surgeons, Columbia
University, New York, NY, USA.,G.H. Sergievsky Center, Vagelos College of Physicians and
Surgeons, Columbia University, New York, NY, USA.,Department of Neurology, Vagelos College of Physicians and
Surgeons, New York-Presbyterian Hospital, Columbia University Medical Center, New
York, NY, USA
| | - Gerard D. Schellenberg
- Department of Pathology and Laboratory Medicine,
University of Pennsylvania, Philadelphia, PA, USA
| | - Richard Mayeux
- Taub Institute for Research on Alzheimer’s Disease
and the Aging Brain, Vagelos College of Physicians and Surgeons, Columbia
University, New York, NY, USA.,G.H. Sergievsky Center, Vagelos College of Physicians and
Surgeons, Columbia University, New York, NY, USA.,Department of Neurology, Vagelos College of Physicians and
Surgeons, New York-Presbyterian Hospital, Columbia University Medical Center, New
York, NY, USA
| | - Sandra Barral
- Taub Institute for Research on Alzheimer’s Disease
and the Aging Brain, Vagelos College of Physicians and Surgeons, Columbia
University, New York, NY, USA.,G.H. Sergievsky Center, Vagelos College of Physicians and
Surgeons, Columbia University, New York, NY, USA.,Department of Neurology, Vagelos College of Physicians and
Surgeons, New York-Presbyterian Hospital, Columbia University Medical Center, New
York, NY, USA
| | -
- Taub Institute for Research on Alzheimer's Disease and the Aging Brain, Vagelos College of Physicians and Surgeons, Columbia University, New York, New York, USA
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7
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Washington C, Dapas M, Biddanda A, Magnaye KM, Aneas I, Helling BA, Szczesny B, Boorgula MP, Taub MA, Kenny E, Mathias RA, Barnes KC, Khurana Hershey GK, Kercsmar CM, Gereige JD, Makhija M, Gruchalla RS, Gill MA, Liu AH, Rastogi D, Busse W, Gergen PJ, Visness CM, Gold DR, Hartert T, Johnson CC, Lemanske RF, Martinez FD, Miller RL, Ownby D, Seroogy CM, Wright AL, Zoratti EM, Bacharier LB, Kattan M, O'Connor GT, Wood RA, Nobrega MA, Altman MC, Jackson DJ, Gern JE, McKennan CG, Ober C. African-specific alleles modify risk for asthma at the 17q12-q21 locus in African Americans. Genome Med 2022; 14:112. [PMID: 36175932 PMCID: PMC9520885 DOI: 10.1186/s13073-022-01114-x] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2022] [Accepted: 09/15/2022] [Indexed: 02/02/2023] Open
Abstract
BACKGROUND Asthma is the most common chronic disease in children, occurring at higher frequencies and with more severe disease in children with African ancestry. METHODS We tested for association with haplotypes at the most replicated and significant childhood-onset asthma locus at 17q12-q21 and asthma in European American and African American children. Following this, we used whole-genome sequencing data from 1060 African American and 100 European American individuals to identify novel variants on a high-risk African American-specific haplotype. We characterized these variants in silico using gene expression and ATAC-seq data from airway epithelial cells, functional annotations from ENCODE, and promoter capture (pc)Hi-C maps in airway epithelial cells. Candidate causal variants were then assessed for correlation with asthma-associated phenotypes in African American children and adults. RESULTS Our studies revealed nine novel African-specific common variants, enriched on a high-risk asthma haplotype, which regulated the expression of GSDMA in airway epithelial cells and were associated with features of severe asthma. Using ENCODE annotations, ATAC-seq, and pcHi-C, we narrowed the associations to two candidate causal variants that are associated with features of T2 low severe asthma. CONCLUSIONS Previously unknown genetic variation at the 17q12-21 childhood-onset asthma locus contributes to asthma severity in individuals with African ancestries. We suggest that many other population-specific variants that have not been discovered in GWAS contribute to the genetic risk for asthma and other common diseases.
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Affiliation(s)
- Charles Washington
- Department of Human Genetics, The University of Chicago, 928 E. 58th St. CLSC 507C, Chicago, IL, 60637, USA
| | - Matthew Dapas
- Department of Human Genetics, The University of Chicago, 928 E. 58th St. CLSC 507C, Chicago, IL, 60637, USA
| | - Arjun Biddanda
- Department of Human Genetics, The University of Chicago, 928 E. 58th St. CLSC 507C, Chicago, IL, 60637, USA
| | - Kevin M Magnaye
- Department of Human Genetics, The University of Chicago, 928 E. 58th St. CLSC 507C, Chicago, IL, 60637, USA
| | - Ivy Aneas
- Department of Human Genetics, The University of Chicago, 928 E. 58th St. CLSC 507C, Chicago, IL, 60637, USA
| | - Britney A Helling
- Department of Human Genetics, The University of Chicago, 928 E. 58th St. CLSC 507C, Chicago, IL, 60637, USA
| | - Brooke Szczesny
- Department of Medicine, Johns Hopkins University, Baltimore, MD, USA
| | | | - Margaret A Taub
- Department of Biostatistics, Bloomberg School of Public Health, Johns Hopkins University, Baltimore, MD, USA
| | - Eimear Kenny
- Department of Medicine, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Rasika A Mathias
- Department of Medicine, Johns Hopkins University, Baltimore, MD, USA
| | - Kathleen C Barnes
- Department of Medicine, University of Colorado Denver, Aurora, CO, USA
| | | | - Carolyn M Kercsmar
- Division of Asthma Research, Cincinnati Children's Hospital, Cincinnati, OH, USA
| | - Jessica D Gereige
- Department of Medicine, Division of Pulmonary, Allergy, Sleep, and Critical Care Medicine, Boston University School of Medicine, Boston, MA, USA
| | - Melanie Makhija
- Ann and Robert H. Lurie Children's Hospital of Chicago, Chicago, IL, USA
| | | | - Michelle A Gill
- University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Andrew H Liu
- Children's Hospital Colorado and University of Colorado School of Medicine, Aurora, CO, USA
| | - Deepa Rastogi
- Children's National Hospital and George Washington University School of Medicine and Health Sciences, Washington, DC, USA
| | - William Busse
- University of Wisconsin School of Medicine and Public Health, Madison, WI, USA
| | | | | | - Diane R Gold
- The Channing Division of Network Medicine, Department of Medicine, Brigham and Women's Hospital and Department of Environmental Health, Harvard T.H. Chan School of Public Health, Harvard University, Boston, MA, USA
| | - Tina Hartert
- Department of Medicine, Vanderbilt University School of Medicine, Nashville, TN, USA
| | - Christine C Johnson
- Department of Public Health Sciences, Henry Ford Health Systems, Detroit, MI, USA
| | - Robert F Lemanske
- Department of Pediatrics, University of Wisconsin School of Medicine and Public Health, Madison, WI, USA
| | - Fernando D Martinez
- Asthma and Airway Disease Research Center, University of Arizona, Tucson, AZ, USA
| | - Rachel L Miller
- Department of Medicine, Division of Clinical Immunology Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Dennis Ownby
- Department of Public Health Sciences, Henry Ford Health Systems, Detroit, MI, USA
| | - Christine M Seroogy
- Department of Pediatrics, University of Wisconsin School of Medicine and Public Health, Madison, WI, USA
| | - Anne L Wright
- Asthma and Airway Disease Research Center, University of Arizona, Tucson, AZ, USA
| | - Edward M Zoratti
- Department of Medicine, Henry Ford Health Systems, Detroit, MI, USA
| | - Leonard B Bacharier
- Department of Pediatrics, Monroe Carell Jr Children's Hospital at Vanderbilt University Medical Center, Nashville, TN, USA
| | - Meyer Kattan
- Department of Pediatrics, Columbia University Medical Center, New York, NY, USA
| | - George T O'Connor
- Pulmonary Center, Boston University School of Medicine, Boston, MA, USA
| | - Robert A Wood
- Department of Pediatrics, Johns Hopkins University, Baltimore, MD, USA
| | - Marcelo A Nobrega
- Department of Human Genetics, The University of Chicago, 928 E. 58th St. CLSC 507C, Chicago, IL, 60637, USA
| | - Matthew C Altman
- Immunology Division, Benaroya Research Institute Systems, Seattle, WA, USA
- Department of Medicine, University of Washington, Seattle, WA, USA
| | - Daniel J Jackson
- Department of Pediatrics, University of Wisconsin School of Medicine and Public Health, Madison, WI, USA
| | - James E Gern
- Department of Pediatrics, University of Wisconsin School of Medicine and Public Health, Madison, WI, USA
| | | | - Carole Ober
- Department of Human Genetics, The University of Chicago, 928 E. 58th St. CLSC 507C, Chicago, IL, 60637, USA.
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8
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Liu Y, Qu HQ, Qu J, Chang X, Mentch FD, Nguyen K, Tian L, Glessner J, Sleiman PMA, Hakonarson H. Burden of rare coding variants reveals genetic heterogeneity between obese and non-obese asthma patients in the African American population. Respir Res 2022; 23:116. [PMID: 35524249 PMCID: PMC9078008 DOI: 10.1186/s12931-022-02039-0] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2021] [Accepted: 04/19/2022] [Indexed: 11/23/2022] Open
Abstract
Background Asthma is a complex condition largely attributed to the interactions among genes and environments as a heterogeneous phenotype. Obesity is significantly associated with asthma development, and genetic studies on obese vs. non-obese asthma are warranted. Methods To investigate asthma in the minority African American (AA) population with or without obesity, we performed a whole genome sequencing (WGS) study on blood-derived DNA of 4289 AA individuals, included 2226 asthma patients (1364 with obesity and 862 without obesity) and 2006 controls without asthma. The burden analysis of functional rare coding variants was performed by comparing asthma vs. controls and by stratified analysis of obese vs. non-obese asthma, respectively. Results Among the top 66 genes with P < 0.01 in the asthma vs. control analysis, stratified analysis by obesity showed inverse correlation of natural logarithm (LN) of P value between obese and non-obese asthma (r = − 0.757, P = 1.90E−13). Five genes previously reported in a genome-wide association study (GWAS) on asthma, including TSLP, SLC9A4, PSMB8, IGSF5, and IKZF4 were demonstrated association in the asthma vs. control analysis. The associations of IKZF4 and IGSF5 are only associated with obese asthma; and the association of SLC9A4 is only observed in non-obese asthma. In addition, the association of RSPH3 (the gene is related to primary ciliary dyskinesia) is observed in non-obese asthma. Conclusions These findings highlight genetic heterogeneity between obese and non-obese asthma in patients of AA ancestry. Supplementary Information The online version contains supplementary material available at 10.1186/s12931-022-02039-0.
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Affiliation(s)
- Yichuan Liu
- Center for Applied Genomics, Children's Hospital of Philadelphia, Philadelphia, PA, 19104, USA
| | - Hui-Qi Qu
- Center for Applied Genomics, Children's Hospital of Philadelphia, Philadelphia, PA, 19104, USA
| | - Jingchun Qu
- Center for Applied Genomics, Children's Hospital of Philadelphia, Philadelphia, PA, 19104, USA
| | - Xiao Chang
- Center for Applied Genomics, Children's Hospital of Philadelphia, Philadelphia, PA, 19104, USA
| | - Frank D Mentch
- Center for Applied Genomics, Children's Hospital of Philadelphia, Philadelphia, PA, 19104, USA
| | - Kenny Nguyen
- Center for Applied Genomics, Children's Hospital of Philadelphia, Philadelphia, PA, 19104, USA
| | - Lifeng Tian
- Center for Applied Genomics, Children's Hospital of Philadelphia, Philadelphia, PA, 19104, USA
| | - Joseph Glessner
- Center for Applied Genomics, Children's Hospital of Philadelphia, Philadelphia, PA, 19104, USA
| | - Patrick M A Sleiman
- Center for Applied Genomics, Children's Hospital of Philadelphia, Philadelphia, PA, 19104, USA.,Department of Pediatrics, The Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA.,Division of Human Genetics, Children's Hospital of Philadelphia, Philadelphia, PA, 19104, USA
| | - Hakon Hakonarson
- Center for Applied Genomics, Children's Hospital of Philadelphia, Philadelphia, PA, 19104, USA. .,Department of Pediatrics, The Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA. .,Division of Human Genetics, Children's Hospital of Philadelphia, Philadelphia, PA, 19104, USA. .,Division of Pulmonary Medicine, Children's Hospital of Philadelphia, Philadelphia, PA, 19104, USA. .,Faculty of Medicine, University of Iceland, 101, Reykjavik, Iceland.
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9
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Lee HS, Kim B, Park T. Transethnic meta-analysis of exome-wide variants identifies new loci associated with male-specific metabolic syndrome. Genes Genomics 2022; 44:629-636. [PMID: 35384631 DOI: 10.1007/s13258-021-01214-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2021] [Accepted: 12/29/2021] [Indexed: 11/04/2022]
Abstract
BACKGROUND Metabolic syndrome (MetS) is a group of very common human conditions promoting strong understand the impact of rare variants, beyond exome-wide association studies, to potentially discover causative variants, across different ethnic populations. OBJECTIVE We performed transethnic, exome-wide MetS association studies on MetS in men. METHODS We analyzed genotype data of 5302 European subjects (2658 cases and 2644 controls), in the discovery stage of the European METabolic Syndrome In Men study, generated from exome chips, and 2481 subjects (714 cases and 1767 controls), in the replication stage, across 6 independent cohorts of 5 ancestries (T2D-GENES consortium), using whole-exome sequencing. We therefore evaluated gene-level and variant-level associations, of rare variants for MetS, using logistic regression (LR) and multivariate analyses (MulA). RESULTS Gene-based association found the gene for the cholesteryl ester transfer protein (CETP) (from MulA, p value = 4.67 × 10-9; from LR, p value = 0.009) to well associate with MetS. At two missense variants, from 8 rare variants in CETP, Ala390Pro (rs5880) (from MulA, p value = 1.28 × 10-7; from LR, p value = 1.34 × 10-4) and Arg468Gln (rs1800777) (from MulA, p value = 2.40 × 10-5; from LR, p value = 1.49 × 10-3) significantly associated with MetS across five ancestries. CONCLUSIONS Our findings highlight novel rare variants of genes that confer MetS susceptibility, in Europeans, that are shared with diverse populations, emphasizing an opportunity to further understand the biological target or genes that underlie MetS, across populations.
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Affiliation(s)
- Ho-Sun Lee
- Interdisciplinary Program in Bioinformatics, Seoul National University, Seoul, 08826, Republic of Korea
- Daegu Institution, National Forensic Service, 33-14, Hogukro, Waegwon-eup, Chilgok-gun, Gyeomgsamgbuk-do, Republic of Korea
| | - Boram Kim
- Interdisciplinary Program in Bioinformatics, Seoul National University, Seoul, 08826, Republic of Korea
| | - Taesung Park
- Interdisciplinary Program in Bioinformatics, Seoul National University, Seoul, 08826, Republic of Korea.
- Department of Statistics, Seoul National University, Seoul, 08826, Republic of Korea.
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10
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Chang D, Hunkapiller J, Bhangale T, Reeder J, Mukhyala K, Tom J, Cowgill A, Vogel J, Forrest WF, Khan Z, Stockwell A, McCarthy MI, Staton TL, Olsson J, Holweg CTJ, Cheung DS, Chen H, Brauer MJ, Graham RR, Behrens T, Wilson MS, Arron JR, Choy DF, Yaspan BL. A whole genome sequencing study of moderate to severe asthma identifies a lung function locus associated with asthma risk. Sci Rep 2022; 12:5574. [PMID: 35368043 PMCID: PMC8976834 DOI: 10.1038/s41598-022-09447-8] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2021] [Accepted: 03/23/2022] [Indexed: 11/09/2022] Open
Abstract
AbstractGenome-wide association studies (GWAS) have identified many common variant loci associated with asthma susceptibility, but few studies investigate the genetics underlying moderate-to-severe asthma risk. Here, we present a whole-genome sequencing study comparing 3181 moderate-to-severe asthma patients to 3590 non-asthma controls. We demonstrate that asthma risk is genetically correlated with lung function measures and that this component of asthma risk is orthogonal to the eosinophil genetics that also contribute to disease susceptibility. We find that polygenic scores for reduced lung function are associated with younger asthma age of onset. Genome-wide, seven previously reported common asthma variant loci and one previously reported lung function locus, near THSD4, reach significance. We replicate association of the lung function locus in a recently published GWAS of moderate-to-severe asthma patients. We additionally replicate the association of a previously reported rare (minor allele frequency < 1%) coding variant in IL33 and show significant enrichment of rare variant burden in genes from common variant allergic disease loci. Our findings highlight the contribution of lung function genetics to moderate-to-severe asthma risk, and provide initial rare variant support for associations with moderate-to-severe asthma risk at several candidate genes from common variant loci.
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11
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Kothalawala DM, Kadalayil L, Curtin JA, Murray CS, Simpson A, Custovic A, Tapper WJ, Arshad SH, Rezwan FI, Holloway JW. Integration of Genomic Risk Scores to Improve the Prediction of Childhood Asthma Diagnosis. J Pers Med 2022; 12:75. [PMID: 35055391 PMCID: PMC8777841 DOI: 10.3390/jpm12010075] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2021] [Revised: 12/18/2021] [Accepted: 12/31/2021] [Indexed: 01/24/2023] Open
Abstract
Genome-wide and epigenome-wide association studies have identified genetic variants and differentially methylated nucleotides associated with childhood asthma. Incorporation of such genomic data may improve performance of childhood asthma prediction models which use phenotypic and environmental data. Using genome-wide genotype and methylation data at birth from the Isle of Wight Birth Cohort (n = 1456), a polygenic risk score (PRS), and newborn (nMRS) and childhood (cMRS) methylation risk scores, were developed to predict childhood asthma diagnosis. Each risk score was integrated with two previously published childhood asthma prediction models (CAPE and CAPP) and were validated in the Manchester Asthma and Allergy Study. Individually, the genomic risk scores demonstrated modest-to-moderate discriminative performance (area under the receiver operating characteristic curve, AUC: PRS = 0.64, nMRS = 0.55, cMRS = 0.54), and their integration only marginally improved the performance of the CAPE (AUC: 0.75 vs. 0.71) and CAPP models (AUC: 0.84 vs. 0.82). The limited predictive performance of each genomic risk score individually and their inability to substantially improve upon the performance of the CAPE and CAPP models suggests that genetic and epigenetic predictors of the broad phenotype of asthma are unlikely to have clinical utility. Hence, further studies predicting specific asthma endotypes are warranted.
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Affiliation(s)
- Dilini M. Kothalawala
- Human Development and Health, Faculty of Medicine, University of Southampton, Southampton SO16 6YD, UK; (D.M.K.); (L.K.); (W.J.T.); (F.I.R.)
- NIHR Southampton Biomedical Research Centre, University Hospital Southampton, Southampton SO16 6YD, UK;
| | - Latha Kadalayil
- Human Development and Health, Faculty of Medicine, University of Southampton, Southampton SO16 6YD, UK; (D.M.K.); (L.K.); (W.J.T.); (F.I.R.)
- Clinical and Experimental Sciences, Faculty of Medicine, University of Southampton, Southampton SO16 6YD, UK
| | - John A. Curtin
- Division of Infection, Immunity, and Respiratory Medicine, School of Biological Sciences, Manchester University Hospital NHS Foundation Trust, University of Manchester, Manchester Academic Health Science Centre, Manchester M13 9PL, UK; (J.A.C.); (C.S.M.); (A.S.)
| | - Clare S. Murray
- Division of Infection, Immunity, and Respiratory Medicine, School of Biological Sciences, Manchester University Hospital NHS Foundation Trust, University of Manchester, Manchester Academic Health Science Centre, Manchester M13 9PL, UK; (J.A.C.); (C.S.M.); (A.S.)
| | - Angela Simpson
- Division of Infection, Immunity, and Respiratory Medicine, School of Biological Sciences, Manchester University Hospital NHS Foundation Trust, University of Manchester, Manchester Academic Health Science Centre, Manchester M13 9PL, UK; (J.A.C.); (C.S.M.); (A.S.)
| | - Adnan Custovic
- National Heart and Lung Institute, Imperial College of Science, Technology, and Medicine, London SW3 6LY, UK;
| | - William J. Tapper
- Human Development and Health, Faculty of Medicine, University of Southampton, Southampton SO16 6YD, UK; (D.M.K.); (L.K.); (W.J.T.); (F.I.R.)
| | - S. Hasan Arshad
- NIHR Southampton Biomedical Research Centre, University Hospital Southampton, Southampton SO16 6YD, UK;
- Clinical and Experimental Sciences, Faculty of Medicine, University of Southampton, Southampton SO16 6YD, UK
- The David Hide Asthma and Allergy Research Centre, St. Mary’s Hospital, Isle of Wight PO30 5TG, UK
| | - Faisal I. Rezwan
- Human Development and Health, Faculty of Medicine, University of Southampton, Southampton SO16 6YD, UK; (D.M.K.); (L.K.); (W.J.T.); (F.I.R.)
- Department of Computer Science, Aberystwyth University, Aberystwyth SY23 3DB, UK
| | - John W. Holloway
- Human Development and Health, Faculty of Medicine, University of Southampton, Southampton SO16 6YD, UK; (D.M.K.); (L.K.); (W.J.T.); (F.I.R.)
- NIHR Southampton Biomedical Research Centre, University Hospital Southampton, Southampton SO16 6YD, UK;
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12
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Xia R, Cheng Y, Han X, Wei Y, Wei X. Ikaros Proteins in Tumor: Current Perspectives and New Developments. Front Mol Biosci 2021; 8:788440. [PMID: 34950704 PMCID: PMC8689071 DOI: 10.3389/fmolb.2021.788440] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2021] [Accepted: 11/09/2021] [Indexed: 02/05/2023] Open
Abstract
Ikaros is a zinc finger transcription factor (TF) of the Krüppel family member, which significantly regulates normal lymphopoiesis and tumorigenesis. Ikaros can directly initiate or suppress tumor suppressors or oncogenes, consequently regulating the survival and proliferation of cancer cells. Over recent decades, a series of studies have been devoted to exploring and clarifying the relationship between Ikaros and associated tumors. Therapeutic strategies targeting Ikaros have shown promising therapeutic effects in both pre-clinical and clinical trials. Nevertheless, the increasingly prominent problem of drug resistance targeted to Ikaros and its analog is gradually appearing in our field of vision. This article reviews the role of Ikaros in tumorigenesis, the mechanism of drug resistance, the progress of targeting Ikaros in both pre-clinical and clinical trials, and the potential use of associated therapy in cancer therapy.
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Affiliation(s)
- Ruolan Xia
- Laboratory of Aging Research and Cancer Drug Target, State Key Laboratory of Biotherapy, National Clinical Research Center for Geriatrics, West China Hospital, Sichuan University, Chengdu, China
| | - Yuan Cheng
- Laboratory of Aging Research and Cancer Drug Target, State Key Laboratory of Biotherapy, National Clinical Research Center for Geriatrics, West China Hospital, Sichuan University, Chengdu, China
| | - Xuejiao Han
- Laboratory of Aging Research and Cancer Drug Target, State Key Laboratory of Biotherapy, National Clinical Research Center for Geriatrics, West China Hospital, Sichuan University, Chengdu, China
| | - Yuquan Wei
- Laboratory of Aging Research and Cancer Drug Target, State Key Laboratory of Biotherapy, National Clinical Research Center for Geriatrics, West China Hospital, Sichuan University, Chengdu, China
| | - Xiawei Wei
- Laboratory of Aging Research and Cancer Drug Target, State Key Laboratory of Biotherapy, National Clinical Research Center for Geriatrics, West China Hospital, Sichuan University, Chengdu, China
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13
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An Overview of Health Disparities in Asthma. THE YALE JOURNAL OF BIOLOGY AND MEDICINE 2021; 94:497-507. [PMID: 34602887 PMCID: PMC8461584] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
Asthma is a heterogeneous disease characterized by inflammation in the respiratory airways which manifests clinically with wheezing, cough, and episodic periods of chest tightness; if left untreated it can lead to permanent obstruction or death. In the US, asthma affects all ages and genders, and individuals from racial and ethnic minority groups are disproportionately burdened by this disease. The financial cost of asthma exceeds $81 billion every year and despite all the resources invested, asthma is responsible for over 3,500 deaths annually in the nation. In this overview, we highlight important factors associated with health disparities in asthma. While they are complex and overlap, we group these factors in five domains: biological, behavioral, socio-cultural, built environment, and health systems. We review the biological domain in detail, which traditionally has been best studied. We also acknowledge that implicit and explicit racism is an important contributor to asthma disparities and responsible for many of the socio-environmental factors that worsen outcomes in this disease.
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14
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Sariya S, Felsky D, Reyes-Dumeyer D, Lali R, Lantigua RA, Vardarajan B, Jiménez-Velázquez IZ, Haines JL, Shellenberg GD, Pericak-Vance MA, Paré G, Mayeux R, Tosto G. Polygenic Risk Score for Alzheimer's Disease in Caribbean Hispanics. Ann Neurol 2021; 90:366-376. [PMID: 34038570 PMCID: PMC8435026 DOI: 10.1002/ana.26131] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2021] [Revised: 05/17/2021] [Accepted: 05/19/2021] [Indexed: 11/07/2022]
Abstract
OBJECTIVE Polygenic risk scores (PRSs) assess the individual genetic propensity to a condition by combining sparse information scattered across genetic loci, often displaying small effect sizes. Most PRSs are constructed in European-ancestry populations, limiting their use in other ethnicities. Here we constructed and validated a PRS for late-onset Alzheimer's Disease (LOAD) in Caribbean Hispanics (CH). METHODS We used a CH discovery (n = 4,312) and independent validation sample (n = 1,850) to construct an ancestry-specific PRS ("CH-PRS") and evaluated its performance alone and with other predictors using the area under curve (AUC) and logistic regression (strength of association with LOAD and statistical significance). We tested if CH-PRS predicted conversion to LOAD in a subsample with longitudinal data (n = 1,239). We also tested the CH-PRS in an independent replication CH cohort (n = 200) and brain autopsy cohort (n = 33). Finally, we tested the effect of ancestry on PRS by using European and African American discovery cohorts to construct alternative PRSs ("EUR-PRS", "AA-PRS"). RESULTS The full model (LOAD ~ CH-PRS + sex + age + APOE-ɛ4), achieved an AUC = 74% (ORCH-PRS = 1.51 95%CI = 1.36-1.68), raising to >75% in APOE-ɛ4 non-carriers. CH-PRS alone achieved an AUC = 72% in the autopsy cohort, raising to AUC = 83% in full model. Higher CH-PRS was significantly associated with clinical LOAD in the replication CH cohort (OR = 1.61, 95%CI = 1.19-2.17) and significantly predicted conversion to LOAD (HR = 1.93, CI = 1.70-2.20) in the longitudinal subsample. EUR-PRS and AA-PRS reached lower prediction accuracy (AUC = 58% and 53%, respectively). INTERPRETATION Enriching diversity in genetic studies is critical to provide an effective PRS in profiling LOAD risk across populations. ANN NEUROL 2021;90:366-376.
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Affiliation(s)
- Sanjeev Sariya
- Taub Institute for Research on Alzheimer’s Disease and the Aging Brain, College of Physicians and Surgeons, Columbia University, New York, NY
- The Gertrude H. Sergievsky Center, College of Physicians and Surgeons, Columbia University, New York, NY
- Department of Neurology, College of Physicians and Surgeons, Columbia University and the New York Presbyterian Hospital, New York, NY
| | - Daniel Felsky
- Krembil Centre for Neuroinformatics, Centre for Addiction and Mental Health, Toronto, ON, Canada
| | - Dolly Reyes-Dumeyer
- Taub Institute for Research on Alzheimer’s Disease and the Aging Brain, College of Physicians and Surgeons, Columbia University, New York, NY
- The Gertrude H. Sergievsky Center, College of Physicians and Surgeons, Columbia University, New York, NY
- Department of Neurology, College of Physicians and Surgeons, Columbia University and the New York Presbyterian Hospital, New York, NY
| | - Ricky Lali
- Population Health Research Institute, McMaster University, Hamilton, ON, Canada
| | - Rafael A. Lantigua
- Taub Institute for Research on Alzheimer’s Disease and the Aging Brain, College of Physicians and Surgeons, Columbia University, New York, NY
- Department of Medicine, College of Physicians and Surgeons, Columbia University, and the New York Presbyterian Hospital, New York, NY
| | - Badri Vardarajan
- Taub Institute for Research on Alzheimer’s Disease and the Aging Brain, College of Physicians and Surgeons, Columbia University, New York, NY
- The Gertrude H. Sergievsky Center, College of Physicians and Surgeons, Columbia University, New York, NY
- Department of Neurology, College of Physicians and Surgeons, Columbia University and the New York Presbyterian Hospital, New York, NY
| | | | - Jonathan L. Haines
- Department of Population & Quantitative Health SciencesCleveland Institute for Computational Biology, Case Western Reserve University, Cleveland, OH
| | | | - Margaret A Pericak-Vance
- John P. Hussman Institute for Human Genomics, Miller School of Medicine, University of Miami, Miami, FL
| | - Guillaume Paré
- Population Health Research Institute, McMaster University, Hamilton, ON, Canada
| | - Richard Mayeux
- Taub Institute for Research on Alzheimer’s Disease and the Aging Brain, College of Physicians and Surgeons, Columbia University, New York, NY
- The Gertrude H. Sergievsky Center, College of Physicians and Surgeons, Columbia University, New York, NY
- Department of Neurology, College of Physicians and Surgeons, Columbia University and the New York Presbyterian Hospital, New York, NY
- Department of Medicine, College of Physicians and Surgeons, Columbia University, and the New York Presbyterian Hospital, New York, NY
- Department of Psychiatry, College of Physicians and Surgeons, Columbia University, New York, NY
| | - Giuseppe Tosto
- Taub Institute for Research on Alzheimer’s Disease and the Aging Brain, College of Physicians and Surgeons, Columbia University, New York, NY
- The Gertrude H. Sergievsky Center, College of Physicians and Surgeons, Columbia University, New York, NY
- Department of Neurology, College of Physicians and Surgeons, Columbia University and the New York Presbyterian Hospital, New York, NY
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15
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Liu J, Deng Y, Yu B, Mo B, Luo L, Yang J, Zhang X, Wang Z, Wang Y, Zhu J, Yang H, Fang S, Cheng Z, Li J, Shu Y, Luo G, Xiong W, Wei J, Li Z. Targeted resequencing showing novel common and rare genetic variants increases the risk of asthma in the Chinese Han population. J Clin Lab Anal 2021; 35:e23813. [PMID: 33969541 DOI: 10.1002/jcla.23813] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2021] [Revised: 04/16/2021] [Indexed: 11/11/2022] Open
Abstract
BACKGROUND Although studies have identified hundreds of genetic variants associated with asthma risk, a large fraction of heritability remains unexplained, especially in Chinese individuals. METHODS To identify genetic risk factors for asthma in a Han Chinese population, 211 asthma-related genes were first selected based on database searches. The genes were then sequenced for subjects in a Discovery Cohort (284 asthma patients and 205 older healthy controls) using targeted next-generation sequencing. Bioinformatics analysis and statistical association analyses were performed to reveal the associations between rare/common variants and asthma, respectively. The identified common risk variants underwent a validation analysis using a Replication Cohort (664 patients and 650 controls). RESULTS First, we identified 18 potentially functional rare loss-of-function (LOF) variants in 21/284 (7.4%) of the asthma cases. Second, using burden tests, we found that the asthma group had nominally significant (p < 0.05) burdens of rare nonsynonymous variants in 10 genes. Third, 23 common single-nucleotide polymorphisms were associated with the risk of asthma, 7/23 (30.4%) and 9/23 (39.1%) of which were modestly significant (p < 9.1 × 10-4 ) in the Replication Cohort and Combined Cohort, respectively. According to our cumulative risk model involving the modestly associated alleles, middle- and high-risk subjects had a 2.0-fold (95% CI: 1.621-2.423, p = 2.624 × 10-11 ) and 6.0-fold (95% CI: 3.623-10.156, p = 7.086 × 10-12 ) increased risk of asthma, respectively, compared with low-risk subjects. CONCLUSION This study revealed novel rare and common genetic risk factors for asthma, and provided a cumulative risk model for asthma risk prediction and stratification in Han Chinese individuals.
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Affiliation(s)
- Juan Liu
- Department of Respiratory and Critical Care Medicine, Key Laboratory of Pulmonary Diseases of Health Ministry, Key Cite of National Clinical Research Center for Respiratory Disease, Wuhan Clinical Medical Research Center for Chronic Airway Diseases, Tongji Hospital, Tongji Medical College, Huazhong University of Sciences and Technology, Wuhan, China
| | - Yanhan Deng
- Department of Respiratory and Critical Care Medicine, Key Laboratory of Pulmonary Diseases of Health Ministry, Key Cite of National Clinical Research Center for Respiratory Disease, Wuhan Clinical Medical Research Center for Chronic Airway Diseases, Tongji Hospital, Tongji Medical College, Huazhong University of Sciences and Technology, Wuhan, China
| | - Bo Yu
- Division of Cardiology, Departments of Internal Medicine and Genetic Diagnosis Center, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Biwen Mo
- Department of Respiratory Medicine, Affiliated Hospital of Guilin Medical University, Guilin, China
| | - Liman Luo
- Department of Pediatrics, The 306 Hospital of People's Liberation Army, Beijing, China
| | - Jingping Yang
- Department of Respiratory and Critical Care Medicine, The Third Affiliated Hospital of Inner Mongolia Medical University, Baotou, China
| | - Xiaoju Zhang
- Department of Respiratory Medicine, Henan Provincial People's Hospital & the People's Hospital of Zhengzhou University, Zhengzhou, China
| | - Zheng Wang
- Department of Respiratory Medicine, Henan Provincial People's Hospital & the People's Hospital of Zhengzhou University, Zhengzhou, China
| | - Yingnan Wang
- Department of Respiratory and Critical Care Medicine, Renmin Hospital of Three Gorges University, Yichang, China
| | - Jing Zhu
- Department of Respiratory and Critical Care Medicine, Renmin Hospital of Three Gorges University, Yichang, China
| | - Hua Yang
- Department of Respiratory Medicine, University Hospital of Hubei University for Nationalities, Enshi, China
| | - Shirong Fang
- Department of Respiratory Medicine, University Hospital of Hubei University for Nationalities, Enshi, China
| | - Zhenshun Cheng
- Department of Respiratory Medicine, Zhongnan Hospital of Wuhan University, Wuhan University, Wuhan, China
| | - Jingping Li
- Department of Respiratory Medicine, Qianjiang Central Hospital, Qianjiang, China
| | - Ying Shu
- Department of Respiratory Medicine, Qianjiang Central Hospital, Qianjiang, China
| | - Guangwei Luo
- Department of Respiratory Medicine, Wuhan No. 1 Hospital, Wuhan, China
| | - Weining Xiong
- Department of Respiratory and Critical Care Medicine, Key Laboratory of Pulmonary Diseases of Health Ministry, Key Cite of National Clinical Research Center for Respiratory Disease, Wuhan Clinical Medical Research Center for Chronic Airway Diseases, Tongji Hospital, Tongji Medical College, Huazhong University of Sciences and Technology, Wuhan, China.,Department of Respiratory Medicine, Shanghai Ninth People's Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Jianghong Wei
- Department of Respiratory Medicine, Affiliated Hospital of Guilin Medical University, Guilin, China
| | - Zongzhe Li
- Division of Cardiology, Departments of Internal Medicine and Genetic Diagnosis Center, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
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16
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Qian Q, Chowdhury BP, Sun Z, Lenberg J, Alam R, Vivier E, Gorska MM. Maternal diesel particle exposure promotes offspring asthma through NK cell-derived granzyme B. J Clin Invest 2021; 130:4133-4151. [PMID: 32407293 DOI: 10.1172/jci130324] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2019] [Accepted: 04/29/2020] [Indexed: 12/31/2022] Open
Abstract
Mothers living near high-traffic roads before or during pregnancy are more likely to have children with asthma. Mechanisms are unknown. Using a mouse model, here we showed that maternal exposure to diesel exhaust particles (DEP) predisposed offspring to allergic airway disease (AAD, murine counterpart of human asthma) through programming of their NK cells; predisposition to AAD did not develop in DEP pups that lacked NK cells and was induced in normal pups receiving NK cells from WT DEP pups. DEP NK cells expressed GATA3 and cosecreted IL-13 and the killer protease granzyme B in response to allergen challenge. Extracellular granzyme B did not kill, but instead stimulated protease-activated receptor 2 (PAR2) to cooperate with IL-13 in the induction of IL-25 in airway epithelial cells. Through loss-of-function and reconstitution experiments in pups, we showed that NK cells and granzyme B were required for IL-25 induction and activation of the type 2 immune response and that IL-25 mediated NK cell effects on type 2 response and AAD. Finally, experiments using human cord blood and airway epithelial cells suggested that DEP might induce an identical pathway in humans. Collectively, we describe an NK cell-dependent endotype of AAD that emerged in early life as a result of maternal exposure to DEP.
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Affiliation(s)
- Qian Qian
- Division of Allergy and Clinical Immunology, Department of Medicine, National Jewish Health (NJH), Denver, Colorado, USA
| | - Bidisha Paul Chowdhury
- Division of Allergy and Clinical Immunology, Department of Medicine, National Jewish Health (NJH), Denver, Colorado, USA
| | - Zehua Sun
- Division of Allergy and Clinical Immunology, Department of Medicine, National Jewish Health (NJH), Denver, Colorado, USA
| | - Jerica Lenberg
- Division of Allergy and Clinical Immunology, Department of Medicine, National Jewish Health (NJH), Denver, Colorado, USA
| | - Rafeul Alam
- Division of Allergy and Clinical Immunology, Department of Medicine, National Jewish Health (NJH), Denver, Colorado, USA.,Division of Allergy and Clinical Immunology, Department of Medicine, University of Colorado Anschutz Medical Campus, Aurora, Colorado, USA
| | - Eric Vivier
- Innate Pharma Research Labs, Innate Pharma, Marseille, France.,Centre d'Immunologie de Marseille-Luminy, CNRS, INSERM, Aix Marseille University, Marseille, France.,Service d'Immunologie, Marseille Immunopole, Hôpital de la Timone, Assistance Publique des Hôpitaux de Marseille, Marseille, France
| | - Magdalena M Gorska
- Division of Allergy and Clinical Immunology, Department of Medicine, National Jewish Health (NJH), Denver, Colorado, USA.,Division of Allergy and Clinical Immunology, Department of Medicine, University of Colorado Anschutz Medical Campus, Aurora, Colorado, USA
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17
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Ahluwalia TS, Eliasen AU, Sevelsted A, Pedersen CET, Stokholm J, Chawes B, Bork-Jensen J, Grarup N, Pedersen O, Hansen T, Linneberg A, Sharma A, Weiss ST, Evans MD, Jackson DJ, Morin A, Krogfelt KA, Schjørring S, Mortensen PB, Hougaard DM, Bybjerg-Grauholm J, Bækvad-Hansen M, Mors O, Nordentoft M, Børglum AD, Werge T, Agerbo E, Gern JE, Lemanske RF, Ober C, Pedersen AG, Bisgaard H, Bønnelykke K. FUT2-ABO epistasis increases the risk of early childhood asthma and Streptococcus pneumoniae respiratory illnesses. Nat Commun 2020; 11:6398. [PMID: 33328473 PMCID: PMC7744576 DOI: 10.1038/s41467-020-19814-6] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2019] [Accepted: 10/29/2020] [Indexed: 12/17/2022] Open
Abstract
Asthma with severe exacerbation is the most common cause of hospitalization among young children. We aim to increase the understanding of this clinically important disease entity through a genome-wide association study. The discovery analysis comprises 2866 children experiencing severe asthma exacerbation between ages 2 and 6 years, and 65,415 non-asthmatic controls, and we replicate findings in 918 children from the Copenhagen Prospective Studies on Asthma in Childhood (COPSAC) birth cohorts. We identify rs281379 near FUT2/MAMSTR on chromosome 19 as a novel risk locus (OR = 1.18 (95% CI = 1.11-1.25), Pdiscovery = 2.6 × 10-9) as well as a biologically plausible interaction between functional variants in FUT2 and ABO. We further discover and replicate a potential causal mechanism behind this interaction related to S. pneumoniae respiratory illnesses. These results suggest a novel mechanism of early childhood asthma and demonstrates the importance of phenotype-specificity for discovery of asthma genes and epistasis.
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Affiliation(s)
- Tarunveer S Ahluwalia
- COPSAC, Copenhagen Prospective Studies on Asthma in Childhood, Herlev and Gentofte Hospital, University of Copenhagen, Copenhagen, Denmark
- Steno Diabetes Center Copenhagen, Gentofte, Denmark
- Department of Biology, The Bioinformatics Center, University of Copenhagen, Copenhagen, Denmark
| | - Anders U Eliasen
- COPSAC, Copenhagen Prospective Studies on Asthma in Childhood, Herlev and Gentofte Hospital, University of Copenhagen, Copenhagen, Denmark
- Section for Bioinformatics, Department of Health Technology, Technical University of Denmark, Copenhagen, Denmark
| | - Astrid Sevelsted
- COPSAC, Copenhagen Prospective Studies on Asthma in Childhood, Herlev and Gentofte Hospital, University of Copenhagen, Copenhagen, Denmark
| | - Casper-Emil T Pedersen
- COPSAC, Copenhagen Prospective Studies on Asthma in Childhood, Herlev and Gentofte Hospital, University of Copenhagen, Copenhagen, Denmark
| | - Jakob Stokholm
- COPSAC, Copenhagen Prospective Studies on Asthma in Childhood, Herlev and Gentofte Hospital, University of Copenhagen, Copenhagen, Denmark
| | - Bo Chawes
- COPSAC, Copenhagen Prospective Studies on Asthma in Childhood, Herlev and Gentofte Hospital, University of Copenhagen, Copenhagen, Denmark
| | - Jette Bork-Jensen
- Novo Nordisk Foundation Center for Basic Metabolic Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Niels Grarup
- Novo Nordisk Foundation Center for Basic Metabolic Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Oluf Pedersen
- Novo Nordisk Foundation Center for Basic Metabolic Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Torben Hansen
- Novo Nordisk Foundation Center for Basic Metabolic Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Allan Linneberg
- Center for Clinical Research and Disease Prevention, Bispebjerg and Frederiksberg Hospital, The Capital Region, Copenhagen, Denmark
- Department of Clinical Medicine, University of Copenhagen, Copenhagen, Denmark
| | - Amitabh Sharma
- Channing Division of Network Medicine, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | - Scott T Weiss
- Channing Division of Network Medicine, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | - Michael D Evans
- Clinical and Translational Science Institute, University of Minnesota, Minneapolis, MN, USA
| | - Daniel J Jackson
- Department of Pediatrics, University of Wisconsin, Madison, WI, USA
| | - Andreanne Morin
- Department of Human Genetics, University of Chicago, Chicago, IL, USA
| | - Karen A Krogfelt
- Department of Bacteria, Parasites and Fungi, Statens Serum Institut, Copenhagen, Denmark
- Department of Science and Environment, Roskilde University, Roskilde, Denmark
| | - Susanne Schjørring
- Department of Bacteria, Parasites and Fungi, Statens Serum Institut, Copenhagen, Denmark
| | - Preben B Mortensen
- iPSYCH, The Lundbeck Foundation Initiative for Integrated Psychiatric Research, Copenhagen, Denmark
- NCRR, The National Center for Register-based research, Business and Social Sciences, Aarhus University, Aarhus C, Denmark
- CIRRAU-Center for Integrated Register-Based Research at Aarhus University, Aarhus C, Denmark
| | - David M Hougaard
- iPSYCH, The Lundbeck Foundation Initiative for Integrated Psychiatric Research, Copenhagen, Denmark
- Department for Congenital Disorders, Statens Serum Institut, Copenhagen, Denmark
- Den Neonatale Screenings Biobank, SSI, Copenhagen, Denmark
| | - Jonas Bybjerg-Grauholm
- iPSYCH, The Lundbeck Foundation Initiative for Integrated Psychiatric Research, Copenhagen, Denmark
- Department for Congenital Disorders, Statens Serum Institut, Copenhagen, Denmark
- Den Neonatale Screenings Biobank, SSI, Copenhagen, Denmark
| | - Marie Bækvad-Hansen
- iPSYCH, The Lundbeck Foundation Initiative for Integrated Psychiatric Research, Copenhagen, Denmark
- Department for Congenital Disorders, Statens Serum Institut, Copenhagen, Denmark
- Den Neonatale Screenings Biobank, SSI, Copenhagen, Denmark
| | - Ole Mors
- iPSYCH, The Lundbeck Foundation Initiative for Integrated Psychiatric Research, Copenhagen, Denmark
- Psychosis Research Unit, Aarhus University Hospital-Psychiatry, Risskov, Denmark
| | - Merete Nordentoft
- iPSYCH, The Lundbeck Foundation Initiative for Integrated Psychiatric Research, Copenhagen, Denmark
- Mental Health Center Copenhagen, Capital Region of Denmark, Copenhagen University Hospital, Copenhagen, Denmark
| | - Anders D Børglum
- iPSYCH, The Lundbeck Foundation Initiative for Integrated Psychiatric Research, Copenhagen, Denmark
- Department of Biomedicine and iSEQ, Center for Integrative Sequencing, Aarhus University, Aarhus C, Denmark
- Center for Genomics and Personalized Medicine, Central Region Denmark, Aarhus C, Denmark
| | - Thomas Werge
- iPSYCH, The Lundbeck Foundation Initiative for Integrated Psychiatric Research, Copenhagen, Denmark
- Mental Health Center Copenhagen, Capital Region of Denmark, Copenhagen University Hospital, Copenhagen, Denmark
- Institute of Biological Psychiatry, Copenhagen Mental Health Services, Copenhagen, Denmark
- Center for GeoGenetics, GLOBE Institute, University of Copenhagen, Copenhagen, Denmark
| | - Esben Agerbo
- iPSYCH, The Lundbeck Foundation Initiative for Integrated Psychiatric Research, Copenhagen, Denmark
- NCRR, The National Center for Register-based research, Business and Social Sciences, Aarhus University, Aarhus C, Denmark
- CIRRAU-Center for Integrated Register-Based Research at Aarhus University, Aarhus C, Denmark
| | - James E Gern
- Department of Pediatrics, University of Wisconsin, Madison, WI, USA
| | | | - Carole Ober
- Department of Human Genetics, University of Chicago, Chicago, IL, USA
| | - Anders G Pedersen
- Section for Bioinformatics, Department of Health Technology, Technical University of Denmark, Copenhagen, Denmark
| | - Hans Bisgaard
- COPSAC, Copenhagen Prospective Studies on Asthma in Childhood, Herlev and Gentofte Hospital, University of Copenhagen, Copenhagen, Denmark
| | - Klaus Bønnelykke
- COPSAC, Copenhagen Prospective Studies on Asthma in Childhood, Herlev and Gentofte Hospital, University of Copenhagen, Copenhagen, Denmark.
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18
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Han Y, Jia Q, Jahani PS, Hurrell BP, Pan C, Huang P, Gukasyan J, Woodward NC, Eskin E, Gilliland FD, Akbari O, Hartiala JA, Allayee H. Genome-wide analysis highlights contribution of immune system pathways to the genetic architecture of asthma. Nat Commun 2020; 11:1776. [PMID: 32296059 PMCID: PMC7160128 DOI: 10.1038/s41467-020-15649-3] [Citation(s) in RCA: 100] [Impact Index Per Article: 25.0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2019] [Accepted: 03/17/2020] [Indexed: 12/20/2022] Open
Abstract
Asthma is a chronic and genetically complex respiratory disease that affects over 300 million people worldwide. Here, we report a genome-wide analysis for asthma using data from the UK Biobank and the Trans-National Asthma Genetic Consortium. We identify 66 previously unknown asthma loci and demonstrate that the susceptibility alleles in these regions are, either individually or as a function of cumulative genetic burden, associated with risk to a greater extent in men than women. Bioinformatics analyses prioritize candidate causal genes at 52 loci, including CD52, and demonstrate that asthma-associated variants are enriched in regions of open chromatin in immune cells. Lastly, we show that a murine anti-CD52 antibody mimics the immune cell-depleting effects of a clinically used human anti-CD52 antibody and reduces allergen-induced airway hyperreactivity in mice. These results further elucidate the genetic architecture of asthma and provide important insight into the immunological and sex-specific relevance of asthma-associated risk variants. Asthma is a common disease of the airways for which numerous genetic loci have been identified. Here, Han et al. carry out a genome-wide analysis for asthma to identify additional loci, report sex-stratified and genetic risk score analyses, and functionally follow-up one locus using a murine model of airway hyperreactivity.
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Affiliation(s)
- Yi Han
- Department of Preventive Medicine, Keck School of Medicine, University of Southern California, Los Angeles, CA, 90033, USA.,Department of Biochemistry & Molecular Medicine, Keck School of Medicine, University of Southern California, Los Angeles, CA, 90033, USA
| | - Qiong Jia
- Department of Preventive Medicine, Keck School of Medicine, University of Southern California, Los Angeles, CA, 90033, USA.,Department of Biochemistry & Molecular Medicine, Keck School of Medicine, University of Southern California, Los Angeles, CA, 90033, USA
| | - Pedram Shafiei Jahani
- Department of Molecular Microbiology and Immunology, Keck School of Medicine, University of Southern California, Los Angeles, CA, 90033, USA
| | - Benjamin P Hurrell
- Department of Molecular Microbiology and Immunology, Keck School of Medicine, University of Southern California, Los Angeles, CA, 90033, USA
| | - Calvin Pan
- Department of Human Genetics, David Geffen School of Medicine at UCLA, Los Angeles, CA, 90095, USA
| | - Pin Huang
- Department of Preventive Medicine, Keck School of Medicine, University of Southern California, Los Angeles, CA, 90033, USA.,Department of Biochemistry & Molecular Medicine, Keck School of Medicine, University of Southern California, Los Angeles, CA, 90033, USA
| | - Janet Gukasyan
- Department of Preventive Medicine, Keck School of Medicine, University of Southern California, Los Angeles, CA, 90033, USA.,Department of Biochemistry & Molecular Medicine, Keck School of Medicine, University of Southern California, Los Angeles, CA, 90033, USA
| | - Nicholas C Woodward
- Department of Preventive Medicine, Keck School of Medicine, University of Southern California, Los Angeles, CA, 90033, USA.,Department of Biochemistry & Molecular Medicine, Keck School of Medicine, University of Southern California, Los Angeles, CA, 90033, USA
| | - Eleazar Eskin
- Department of Computer Science and Inter-Departmental Program in Bioinformatics, University of California, Los Angeles, Los Angeles, CA, 90095, USA
| | - Frank D Gilliland
- Department of Preventive Medicine, Keck School of Medicine, University of Southern California, Los Angeles, CA, 90033, USA
| | - Omid Akbari
- Department of Molecular Microbiology and Immunology, Keck School of Medicine, University of Southern California, Los Angeles, CA, 90033, USA
| | - Jaana A Hartiala
- Department of Preventive Medicine, Keck School of Medicine, University of Southern California, Los Angeles, CA, 90033, USA.,Department of Biochemistry & Molecular Medicine, Keck School of Medicine, University of Southern California, Los Angeles, CA, 90033, USA
| | - Hooman Allayee
- Department of Preventive Medicine, Keck School of Medicine, University of Southern California, Los Angeles, CA, 90033, USA. .,Department of Biochemistry & Molecular Medicine, Keck School of Medicine, University of Southern California, Los Angeles, CA, 90033, USA.
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19
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Gao Y, Li J, Zhang Y, Zhang L. Replication study of susceptibility variants associated with allergic rhinitis and allergy in Han Chinese. Allergy Asthma Clin Immunol 2020; 16:13. [PMID: 32082391 PMCID: PMC7014941 DOI: 10.1186/s13223-020-0411-9] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2019] [Accepted: 01/28/2020] [Indexed: 12/12/2022] Open
Abstract
Background Allergic rhinitis (AR) is believed to be a complex genetic disease. The last decade has been marked by the publication of more than 20 genome-wide association studies (GWASs) of AR and associated allergic phenotypes and allergic diseases, which have shown allergic diseases and traits to share a large number of genetic susceptibility loci. The aim of present study was therefore to investigate the highly replicated allergy related genes and variants as candidates for AR in Han Chinese subjects. Methods A total of 762 AR patients and 760 control subjects were recruited, and a total of 58 susceptible variants previously reported to be associated with allergic traits were choose for replication. Results Logistic regression analyses revealed that in the co-dominant-effect model as assessed by the AIC, compared with wild-type carriers, significant AR risk were associated with rs9865818 in LPP (P = 0.029, OR = 1.469 for GG vs. AA); rs6554809 in DNAH5 (P = 0.000, OR = 1.597 for TC vs. CC); rs1438673 in WDR36-CAMK4 loci (P = 0.037, OR = 1.396 for CC vs.TT), rs7775228 in HLA region (P = 0.000, OR = 1.589 for TC vs.TT), rs7203459 in CLEC16A (P = 0.025, OR = 0.731 for TC vs. TT). Conclusion We replicated Han Chinese AR-specific susceptibility loci in LPP, DNAH5, HLA, CLEC16A and WDR36-CAMK4. Further understanding the molecular mechanisms underlying these associations may provide new insights into the etiology of allergic disease.
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Affiliation(s)
- Yunbo Gao
- 1Department of Otolaryngology Head and Neck Surgery, Beijing TongRen Hospital, Capital Medical University, Beijing, 100730 People's Republic of China
| | - Jingyun Li
- 1Department of Otolaryngology Head and Neck Surgery, Beijing TongRen Hospital, Capital Medical University, Beijing, 100730 People's Republic of China.,2Beijing Key Laboratory of Nasal Diseases, Beijing Institute of Otolaryngology, No. 17, HouGouHuTong, DongCheng District, Beijing, 100005 People's Republic of China
| | - Yuan Zhang
- 1Department of Otolaryngology Head and Neck Surgery, Beijing TongRen Hospital, Capital Medical University, Beijing, 100730 People's Republic of China.,2Beijing Key Laboratory of Nasal Diseases, Beijing Institute of Otolaryngology, No. 17, HouGouHuTong, DongCheng District, Beijing, 100005 People's Republic of China.,3Department of Allergy, Beijing TongRen Hospital, Capital Medical University, Beijing, 100730 People's Republic of China
| | - Luo Zhang
- 1Department of Otolaryngology Head and Neck Surgery, Beijing TongRen Hospital, Capital Medical University, Beijing, 100730 People's Republic of China.,2Beijing Key Laboratory of Nasal Diseases, Beijing Institute of Otolaryngology, No. 17, HouGouHuTong, DongCheng District, Beijing, 100005 People's Republic of China.,3Department of Allergy, Beijing TongRen Hospital, Capital Medical University, Beijing, 100730 People's Republic of China
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20
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Dapas M, Sisk R, Legro RS, Urbanek M, Dunaif A, Hayes MG. Family-Based Quantitative Trait Meta-Analysis Implicates Rare Noncoding Variants in DENND1A in Polycystic Ovary Syndrome. J Clin Endocrinol Metab 2019; 104:3835-3850. [PMID: 31038695 PMCID: PMC6660913 DOI: 10.1210/jc.2018-02496] [Citation(s) in RCA: 38] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/19/2018] [Accepted: 04/17/2019] [Indexed: 02/07/2023]
Abstract
CONTEXT Polycystic ovary syndrome (PCOS) is among the most common endocrine disorders of premenopausal women, affecting 5% to15% of this population depending on the diagnostic criteria applied. It is characterized by hyperandrogenism, ovulatory dysfunction, and polycystic ovarian morphology. PCOS is highly heritable, but only a small proportion of this heritability can be accounted for by the common genetic susceptibility variants identified to date. OBJECTIVE The objective of this study was to test whether rare genetic variants contribute to PCOS pathogenesis. DESIGN, PATIENTS, AND METHODS We performed whole-genome sequencing on DNA from 261 individuals from 62 families with one or more daughters with PCOS. We tested for associations of rare variants with PCOS and its concomitant hormonal traits using a quantitative trait meta-analysis. RESULTS We found rare variants in DENND1A (P = 5.31 × 10-5, adjusted P = 0.039) that were significantly associated with reproductive and metabolic traits in PCOS families. CONCLUSIONS Common variants in DENND1A have previously been associated with PCOS diagnosis in genome-wide association studies. Subsequent studies indicated that DENND1A is an important regulator of human ovarian androgen biosynthesis. Our findings provide additional evidence that DENND1A plays a central role in PCOS and suggest that rare noncoding variants contribute to disease pathogenesis.
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Affiliation(s)
- Matthew Dapas
- Division of Endocrinology, Metabolism, and Molecular Medicine, Department of Medicine, Northwestern University Feinberg School of Medicine, Chicago, Illinois
| | - Ryan Sisk
- Division of Endocrinology, Metabolism, and Molecular Medicine, Department of Medicine, Northwestern University Feinberg School of Medicine, Chicago, Illinois
| | - Richard S Legro
- Department of Obstetrics and Gynecology, Penn State College of Medicine, Hershey, Pennsylvania
| | - Margrit Urbanek
- Division of Endocrinology, Metabolism, and Molecular Medicine, Department of Medicine, Northwestern University Feinberg School of Medicine, Chicago, Illinois
- Center for Genetic Medicine, Northwestern University Feinberg School of Medicine, Chicago, Illinois
- Center for Reproductive Science, Northwestern University Feinberg School of Medicine, Chicago, Illinois
| | - Andrea Dunaif
- Division of Endocrinology, Diabetes, and Bone Disease, Icahn School of Medicine at Mount Sinai, New York, New York
| | - M Geoffrey Hayes
- Division of Endocrinology, Metabolism, and Molecular Medicine, Department of Medicine, Northwestern University Feinberg School of Medicine, Chicago, Illinois
- Center for Genetic Medicine, Northwestern University Feinberg School of Medicine, Chicago, Illinois
- Department of Anthropology, Northwestern University, Evanston, Illinois
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21
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Tosto G, Vardarajan B, Sariya S, Brickman AM, Andrews H, Manly JJ, Schupf N, Reyes-Dumeyer D, Lantigua R, Bennett DA, De Jager PL, Mayeux R. Association of Variants in PINX1 and TREM2 With Late-Onset Alzheimer Disease. JAMA Neurol 2019; 76:942-948. [PMID: 31058951 DOI: 10.1001/jamaneurol.2019.1066] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
Importance Genetic causes of late-onset Alzheimer disease (LOAD) are not completely explained by known genetic loci. Whole-exome and whole-genome sequencing can improve the understanding of the causes of LOAD and provide initial steps required to identify potential therapeutic targets. Objective To identify the genetic loci for LOAD across different ethnic groups. Design, Setting, and Participants This multicenter cohort study was designed to analyze whole-exome sequencing data from a multiethnic cohort using a transethnic gene-kernel association test meta-analysis, adjusted for sex, age, and principal components, to identify genetic variants associated with LOAD. A meta-analysis was conducted on the results of 2 independent studies of whole-exome and whole-genome sequence data from individuals of European ancestry. This group of European American, African American, and Caribbean Hispanic individuals participating in an urban population-based study were the discovery cohort; the additional cohorts included affected individuals and control participants from 2 publicly available data sets. Replication was achieved using independent data sets from Caribbean Hispanic families with multiple family members affected by LOAD and the International Genetics of Alzheimer Project. Main Outcomes and Measures Late-onset Alzheimer disease. Results The discovery cohort included 3595 affected individuals, while the additional cohorts included 5931 individuals with LOAD and 5504 control participants. Of 3916 individuals in the discovery cohort, we included 3595 individuals (1397 with LOAD and 2198 cognitively healthy controls; 2451 [68.2%] women; mean [SD] age, 80.3 [6.83] years). Another 321 individuals (8.2%) were excluded because of non-LOAD diagnosis, age younger than 60 years, missing covariates, duplicate data, or genetic outlier status. Gene-based tests that compared affected individuals (n = 7328) and control participants (n = 7702) and included only rare and uncommon variants annotated as having moderate-high functional effect supported PINX1 (8p23.1) as a locus with gene-wide significance (P = 2.81 × 10-6) after meta-analysis across the 3 studies. The PINX1 finding was replicated using data from the family-based study and the International Genetics of Alzheimer Project. Full meta-analysis of discovery and replication cohorts reached a P value of 6.16 × 10-7 for PINX1 (in 7620 affected individuals vs 7768 control participants). We also identified TREM2 in an annotation model that prioritized highly deleterious variants with a combined annotation dependent depletion greater than 20 (P= 1.0 × 10-7). Conclusions and Relevance This gene-based, transethnic approach identified PINX1, a gene involved in telomere integrity, and TREM2, a gene with a product of an immune receptor found in microglia, as associated with LOAD. Both genes have well-established roles in aging and neurodegeneration.
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Affiliation(s)
- Giuseppe Tosto
- Taub Institute for Research on Alzheimer's Disease and the Aging Brain, College of Physicians and Surgeons, Columbia University, New York, New York.,The Gertrude H. Sergievsky Center, College of Physicians and Surgeons, Columbia University, New York, New York.,Department of Neurology, College of Physicians and Surgeons, Columbia University, the New York Presbyterian Hospital, New York
| | - Badri Vardarajan
- Taub Institute for Research on Alzheimer's Disease and the Aging Brain, College of Physicians and Surgeons, Columbia University, New York, New York.,The Gertrude H. Sergievsky Center, College of Physicians and Surgeons, Columbia University, New York, New York
| | - Sanjeev Sariya
- Taub Institute for Research on Alzheimer's Disease and the Aging Brain, College of Physicians and Surgeons, Columbia University, New York, New York.,The Gertrude H. Sergievsky Center, College of Physicians and Surgeons, Columbia University, New York, New York
| | - Adam M Brickman
- Taub Institute for Research on Alzheimer's Disease and the Aging Brain, College of Physicians and Surgeons, Columbia University, New York, New York.,The Gertrude H. Sergievsky Center, College of Physicians and Surgeons, Columbia University, New York, New York.,Department of Neurology, College of Physicians and Surgeons, Columbia University, the New York Presbyterian Hospital, New York
| | - Howard Andrews
- Taub Institute for Research on Alzheimer's Disease and the Aging Brain, College of Physicians and Surgeons, Columbia University, New York, New York.,The Gertrude H. Sergievsky Center, College of Physicians and Surgeons, Columbia University, New York, New York.,Department of Psychiatry, College of Physicians and Surgeons, Columbia University, New York, New York
| | - Jennifer J Manly
- Taub Institute for Research on Alzheimer's Disease and the Aging Brain, College of Physicians and Surgeons, Columbia University, New York, New York.,The Gertrude H. Sergievsky Center, College of Physicians and Surgeons, Columbia University, New York, New York.,Department of Neurology, College of Physicians and Surgeons, Columbia University, the New York Presbyterian Hospital, New York
| | - Nicole Schupf
- Taub Institute for Research on Alzheimer's Disease and the Aging Brain, College of Physicians and Surgeons, Columbia University, New York, New York.,The Gertrude H. Sergievsky Center, College of Physicians and Surgeons, Columbia University, New York, New York.,Department of Neurology, College of Physicians and Surgeons, Columbia University, the New York Presbyterian Hospital, New York.,Department of Epidemiology, Mailman School of Public Health, Columbia University, New York, New York
| | - Dolly Reyes-Dumeyer
- Taub Institute for Research on Alzheimer's Disease and the Aging Brain, College of Physicians and Surgeons, Columbia University, New York, New York.,The Gertrude H. Sergievsky Center, College of Physicians and Surgeons, Columbia University, New York, New York
| | - Rafael Lantigua
- Taub Institute for Research on Alzheimer's Disease and the Aging Brain, College of Physicians and Surgeons, Columbia University, New York, New York.,The Gertrude H. Sergievsky Center, College of Physicians and Surgeons, Columbia University, New York, New York.,Department of Medicine, College of Physicians and Surgeons, Columbia University, The New York Presbyterian Hospital, New York
| | - David A Bennett
- Rush Alzheimer's Disease Center, Rush University Medical Center, Chicago, Illinois
| | - Phillip L De Jager
- Taub Institute for Research on Alzheimer's Disease and the Aging Brain, College of Physicians and Surgeons, Columbia University, New York, New York.,The Gertrude H. Sergievsky Center, College of Physicians and Surgeons, Columbia University, New York, New York.,Department of Neurology, College of Physicians and Surgeons, Columbia University, the New York Presbyterian Hospital, New York
| | - Richard Mayeux
- Taub Institute for Research on Alzheimer's Disease and the Aging Brain, College of Physicians and Surgeons, Columbia University, New York, New York.,The Gertrude H. Sergievsky Center, College of Physicians and Surgeons, Columbia University, New York, New York.,Department of Neurology, College of Physicians and Surgeons, Columbia University, the New York Presbyterian Hospital, New York.,Department of Psychiatry, College of Physicians and Surgeons, Columbia University, New York, New York.,Department of Epidemiology, Mailman School of Public Health, Columbia University, New York, New York
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22
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Lu SY, He ZZ, Xu JX, Yang C, Chen LJ, Gong B. Association of Polymorphisms at the SIX1-SIX6 Locus With Primary Open-Angle Glaucoma. ACTA ACUST UNITED AC 2019; 60:2914-2924. [PMID: 31284308 DOI: 10.1167/iovs.18-26489] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Affiliation(s)
- Shi Yao Lu
- Department of Ophthalmology and Visual Sciences, The Chinese University of Hong Kong, Hong Kong, China
| | - Zong Ze He
- Department of Neurosurgery, Sichuan Academy of Medical Sciences and Sichuan Provincial People's Hospital, School of Medicine, University of Electronic Science and Technology of China, Chengdu, Sichuan, China
| | - Jia Xin Xu
- School of Clinic Medicine, Southwest Medical University, Luzhou, Sichuan, China
| | - Chen Yang
- The Key Laboratory for Human Disease Gene Study of Sichuan Province and Department of Laboratory Medicine, Sichuan Academy of Medical Sciences and Sichuan Provincial People's Hospital, School of Medicine, University of Electronic Science and Technology of China, Chengdu, Sichuan, China
| | - Li Jia Chen
- Department of Ophthalmology and Visual Sciences, The Chinese University of Hong Kong, Hong Kong, China
| | - Bo Gong
- The Key Laboratory for Human Disease Gene Study of Sichuan Province and Department of Laboratory Medicine, Sichuan Academy of Medical Sciences and Sichuan Provincial People's Hospital, School of Medicine, University of Electronic Science and Technology of China, Chengdu, Sichuan, China
- Institute of Chengdu Biology, Sichuan Translational Medicine Hospital, Chinese Academy of Sciences, Chengdu, Sichuan, China
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23
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Sariya S, Lee JH, Mayeux R, Vardarajan BN, Reyes-Dumeyer D, Manly JJ, Brickman AM, Lantigua R, Medrano M, Jimenez-Velazquez IZ, Tosto G. Rare Variants Imputation in Admixed Populations: Comparison Across Reference Panels and Bioinformatics Tools. Front Genet 2019; 10:239. [PMID: 31001313 PMCID: PMC6456789 DOI: 10.3389/fgene.2019.00239] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2018] [Accepted: 03/04/2019] [Indexed: 11/13/2022] Open
Abstract
Background Imputation has become a standard approach in genome-wide association studies (GWAS) to infer in silico untyped markers. Although feasibility for common variants imputation is well established, we aimed to assess rare and ultra-rare variants’ imputation in an admixed Caribbean Hispanic population (CH). Methods We evaluated imputation accuracy in CH (N = 1,000), focusing on rare (0.1% ≤ minor allele frequency (MAF) ≤ 1%) and ultra-rare (MAF < 0.1%) variants. We used two reference panels, the Haplotype Reference Consortium (HRC; N = 27,165) and 1000 Genome Project (1000G phase 3; N = 2,504) and multiple phasing (SHAPEIT, Eagle2) and imputation algorithms (IMPUTE2, MACH-Admix). To assess imputation quality, we reported: (a) high-quality variant counts according to imputation tools’ internal indexes (e.g., IMPUTE2 “Info” ≥ 80%). (b) Wilcoxon Signed-Rank Test comparing imputation quality for genotyped variants that were masked and imputed; (c) Cohen’s kappa coefficient to test agreement between imputed and whole-exome sequencing (WES) variants; (d) imputation of G206A mutation in the PSEN1 (ultra-rare in the general population an more frequent in CH) followed by confirmation genotyping. We also tested ancestry proportion (European, African and Native American) against WES-imputation mismatches in a Poisson regression fashion. Results SHAPEIT2 retrieved higher percentage of imputed high-quality variants than Eagle2 (rare: 51.02% vs. 48.60%; ultra-rare 0.66% vs. 0.65%, Wilcoxon p-value < 0.001). SHAPEIT-IMPUTE2 employing HRC outperformed 1000G (64.50% vs. 59.17%; 1.69% vs. 0.75% for high-quality rare and ultra-rare variants, respectively, Wilcoxon p-value < 0.001). SHAPEIT-IMPUTE2 outperformed MaCH-Admix. Compared to 1000G, HRC-imputation retrieved a higher number of high-quality rare and ultra-rare variants, despite showing lower agreement between imputed and WES variants (e.g., rare: 98.86% for HRC vs. 99.02% for 1000G). High Kappa (K = 0.99) was observed for both reference panels. Twelve G206A mutation carriers were imputed and all validated by confirmation genotyping. African ancestry was associated with higher imputation errors for uncommon and rare variants (p-value < 1e-05). Conclusion Reference panels with larger numbers of haplotypes can improve imputation quality for rare and ultra-rare variants in admixed populations such as CH. Ethnic composition is an important predictor of imputation accuracy, with higher African ancestry associated with poorer imputation accuracy.
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Affiliation(s)
- Sanjeev Sariya
- Taub Institute for Research on Alzheimer's Disease and the Aging Brain, Vagelos College of Physicians and Surgeons, Columbia University, New York, NY, United States.,The Gertrude H. Sergievsky Center, College of Physicians and Surgeons, Columbia University, New York, NY, United States
| | - Joseph H Lee
- Taub Institute for Research on Alzheimer's Disease and the Aging Brain, Vagelos College of Physicians and Surgeons, Columbia University, New York, NY, United States.,The Gertrude H. Sergievsky Center, College of Physicians and Surgeons, Columbia University, New York, NY, United States.,Department of Neurology, College of Physicians and Surgeons, New York-Presbyterian Hospital, Columbia University Medical Center, New York, NY, United States
| | - Richard Mayeux
- Taub Institute for Research on Alzheimer's Disease and the Aging Brain, Vagelos College of Physicians and Surgeons, Columbia University, New York, NY, United States.,The Gertrude H. Sergievsky Center, College of Physicians and Surgeons, Columbia University, New York, NY, United States.,Department of Neurology, College of Physicians and Surgeons, New York-Presbyterian Hospital, Columbia University Medical Center, New York, NY, United States
| | - Badri N Vardarajan
- Taub Institute for Research on Alzheimer's Disease and the Aging Brain, Vagelos College of Physicians and Surgeons, Columbia University, New York, NY, United States.,The Gertrude H. Sergievsky Center, College of Physicians and Surgeons, Columbia University, New York, NY, United States
| | - Dolly Reyes-Dumeyer
- Taub Institute for Research on Alzheimer's Disease and the Aging Brain, Vagelos College of Physicians and Surgeons, Columbia University, New York, NY, United States.,The Gertrude H. Sergievsky Center, College of Physicians and Surgeons, Columbia University, New York, NY, United States
| | - Jennifer J Manly
- Taub Institute for Research on Alzheimer's Disease and the Aging Brain, Vagelos College of Physicians and Surgeons, Columbia University, New York, NY, United States.,The Gertrude H. Sergievsky Center, College of Physicians and Surgeons, Columbia University, New York, NY, United States.,Department of Neurology, College of Physicians and Surgeons, New York-Presbyterian Hospital, Columbia University Medical Center, New York, NY, United States
| | - Adam M Brickman
- Taub Institute for Research on Alzheimer's Disease and the Aging Brain, Vagelos College of Physicians and Surgeons, Columbia University, New York, NY, United States.,The Gertrude H. Sergievsky Center, College of Physicians and Surgeons, Columbia University, New York, NY, United States.,Department of Neurology, College of Physicians and Surgeons, New York-Presbyterian Hospital, Columbia University Medical Center, New York, NY, United States
| | - Rafael Lantigua
- Medicine College of Physicians and Surgeons, and The Department of Epidemiology, School of Public Health, Columbia University, New York, NY, United States
| | - Martin Medrano
- School of Medicine, Pontificia Universidad Catolica Madre y Maestra, Santiago, Dominican Republic
| | - Ivonne Z Jimenez-Velazquez
- Department of Medicine, Geriatrics Program, University of Puerto Rico School of Medicine, San Juan, Puerto Rico
| | - Giuseppe Tosto
- Taub Institute for Research on Alzheimer's Disease and the Aging Brain, Vagelos College of Physicians and Surgeons, Columbia University, New York, NY, United States.,The Gertrude H. Sergievsky Center, College of Physicians and Surgeons, Columbia University, New York, NY, United States.,Department of Neurology, College of Physicians and Surgeons, New York-Presbyterian Hospital, Columbia University Medical Center, New York, NY, United States
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24
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Lyon de Ana C, Arakcheeva K, Agnihotri P, Derosia N, Winandy S. Lack of Ikaros Deregulates Inflammatory Gene Programs in T Cells. THE JOURNAL OF IMMUNOLOGY 2019; 202:1112-1123. [PMID: 30635395 DOI: 10.4049/jimmunol.1801270] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/18/2018] [Accepted: 12/10/2018] [Indexed: 12/15/2022]
Abstract
CD4 Th cells are organizers of the immune response, directing other immune cells to initiate and maintain effective humoral and cellular immunity. CD4 T cells differentiate into distinct Th effector or regulatory subsets in response to signals delivered to them during the course of infection. Ikaros is a transcription factor that is expressed in blood cells from the level of the hematopoietic stem cell. It is required for normal thymic T cell development and serves as a tumor suppressor, as lack of Ikaros in developing lymphoid cells results in leukemia. To study the role of Ikaros in CD4 T cell differentiation and function, an Ikaros conditional knockout mouse was developed such that Ikaros expression was deleted specifically in mature T cells, thus avoiding defects observed in germline Ikaros mutant mice. Using this model system, we have shown that in the absence of Ikaros, CD4 T cells are able to attain Th1, Th2, and Th17, but not inducible regulatory T, cell fates. However, they show enhanced expression of a cohort of proinflammatory cytokines, resulting in differentiation of Th17 cells with a phenotype that has been associated with autoimmunity and pathological inflammation. In addition, we define Ikaros as a repressor of the gene program associated with the response to type I IFNs, another key pathway whose deregulation is linked to autoimmunity. Taken together, these data definitively define Ikaros as a critical regulator at the center of the inflammatory response in T cells and highlight a potential role in suppressing autoimmunity.
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Affiliation(s)
- Carolina Lyon de Ana
- Department of Pathology and Laboratory Medicine, Immunology Training Program, Boston University School of Medicine, Boston, MA 02118
| | - Ksenia Arakcheeva
- Department of Pathology and Laboratory Medicine, Immunology Training Program, Boston University School of Medicine, Boston, MA 02118
| | - Parul Agnihotri
- Department of Pathology and Laboratory Medicine, Immunology Training Program, Boston University School of Medicine, Boston, MA 02118
| | - Nicole Derosia
- Department of Pathology and Laboratory Medicine, Immunology Training Program, Boston University School of Medicine, Boston, MA 02118
| | - Susan Winandy
- Department of Pathology and Laboratory Medicine, Immunology Training Program, Boston University School of Medicine, Boston, MA 02118
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25
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Park JS, Son JH, Park CS, Chang HS. Clinical Implications of Single Nucleotide Polymorphisms in Diagnosis of Asthma and its Subtypes. Yonsei Med J 2019; 60:1-9. [PMID: 30554485 PMCID: PMC6298887 DOI: 10.3349/ymj.2019.60.1.1] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/23/2018] [Revised: 09/11/2018] [Accepted: 09/15/2018] [Indexed: 11/27/2022] Open
Abstract
For the past three decades, a large number of genetic studies have been performed to examine genetic variants associated with asthma and its subtypes in hopes of gaining better understanding of the mechanisms underlying disease pathology and to identify genetic biomarkers predictive of disease outcomes. Various methods have been used to achieve these objectives, including linkage analysis, candidate gene polymorphism analysis, and genome-wide association studies (GWAS); however, the degree to which genetic variants contribute to asthma pathogenesis has proven to be much less significant than originally expected. Subsequent application of GWAS to well-defined phenotypes, such as occupational asthma and non-steroidal anti-inflammatory drugexacerbated respiratory diseases, has overcome some of these limitations, although with only partial success. Recently, a combinatorial analysis of single nucleotide polymorphisms (SNPs) identified by GWAS has been used to develop sets of genetic markers able to more accurately stratify asthma subtypes. In this review, we discuss the implications of the identified SNPs in diagnosis of asthma and its subtypes and the progress being made in combinatorial analysis of genetic variants.
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Affiliation(s)
- Jong Sook Park
- Division of Allergy and Respiratory Medicine, Department of Internal Medicine, Soonchunhyang University Bucheon Hospital, Bucheon, Korea
| | - Ji Hye Son
- Department of Interdisciplinary Program in Biomedical Science, Graduate School, Soonchunhyang University, Bucheon, Korea
| | - Choon Sik Park
- Division of Allergy and Respiratory Medicine, Department of Internal Medicine, Soonchunhyang University Bucheon Hospital, Bucheon, Korea
| | - Hun Soo Chang
- Department of Interdisciplinary Program in Biomedical Science, Graduate School, Soonchunhyang University, Bucheon, Korea.
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26
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Kim KW, Ober C. Lessons Learned From GWAS of Asthma. ALLERGY, ASTHMA & IMMUNOLOGY RESEARCH 2019; 11:170-187. [PMID: 30661310 PMCID: PMC6340805 DOI: 10.4168/aair.2019.11.2.170] [Citation(s) in RCA: 69] [Impact Index Per Article: 13.8] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/16/2018] [Accepted: 09/05/2018] [Indexed: 02/05/2023]
Abstract
Asthma is a common complex disease of the airways. Genome-wide association studies (GWASs) of asthma have identified many risk alleles and loci that have been replicated in worldwide populations. Although the risk alleles identified by GWAS have small effects and explain only a small portion of prevalence, the discovery of asthma loci can provide an understanding of its genetic architecture and the molecular pathways involved in disease pathogenesis. These discoveries can translate into advances in clinical care by identifying therapeutic targets, preventive strategies and ultimately approaches for personalized medicine. In this review, we summarize results from GWAS of asthma from the past 10 years and the insights gleaned from these discoveries.
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Affiliation(s)
- Kyung Won Kim
- Department of Pediatrics, Severance Hospital, Institute of Allergy, Brain Korea 21 PLUS project for Medical Science, Yonsei University College of Medicine, Seoul, Korea.
| | - Carole Ober
- Department of Human Genetics, University of Chicago, Chicago, IL, USA
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27
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Hernandez-Pacheco N, Pino-Yanes M, Flores C. Genomic Predictors of Asthma Phenotypes and Treatment Response. Front Pediatr 2019; 7:6. [PMID: 30805318 PMCID: PMC6370703 DOI: 10.3389/fped.2019.00006] [Citation(s) in RCA: 48] [Impact Index Per Article: 9.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/09/2018] [Accepted: 01/10/2019] [Indexed: 12/11/2022] Open
Abstract
Asthma is a complex respiratory disease considered as the most common chronic condition in children. A large genetic contribution to asthma susceptibility is predicted by the clustering of asthma and allergy symptoms among relatives and the large disease heritability estimated from twin studies, ranging from 55 to 90%. Genetic basis of asthma has been extensively investigated in the past 40 years using linkage analysis and candidate-gene association studies. However, the development of dense arrays for polymorphism genotyping has enabled the transition toward genome-wide association studies (GWAS), which have led the discovery of several unanticipated asthma genes in the last 11 years. Despite this, currently known risk variants identified using many thousand samples from distinct ethnicities only explain a small proportion of asthma heritability. This review examines the main findings of the last 2 years in genomic studies of asthma using GWAS and admixture mapping studies, as well as the direction of studies fostering integrative perspectives involving omics data. Additionally, we discuss the need for assessing the whole spectrum of genetic variation in association studies of asthma susceptibility, severity, and treatment response in order to further improve our knowledge of asthma genes and predictive biomarkers. Leveraging the individual's genetic information will allow a better understanding of asthma pathogenesis and will facilitate the transition toward a more precise diagnosis and treatment.
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Affiliation(s)
- Natalia Hernandez-Pacheco
- Research Unit, Hospital Universitario N.S. de Candelaria, Universidad de La Laguna, Santa Cruz de Tenerife, Spain.,Genomics and Health Group, Department of Biochemistry, Microbiology, Cell Biology and Genetics, Universidad de La Laguna, Santa Cruz de Tenerife, Spain
| | - Maria Pino-Yanes
- Research Unit, Hospital Universitario N.S. de Candelaria, Universidad de La Laguna, Santa Cruz de Tenerife, Spain.,Genomics and Health Group, Department of Biochemistry, Microbiology, Cell Biology and Genetics, Universidad de La Laguna, Santa Cruz de Tenerife, Spain.,CIBER de Enfermedades Respiratorias, Instituto de Salud Carlos III, Madrid, Spain
| | - Carlos Flores
- Research Unit, Hospital Universitario N.S. de Candelaria, Universidad de La Laguna, Santa Cruz de Tenerife, Spain.,CIBER de Enfermedades Respiratorias, Instituto de Salud Carlos III, Madrid, Spain.,Genomics Division, Instituto Tecnológico y de Energías Renovables, Santa Cruz de Tenerife, Spain
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28
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Neville MDC, Choi J, Lieberman J, Duan QL. Identification of deleterious and regulatory genomic variations in known asthma loci. Respir Res 2018; 19:248. [PMID: 30541564 PMCID: PMC6292105 DOI: 10.1186/s12931-018-0953-2] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2018] [Accepted: 11/23/2018] [Indexed: 11/25/2022] Open
Abstract
Background Candidate gene and genome-wide association studies have identified hundreds of asthma risk loci. The majority of associated variants, however, are not known to have any biological function and are believed to represent markers rather than true causative mutations. We hypothesized that many of these associated markers are in linkage disequilibrium (LD) with the elusive causative variants. Methods We compiled a comprehensive list of 449 asthma-associated variants previously reported in candidate gene and genome-wide association studies. Next, we identified all sequence variants located within the 305 unique genes using whole-genome sequencing data from the 1000 Genomes Project. Then, we calculated the LD between known asthma variants and the sequence variants within each gene. LD variants identified were then annotated to determine those that are potentially deleterious and/or functional (i.e. coding or regulatory effects on the encoded transcript or protein). Results We identified 10,130 variants in LD (r2 > 0.6) with known asthma variants. Annotations of these LD variants revealed that several have potentially deleterious effects including frameshift, alternate splice site, stop-lost, and missense. Moreover, 24 of the LD variants have been reported to regulate gene expression as expression quantitative trait loci (eQTLs). Conclusions This study is proof of concept that many of the genetic loci previously associated with complex diseases such as asthma are not causative but represent markers of disease, which are in LD with the elusive causative variants. We hereby report a number of potentially deleterious and regulatory variants that are in LD with the reported asthma loci. These reported LD variants could account for the original association signals with asthma and represent the true causative mutations at these loci. Electronic supplementary material The online version of this article (10.1186/s12931-018-0953-2) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Matthew D C Neville
- Department of Biomedical and Molecular Sciences, Queen's University, Botterell Hall, Room 530 - 18 Stuart St, Kingston, ON, K7L3N6, Canada
| | - Jihoon Choi
- Department of Biomedical and Molecular Sciences, Queen's University, Botterell Hall, Room 530 - 18 Stuart St, Kingston, ON, K7L3N6, Canada
| | - Jonathan Lieberman
- Department of Biomedical and Molecular Sciences, Queen's University, Botterell Hall, Room 530 - 18 Stuart St, Kingston, ON, K7L3N6, Canada
| | - Qing Ling Duan
- Department of Biomedical and Molecular Sciences, Queen's University, Botterell Hall, Room 530 - 18 Stuart St, Kingston, ON, K7L3N6, Canada. .,School of Computing, Queen's University, 557 Goodwin Hall, Room 531, Kingston, ON, K7L 2N8, Canada.
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29
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Panganiban RA, Sun M, Dahlin A, Park HR, Kan M, Himes BE, Mitchel JA, Iribarren C, Jorgenson E, Randell SH, Israel E, Tantisira K, Shore S, Park JA, Weiss ST, Wu AC, Lu Q. A functional splice variant associated with decreased asthma risk abolishes the ability of gasdermin B to induce epithelial cell pyroptosis. J Allergy Clin Immunol 2018; 142:1469-1478.e2. [PMID: 29330013 PMCID: PMC6037620 DOI: 10.1016/j.jaci.2017.11.040] [Citation(s) in RCA: 114] [Impact Index Per Article: 19.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2017] [Revised: 11/12/2017] [Accepted: 11/22/2017] [Indexed: 12/17/2022]
Abstract
BACKGROUND Genetic variants in the chromosomal region 17q21 are consistently associated with asthma. However, mechanistic studies have not yet linked any of the associated variants to a function that could influence asthma, and as a result, the identity of the asthma gene(s) remains elusive. OBJECTIVES We sought to identify and characterize functional variants in the 17q21 locus. METHODS We used the Exome Aggregation Consortium browser to identify coding (amino acid-changing) variants in the 17q21 locus. We obtained asthma association measures for these variants in both the Genetic Epidemiology Research in Adult Health and Aging (GERA) cohort (16,274 cases and 38,269 matched controls) and the EVE Consortium study (5,303 asthma cases and 12,560 individuals). Gene expression and protein localization were determined by quantitative RT-PCR and fluorescence immunostaining, respectively. Molecular and cellular studies were performed to determine the functional effects of coding variants. RESULTS Two coding variants (rs2305480 and rs11078928) of the gasdermin B (GSDMB) gene in the 17q21 locus were associated with lower asthma risk in both GERA (odds ratio, 0.92; P = 1.01 × 10-6) and EVE (odds ratio, 0.85; joint PEVE = 1.31 × 10-13). In GERA, rs11078928 had a minor allele frequency (MAF) of 0.45 in unaffected (nonasthmatic) controls and 0.43 in asthma cases. For European Americans in EVE, the MAF of rs2305480 was 0.45 for controls and 0.39 for cases; for all EVE subjects, the MAF was 0.32 for controls and 0.27 for cases. GSDMB is highly expressed in differentiated airway epithelial cells, including the ciliated cells. We found that, when the GSDMB protein is cleaved by inflammatory caspase-1 to release its N-terminal fragment, potent pyroptotic cell death is induced. The splice variant rs11078928 deletes the entire exon 6, which encodes 13 amino acids in the critical N-terminus, and abolishes the pyroptotic activity of the GSDMB protein. CONCLUSIONS Our study identified a functional asthma variant in the GSDMB gene of the 17q21 locus and implicates GSDMB-mediated epithelial cell pyroptosis in pathogenesis.
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Affiliation(s)
- Ronald A Panganiban
- Program in Molecular and Integrative Physiological Sciences, Departments of Environmental Health and Genetics & Complex Diseases, Harvard T.H. Chan School of Public Health, Boston, Mass
| | - Maoyun Sun
- Program in Molecular and Integrative Physiological Sciences, Departments of Environmental Health and Genetics & Complex Diseases, Harvard T.H. Chan School of Public Health, Boston, Mass
| | - Amber Dahlin
- Channing Division of Network Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, Mass
| | - Hae-Ryung Park
- Program in Molecular and Integrative Physiological Sciences, Departments of Environmental Health and Genetics & Complex Diseases, Harvard T.H. Chan School of Public Health, Boston, Mass
| | - Mengyuan Kan
- Department of Biostatistics, Epidemiology and Informatics, University of Pennsylvania, Philadelphia, Pennsylvania
| | - Blanca E Himes
- Department of Biostatistics, Epidemiology and Informatics, University of Pennsylvania, Philadelphia, Pennsylvania
| | - Jennifer A Mitchel
- Program in Molecular and Integrative Physiological Sciences, Departments of Environmental Health and Genetics & Complex Diseases, Harvard T.H. Chan School of Public Health, Boston, Mass
| | - Carlos Iribarren
- Division of Research, Kaiser Permanente Northern California, Oakland, Calif
| | - Eric Jorgenson
- Division of Research, Kaiser Permanente Northern California, Oakland, Calif
| | - Scott H Randell
- Marsico Lung Institute/Cystic Fibrosis Center, University of North Carolina, Chapel Hill, NC
| | - Elliot Israel
- Asthma Research Center, Brigham and Women's Hospital and Harvard Medical School, Boston, Mass
| | - Kelan Tantisira
- Channing Division of Network Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, Mass
| | - Stephanie Shore
- Program in Molecular and Integrative Physiological Sciences, Departments of Environmental Health and Genetics & Complex Diseases, Harvard T.H. Chan School of Public Health, Boston, Mass
| | - Jin-Ah Park
- Program in Molecular and Integrative Physiological Sciences, Departments of Environmental Health and Genetics & Complex Diseases, Harvard T.H. Chan School of Public Health, Boston, Mass
| | - Scott T Weiss
- Channing Division of Network Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, Mass
| | - Ann Chen Wu
- Channing Division of Network Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, Mass; Precision Medicine Translational Research Center, Department of Population Medicine, Harvard Medical School, Boston, Mass
| | - Quan Lu
- Program in Molecular and Integrative Physiological Sciences, Departments of Environmental Health and Genetics & Complex Diseases, Harvard T.H. Chan School of Public Health, Boston, Mass.
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Wojcik GL, Fuchsberger C, Taliun D, Welch R, Martin AR, Shringarpure S, Carlson CS, Abecasis G, Kang HM, Boehnke M, Bustamante CD, Gignoux CR, Kenny EE. Imputation-Aware Tag SNP Selection To Improve Power for Large-Scale, Multi-ethnic Association Studies. G3 (BETHESDA, MD.) 2018; 8:3255-3267. [PMID: 30131328 PMCID: PMC6169386 DOI: 10.1534/g3.118.200502] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/14/2018] [Accepted: 08/03/2018] [Indexed: 01/26/2023]
Abstract
The emergence of very large cohorts in genomic research has facilitated a focus on genotype-imputation strategies to power rare variant association. These strategies have benefited from improvements in imputation methods and association tests, however little attention has been paid to ways in which array design can increase rare variant association power. Therefore, we developed a novel framework to select tag SNPs using the reference panel of 26 populations from Phase 3 of the 1000 Genomes Project. We evaluate tag SNP performance via mean imputed r2 at untyped sites using leave-one-out internal validation and standard imputation methods, rather than pairwise linkage disequilibrium. Moving beyond pairwise metrics allows us to account for haplotype diversity across the genome for improve imputation accuracy and demonstrates population-specific biases from pairwise estimates. We also examine array design strategies that contrast multi-ethnic cohorts vs. single populations, and show a boost in performance for the former can be obtained by prioritizing tag SNPs that contribute information across multiple populations simultaneously. Using our framework, we demonstrate increased imputation accuracy for rare variants (frequency < 1%) by 0.5-3.1% for an array of one million sites and 0.7-7.1% for an array of 500,000 sites, depending on the population. Finally, we show how recent explosive growth in non-African populations means tag SNPs capture on average 30% fewer other variants than in African populations. The unified framework presented here will enable investigators to make informed decisions for the design of new arrays, and help empower the next phase of rare variant association for global health.
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Affiliation(s)
- Genevieve L Wojcik
- Department of Genetics, Stanford University School of Medicine, 365 Lasuen Street, Littlefield Center MC2069, Stanford, CA 94305
| | - Christian Fuchsberger
- Department of Biostatistics and Center for Statistical Genetics, School of Public Health, University of Michigan, 1415 Washington Heights, Ann Arbor, MI 48109
- Center for Biomedicine, European Academy of Bolzano/Bozen (EURAC), affiliated with the University of Lübeck, Bolzano, Bozen, 39100, Italy
| | - Daniel Taliun
- Department of Biostatistics and Center for Statistical Genetics, School of Public Health, University of Michigan, 1415 Washington Heights, Ann Arbor, MI 48109
| | - Ryan Welch
- Department of Biostatistics and Center for Statistical Genetics, School of Public Health, University of Michigan, 1415 Washington Heights, Ann Arbor, MI 48109
| | - Alicia R Martin
- Department of Genetics, Stanford University School of Medicine, 365 Lasuen Street, Littlefield Center MC2069, Stanford, CA 94305
| | - Suyash Shringarpure
- Department of Genetics, Stanford University School of Medicine, 365 Lasuen Street, Littlefield Center MC2069, Stanford, CA 94305
| | - Christopher S Carlson
- Fred Hutchinson Cancer Center, University of Washington, 1100 Fairview Ave. N., Seattle, WA 98109
| | - Goncalo Abecasis
- Department of Biostatistics and Center for Statistical Genetics, School of Public Health, University of Michigan, 1415 Washington Heights, Ann Arbor, MI 48109
| | - Hyun Min Kang
- Department of Biostatistics and Center for Statistical Genetics, School of Public Health, University of Michigan, 1415 Washington Heights, Ann Arbor, MI 48109
| | - Michael Boehnke
- Department of Biostatistics and Center for Statistical Genetics, School of Public Health, University of Michigan, 1415 Washington Heights, Ann Arbor, MI 48109
| | - Carlos D Bustamante
- Department of Genetics, Stanford University School of Medicine, 365 Lasuen Street, Littlefield Center MC2069, Stanford, CA 94305
- Department of Biomedical Data Science, Stanford University School of Medicine, 365 Lasuen Street, Littlefield Center MC2069, Stanford, CA 94305
| | - Christopher R Gignoux
- Department of Genetics, Stanford University School of Medicine, 365 Lasuen Street, Littlefield Center MC2069, Stanford, CA 94305
| | - Eimear E Kenny
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, 1 Gustave L. Levy Place, New York, NY 10029
- The Charles Bronfman Institute for Personalized Medicine, Icahn School of Medicine at Mount Sinai, 1 Gustave L. Levy Place, New York, NY 10029
- The Icahn Institute of Multiscale Biology and Genomics, Icahn School of Medicine at Mount Sinai, 1 Gustave L. Levy Place, New York, NY 10029
- The Center for Statistical Genetics, Icahn School of Medicine at Mount Sinai, 1 Gustave L. Levy Place, New York, NY 10029
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31
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Morin A, Madore AM, Kwan T, Ban M, Partanen J, Rönnblom L, Syvänen AC, Sawcer S, Stunnenberg H, Lathrop M, Pastinen T, Laprise C. Exploring rare and low-frequency variants in the Saguenay-Lac-Saint-Jean population identified genes associated with asthma and allergy traits. Eur J Hum Genet 2018; 27:90-101. [PMID: 30206357 PMCID: PMC6303288 DOI: 10.1038/s41431-018-0266-4] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2017] [Revised: 08/08/2018] [Accepted: 08/19/2018] [Indexed: 12/13/2022] Open
Abstract
The Saguenay–Lac-Saint-Jean (SLSJ) region is located in northeastern Quebec and is known for its unique demographic history and founder effect. As founder populations are enriched with population-specific variants, we characterized the variants distribution in SLSJ and compared it with four European populations (Finnish, Sweden, United Kingdom and France), of which the Finnish population is another founder population. Targeted sequencing of the coding and non-coding immune regulatory regions of the SLSJ asthma familial cohort and the four European populations were performed. Rare and low-frequency coding and non-coding regulatory variants identified in the SLSJ population were then investigated for variant- and gene-level associations with asthma and allergy-related traits (eosinophil percentage, immunoglobulin (Ig) E levels and lung function). Our data showed that (1) rare or deleterious variants were not enriched in the two founder populations as compared with the three non-founder European populations; (2) a larger proportion of founder population-specific variants occurred with higher frequencies; and (3) low-frequency variants appeared to be more deleterious. Furthermore, a rare variant, rs1386931, located in the 3ʹ-UTR of CXCR6 and intron of FYCO1 was found to be associated with eosinophil percentage. Gene-based analyses identified NRP2, MRPL44 and SERPINE2 to be associated with various asthma and allergy-related traits. Our study demonstrated the usefulness of using a founder population to identify new genes associated with asthma and allergy-related traits; thus better understand the genes and pathways implicated in pathophysiology.
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Affiliation(s)
- Andréanne Morin
- Department of Human Genetics, McGill University, Montréal, QC, Canada.,McGill University and Genome Québec Innovation Centre, Montréal, QC, Canada.,Département des Sciences Fondamentales, Université du Québec à Chicoutimi, Saguenay, QC, Canada
| | - Anne-Marie Madore
- Département des Sciences Fondamentales, Université du Québec à Chicoutimi, Saguenay, QC, Canada
| | - Tony Kwan
- Department of Human Genetics, McGill University, Montréal, QC, Canada.,McGill University and Genome Québec Innovation Centre, Montréal, QC, Canada
| | - Maria Ban
- Department of Clinical Neurosciences, University of Cambridge, Cambridge, UK
| | - Jukka Partanen
- Research & Development, Finnish Red Cross Blood Service, Helsinki, Finland
| | - Lars Rönnblom
- Department of Medical Sciences, Section of Rheumatology, Uppsala University, Uppsala, Sweden
| | - Ann-Christine Syvänen
- Department of Medical Sciences, Molecular Medicine and Science for Life Laboratory, Uppsala University, Uppsala, Sweden
| | - Stephen Sawcer
- Department of Clinical Neurosciences, University of Cambridge, Cambridge, UK
| | - Hendrik Stunnenberg
- Department of Molecular Biology, Faculty of Science, Radboud University, Nijmegen, The Netherlands
| | - Mark Lathrop
- Department of Human Genetics, McGill University, Montréal, QC, Canada.,McGill University and Genome Québec Innovation Centre, Montréal, QC, Canada
| | - Tomi Pastinen
- Department of Human Genetics, McGill University, Montréal, QC, Canada.,McGill University and Genome Québec Innovation Centre, Montréal, QC, Canada.,Center for Pediatric Genomic Medicine, Kansas City, MO, USA
| | - Catherine Laprise
- Département des Sciences Fondamentales, Université du Québec à Chicoutimi, Saguenay, QC, Canada. .,Centre Intégré Universitaire de Santé et de Services Sociaux du Saguenay-Lac-Saint-Jean, Saguenay, QC, Canada.
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32
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A decade of research on the 17q12-21 asthma locus: Piecing together the puzzle. J Allergy Clin Immunol 2018; 142:749-764.e3. [PMID: 29307657 PMCID: PMC6172038 DOI: 10.1016/j.jaci.2017.12.974] [Citation(s) in RCA: 119] [Impact Index Per Article: 19.8] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2017] [Revised: 12/13/2017] [Accepted: 12/16/2017] [Indexed: 12/20/2022]
Abstract
Chromosome 17q12–21 remains the most highly replicated and significant asthma locus. Genotypes in the core region defined by the first genome-wide association study correlate with expression of 2 genes, ORM1-like 3 (ORMDL3) and gasdermin B (GSDMB), making these prime candidate asthma genes, although recent studies have implicated gasdermin A (GSDMA) distal to and post-GPI attachment to proteins 3 (PGAP3) proximal to the core region as independent loci. We review 10 years of studies on the 17q12–21 locus and suggest that genotype-specific risks for asthma at the proximal and distal loci are not specific to early-onset asthma and mediated by PGAP3, ORMDL3, and/or GSDMA expression. We propose that the weak and inconsistent associations of 17q single nucleotide polymorphisms with asthma in African Americans is due to the high frequency of some 17q alleles, the breakdown of linkage disequilibrium on African-derived chromosomes, and possibly different early-life asthma endotypes in these children. Finally, the inconsistent association between asthma and gene expression levels in blood or lung cells from older children and adults suggests that genotype effects may mediate asthma risk or protection during critical developmental windows and/or in response to relevant exposures in early life. Thus studies of young children and ethnically diverse populations are required to fully understand the relationship between genotype and asthma phenotype and the gene regulatory architecture at this locus. (J Allergy Clin Immunol 2018;142:749–64.)
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33
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Demenais F, Margaritte-Jeannin P, Barnes KC, Cookson WOC, Altmüller J, Ang W, Barr RG, Beaty TH, Becker AB, Beilby J, Bisgaard H, Bjornsdottir US, Bleecker E, Bønnelykke K, Boomsma DI, Bouzigon E, Brightling CE, Brossard M, Brusselle GG, Burchard E, Burkart KM, Bush A, Chan-Yeung M, Chung KF, Couto Alves A, Curtin JA, Custovic A, Daley D, de Jongste JC, Del-Rio-Navarro BE, Donohue KM, Duijts L, Eng C, Eriksson JG, Farrall M, Fedorova Y, Feenstra B, Ferreira MA, Freidin MB, Gajdos Z, Gauderman J, Gehring U, Geller F, Genuneit J, Gharib SA, Gilliland F, Granell R, Graves PE, Gudbjartsson DF, Haahtela T, Heckbert SR, Heederik D, Heinrich J, Heliövaara M, Henderson J, Himes BE, Hirose H, Hirschhorn JN, Hofman A, Holt P, Hottenga J, Hudson TJ, Hui J, Imboden M, Ivanov V, Jaddoe VWV, James A, Janson C, Jarvelin MR, Jarvis D, Jones G, Jonsdottir I, Jousilahti P, Kabesch M, Kähönen M, Kantor DB, Karunas AS, Khusnutdinova E, Koppelman GH, Kozyrskyj AL, Kreiner E, Kubo M, Kumar R, Kumar A, Kuokkanen M, Lahousse L, Laitinen T, Laprise C, Lathrop M, Lau S, Lee YA, Lehtimäki T, Letort S, Levin AM, Li G, Liang L, Loehr LR, London SJ, Loth DW, Manichaikul A, Marenholz I, Martinez FJ, Matheson MC, Mathias RA, Matsumoto K, Mbarek H, McArdle WL, Melbye M, Melén E, Meyers D, Michel S, Mohamdi H, Musk AW, Myers RA, Nieuwenhuis MAE, Noguchi E, O'Connor GT, Ogorodova LM, Palmer CD, Palotie A, Park JE, Pennell CE, Pershagen G, Polonikov A, Postma DS, Probst-Hensch N, Puzyrev VP, Raby BA, Raitakari OT, Ramasamy A, Rich SS, Robertson CF, Romieu I, Salam MT, Salomaa V, Schlünssen V, Scott R, Selivanova PA, Sigsgaard T, Simpson A, Siroux V, Smith LJ, Solodilova M, Standl M, Stefansson K, Strachan DP, Stricker BH, Takahashi A, Thompson PJ, Thorleifsson G, Thorsteinsdottir U, Tiesler CMT, Torgerson DG, Tsunoda T, Uitterlinden AG, van der Valk RJP, Vaysse A, Vedantam S, von Berg A, von Mutius E, Vonk JM, Waage J, Wareham NJ, Weiss ST, White WB, Wickman M, Widén E, Willemsen G, Williams LK, Wouters IM, Yang JJ, Zhao JH, Moffatt MF, Ober C, Nicolae DL. Multiancestry association study identifies new asthma risk loci that colocalize with immune-cell enhancer marks. Nat Genet 2017; 50:42-53. [PMID: 29273806 PMCID: PMC5901974 DOI: 10.1038/s41588-017-0014-7] [Citation(s) in RCA: 326] [Impact Index Per Article: 46.6] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2016] [Accepted: 11/08/2017] [Indexed: 12/11/2022]
Abstract
We examined common variation in asthma risk by conducting a meta-analysis of worldwide asthma genome-wide association studies (23,948 cases, 118,538 controls) from ethnically-diverse populations. We identified five new asthma loci, uncovered two additional novel associations at two known asthma loci, established asthma associations at two loci implicated previously in comorbidity of asthma plus hay fever, and confirmed nine known loci. Investigation of pleiotropy showed large overlaps in genetic variants with autoimmune and inflammatory diseases. Enrichment of asthma risk loci in enhancer marks, especially in immune cells, suggests a major role of these loci in the regulation of immune-related mechanisms.
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Affiliation(s)
- Florence Demenais
- Genetic Variation and Human Diseases Unit (UMR-946), Institut National de la Santé et de la Recherche Médicale (INSERM), Paris, France. .,Institut Universitaire d'Hématologie, Université Paris Diderot, Université Sorbonne Paris Cité, Paris, France.
| | - Patricia Margaritte-Jeannin
- Genetic Variation and Human Diseases Unit (UMR-946), Institut National de la Santé et de la Recherche Médicale (INSERM), Paris, France.,Institut Universitaire d'Hématologie, Université Paris Diderot, Université Sorbonne Paris Cité, Paris, France
| | - Kathleen C Barnes
- Division of Biomedical Informatics and Personalized Medicine, Colorado Center for Personalized Medicine, University of Colorado, Denver, CO, USA
| | | | - Janine Altmüller
- Cologne Center for Genomics and Center for Molecular Medicine Cologne (CMMC), University of Cologne, Cologne, Germany
| | - Wei Ang
- School of Women's and Infants' Health, University of Western Australia, Perth, Western Australia, Australia
| | - R Graham Barr
- Departments of Medicine and Epidemiology, Columbia University, New York, NY, USA
| | - Terri H Beaty
- Division of Genetic Epidemiology, Department of Epidemiology, Bloomberg School of Public Health, Johns Hopkins University, Baltimore, MD, USA
| | - Allan B Becker
- Department of Pediatrics and Child Health, University of Manitoba, Winnipeg, Manitoba, Canada
| | - John Beilby
- Department of the Diagnostic Genomics Laboratory, PathWest Laboratory Medicine, Queen Elizabeth II Medical Centre, Nedlands, Western Australia, Australia
| | - Hans Bisgaard
- Copenhagen Prospective Studies on Asthma in Childhood, Herlev and Gentofte Hospital, University of Copenhagen, Copenhagen, Denmark
| | | | - Eugene Bleecker
- Center for Genomics, Wake Forest University School of Medicine, Winston-Salem, NC, USA
| | - Klaus Bønnelykke
- Copenhagen Prospective Studies on Asthma in Childhood, Herlev and Gentofte Hospital, University of Copenhagen, Copenhagen, Denmark
| | - Dorret I Boomsma
- Department of Biological Psychology, Amsterdam Public Health Research Institute, Vrjie Universiteit, Amsterdam, The Netherlands
| | - Emmanuelle Bouzigon
- Genetic Variation and Human Diseases Unit (UMR-946), Institut National de la Santé et de la Recherche Médicale (INSERM), Paris, France.,Institut Universitaire d'Hématologie, Université Paris Diderot, Université Sorbonne Paris Cité, Paris, France
| | | | - Myriam Brossard
- Genetic Variation and Human Diseases Unit (UMR-946), Institut National de la Santé et de la Recherche Médicale (INSERM), Paris, France.,Institut Universitaire d'Hématologie, Université Paris Diderot, Université Sorbonne Paris Cité, Paris, France
| | - Guy G Brusselle
- Department of Respiratory Medicine, Ghent University Hospital, Ghent, Belgium.,Department of Epidemiology, Erasmus MC-University Medical Center Rotterdam, Rotterdam, The Netherlands.,Department of Respiratory Medicine, Erasmus MC-University Medical Center Rotterdam, Rotterdam, The Netherlands
| | - Esteban Burchard
- Department of Bioengineering & Therapeutic Sciences and Medicine, University of California, San Francisco, San Francisco, CA, USA
| | - Kristin M Burkart
- Division of Pulmonary, Allergy and Critical Care, College of Physicians and Surgeons, Columbia University, New York, NY, USA
| | - Andrew Bush
- National Heart and Lung Institute, Imperial College London, London, UK.,Royal Brompton Harefield National Health Service (NHS) Foundation Trust, London, UK
| | - Moira Chan-Yeung
- Department of Medicine, University of British Columbia, Vancouver, British Columbia, Canada
| | - Kian Fan Chung
- National Heart and Lung Institute, Imperial College London, London, UK.,Biomedical Research Unit, Royal Brompton & Harefield National Health Service (NHS) Trust, London, UK
| | | | - John A Curtin
- Division of Infection, Immunity and Respiratory Medicine, School of Biological Sciences, Faculty of Biology, Medicine and Health, Manchester Academic Health Science Centre, University of Manchester, Manchester, UK
| | - Adnan Custovic
- Department of Paediatrics, Imperial College London, London, UK
| | - Denise Daley
- Department of Medicine, University of British Columbia, Vancouver, British Columbia, Canada.,Centre for Heart and Lung Innovation, University of British Columbia, Vancouver, BC, Canada
| | - Johan C de Jongste
- Department of Pediatrics, Division of Respiratory Medicine, Erasmus MC-University Medical Center Rotterdam, Rotterdam, The Netherlands
| | | | - Kathleen M Donohue
- Departments of Medicine and Epidemiology, Columbia University, New York, NY, USA
| | - Liesbeth Duijts
- Department of Pediatrics, Division of Respiratory Medicine, and Department of Pediatrics, Division of Neonatology, Erasmus MC-University Medical Center Rotterdam, Rotterdam, The Netherlands
| | - Celeste Eng
- Department of Medicine, University of California, San Francisco, San Francisco, CA, USA
| | - Johan G Eriksson
- Department of General Practice and Primary Health Care, University of Helsinki and Helsinki University Hospital, Helsinki, Finland
| | - Martin Farrall
- Division of Cardiovascular Medicine, Radcliffe Department of Medicine, University of Oxford, Oxford, UK.,Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, UK
| | - Yuliya Fedorova
- Institute of Biochemistry and Genetics, Ufa Scientific Center of the Russian Academy of Sciences, Ufa, Russian Federation
| | - Bjarke Feenstra
- Department of Epidemiology Research, Statens Serum Institut, Copenhagen, Denmark
| | - Manuel A Ferreira
- Genetics and Computational Biology, QIMR Berghofer Medical Research Institute, Brisbane, Queensland, Australia
| | | | - Maxim B Freidin
- Population Genetics Laboratory, Research Institute of Medical Genetics, Tomsk NRMC, Tomsk, Russian Federation
| | - Zofia Gajdos
- Divisions of Genetics and Endocrinology, Children's Hospital, Boston, MA, USA.,Broad Institute, Cambridge, MA, USA
| | - Jim Gauderman
- Department of Preventive Medicine, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
| | - Ulrike Gehring
- Division of Environmental Epidemiology, Institute for Risk Assessment Sciences, Utrecht University, Utrecht, The Netherlands
| | - Frank Geller
- Department of Epidemiology Research, Statens Serum Institut, Copenhagen, Denmark
| | - Jon Genuneit
- Institute of Epidemiology and Medical Biometry, Ulm University, Ulm, Germany
| | - Sina A Gharib
- Department of Medicine, University of Washington, Seattle, WA, USA
| | - Frank Gilliland
- Department of Preventive Medicine, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA
| | - Raquel Granell
- Population Health Sciences, Bristol Medical School, University of Bristol, Bristol, UK.,MRC Integrative Epidemiology Unit, University of Bristol, Bristol, UK
| | - Penelope E Graves
- Asthma and Airway Disease Research Center and BIO5 Institute, University of Arizona, Tucson, AZ, USA
| | - Daniel F Gudbjartsson
- deCODE genetics, Amgen Inc., Reykjavik, Iceland.,School of Engineering and Natural Sciences, University of Iceland, Reykjavik, Iceland
| | - Tari Haahtela
- Skin and Allergy Hospital, University of Helsinki, Helsinki, Finland
| | - Susan R Heckbert
- Department of Epidemiology, University of Washington, Seattle, WA, USA
| | - Dick Heederik
- Division of Environmental Epidemiology, Institute for Risk Assessment Sciences, Utrecht University, Utrecht, The Netherlands
| | - Joachim Heinrich
- Institute and Outpatient Clinic for Occupational, Social and Environmental Medicine, University Hospital in Munich, Munich, Germany.,Institute of Epidemiology I, Helmholtz Zentrum München, German Research Centre for Environmental Health, Neuherberg, Germany
| | | | - John Henderson
- Population Health Sciences, Bristol Medical School, University of Bristol, Bristol, UK.,MRC Integrative Epidemiology Unit, University of Bristol, Bristol, UK
| | - Blanca E Himes
- Department of Biostatistics, Epidemiology and Informatics, University of Pennsylvania, Philadelphia, PA, USA
| | - Hiroshi Hirose
- Health Center, Department of Internal Medicine, Keio University, Tokyo, Japan
| | - Joel N Hirschhorn
- Broad Institute, Cambridge, MA, USA.,Division of Endocrinology and Center for Basic and Translational Obesity Research, Boston Children's Hospital, Boston, MA, USA.,Departments of Pediatrics and Genetics, Harvard Medical School, Boston, MA, USA
| | - Albert Hofman
- Department of Epidemiology, Erasmus MC-University Medical Center Rotterdam, Rotterdam, The Netherlands.,Department of Epidemiology, Harvard T.H. Chan School of Public Health, Boston, MA, USA
| | - Patrick Holt
- Cell Biology Telethon Kids Institute, University of Western Australia, Subiaco, Western Australia, Australia
| | - Jouke Hottenga
- Department of Biological Psychology, Amsterdam Public Health Research Institute, Vrjie Universiteit, Amsterdam, The Netherlands
| | - Thomas J Hudson
- Ontario Institute for Cancer Research, Toronto, Ontario, Canada.,AbbVie Inc., Redwood City, CA, USA
| | - Jennie Hui
- Department of the Diagnostic Genomics Laboratory, PathWest Laboratory Medicine, Queen Elizabeth II Medical Centre, Nedlands, Western Australia, Australia.,Busselton Population Medical Research Institute, Perth, Western Australia, Australia.,School of Population and Global Health, University of Western Australia, Nedlands, Western Australia, Australia
| | - Medea Imboden
- Department of Epidemiology and Public Health, Swiss Tropical and Public Health Institute, Basel, Switzerland.,University of Basel, Basel, Switzerland
| | - Vladimir Ivanov
- Department of Biology, Medical Genetics and Ecology, Kursk State Medical University, Kursk, Russian Federation
| | - Vincent W V Jaddoe
- The Generation R Study Group, Department of Pediatrics and Department of Epidemiology, Erasmus MC-University Medical Center Rotterdam, Rotterdam, The Netherlands
| | - Alan James
- Department of Pulmonary Physiology and Sleep Medicine, Busselton Population Medical Research Institute, Sir Charles Gairdner Hospital, Nedlands, Western Australia, Australia.,School of Medicine and Pharmacology, University of Western Australia, Crawley, Western Australia, Australia
| | - Christer Janson
- Department of Medical Sciences: Respiratory, Allergy & Sleep Research, Uppsala University, Uppsala, Sweden
| | - Marjo-Riitta Jarvelin
- Department of Epidemiology and Biostatistics, MRC-PHE Centre for Environment & Health, School of Public Health, Imperial College London, London, UK.,Center for Life Course Health Research, Faculty of Medicine, University of Oulu, Oulu, Finland.,Biocenter Oulu, University of Oulu, Oulu, Finland.,Unit of Primary Care, Oulu University Hospital, Oulu, Finland
| | - Deborah Jarvis
- National Heart and Lung Institute, Imperial College London, London, UK.,MRC-PHE Centre for Environment and Health, Imperial College London, London, UK
| | - Graham Jones
- School of Science and Health, Western Sydney University, Sydney, New South Wales, Australia
| | - Ingileif Jonsdottir
- deCODE genetics, Amgen Inc., Reykjavik, Iceland.,Faculty of Medicine, University of Iceland, Reykjavik, Iceland
| | - Pekka Jousilahti
- National Institute for Health and Welfare (THL), Helsinki, Finland
| | - Michael Kabesch
- Department of Pediatric Pneumology and Allergy, University Children's Hospital Regensburg (KUNO), Regensburg, Germany
| | - Mika Kähönen
- Department of Clinical Physiology, University of Tampere and Tampere University Hospital, Tampere, Finland
| | - David B Kantor
- Department of Anesthesiology, Perioperative and Pain Medicine, Division of Critical Care Medicine, Boston Children's Hospital, Boston, MA, USA.,Department of Anaesthesia, Harvard Medical School, Boston, MA, USA
| | - Alexandra S Karunas
- Institute of Biochemistry and Genetics, Ufa Scientific Center of the Russian Academy of Sciences, Ufa, Russian Federation.,Department of Genetics and Fundamental Medicine, Bashkir State University, Ufa, Russian Federation
| | - Elza Khusnutdinova
- Institute of Biochemistry and Genetics, Ufa Scientific Center of the Russian Academy of Sciences, Ufa, Russian Federation.,Department of Genetics and Fundamental Medicine, Bashkir State University, Ufa, Russian Federation
| | - Gerard H Koppelman
- University of Groningen, University Medical Center Groningen, Department of Pediatric Pulmonology and Pediatric Allergology, Beatrix Children's Hospital, Groningen, The Netherlands.,Groningen Research Institute for Asthma and COPD (GRIAC), Groningen, The Netherlands
| | - Anita L Kozyrskyj
- Department of Pediatrics, University of Alberta, Edmonton, Alberta, Canada
| | - Eskil Kreiner
- Copenhagen Prospective Studies on Asthma in Childhood, Herlev and Gentofte Hospital, University of Copenhagen, Copenhagen, Denmark
| | - Michiaki Kubo
- RIKEN Center for Integrative Medical Sciences, Yokohama, Japan
| | - Rajesh Kumar
- Ann & Robert H. Lurie Children's Hospital of Chicago, Chicago, IL, USA.,Divison of Allergy and Clinical Immunology, Department of Pediatrics, Northwestern University Feinberg School of Medicine, Chicago, IL, USA
| | - Ashish Kumar
- Department of Epidemiology and Public Health, Swiss Tropical and Public Health Institute, Basel, Switzerland.,University of Basel, Basel, Switzerland.,Institute of Environmental Medicine, Karolinska Institutet, Stockholm, Sweden
| | - Mikko Kuokkanen
- National Institute for Health and Welfare (THL), Helsinki, Finland.,Institute for Molecular Medicine Finland (FIMM), University of Helsinki, Helsinki, Finland
| | - Lies Lahousse
- Department of Epidemiology, Erasmus MC-University Medical Center Rotterdam, Rotterdam, The Netherlands.,Pharmaceutical Care Unit, Faculty of Pharmaceutical Sciences, Ghent University, Ghent, Belgium
| | - Tarja Laitinen
- Department of Pulmonary Medicine, University of Turku and Turku University Hospital, Turku, Finland
| | - Catherine Laprise
- Département des Sciences Fondamentales, Université du Québec à Chicoutimi, Chicoutimi, Quebec, Canada.,Centre de Santé et de Services Sociaux du Saguenay-Lac-Saint-Jean, Saguenay, QC, Canada
| | - Mark Lathrop
- McGill University and Genome Quebec Innovation Centre, Montréal, QC, Canada
| | - Susanne Lau
- Pediatric Pneumology and Immunology, Charité Universitätsmedizin, Berlin, Germany
| | - Young-Ae Lee
- Max-Delbrück-Centrum (MDC) for Molecular Medicine, Berlin, Germany.,Pediatric Allergology, Experimental and Clinical Research Center, Charité Universitätsmedizin, Berlin, Germany
| | - Terho Lehtimäki
- Department of Clinical Chemistry, Fimlab Laboratories, Faculty of Medicine and Life Sciences, University of Tampere, Tampere, Finland
| | - Sébastien Letort
- Genetic Variation and Human Diseases Unit (UMR-946), Institut National de la Santé et de la Recherche Médicale (INSERM), Paris, France.,Institut Universitaire d'Hématologie, Université Paris Diderot, Université Sorbonne Paris Cité, Paris, France
| | - Albert M Levin
- Department of Public Health Sciences, Henry Ford Health System, Detroit, MI, USA
| | - Guo Li
- Department of Medicine, University of Washington, Seattle, WA, USA
| | - Liming Liang
- Department of Epidemiology, Harvard T.H. Chan School of Public Health, Boston, MA, USA.,Department of Biostatistics, Harvard T.H. Chan School of Public Health, Boston, MA, USA
| | - Laura R Loehr
- Division of General Medicine, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Stephanie J London
- National Institute of Environmental Health Sciences, National Institutes of Health, Department of Health and Human Services, Research Triangle Park, NC, USA
| | - Daan W Loth
- Department of Epidemiology, Erasmus MC-University Medical Center Rotterdam, Rotterdam, The Netherlands
| | - Ani Manichaikul
- Center for Public Health Genomics, University of Virginia, Charlottesville, VA, USA
| | - Ingo Marenholz
- Max-Delbrück-Centrum (MDC) for Molecular Medicine, Berlin, Germany.,Pediatric Allergology, Experimental and Clinical Research Center, Charité Universitätsmedizin, Berlin, Germany
| | - Fernando J Martinez
- Asthma and Airway Disease Research Center and BIO5 Institute, University of Arizona, Tucson, AZ, USA
| | - Melanie C Matheson
- Melbourne School of Population and Global Health, University of Melbourne, Melbourne, Victoria, Australia
| | - Rasika A Mathias
- Division of Allergy & Clinical Immunology, Department of Medicine, Johns Hopkins University, Baltimore, MD, USA
| | - Kenji Matsumoto
- Department of Allergy and Clinical Immunology, National Research Institute for Child Health and Development, Tokyo, Japan
| | - Hamdi Mbarek
- Department of Biological Psychology, Amsterdam Public Health Research Institute, Vrjie Universiteit, Amsterdam, The Netherlands
| | - Wendy L McArdle
- Bristol Bioresource Laboratories, School of Social and Community Medicine, University of Bristol, Bristol, UK
| | - Mads Melbye
- Department of Epidemiology Research, Statens Serum Institut, Copenhagen, Denmark.,Department of Clinical Medicine, University of Copenhagen, Copenhagen, Denmark.,Department of Medicine, Stanford University School of Medicine, Stanford, CA, USA
| | - Erik Melén
- Institute of Environmental Medicine, Karolinska Institutet, Stockholm, Sweden.,Centre for Occupational and Environmental Medicine, Stockholm County Council, Stockholm, Sweden.,Sachs Children's Hospital, Stockholm, Sweden
| | - Deborah Meyers
- Center for Genomics, Wake Forest University School of Medicine, Winston-Salem, NC, USA
| | - Sven Michel
- Department of Pediatric Pneumology and Allergy, University Children's Hospital Regensburg (KUNO), Regensburg, Germany
| | - Hamida Mohamdi
- Genetic Variation and Human Diseases Unit (UMR-946), Institut National de la Santé et de la Recherche Médicale (INSERM), Paris, France.,Institut Universitaire d'Hématologie, Université Paris Diderot, Université Sorbonne Paris Cité, Paris, France
| | - Arthur W Musk
- Department of Respiratory Medicine, Sir Charles Gairdner Hospital, Nedlands, Western Australia, Australia.,Schools of Population Health and of Medicine and Pharmacology, University of Western Australia, Perth, Western Australia, Australia
| | - Rachel A Myers
- Center for Applied Genomics and Precision Medicine, Duke University School of Medicine, Durham, NC, USA
| | - Maartje A E Nieuwenhuis
- Groningen Research Institute for Asthma and COPD (GRIAC), Groningen, The Netherlands.,University Medical Center Groningen, Department of Pulmonology, University of Groningen, Groningen, The Netherlands
| | - Emiko Noguchi
- Department of Medical Genetics, Faculty of Medicine, University of Tsukuba, Tsukuba, Japan
| | - George T O'Connor
- Pulmonary Center, Department of Medicine, Boston University School of Medicine, Boston, MA, USA.,The National Heart, Lung, and Blood Institute's Framingham Heart Study, Framingham, MA, USA
| | - Ludmila M Ogorodova
- Department of Faculty Pediatrics, Siberian State Medical University, Tomsk, Russian Federation
| | - Cameron D Palmer
- Broad Institute, Cambridge, MA, USA.,Division of Endocrinology and Center for Basic and Translational Obesity Research, Boston Children's Hospital, Boston, MA, USA
| | - Aarno Palotie
- Institute for Molecular Medicine Finland (FIMM), University of Helsinki, Helsinki, Finland.,Analytic and Translational Genetics Unit, Departments of Medicine, of Neurology and of Psychiatry, Massachusetts General Hospital, Boston, MA, USA.,The Stanley Center for Psychiatric Research and Program in Medical and Population Genetics, Broad Institute, Cambridge, MA, USA
| | - Julie E Park
- Department of Medicine, University of British Columbia, Vancouver, British Columbia, Canada
| | - Craig E Pennell
- School of Women's and Infants' Health, University of Western Australia, Perth, Western Australia, Australia
| | - Göran Pershagen
- Institute of Environmental Medicine, Karolinska Institutet, Stockholm, Sweden.,Centre for Occupational and Environmental Medicine, Stockholm County Council, Stockholm, Sweden
| | - Alexey Polonikov
- Department of Biology, Medical Genetics and Ecology, Kursk State Medical University, Kursk, Russian Federation
| | - Dirkje S Postma
- Groningen Research Institute for Asthma and COPD (GRIAC), Groningen, The Netherlands.,University Medical Center Groningen, Department of Pulmonology, University of Groningen, Groningen, The Netherlands
| | - Nicole Probst-Hensch
- Department of Epidemiology and Public Health, Swiss Tropical and Public Health Institute, Basel, Switzerland.,University of Basel, Basel, Switzerland
| | - Valery P Puzyrev
- Population Genetics Laboratory, Research Institute of Medical Genetics, Tomsk NRMC, Tomsk, Russian Federation
| | - Benjamin A Raby
- Channing Division of Network Medicine, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA
| | - Olli T Raitakari
- Department of Clinical Physiology and Nuclear Medicine, University of Turku and Turku University Hospital, Turku, Finland
| | - Adaikalavan Ramasamy
- Department of Epidemiology and Biostatistics, Imperial College London, London, UK.,Department of Medical and Molecular Genetics, King's College London, London, UK
| | - Stephen S Rich
- Center for Public Health Genomics, University of Virginia, Charlottesville, VA, USA
| | - Colin F Robertson
- Respiratory Medicine, Murdoch Children's Research Institute, Melbourne, Victoria, Australia
| | - Isabelle Romieu
- Hubert Department of Global Health, Mory University, Atlanta, GA, USA.,Center for Population Health Research, National Institute of Public Health, Cuernavaca, Mexico
| | - Muhammad T Salam
- Department of Preventive Medicine, Keck School of Medicine, University of Southern California, Los Angeles, CA, USA.,Department of Psychiatry, Kern Medical, Bakersfield, CA, USA
| | - Veikko Salomaa
- National Institute for Health and Welfare (THL), Helsinki, Finland
| | - Vivi Schlünssen
- Department of Public Health, Section for Environment, Occupation & Health, Aarhus University, Aarhus, Denmark
| | - Robert Scott
- MRC Epidemiology Unit, University of Cambridge School of Clinical Medicine, Institute of Metabolic Science, Cambridge Biomedical Campus, Cambridge, UK
| | - Polina A Selivanova
- Department of Faculty Therapy, Siberian State Medical University, Tomsk, Russian Federation
| | - Torben Sigsgaard
- Department of Public Health, Section for Environment, Occupation & Health, Aarhus University, Aarhus, Denmark
| | - Angela Simpson
- Division of Infection, Immunity and Respiratory Medicine, School of Biological Sciences, Faculty of Biology, Medicine and Health, Manchester Academic Health Science Centre, University of Manchester, Manchester, UK.,University Hospital of South Manchester, National Health Service (NHS) Foundation Trust, Manchester, UK
| | - Valérie Siroux
- Institut National de la Santé et de la Recherche Médicale (INSERM) U1209, Institute for Advanced Biosciences, Team of Environmental Epidemiology Applied to Reproduction and Respiratory Health, Grenoble, France.,Université de Grenoble Alpes/CNRS UMR5309, Institute for Advanced Biosciences, Team of Environmental Epidemiology Applied to Reproduction and Respiratory Health, Grenoble, France
| | - Lewis J Smith
- Division of Pulmonary and Critical Care Medicine, Feinberg School of Medicine, Northwestern University, Chicago, IL, USA
| | - Maria Solodilova
- Department of Biology, Medical Genetics and Ecology, Kursk State Medical University, Kursk, Russian Federation
| | - Marie Standl
- Institute of Epidemiology I, Helmholtz Zentrum München, German Research Centre for Environmental Health, Neuherberg, Germany
| | - Kari Stefansson
- deCODE genetics, Amgen Inc., Reykjavik, Iceland.,Faculty of Medicine, University of Iceland, Reykjavik, Iceland
| | - David P Strachan
- Population Health Research Institute, St George's University of London, London, UK
| | - Bruno H Stricker
- Department of Epidemiology, Erasmus MC-University Medical Center Rotterdam, Rotterdam, The Netherlands.,Netherlands Healthcare Inspectorate, The Hague, The Netherlands.,Department of Internal Medicine, Erasmus MC-University Medical Center Rotterdam, Rotterdam, The Netherlands
| | | | - Philip J Thompson
- Institute for Respiratory Health and Harry Perkins Institute of Medical Research, University of Western Australia and The Lung Health Clinic, Nedlands, Western Australia, Australia
| | | | - Unnur Thorsteinsdottir
- deCODE genetics, Amgen Inc., Reykjavik, Iceland.,Faculty of Medicine, University of Iceland, Reykjavik, Iceland
| | - Carla M T Tiesler
- Institute of Epidemiology I, Helmholtz Zentrum München, German Research Centre for Environmental Health, Neuherberg, Germany.,Division of Metabolic Diseases and Nutritional Medicine, Dr. von Hauner Children's Hospital, Ludwig-Maximilians-University of Munich, Munich, Germany
| | - Dara G Torgerson
- Department of Medicine, University of California, San Francisco, San Francisco, CA, USA
| | - Tatsuhiko Tsunoda
- RIKEN Center for Integrative Medical Sciences, Yokohama, Japan.,Department of Medical Science Mathematics, Medical Research Institute, Tokyo Medical and Dental University, Tokyo, Japan
| | - André G Uitterlinden
- Department of Internal Medicine, Erasmus MC-University Medical Center Rotterdam, Rotterdam, The Netherlands
| | - Ralf J P van der Valk
- The Generation R Study Group, Department of Pediatrics, Division of Respiratory Medicine and Department of Epidemiology, Erasmus MC-University Medical Center Rotterdam, Rotterdam, The Netherlands
| | - Amaury Vaysse
- Genetic Variation and Human Diseases Unit (UMR-946), Institut National de la Santé et de la Recherche Médicale (INSERM), Paris, France.,Institut Universitaire d'Hématologie, Université Paris Diderot, Université Sorbonne Paris Cité, Paris, France
| | - Sailaja Vedantam
- Divisions of Genetics and Endocrinology, Children's Hospital, Boston, MA, USA.,Broad Institute, Cambridge, MA, USA
| | - Andrea von Berg
- Department of Pediatrics, Marien-Hospital Wesel, Wesel, Germany
| | - Erika von Mutius
- Dr. Von Hauner Children's Hospital, Ludwig Maximilians University Munich, Munich, Germany.,German Center for Lung Research, Munich, Germany
| | - Judith M Vonk
- Groningen Research Institute for Asthma and COPD (GRIAC), Groningen, The Netherlands.,University of Groningen, University Medical Center Groningen, Department of Epidemiology, Groningen, The Netherlands
| | - Johannes Waage
- Copenhagen Prospective Studies on Asthma in Childhood, Herlev and Gentofte Hospital, University of Copenhagen, Copenhagen, Denmark
| | - Nick J Wareham
- MRC Epidemiology Unit, University of Cambridge School of Clinical Medicine, Institute of Metabolic Science, Cambridge Biomedical Campus, Cambridge, UK
| | - Scott T Weiss
- Channing Division of Network Medicine, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA
| | - Wendy B White
- Undergraduate Training and Education Center (UTEC), Jackson Heart Study, Tougaloo College, Jackson, MI, USA
| | - Magnus Wickman
- Institute of Environmental Medicine, Karolinska Institutet, Stockholm, Sweden.,Centre for Clinical Research Sörmland, Uppsala University, Eskilstuna, Sweden
| | - Elisabeth Widén
- Institute for Molecular Medicine Finland (FIMM), University of Helsinki, Helsinki, Finland
| | - Gonneke Willemsen
- Department of Biological Psychology, Amsterdam Public Health Research Institute, Vrjie Universiteit, Amsterdam, The Netherlands
| | - L Keoki Williams
- Center for Health Policy and Health Services Research, Henry Ford Health System, Detroit, MI, USA.,Department of Internal Medicine, Henry Ford Health System, Detroit, MI, USA
| | - Inge M Wouters
- Division of Environmental Epidemiology, Institute for Risk Assessment Sciences, Utrecht University, Utrecht, The Netherlands
| | - James J Yang
- School of Nursing, University of Michigan, Ann Arbor, MI, USA
| | - Jing Hua Zhao
- MRC Epidemiology Unit, University of Cambridge School of Clinical Medicine, Institute of Metabolic Science, Cambridge Biomedical Campus, Cambridge, UK
| | - Miriam F Moffatt
- Section of Genomic Medicine, National Heart and Lung Institute, London, UK
| | - Carole Ober
- Department of Human Genetics, University of Chicago, Chicago, IL, USA
| | - Dan L Nicolae
- Departments of Statistics, Human Genetics and Medicine, Section of Genetic Medicine, University of Chicago, Chicago, IL, USA.
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Seyerle AA, Lin HJ, Gogarten SM, Stilp A, Méndez Giráldez R, Soliman E, Baldassari A, Graff M, Heckbert S, Kerr KF, Kooperberg C, Rodriguez C, Guo X, Yao J, Sotoodehnia N, Taylor KD, Whitsel EA, Rotter JI, Laurie CC, Avery CL. Genome-wide association study of PR interval in Hispanics/Latinos identifies novel locus at ID2. Heart 2017; 104:904-911. [PMID: 29127183 DOI: 10.1136/heartjnl-2017-312045] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/28/2017] [Revised: 10/10/2017] [Accepted: 10/16/2017] [Indexed: 01/12/2023] Open
Abstract
OBJECTIVE PR interval (PR) is a heritable electrocardiographic measure of atrial and atrioventricular nodal conduction. Changes in PR duration may be associated with atrial fibrillation, heart failure and all-cause mortality. Hispanic/Latino populations have high burdens of cardiovascular morbidity and mortality, are highly admixed and represent exceptional opportunities for novel locus identification. However, they remain chronically understudied. We present the first genome-wide association study (GWAS) of PR in 14 756 participants of Hispanic/Latino ancestry from three studies. METHODS Study-specific summary results of the association between 1000 Genomes Phase 1 imputed single-nucleotide polymorphisms (SNPs) and PR assumed an additive genetic model and were adjusted for global ancestry, study centre/region and clinical covariates. Results were combined using fixed-effects, inverse variance weighted meta-analysis. Sequential conditional analyses were used to identify independent signals. Replication of novel loci was performed in populations of Asian, African and European descent. ENCODE and RoadMap data were used to annotate results. RESULTS We identified a novel genome-wide association (P<5×10-8) with PR at ID2 (rs6730558), which replicated in Asian and European populations (P<0.017). Additionally, we generalised 10 previously identified PR loci to Hispanics/Latinos. Bioinformatics annotation provided evidence for regulatory function in cardiac tissue. Further, for six loci that generalised, the Hispanic/Latino index SNP was genome-wide significant and identical to (or in high linkage disequilibrium with) the previously identified GWAS lead SNP. CONCLUSIONS Our results suggest that genetic determinants of PR are consistent across race/ethnicity, but extending studies to admixed populations can identify novel associations, underscoring the importance of conducting genetic studies in diverse populations.
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Affiliation(s)
- Amanda A Seyerle
- Department of Epidemiology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA.,Division of Epidemiology and Community Health, University of Minnesota, Minneapolis, Minnesota, USA
| | - Henry J Lin
- Institute for Translational Genomics and Population Sciences, Los Angeles Biomedical Research Institute at Harbor-UCLA Medical Center, Torrance, California, USA.,Department of Pediatrics, Division of Medical Genetics, Harbor-UCLA Medical Center, Torrance, California, USA
| | | | - Adrienne Stilp
- Department of Biostatistics, University of Washington, Seattle, Washington, USA
| | - Raul Méndez Giráldez
- Department of Epidemiology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
| | - Elsayed Soliman
- Division of Public Health Sciences, Wake Forest School of Medicine, Epidemiology Cardiology Research Center (EPICARE), Winston-Salem, North Carolina, USA.,Department of Medicine, Section of Cardiology, Wake Forest School of Medicine, Winston-Salem, North Carolina, USA
| | - Antoine Baldassari
- Department of Epidemiology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
| | - Mariaelisa Graff
- Department of Epidemiology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
| | - Susan Heckbert
- Department of Epidemiology, University of Washington, Seattle, Washington, USA.,Cardiovascular Health Research Unit, University of Washington, Seattle, Washington, USA
| | - Kathleen F Kerr
- Department of Biostatistics, University of Washington, Seattle, Washington, USA
| | - Charles Kooperberg
- Division of Public Health Sciences, Fred Hutchinson Cancer Research Center, Seattle, Washington, USA
| | - Carlos Rodriguez
- Department of Medicine, Section of Cardiology, Wake Forest School of Medicine, Winston-Salem, North Carolina, USA.,Department of Epidemiology and Prevention, Division of Public Health Sciences, Wake Forest University School of Medicine, Winston-Salem, North Carolina, USA
| | - Xiuqing Guo
- Institute for Translational Genomics and Population Sciences, Los Angeles Biomedical Research Institute at Harbor-UCLA Medical Center, Torrance, California, USA.,Department of Pediatrics, Division of Medical Genetics, Harbor-UCLA Medical Center, Torrance, California, USA
| | - Jie Yao
- Institute for Translational Genomics and Population Sciences, Los Angeles Biomedical Research Institute at Harbor-UCLA Medical Center, Torrance, California, USA.,Department of Pediatrics, Division of Medical Genetics, Harbor-UCLA Medical Center, Torrance, California, USA
| | - Nona Sotoodehnia
- Cardiovascular Health Research Unit, University of Washington, Seattle, Washington, USA.,Division of Cardiology, University of Washington, Seattle, Washington, USA
| | - Kent D Taylor
- Division of Genomic Outcomes and Institute for Translational Genomics and Population Sciences, Los Angeles Biomedical Research Institute at Harbor-UCLA Medical Center, Torrance, California, USA
| | - Eric A Whitsel
- Department of Epidemiology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA.,Department of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
| | - Jerome I Rotter
- Institute for Translational Genomics and Population Sciences, Los Angeles Biomedical Research Institute at Harbor-UCLA Medical Center, Torrance, California, USA.,Department of Pediatrics, Division of Medical Genetics, Harbor-UCLA Medical Center, Torrance, California, USA
| | - Cathy C Laurie
- Department of Biostatistics, University of Washington, Seattle, Washington, USA
| | - Christy L Avery
- Department of Epidemiology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA.,Carolina Population Center, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
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35
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Talwar A, Garcia JGN, Tsai H, Moreno M, Lahm T, Zamanian RT, Machado R, Kawut SM, Selej M, Mathai S, D'Anna LH, Sahni S, Rodriquez EJ, Channick R, Fagan K, Gray M, Armstrong J, Rodriguez Lopez J, de Jesus Perez V. Health Disparities in Patients with Pulmonary Arterial Hypertension: A Blueprint for Action. An Official American Thoracic Society Statement. Am J Respir Crit Care Med 2017; 196:e32-e47. [PMID: 29028375 DOI: 10.1164/rccm.201709-1821st] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
BACKGROUND Health disparities have a major impact in the quality of life and clinical care received by minorities in the United States. Pulmonary arterial hypertension (PAH) is a rare cardiopulmonary disorder that affects children and adults and that, if untreated, results in premature death. The impact of health disparities in the diagnosis, treatment, and clinical outcome of patients with PAH has not been systematically investigated. OBJECTIVES The specific goals of this research statement were to conduct a critical review of the literature concerning health disparities in PAH, identify major research gaps and prioritize direction for future research. METHODS Literature searches from multiple reference databases were performed using medical subject headings and text words for pulmonary hypertension and health disparities. Members of the committee discussed the evidence and provided recommendations for future research. RESULTS Few studies were found discussing the impact of health disparities in PAH. Using recent research statements focused on health disparities, the group identified six major study topics that would help address the contribution of health disparities to PAH. Representative studies in each topic were discussed and specific recommendations were made by the group concerning the most urgent questions to address in future research studies. CONCLUSIONS At present, there are few studies that address health disparities in PAH. Given the potential adverse impact of health disparities, we recommend that research efforts be undertaken to address the topics discussed in the document. Awareness of health disparities will likely improve advocacy efforts, public health policy and the quality of care of vulnerable populations with PAH.
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36
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Sims R, van der Lee SJ, Naj AC, Bellenguez C, Badarinarayan N, Jakobsdottir J, Kunkle BW, Boland A, Raybould R, Bis JC, Martin ER, Grenier-Boley B, Heilmann-Heimbach S, Chouraki V, Kuzma AB, Sleegers K, Vronskaya M, Ruiz A, Graham RR, Olaso R, Hoffmann P, Grove ML, Vardarajan BN, Hiltunen M, Nöthen MM, White CC, Hamilton-Nelson KL, Epelbaum J, Maier W, Choi SH, Beecham GW, Dulary C, Herms S, Smith AV, Funk CC, Derbois C, Forstner AJ, Ahmad S, Li H, Bacq D, Harold D, Satizabal CL, Valladares O, Squassina A, Thomas R, Brody JA, Qu L, Sánchez-Juan P, Morgan T, Wolters FJ, Zhao Y, Garcia FS, Denning N, Fornage M, Malamon J, Naranjo MCD, Majounie E, Mosley TH, Dombroski B, Wallon D, Lupton MK, Dupuis J, Whitehead P, Fratiglioni L, Medway C, Jian X, Mukherjee S, Keller L, Brown K, Lin H, Cantwell LB, Panza F, McGuinness B, Moreno-Grau S, Burgess JD, Solfrizzi V, Proitsi P, Adams HH, Allen M, Seripa D, Pastor P, Cupples LA, Price ND, Hannequin D, Frank-García A, Levy D, Chakrabarty P, Caffarra P, Giegling I, Beiser AS, Giedraitis V, Hampel H, Garcia ME, Wang X, Lannfelt L, Mecocci P, Eiriksdottir G, Crane PK, Pasquier F, Boccardi V, Henández I, Barber RC, Scherer M, Tarraga L, Adams PM, Leber M, Chen Y, Albert MS, Riedel-Heller S, Emilsson V, Beekly D, Braae A, Schmidt R, Blacker D, Masullo C, Schmidt H, Doody RS, Spalletta G, Longstreth WT, Fairchild TJ, Bossù P, Lopez OL, Frosch MP, Sacchinelli E, Ghetti B, Yang Q, Huebinger RM, Jessen F, Li S, Kamboh MI, Morris J, Sotolongo-Grau O, Katz MJ, Corcoran C, Dunstan M, Braddel A, Thomas C, Meggy A, Marshall R, Gerrish A, Chapman J, Aguilar M, Taylor S, Hill M, Fairén MD, Hodges A, Vellas B, Soininen H, Kloszewska I, Daniilidou M, Uphill J, Patel Y, Hughes JT, Lord J, Turton J, Hartmann AM, Cecchetti R, Fenoglio C, Serpente M, Arcaro M, Caltagirone C, Orfei MD, Ciaramella A, Pichler S, Mayhaus M, Gu W, Lleó A, Fortea J, Blesa R, Barber IS, Brookes K, Cupidi C, Maletta RG, Carrell D, Sorbi S, Moebus S, Urbano M, Pilotto A, Kornhuber J, Bosco P, Todd S, Craig D, Johnston J, Gill M, Lawlor B, Lynch A, Fox NC, Hardy J, Albin RL, Apostolova LG, Arnold SE, Asthana S, Atwood CS, Baldwin CT, Barnes LL, Barral S, Beach TG, Becker JT, Bigio EH, Bird TD, Boeve BF, Bowen JD, Boxer A, Burke JR, Burns JM, Buxbaum JD, Cairns NJ, Cao C, Carlson CS, Carlsson CM, Carney RM, Carrasquillo MM, Carroll SL, Diaz CC, Chui HC, Clark DG, Cribbs DH, Crocco EA, DeCarli C, Dick M, Duara R, Evans DA, Faber KM, Fallon KB, Fardo DW, Farlow MR, Ferris S, Foroud TM, Galasko DR, Gearing M, Geschwind DH, Gilbert JR, Graff-Radford NR, Green RC, Growdon JH, Hamilton RL, Harrell LE, Honig LS, Huentelman MJ, Hulette CM, Hyman BT, Jarvik GP, Abner E, Jin LW, Jun G, Karydas A, Kaye JA, Kim R, Kowall NW, Kramer JH, LaFerla FM, Lah JJ, Leverenz JB, Levey AI, Li G, Lieberman AP, Lunetta KL, Lyketsos CG, Marson DC, Martiniuk F, Mash DC, Masliah E, McCormick WC, McCurry SM, McDavid AN, McKee AC, Mesulam M, Miller BL, Miller CA, Miller JW, Morris JC, Murrell JR, Myers AJ, O'Bryant S, Olichney JM, Pankratz VS, Parisi JE, Paulson HL, Perry W, Peskind E, Pierce A, Poon WW, Potter H, Quinn JF, Raj A, Raskind M, Reisberg B, Reitz C, Ringman JM, Roberson ED, Rogaeva E, Rosen HJ, Rosenberg RN, Sager MA, Saykin AJ, Schneider JA, Schneider LS, Seeley WW, Smith AG, Sonnen JA, Spina S, Stern RA, Swerdlow RH, Tanzi RE, Thornton-Wells TA, Trojanowski JQ, Troncoso JC, Van Deerlin VM, Van Eldik LJ, Vinters HV, Vonsattel JP, Weintraub S, Welsh-Bohmer KA, Wilhelmsen KC, Williamson J, Wingo TS, Woltjer RL, Wright CB, Yu CE, Yu L, Garzia F, Golamaully F, Septier G, Engelborghs S, Vandenberghe R, De Deyn PP, Fernadez CM, Benito YA, Thonberg H, Forsell C, Lilius L, Kinhult-Stählbom A, Kilander L, Brundin R, Concari L, Helisalmi S, Koivisto AM, Haapasalo A, Dermecourt V, Fievet N, Hanon O, Dufouil C, Brice A, Ritchie K, Dubois B, Himali JJ, Keene CD, Tschanz J, Fitzpatrick AL, Kukull WA, Norton M, Aspelund T, Larson EB, Munger R, Rotter JI, Lipton RB, Bullido MJ, Hofman A, Montine TJ, Coto E, Boerwinkle E, Petersen RC, Alvarez V, Rivadeneira F, Reiman EM, Gallo M, O'Donnell CJ, Reisch JS, Bruni AC, Royall DR, Dichgans M, Sano M, Galimberti D, St George-Hyslop P, Scarpini E, Tsuang DW, Mancuso M, Bonuccelli U, Winslow AR, Daniele A, Wu CK, Peters O, Nacmias B, Riemenschneider M, Heun R, Brayne C, Rubinsztein DC, Bras J, Guerreiro R, Al-Chalabi A, Shaw CE, Collinge J, Mann D, Tsolaki M, Clarimón J, Sussams R, Lovestone S, O'Donovan MC, Owen MJ, Behrens TW, Mead S, Goate AM, Uitterlinden AG, Holmes C, Cruchaga C, Ingelsson M, Bennett DA, Powell J, Golde TE, Graff C, De Jager PL, Morgan K, Ertekin-Taner N, Combarros O, Psaty BM, Passmore P, Younkin SG, Berr C, Gudnason V, Rujescu D, Dickson DW, Dartigues JF, DeStefano AL, Ortega-Cubero S, Hakonarson H, Campion D, Boada M, Kauwe JK, Farrer LA, Van Broeckhoven C, Ikram MA, Jones L, Haines JL, Tzourio C, Launer LJ, Escott-Price V, Mayeux R, Deleuze JF, Amin N, Holmans PA, Pericak-Vance MA, Amouyel P, van Duijn CM, Ramirez A, Wang LS, Lambert JC, Seshadri S, Williams J, Schellenberg GD. Rare coding variants in PLCG2, ABI3, and TREM2 implicate microglial-mediated innate immunity in Alzheimer's disease. Nat Genet 2017; 49:1373-1384. [PMID: 28714976 PMCID: PMC5669039 DOI: 10.1038/ng.3916] [Citation(s) in RCA: 637] [Impact Index Per Article: 91.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2016] [Accepted: 06/16/2017] [Indexed: 02/02/2023]
Abstract
We identified rare coding variants associated with Alzheimer's disease in a three-stage case-control study of 85,133 subjects. In stage 1, we genotyped 34,174 samples using a whole-exome microarray. In stage 2, we tested associated variants (P < 1 × 10-4) in 35,962 independent samples using de novo genotyping and imputed genotypes. In stage 3, we used an additional 14,997 samples to test the most significant stage 2 associations (P < 5 × 10-8) using imputed genotypes. We observed three new genome-wide significant nonsynonymous variants associated with Alzheimer's disease: a protective variant in PLCG2 (rs72824905: p.Pro522Arg, P = 5.38 × 10-10, odds ratio (OR) = 0.68, minor allele frequency (MAF)cases = 0.0059, MAFcontrols = 0.0093), a risk variant in ABI3 (rs616338: p.Ser209Phe, P = 4.56 × 10-10, OR = 1.43, MAFcases = 0.011, MAFcontrols = 0.008), and a new genome-wide significant variant in TREM2 (rs143332484: p.Arg62His, P = 1.55 × 10-14, OR = 1.67, MAFcases = 0.0143, MAFcontrols = 0.0089), a known susceptibility gene for Alzheimer's disease. These protein-altering changes are in genes highly expressed in microglia and highlight an immune-related protein-protein interaction network enriched for previously identified risk genes in Alzheimer's disease. These genetic findings provide additional evidence that the microglia-mediated innate immune response contributes directly to the development of Alzheimer's disease.
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Affiliation(s)
- Rebecca Sims
- Institute of Psychological Medicine and Clinical Neurosciences, MRC Centre for Neuropsychiatric Genetics and Genomics, Cardiff University, Cardiff, UK
| | - Sven J van der Lee
- Department of Epidemiology, Erasmus Medical Center, Rotterdam, the Netherlands
| | - Adam C Naj
- Department of Biostatistics and Epidemiology/Center for Clinical Epidemiology and Biostatistics, University of Pennsylvania Perelman School of Medicine, Philadelphia, Pennsylvania, USA
| | - Céline Bellenguez
- INSERM, U1167, RID-AGE-Risk Factors and Molecular Determinants of Aging-Related Diseases, Lille, France
- Institut Pasteur de Lille, Lille, France
- University Lille, U1167-Excellence Laboratory LabEx DISTALZ, Lille, France
| | - Nandini Badarinarayan
- Institute of Psychological Medicine and Clinical Neurosciences, MRC Centre for Neuropsychiatric Genetics and Genomics, Cardiff University, Cardiff, UK
| | | | - Brian W Kunkle
- John P. Hussman Institute for Human Genomics, University of Miami, Miami, Florida, USA
| | - Anne Boland
- CEA/Institut de Génomique, Centre National de Génotypage, Evry, France
| | - Rachel Raybould
- Institute of Psychological Medicine and Clinical Neurosciences, MRC Centre for Neuropsychiatric Genetics and Genomics, Cardiff University, Cardiff, UK
| | - Joshua C Bis
- Cardiovascular Health Research Unit, Department of Medicine, University of Washington, Seattle, Washington, USA
| | - Eden R Martin
- John P. Hussman Institute for Human Genomics, University of Miami, Miami, Florida, USA
- Dr. John T. Macdonald Foundation, Department of Human Genetics, University of Miami, Miami, Florida, USA
| | - Benjamin Grenier-Boley
- INSERM, U1167, RID-AGE-Risk Factors and Molecular Determinants of Aging-Related Diseases, Lille, France
- Institut Pasteur de Lille, Lille, France
- University Lille, U1167-Excellence Laboratory LabEx DISTALZ, Lille, France
| | - Stefanie Heilmann-Heimbach
- Institute of Human Genetics, University of Bonn, Bonn, Germany
- Department of Genomics, Life &Brain Center, University of Bonn, Bonn, Germany
| | - Vincent Chouraki
- Boston University School of Medicine, Boston, Massachusetts, USA
- Framingham Heart Study, Framingham, Massachusetts, USA
| | - Amanda B Kuzma
- Penn Neurodegeneration Genomics Center, Department of Pathology and Laboratory Medicine, University of Pennsylvania Perelman School of Medicine, Philadelphia, Pennsylvania, USA
| | - Kristel Sleegers
- Neurodegenerative Brain Diseases Group, Department of Molecular Genetics, VIB, Antwerp, Belgium
- Institute Born-Bunge, University of Antwerp, Antwerp, Belgium
| | - Maria Vronskaya
- Institute of Psychological Medicine and Clinical Neurosciences, MRC Centre for Neuropsychiatric Genetics and Genomics, Cardiff University, Cardiff, UK
| | - Agustin Ruiz
- Research Center and Memory Clinic of Fundació ACE, Institut Català de Neurociències Aplicades, Barcelona, Spain
| | - Robert R Graham
- Immunology Biomarkers Group, Genentech, South San Francisco, California, USA
| | - Robert Olaso
- CEA/Institut de Génomique, Centre National de Génotypage, Evry, France
| | - Per Hoffmann
- Institute of Human Genetics, University of Bonn, Bonn, Germany
- Department of Genomics, Life &Brain Center, University of Bonn, Bonn, Germany
- Division of Medical Genetics, University Hospital and Department of Biomedicine, University of Basel, Basel, Switzerland
| | - Megan L Grove
- School of Public Health, Human Genetics Center, University of Texas Health Science Center at Houston, Houston, Texas, USA
| | - Badri N Vardarajan
- Taub Institute on Alzheimer's Disease and the Aging Brain, Department of Neurology, Columbia University, New York, New York, USA
- Gertrude H. Sergievsky Center, Columbia University, New York, New York, USA
- Department of Neurology, Columbia University, New York, New York, USA
| | - Mikko Hiltunen
- Institute of Biomedicine, University of Eastern Finland, Kuopio, Finland
- Department of Neurology, Kuopio University Hospital, Kuopio, Finland
| | - Markus M Nöthen
- Institute of Human Genetics, University of Bonn, Bonn, Germany
- Department of Genomics, Life &Brain Center, University of Bonn, Bonn, Germany
| | - Charles C White
- Program in Translational NeuroPsychiatric Genomics, Institute for the Neurosciences, Departments of Neurology and Psychiatry, Brigham and Women's Hospital, Boston, Massachusetts, USA
| | | | - Jacques Epelbaum
- UMR 894, Center for Psychiatry and Neuroscience, INSERM, Université Paris Descartes, Paris, France
| | - Wolfgang Maier
- German Center for Neurodegenerative Diseases (DZNE), Bonn, Germany
- Department of Psychiatry and Psychotherapy, University of Bonn, Bonn, Germany
| | - Seung-Hoan Choi
- Boston University School of Medicine, Boston, Massachusetts, USA
- Department of Biostatistics, Boston University School of Public Health, Boston, Massachusetts, USA
| | - Gary W Beecham
- John P. Hussman Institute for Human Genomics, University of Miami, Miami, Florida, USA
- Dr. John T. Macdonald Foundation, Department of Human Genetics, University of Miami, Miami, Florida, USA
| | - Cécile Dulary
- CEA/Institut de Génomique, Centre National de Génotypage, Evry, France
| | - Stefan Herms
- Institute of Human Genetics, University of Bonn, Bonn, Germany
- Department of Genomics, Life &Brain Center, University of Bonn, Bonn, Germany
- Division of Medical Genetics, University Hospital and Department of Biomedicine, University of Basel, Basel, Switzerland
| | - Albert V Smith
- Icelandic Heart Association, Kopavogur, Iceland
- Faculty of Medicine, University of Iceland, Reykjavik, Iceland
| | - Cory C Funk
- Institute for Systems Biology, Seattle, Washington, USA
| | - Céline Derbois
- CEA/Institut de Génomique, Centre National de Génotypage, Evry, France
| | - Andreas J Forstner
- Institute of Human Genetics, University of Bonn, Bonn, Germany
- Department of Genomics, Life &Brain Center, University of Bonn, Bonn, Germany
| | - Shahzad Ahmad
- Department of Epidemiology, Erasmus Medical Center, Rotterdam, the Netherlands
| | - Hongdong Li
- Institute for Systems Biology, Seattle, Washington, USA
| | - Delphine Bacq
- CEA/Institut de Génomique, Centre National de Génotypage, Evry, France
| | - Denise Harold
- School of Biotechnology, Dublin City University, Dublin, Ireland
| | - Claudia L Satizabal
- Boston University School of Medicine, Boston, Massachusetts, USA
- Framingham Heart Study, Framingham, Massachusetts, USA
| | - Otto Valladares
- Penn Neurodegeneration Genomics Center, Department of Pathology and Laboratory Medicine, University of Pennsylvania Perelman School of Medicine, Philadelphia, Pennsylvania, USA
| | - Alessio Squassina
- Section of Neuroscience and Clinical Pharmacology, Department of Biomedical Sciences, University of Cagliari, Cagliari, Italy
| | - Rhodri Thomas
- Institute of Psychological Medicine and Clinical Neurosciences, MRC Centre for Neuropsychiatric Genetics and Genomics, Cardiff University, Cardiff, UK
| | - Jennifer A Brody
- Cardiovascular Health Research Unit, Department of Medicine, University of Washington, Seattle, Washington, USA
| | - Liming Qu
- Penn Neurodegeneration Genomics Center, Department of Pathology and Laboratory Medicine, University of Pennsylvania Perelman School of Medicine, Philadelphia, Pennsylvania, USA
| | - Pascual Sánchez-Juan
- Neurology Service and CIBERNED, 'Marqués de Valdecilla' University Hospital (University of Cantabria and IFIMAV), Santander, Spain
| | - Taniesha Morgan
- Institute of Psychological Medicine and Clinical Neurosciences, MRC Centre for Neuropsychiatric Genetics and Genomics, Cardiff University, Cardiff, UK
| | - Frank J Wolters
- Department of Epidemiology, Erasmus Medical Center, Rotterdam, the Netherlands
| | - Yi Zhao
- Penn Neurodegeneration Genomics Center, Department of Pathology and Laboratory Medicine, University of Pennsylvania Perelman School of Medicine, Philadelphia, Pennsylvania, USA
| | | | - Nicola Denning
- Institute of Psychological Medicine and Clinical Neurosciences, MRC Centre for Neuropsychiatric Genetics and Genomics, Cardiff University, Cardiff, UK
| | - Myriam Fornage
- Brown Foundation Institute of Molecular Medicine, University of Texas Health Sciences Center at Houston, Houston, Texas, USA
| | - John Malamon
- Penn Neurodegeneration Genomics Center, Department of Pathology and Laboratory Medicine, University of Pennsylvania Perelman School of Medicine, Philadelphia, Pennsylvania, USA
| | | | - Elisa Majounie
- Institute of Psychological Medicine and Clinical Neurosciences, MRC Centre for Neuropsychiatric Genetics and Genomics, Cardiff University, Cardiff, UK
| | - Thomas H Mosley
- Departments of Medicine, Geriatrics, Gerontology and Neurology, University of Mississippi Medical Center, Jackson, Mississippi, USA
| | - Beth Dombroski
- Penn Neurodegeneration Genomics Center, Department of Pathology and Laboratory Medicine, University of Pennsylvania Perelman School of Medicine, Philadelphia, Pennsylvania, USA
| | - David Wallon
- Centre Hospitalier du Rouvray, Sotteville les Rouen, France
- INSERM U1079, Rouen University, IRIB, Normandy University, Rouen, France
| | - Michelle K Lupton
- Department of Basic and Clinical Neuroscience, Institute of Psychiatry, Psychology and Neuroscience, King's College London, London, UK
- Genetic Epidemiology, QIMR Berghofer Medical Research Institute, Herston, Queensland, Australia
| | - Josée Dupuis
- Department of Biostatistics, Boston University School of Public Health, Boston, Massachusetts, USA
| | - Patrice Whitehead
- John P. Hussman Institute for Human Genomics, University of Miami, Miami, Florida, USA
| | - Laura Fratiglioni
- Department of Geriatric Medicine, Karolinska University Hospital Huddinge, Stockholm, Sweden
- Aging Research Center, Department of Neurobiology, Care Sciences and Society, Karolinska Institutet and Stockholm University, Stockholm, Sweden
| | - Christopher Medway
- Institute of Genetics, Queen's Medical Centre, University of Nottingham, Nottingham, UK
| | - Xueqiu Jian
- Brown Foundation Institute of Molecular Medicine, University of Texas Health Sciences Center at Houston, Houston, Texas, USA
| | | | - Lina Keller
- Aging Research Center, Department of Neurobiology, Care Sciences and Society, Karolinska Institutet and Stockholm University, Stockholm, Sweden
| | - Kristelle Brown
- Institute of Genetics, Queen's Medical Centre, University of Nottingham, Nottingham, UK
| | - Honghuang Lin
- Section of Computational Biomedicine, Department of Medicine, Boston University School of Medicine, Boston, Massachusetts, USA
| | - Laura B Cantwell
- Penn Neurodegeneration Genomics Center, Department of Pathology and Laboratory Medicine, University of Pennsylvania Perelman School of Medicine, Philadelphia, Pennsylvania, USA
| | - Francesco Panza
- Neurodegenerative Disease Unit, Department of Basic Medicine, Neuroscience, and Sense Organs, University of Bari Aldo Moro, Bari, Italy
| | - Bernadette McGuinness
- Centre for Public Health, School of Medicine, Dentistry and Biomedical Sciences, Queen's University, Belfast, UK
| | - Sonia Moreno-Grau
- Research Center and Memory Clinic of Fundació ACE, Institut Català de Neurociències Aplicades, Barcelona, Spain
| | - Jeremy D Burgess
- Department of Neuroscience, Mayo Clinic, Jacksonville, Florida, USA
| | - Vincenzo Solfrizzi
- Geriatric Medicine-Memory Unit and Rare Disease Centre, University of Bari Aldo Moro, Bari, Italy
| | - Petra Proitsi
- Department of Basic and Clinical Neuroscience, Institute of Psychiatry, Psychology and Neuroscience, King's College London, London, UK
| | - Hieab H Adams
- Department of Epidemiology, Erasmus Medical Center, Rotterdam, the Netherlands
| | - Mariet Allen
- Department of Neuroscience, Mayo Clinic, Jacksonville, Florida, USA
| | - Davide Seripa
- Geriatric Unit and Gerontology-Geriatrics Research Laboratory, Department of Medical Sciences, IRCCS Casa Sollievo della Sofferenza, San Giovanni Rotondo, Italy
| | - Pau Pastor
- Section of Gerontology and Geriatrics, Department of Medicine, University of Perugia, Perugia, Italy
| | - L Adrienne Cupples
- Framingham Heart Study, Framingham, Massachusetts, USA
- Department of Biostatistics, Boston University School of Public Health, Boston, Massachusetts, USA
| | | | - Didier Hannequin
- INSERM U1079, Rouen University, IRIB, Normandy University, Rouen, France
- Department of Neurology, Rouen University Hospital, Rouen, France
| | - Ana Frank-García
- Department of Neurology, University Hospital La Paz, Universidad Autónoma de Madrid, Madrid, Spain
- Instituto de Investigación Sanitaria Hospital la Paz (IdiPAZ), Madrid, Spain
- Centro de Investigación Biomédica en Red de Enfermedades Neurodegenerativas (CIBERNED), Instituto de Salud Carlos III, Madrid, Spain
| | - Daniel Levy
- Boston University School of Medicine, Boston, Massachusetts, USA
- Framingham Heart Study, Framingham, Massachusetts, USA
- National Heart, Lung, and Blood Institute, Bethesda, Maryland, USA
| | - Paramita Chakrabarty
- Center for Translational Research in Neurodegenerative Disease, Department of Neuroscience, University of Florida, Gainesville, Florida, USA
| | - Paolo Caffarra
- Department of Neuroscience, University of Parma, Parma, Italy
- Center for Cognitive Disorders AUSL, Parma, Italy
| | - Ina Giegling
- Department of Psychiatry, Martin Luther University Halle-Wittenberg, Halle, Germany
| | - Alexa S Beiser
- Framingham Heart Study, Framingham, Massachusetts, USA
- Department of Biostatistics, Boston University School of Public Health, Boston, Massachusetts, USA
| | | | - Harald Hampel
- AXA Research Fund and UPMC Chair, Paris, France
- Sorbonne Universités, Université Pierre et Marie Curie, Paris, France
- Institut de la Mémoire et de la Maladie d'Alzheimer (IM2A) and Institut du Cerveau et de la Moelle Épinière (ICM), Département de Neurologie, Hôpital de la Pitié-Salpêtrière, Paris, France
| | - Melissa E Garcia
- Laboratory of Epidemiology and Population Sciences, National Institute on Aging, Bethesda, Maryland, USA
| | - Xue Wang
- Department of Neuroscience, Mayo Clinic, Jacksonville, Florida, USA
| | - Lars Lannfelt
- Department of Public Health/Geriatrics, Uppsala University, Uppsala, Sweden
| | - Patrizia Mecocci
- Section of Gerontology and Geriatrics, Department of Medicine, University of Perugia, Perugia, Italy
| | | | - Paul K Crane
- Department of Medicine, University of Washington, Seattle, Washington, USA
| | - Florence Pasquier
- Centre Hospitalier Universitaire de Lille, Epidemiology and Public Health Department, Lille, France
- INSERM UMRS 1171, CNR-Maj, Lille, France
| | - Virginia Boccardi
- Section of Gerontology and Geriatrics, Department of Medicine, University of Perugia, Perugia, Italy
| | - Isabel Henández
- Research Center and Memory Clinic of Fundació ACE, Institut Català de Neurociències Aplicades, Barcelona, Spain
| | - Robert C Barber
- Department of Pharmacology and Neuroscience, University of North Texas Health Science Center, Fort Worth, Texas, USA
| | - Martin Scherer
- Department of Primary Medical Care, University Medical Centre Hamburg-Eppendorf, Hamburg, Germany
| | - Lluis Tarraga
- Research Center and Memory Clinic of Fundació ACE, Institut Català de Neurociències Aplicades, Barcelona, Spain
| | - Perrie M Adams
- Department of Psychiatry, University of Texas Southwestern Medical Center, Dallas, Texas, USA
| | - Markus Leber
- Department of Psychiatry and Psychotherapy, University of Cologne, Cologne, Germany
| | - Yuning Chen
- Department of Biostatistics, Boston University School of Public Health, Boston, Massachusetts, USA
| | - Marilyn S Albert
- Department of Neurology, Johns Hopkins University, Baltimore, Maryland, USA
| | - Steffi Riedel-Heller
- Institute of Social Medicine, Occupational Health and Public Health, University of Leipzig, Leipzig, Germany
| | - Valur Emilsson
- Icelandic Heart Association, Kopavogur, Iceland
- Faculty of Pharmaceutical Sciences, University of Iceland, Reykjavik, Iceland
| | - Duane Beekly
- National Alzheimer's Coordinating Center, University of Washington, Seattle, Washington, USA
| | - Anne Braae
- Schools of Life Sciences and Medicine, University of Nottingham, Nottingham, UK
| | - Reinhold Schmidt
- Department of Neurology, Clinical Division of Neurogeriatrics, Medical University Graz, Graz, Austria
| | - Deborah Blacker
- Department of Epidemiology, Harvard School of Public Health, Boston, Massachusetts, USA
- Department of Psychiatry, Massachusetts General Hospital/Harvard Medical School, Boston, Massachusetts, USA
| | - Carlo Masullo
- Department of Neurology, Catholic University of Rome, Rome, Italy
| | - Helena Schmidt
- Institute of Molecular Biology and Biochemistry, Medical University Graz, Graz, Austria
| | - Rachelle S Doody
- Alzheimer's Disease and Memory Disorders Center, Baylor College of Medicine, Houston, Texas, USA
| | - Gianfranco Spalletta
- Experimental Neuropsychiatry Laboratory, IRCCS Santa Lucia Foundation, Department of Clinical and Behavioural Neurology, Rome, Italy
| | - W T Longstreth
- Department of Neurology, University of Washington, Seattle, Washington, USA
- Department of Epidemiology, University of Washington, Seattle, Washington, USA
| | - Thomas J Fairchild
- Office of Strategy and Measurement, University of North Texas Health Science Center, Fort Worth, Texas, USA
| | - Paola Bossù
- Experimental Neuropsychiatry Laboratory, IRCCS Santa Lucia Foundation, Department of Clinical and Behavioural Neurology, Rome, Italy
| | - Oscar L Lopez
- Department of Psychiatry, University of Pittsburgh, Pittsburgh, Pennsylvania, USA
- Department of Neurology, University of Pittsburgh, Pittsburgh, Pennsylvania, USA
| | - Matthew P Frosch
- C.S. Kubik Laboratory for Neuropathology, Massachusetts General Hospital, Charlestown, Massachusetts, USA
| | - Eleonora Sacchinelli
- Experimental Neuropsychiatry Laboratory, IRCCS Santa Lucia Foundation, Department of Clinical and Behavioural Neurology, Rome, Italy
| | - Bernardino Ghetti
- Department of Pathology and Laboratory Medicine, Indiana University, Indianapolis, Indiana, USA
| | - Qiong Yang
- Department of Biostatistics, Boston University School of Public Health, Boston, Massachusetts, USA
| | - Ryan M Huebinger
- Department of Surgery, University of Texas Southwestern Medical Center, Dallas, Texas, USA
| | - Frank Jessen
- German Center for Neurodegenerative Diseases (DZNE), Bonn, Germany
- Department of Psychiatry and Psychotherapy, University of Bonn, Bonn, Germany
- Department of Psychiatry and Psychotherapy, University of Cologne, Cologne, Germany
| | - Shuo Li
- Department of Biostatistics, Boston University School of Public Health, Boston, Massachusetts, USA
| | - M Ilyas Kamboh
- Alzheimer's Disease Research Center, University of Pittsburgh, Pittsburgh, Pennsylvania, USA
- Department of Human Genetics, University of Pittsburgh, Pittsburgh, Pennsylvania, USA
| | - John Morris
- Department of Psychiatry, Washington University School of Medicine, St. Louis, Missouri, USA
- Hope Center Program on Protein Aggregation and Neurodegeneration, Washington University School of Medicine, St. Louis, Missouri, USA
| | - Oscar Sotolongo-Grau
- Research Center and Memory Clinic of Fundació ACE, Institut Català de Neurociències Aplicades, Barcelona, Spain
| | - Mindy J Katz
- Department of Neurology, Albert Einstein College of Medicine, Bronx, New York, USA
| | - Chris Corcoran
- Department of Mathematics and Statistics, Utah State University, Logan, Utah, USA
| | - Melanie Dunstan
- Institute of Psychological Medicine and Clinical Neurosciences, MRC Centre for Neuropsychiatric Genetics and Genomics, Cardiff University, Cardiff, UK
| | - Amy Braddel
- Institute of Psychological Medicine and Clinical Neurosciences, MRC Centre for Neuropsychiatric Genetics and Genomics, Cardiff University, Cardiff, UK
| | - Charlene Thomas
- Institute of Psychological Medicine and Clinical Neurosciences, MRC Centre for Neuropsychiatric Genetics and Genomics, Cardiff University, Cardiff, UK
| | - Alun Meggy
- Institute of Psychological Medicine and Clinical Neurosciences, MRC Centre for Neuropsychiatric Genetics and Genomics, Cardiff University, Cardiff, UK
| | - Rachel Marshall
- Institute of Psychological Medicine and Clinical Neurosciences, MRC Centre for Neuropsychiatric Genetics and Genomics, Cardiff University, Cardiff, UK
| | - Amy Gerrish
- Institute of Psychological Medicine and Clinical Neurosciences, MRC Centre for Neuropsychiatric Genetics and Genomics, Cardiff University, Cardiff, UK
| | - Jade Chapman
- Institute of Psychological Medicine and Clinical Neurosciences, MRC Centre for Neuropsychiatric Genetics and Genomics, Cardiff University, Cardiff, UK
| | - Miquel Aguilar
- Fundació per la Recerca Biomèdica i Social Mútua Terrassa, Terrassa, Barcelona, Spain
- Memory Unit, Department of Neurology, Hospital Universitario Mútua Terrassa, Terrassa, Barcelona, Spain
| | - Sarah Taylor
- Institute of Psychological Medicine and Clinical Neurosciences, MRC Centre for Neuropsychiatric Genetics and Genomics, Cardiff University, Cardiff, UK
| | - Matt Hill
- Institute of Psychological Medicine and Clinical Neurosciences, MRC Centre for Neuropsychiatric Genetics and Genomics, Cardiff University, Cardiff, UK
| | - Mònica Díez Fairén
- Centro de Investigación Biomédica en Red de Enfermedades Neurodegenerativas (CIBERNED), Instituto de Salud Carlos III, Madrid, Spain
- Fundació per la Recerca Biomèdica i Social Mútua Terrassa, Terrassa, Barcelona, Spain
| | - Angela Hodges
- Department of Old Age Psychiatry, Institute of Psychiatry, Psychology and Neuroscience, King's College London, London, UK
| | - Bruno Vellas
- INSERM U558, University of Toulouse, Toulouse, France
| | - Hilkka Soininen
- Department of Neurology, Kuopio University Hospital, Kuopio, Finland
| | - Iwona Kloszewska
- Elderly and Psychiatric Disorders Department, Medical University of Lodz, Lodz, Poland
| | - Makrina Daniilidou
- Department of Health Sciences, Psychiatry for the Elderly, University of Leicester, Leicester, UK
| | - James Uphill
- Department of Neurodegenerative Disease, MRC Prion Unit, UCL Institute of Neurology, London, UK
| | - Yogen Patel
- Department of Basic and Clinical Neuroscience, Institute of Psychiatry, Psychology and Neuroscience, King's College London, London, UK
| | - Joseph T Hughes
- Department of Basic and Clinical Neuroscience, Institute of Psychiatry, Psychology and Neuroscience, King's College London, London, UK
| | - Jenny Lord
- Institute of Genetics, Queen's Medical Centre, University of Nottingham, Nottingham, UK
| | - James Turton
- Institute of Genetics, Queen's Medical Centre, University of Nottingham, Nottingham, UK
| | - Annette M Hartmann
- Department of Psychiatry, Martin Luther University Halle-Wittenberg, Halle, Germany
| | - Roberta Cecchetti
- Section of Gerontology and Geriatrics, Department of Medicine, University of Perugia, Perugia, Italy
| | - Chiara Fenoglio
- Department of Pathophysiology and Transplantation, University of Milan, Fondazione Ca' Granda, IRCCS Ospedale Policlinico, Milan, Italy
| | - Maria Serpente
- Department of Pathophysiology and Transplantation, University of Milan, Fondazione Ca' Granda, IRCCS Ospedale Policlinico, Milan, Italy
| | - Marina Arcaro
- Department of Pathophysiology and Transplantation, University of Milan, Fondazione Ca' Granda, IRCCS Ospedale Policlinico, Milan, Italy
| | - Carlo Caltagirone
- Experimental Neuropsychiatry Laboratory, IRCCS Santa Lucia Foundation, Department of Clinical and Behavioural Neurology, Rome, Italy
| | - Maria Donata Orfei
- Experimental Neuropsychiatry Laboratory, IRCCS Santa Lucia Foundation, Department of Clinical and Behavioural Neurology, Rome, Italy
| | - Antonio Ciaramella
- Experimental Neuropsychiatry Laboratory, IRCCS Santa Lucia Foundation, Department of Clinical and Behavioural Neurology, Rome, Italy
| | - Sabrina Pichler
- Department of Psychiatry and Psychotherapy, University Hospital, Saarland, Germany
| | - Manuel Mayhaus
- Department of Psychiatry and Psychotherapy, University Hospital, Saarland, Germany
| | - Wei Gu
- Department of Psychiatry and Psychotherapy, University Hospital, Saarland, Germany
| | - Alberto Lleó
- Centro de Investigación Biomédica en Red de Enfermedades Neurodegenerativas (CIBERNED), Instituto de Salud Carlos III, Madrid, Spain
- Memory Unit, Neurology Department and Sant Pau Biomedical Research Institute, Hospital de la Santa Creu i Sant Pau, Autonomous University of Barcelona, Barcelona, Spain
| | - Juan Fortea
- Centro de Investigación Biomédica en Red de Enfermedades Neurodegenerativas (CIBERNED), Instituto de Salud Carlos III, Madrid, Spain
- Memory Unit, Neurology Department and Sant Pau Biomedical Research Institute, Hospital de la Santa Creu i Sant Pau, Autonomous University of Barcelona, Barcelona, Spain
| | - Rafael Blesa
- Centro de Investigación Biomédica en Red de Enfermedades Neurodegenerativas (CIBERNED), Instituto de Salud Carlos III, Madrid, Spain
- Memory Unit, Neurology Department and Sant Pau Biomedical Research Institute, Hospital de la Santa Creu i Sant Pau, Autonomous University of Barcelona, Barcelona, Spain
| | - Imelda S Barber
- Schools of Life Sciences and Medicine, University of Nottingham, Nottingham, UK
| | - Keeley Brookes
- Schools of Life Sciences and Medicine, University of Nottingham, Nottingham, UK
| | - Chiara Cupidi
- Regional Neurogenetic Centre (CRN), ASP Catanzaro, Lamezia Terme, Italy
| | | | - David Carrell
- Department of Psychiatry and Behavioral Sciences, University of Washington School of Medicine, Seattle, Washington, USA
| | - Sandro Sorbi
- NEUROFARBA (Department of Neuroscience, Psychology, Drug Research and Child Health), University of Florence, Florence, Italy
- IRCCS 'Don Carlo Gnocchi', Florence, Italy
| | - Susanne Moebus
- Institute for Medical Informatics, Biometry and Epidemiology, University Hospital of Essen, University Duisburg-Essen, Essen, Germany
| | - Maria Urbano
- Geriatric Unit and Gerontology-Geriatrics Research Laboratory, Department of Medical Sciences, IRCCS Casa Sollievo della Sofferenza, San Giovanni Rotondo, Italy
| | - Alberto Pilotto
- Geriatric Unit and Gerontology-Geriatrics Research Laboratory, Department of Medical Sciences, IRCCS Casa Sollievo della Sofferenza, San Giovanni Rotondo, Italy
| | - Johannes Kornhuber
- Department of Psychiatry and Psychotherapy, University of Erlangen-Nuremberg, Erlangen, Germany
| | - Paolo Bosco
- Istituto di Ricovero e Cura a Carattere Scientifico (IRCCS) Associazione Oasi Maria Santissima Srl, Troina, Italy
| | - Stephen Todd
- Centre for Public Health, School of Medicine, Dentistry and Biomedical Sciences, Queen's University, Belfast, UK
| | - David Craig
- Centre for Public Health, School of Medicine, Dentistry and Biomedical Sciences, Queen's University, Belfast, UK
| | - Janet Johnston
- Centre for Public Health, School of Medicine, Dentistry and Biomedical Sciences, Queen's University, Belfast, UK
| | - Michael Gill
- Mercers Institute for Research on Aging, St. James Hospital and Trinity College, Dublin, Ireland
| | - Brian Lawlor
- Mercers Institute for Research on Aging, St. James Hospital and Trinity College, Dublin, Ireland
| | - Aoibhinn Lynch
- Mercers Institute for Research on Aging, St. James Hospital and Trinity College, Dublin, Ireland
| | - Nick C Fox
- Department of Molecular Neuroscience, UCL, Institute of Neurology, London, UK
| | - John Hardy
- Department of Molecular Neuroscience, UCL, Institute of Neurology, London, UK
| | - Roger L Albin
- Department of Neurology, University of Michigan, Ann Arbor, Michigan, USA
- Geriatric Research, Education and Clinical Center (GRECC), VA Ann Arbor Healthcare System (VAAAHS), Ann Arbor, Michigan, USA
- Michigan Alzheimer Disease Center, Ann Arbor, Michigan, USA
| | - Liana G Apostolova
- Indiana Alzheimer's Disease Center, Indiana University School of Medicine, Indianapolis, Indiana, USA
- Department of Medical and Molecular Genetics, Indiana University, Indianapolis, Indiana, USA
- Department of Neurology, Indiana University, Indianapolis, Indiana, USA
- Department of Radiology and Imaging Sciences, Indiana University, Indianapolis, Indiana, USA
| | - Steven E Arnold
- Department of Psychiatry, University of Pennsylvania Perelman School of Medicine, Philadelphia, Pennsylvania, USA
| | - Sanjay Asthana
- Geriatric Research, Education and Clinical Center (GRECC), University of Wisconsin, Madison, Wisconsin, USA
- Department of Medicine, University of Wisconsin, Madison, Wisconsin, USA
- Wisconsin Alzheimer's Disease Research Center, Madison, Wisconsin, USA
| | - Craig S Atwood
- Geriatric Research, Education and Clinical Center (GRECC), University of Wisconsin, Madison, Wisconsin, USA
- Department of Medicine, University of Wisconsin, Madison, Wisconsin, USA
- Wisconsin Alzheimer's Disease Research Center, Madison, Wisconsin, USA
| | - Clinton T Baldwin
- Department of Medicine (Genetics Program), Boston University, Boston, Massachusetts, USA
| | - Lisa L Barnes
- Department of Neurological Sciences, Rush University Medical Center, Chicago, Illinois, USA
- Department of Behavioral Sciences, Rush University Medical Center, Chicago, Illinois, USA
- Rush Alzheimer's Disease Center, Rush University Medical Center, Chicago, Illinois, USA
| | - Sandra Barral
- Taub Institute on Alzheimer's Disease and the Aging Brain, Department of Neurology, Columbia University, New York, New York, USA
- Gertrude H. Sergievsky Center, Columbia University, New York, New York, USA
- Department of Neurology, Columbia University, New York, New York, USA
| | - Thomas G Beach
- Civin Laboratory for Neuropathology, Banner Sun Health Research Institute, Phoenix, Arizona, USA
| | - James T Becker
- Departments of Psychiatry, Neurology, and Psychology, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, USA
| | - Eileen H Bigio
- Department of Pathology, Northwestern University Feinberg School of Medicine, Chicago, Illinois, USA
- Cognitive Neurology and Alzheimer's Disease Center, Northwestern University Feinberg School of Medicine, Chicago, Illinois, USA
| | - Thomas D Bird
- Department of Neurology, University of Washington, Seattle, Washington, USA
- VA Puget Sound Health Care System/GRECC, Seattle, Washington, USA
| | - Bradley F Boeve
- Department of Neurology, Mayo Clinic, Rochester, Minnesota, USA
| | | | - Adam Boxer
- Department of Neurology, University of California, San Francisco, San Francisco, California, USA
| | - James R Burke
- Department of Medicine, Duke University, Durham, North Carolina, USA
| | - Jeffrey M Burns
- University of Kansas Alzheimer's Disease Center, University of Kansas Medical Center, Kansas City, Kansas, USA
| | - Joseph D Buxbaum
- Department of Genetics and Genomic Sciences, Mount Sinai School of Medicine, New York, New York, USA
- Department of Neuroscience, Mount Sinai School of Medicine, New York, New York, USA
- Department of Psychiatry, Mount Sinai School of Medicine, New York, New York, USA
| | - Nigel J Cairns
- Department of Pathology and Immunology, Washington University, St. Louis, Missouri, USA
| | - Chuanhai Cao
- USF Health Byrd Alzheimer's Institute, University of South Florida, Tampa, Florida, USA
| | - Chris S Carlson
- Fred Hutchinson Cancer Research Center, Seattle, Washington, USA
| | - Cynthia M Carlsson
- Department of Medicine, University of Wisconsin, Madison, Wisconsin, USA
- Wisconsin Alzheimer's Disease Research Center, Madison, Wisconsin, USA
| | - Regina M Carney
- Department of Psychiatry and Behavioral Sciences, Miller School of Medicine, University of Miami, Miami, Florida, USA
| | | | - Steven L Carroll
- Department of Pathology and Laboratory Medicine, Medical University of South Carolina, Charleston, South Carolina, USA
| | - Carolina Ceballos Diaz
- Center for Translational Research in Neurodegenerative Disease, Department of Neuroscience, University of Florida, Gainesville, Florida, USA
| | - Helena C Chui
- Department of Neurology, University of Southern California, Los Angeles, California, USA
| | - David G Clark
- Department of Neurology, Medical University of South Carolina, Charleston, South Carolina, USA
- Department of Neurology, Ralph H. Johnson VA Medical Center, Charleston, South Carolina, USA
| | - David H Cribbs
- Department of Neurology, University of California, Irvine, Irvine, California, USA
| | - Elizabeth A Crocco
- Department of Psychiatry and Behavioral Sciences, Miller School of Medicine, University of Miami, Miami, Florida, USA
| | - Charles DeCarli
- Department of Neurology, University of California, Davis, Sacramento, California, USA
| | - Malcolm Dick
- Institute for Memory Impairments and Neurological Disorders, University of California, Irvine, Irvine, California, USA
| | - Ranjan Duara
- Wien Center for Alzheimer's Disease and Memory Disorders, Mount Sinai Medical Center, Miami Beach, Florida, USA
| | - Denis A Evans
- Rush Institute for Healthy Aging, Department of Internal Medicine, Rush University Medical Center, Chicago, Illinois, USA
| | - Kelley M Faber
- Department of Medical and Molecular Genetics, Indiana University, Indianapolis, Indiana, USA
| | - Kenneth B Fallon
- Department of Pathology, University of Alabama at Birmingham, Birmingham, Alabama, USA
| | - David W Fardo
- Sanders-Brown Center on Aging, Department of Biostatistics, University of Kentucky, Lexington, Kentucky, USA
| | - Martin R Farlow
- Department of Neurology, Indiana University, Indianapolis, Indiana, USA
| | - Steven Ferris
- Department of Psychiatry, New York University, New York, New York, USA
| | - Tatiana M Foroud
- Department of Medical and Molecular Genetics, Indiana University, Indianapolis, Indiana, USA
| | - Douglas R Galasko
- Department of Neurosciences, University of California, San Diego, La Jolla, California, USA
| | - Marla Gearing
- Department of Pathology and Laboratory Medicine, Emory University, Atlanta, Georgia, USA
- Emory Alzheimer's Disease Center, Emory University, Atlanta, Georgia, USA
| | - Daniel H Geschwind
- Neurogenetics Program, University of California, Los Angeles, Los Angeles, California, USA
| | - John R Gilbert
- John P. Hussman Institute for Human Genomics, University of Miami, Miami, Florida, USA
- Dr. John T. Macdonald Foundation, Department of Human Genetics, University of Miami, Miami, Florida, USA
| | - Neill R Graff-Radford
- Department of Neuroscience, Mayo Clinic, Jacksonville, Florida, USA
- Department of Neurology, Mayo Clinic, Jacksonville, Florida, USA
| | - Robert C Green
- Division of Genetics, Department of Medicine and Partners Center for Personalized Genetic Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, Massachusetts, USA
| | - John H Growdon
- Department of Neurology, Massachusetts General Hospital/Harvard Medical School, Boston, Massachusetts, USA
| | - Ronald L Hamilton
- Department of Pathology (Neuropathology), University of Pittsburgh, Pittsburgh, Pennsylvania, USA
| | - Lindy E Harrell
- Department of Neurology, University of Alabama at Birmingham, Birmingham, Alabama, USA
| | - Lawrence S Honig
- Taub Institute on Alzheimer's Disease and the Aging Brain, Department of Neurology, Columbia University, New York, New York, USA
| | - Matthew J Huentelman
- Neurogenomics Division, Translational Genomics Research Institute, Phoenix, Arizona, USA
| | | | - Bradley T Hyman
- Department of Neurology, Massachusetts General Hospital/Harvard Medical School, Boston, Massachusetts, USA
| | - Gail P Jarvik
- Department of Genome Sciences, University of Washington, Seattle, Washington, USA
- Department of Medicine (Medical Genetics), University of Washington, Seattle, Washington, USA
| | - Erin Abner
- Sanders-Brown Center on Aging, College of Public Health, Department of Epidemiology, University of Kentucky, Lexington, Kentucky, USA
| | - Lee-Way Jin
- Department of Pathology and Laboratory Medicine, University of California, Davis, Sacramento, California, USA
| | - Gyungah Jun
- Department of Medicine (Genetics Program), Boston University, Boston, Massachusetts, USA
- Department of Biostatistics, Boston University, Boston, Massachusetts, USA
- Department of Ophthalmology, Boston University, Boston, Massachusetts, USA
| | - Anna Karydas
- Department of Neurology, University of California, San Francisco, San Francisco, California, USA
| | - Jeffrey A Kaye
- Department of Neurology, Oregon Health &Science University, Portland, Oregon, USA
- Department of Neurology, Portland Veterans Affairs Medical Center, Portland, Oregon, USA
| | - Ronald Kim
- Department of Pathology and Laboratory Medicine, University of California, Irvine, Irvine, California, USA
| | - Neil W Kowall
- Department of Neurology, Boston University, Boston, Massachusetts, USA
- Department of Pathology, Boston University, Boston, Massachusetts, USA
| | - Joel H Kramer
- Department of Neuropsychology, University of California, San Francisco, San Francisco, California, USA
| | - Frank M LaFerla
- Department of Neurobiology and Behavior, University of California, Irvine, Irvine, California, USA
| | - James J Lah
- Department of Neurology, Emory University, Atlanta, Georgia, USA
| | - James B Leverenz
- Cleveland Clinic Lou Ruvo Center for Brain Health, Cleveland Clinic, Cleveland, Ohio, USA
| | - Allan I Levey
- Department of Neurology, Emory University, Atlanta, Georgia, USA
| | - Ge Li
- Department of Psychiatry and Behavioral Sciences, University of Washington School of Medicine, Seattle, Washington, USA
- VA Puget Sound Health Care System/GRECC, Seattle, Washington, USA
| | - Andrew P Lieberman
- Department of Pathology, University of Michigan, Ann Arbor, Michigan, USA
| | - Kathryn L Lunetta
- Department of Biostatistics, Boston University, Boston, Massachusetts, USA
| | | | - Daniel C Marson
- Department of Neurology, University of Alabama at Birmingham, Birmingham, Alabama, USA
| | - Frank Martiniuk
- Department of Medicine-Pulmonary, New York University, New York, New York, USA
| | - Deborah C Mash
- Department of Neurology, University of Miami, Miami, Florida, USA
| | - Eliezer Masliah
- Department of Neurosciences, University of California, San Diego, La Jolla, California, USA
- Department of Pathology, University of California, San Diego, La Jolla, California, USA
| | - Wayne C McCormick
- Department of Medicine, University of Washington, Seattle, Washington, USA
| | - Susan M McCurry
- School of Nursing Northwest Research Group on Aging, University of Washington, Seattle, Washington, USA
| | - Andrew N McDavid
- Fred Hutchinson Cancer Research Center, Seattle, Washington, USA
| | - Ann C McKee
- Department of Neurology, Boston University, Boston, Massachusetts, USA
- Department of Pathology, Boston University, Boston, Massachusetts, USA
| | - Marsel Mesulam
- Cognitive Neurology and Alzheimer's Disease Center, Northwestern University Feinberg School of Medicine, Chicago, Illinois, USA
- Department of Neurology, Northwestern University Feinberg School of Medicine, Chicago, Illinois, USA
| | - Bruce L Miller
- Department of Neurology, University of California, San Francisco, San Francisco, California, USA
| | - Carol A Miller
- Department of Pathology, University of Southern California, Los Angeles, California, USA
| | - Joshua W Miller
- Department of Pathology and Laboratory Medicine, University of California, Davis, Sacramento, California, USA
| | - John C Morris
- Department of Pathology and Immunology, Washington University, St. Louis, Missouri, USA
- Department of Neurology, Washington University, St. Louis, Missouri, USA
| | - Jill R Murrell
- Department of Pathology and Laboratory Medicine, Indiana University, Indianapolis, Indiana, USA
- Department of Medical and Molecular Genetics, Indiana University, Indianapolis, Indiana, USA
| | - Amanda J Myers
- Department of Psychiatry and Behavioral Sciences, Miller School of Medicine, University of Miami, Miami, Florida, USA
| | - Sid O'Bryant
- Internal Medicine, Division of Geriatrics, University of North Texas Health Science Center, Fort Worth, Texas, USA
| | - John M Olichney
- Department of Neurology, University of California, Davis, Sacramento, California, USA
| | - Vernon S Pankratz
- Department of Internal Medicine, University of New Mexico Health Sciences Center, Albuquerque, New Mexico, USA
| | - Joseph E Parisi
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, Minnesota, USA
| | - Henry L Paulson
- Department of Neurology, University of Michigan, Ann Arbor, Michigan, USA
- Michigan Alzheimer Disease Center, Ann Arbor, Michigan, USA
| | - William Perry
- John P. Hussman Institute for Human Genomics, University of Miami, Miami, Florida, USA
| | - Elaine Peskind
- Department of Psychiatry and Behavioral Sciences, University of Washington School of Medicine, Seattle, Washington, USA
| | - Aimee Pierce
- Department of Neurology, University of California, Irvine, Irvine, California, USA
| | - Wayne W Poon
- Institute for Memory Impairments and Neurological Disorders, University of California, Irvine, Irvine, California, USA
| | - Huntington Potter
- Department of Neurology, University of Colorado School of Medicine, Aurora, Colorado, USA
| | - Joseph F Quinn
- Department of Neurology, Oregon Health &Science University, Portland, Oregon, USA
- Department of Neurology, Portland Veterans Affairs Medical Center, Portland, Oregon, USA
| | - Ashok Raj
- USF Health Byrd Alzheimer's Institute, University of South Florida, Tampa, Florida, USA
| | - Murray Raskind
- Department of Psychiatry and Behavioral Sciences, University of Washington School of Medicine, Seattle, Washington, USA
| | - Barry Reisberg
- Department of Psychiatry, New York University, New York, New York, USA
- Alzheimer's Disease Center, New York University, New York, New York, USA
| | - Christiane Reitz
- Gertrude H. Sergievsky Center, Columbia University, New York, New York, USA
- Department of Neurology, Columbia University, New York, New York, USA
- Department of Epidemiology, Columbia University, New York, New York, USA
| | - John M Ringman
- Department of Neurology, University of California, Los Angeles, Los Angeles, California, USA
| | - Erik D Roberson
- Department of Neurology, University of Alabama at Birmingham, Birmingham, Alabama, USA
| | - Ekaterina Rogaeva
- Tanz Centre for Research in Neurodegenerative Disease, University of Toronto, Toronto, Ontario, Canada
| | - Howard J Rosen
- Department of Neurology, University of California, San Francisco, San Francisco, California, USA
| | - Roger N Rosenberg
- Department of Neurology, University of Texas Southwestern Medical Center, Dallas, Texas, USA
| | - Mark A Sager
- Department of Medicine, University of Wisconsin, Madison, Wisconsin, USA
| | - Andrew J Saykin
- Department of Medical and Molecular Genetics, Indiana University, Indianapolis, Indiana, USA
- Department of Radiology and Imaging Sciences, Indiana University, Indianapolis, Indiana, USA
| | - Julie A Schneider
- Department of Neurological Sciences, Rush University Medical Center, Chicago, Illinois, USA
- Rush Alzheimer's Disease Center, Rush University Medical Center, Chicago, Illinois, USA
- Department of Pathology (Neuropathology), Rush University Medical Center, Chicago, Illinois, USA
| | - Lon S Schneider
- Department of Neurology, University of Southern California, Los Angeles, California, USA
- Department of Psychiatry, University of Southern California, Los Angeles, California, USA
| | - William W Seeley
- Department of Neurology, University of California, San Francisco, San Francisco, California, USA
| | - Amanda G Smith
- USF Health Byrd Alzheimer's Institute, University of South Florida, Tampa, Florida, USA
| | - Joshua A Sonnen
- Department of Pathology, University of Washington, Seattle, Washington, USA
| | - Salvatore Spina
- Department of Pathology and Laboratory Medicine, Indiana University, Indianapolis, Indiana, USA
| | - Robert A Stern
- Department of Neurology, Boston University, Boston, Massachusetts, USA
| | - Russell H Swerdlow
- University of Kansas Alzheimer's Disease Center, University of Kansas Medical Center, Kansas City, Kansas, USA
| | - Rudolph E Tanzi
- Department of Neurology, Massachusetts General Hospital/Harvard Medical School, Boston, Massachusetts, USA
| | - Tricia A Thornton-Wells
- Translational Medicine, Novartis Institutes for Biomedical Research, Cambridge, Massachusetts, USA
| | - John Q Trojanowski
- Department of Pathology and Laboratory Medicine, University of Pennsylvania Perelman School of Medicine, Philadelphia, Pennsylvania, USA
| | - Juan C Troncoso
- Department of Pathology, Johns Hopkins University, Baltimore, Maryland, USA
| | - Vivianna M Van Deerlin
- Department of Pathology and Laboratory Medicine, University of Pennsylvania Perelman School of Medicine, Philadelphia, Pennsylvania, USA
| | - Linda J Van Eldik
- Sanders-Brown Center on Aging, Department of Anatomy and Neurobiology, University of Kentucky, Lexington, Kentucky, USA
| | - Harry V Vinters
- Department of Neurology, University of California, Los Angeles, Los Angeles, California, USA
- Department of Pathology and Laboratory Medicine, University of California, Los Angeles, Los Angeles, California, USA
| | - Jean Paul Vonsattel
- Taub Institute on Alzheimer's Disease and the Aging Brain, Department of Pathology, Columbia University, New York, New York, USA
| | - Sandra Weintraub
- Cognitive Neurology and Alzheimer's Disease Center, Northwestern University Feinberg School of Medicine, Chicago, Illinois, USA
- Department of Psychiatry, Northwestern University Feinberg School of Medicine, Chicago, Illinois, USA
| | - Kathleen A Welsh-Bohmer
- Department of Medicine, Duke University, Durham, North Carolina, USA
- Department of Psychiatry and Behavioral Sciences, Duke University, Durham, North Carolina, USA
| | - Kirk C Wilhelmsen
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
| | - Jennifer Williamson
- Taub Institute on Alzheimer's Disease and the Aging Brain, Department of Neurology, Columbia University, New York, New York, USA
| | - Thomas S Wingo
- Department of Neurology, Emory University, Atlanta, Georgia, USA
| | - Randall L Woltjer
- Department of Pathology, Oregon Health &Science University, Portland, Oregon, USA
| | - Clinton B Wright
- Evelyn F. McKnight Brain Institute, Department of Neurology, Miller School of Medicine, University of Miami, Miami, Florida, USA
| | - Chang-En Yu
- Department of Medicine, University of Washington, Seattle, Washington, USA
| | - Lei Yu
- Department of Neurological Sciences, Rush University Medical Center, Chicago, Illinois, USA
- Rush Alzheimer's Disease Center, Rush University Medical Center, Chicago, Illinois, USA
| | - Fabienne Garzia
- CEA/Institut de Génomique, Centre National de Génotypage, Evry, France
| | - Feroze Golamaully
- CEA/Institut de Génomique, Centre National de Génotypage, Evry, France
| | - Gislain Septier
- CEA/Institut de Génomique, Centre National de Génotypage, Evry, France
| | - Sebastien Engelborghs
- Institute Born-Bunge, University of Antwerp, Antwerp, Belgium
- Department of Neurology and Memory Clinic, Hospital Network Antwerp, Antwerp, Belgium
| | - Rik Vandenberghe
- Department of Neurology and Memory Clinic, Hospital Network Antwerp, Antwerp, Belgium
- Laboratory for Cognitive Neurology, Department of Neurology, University of Leuven, Leuven, Belgium
| | - Peter P De Deyn
- Institute Born-Bunge, University of Antwerp, Antwerp, Belgium
- Department of Neurology and Memory Clinic, Hospital Network Antwerp, Antwerp, Belgium
| | - Carmen Muñoz Fernadez
- Department of Immunology, Hospital Universitario Doctor Negrín, Las Palmas de Gran Canaria, Spain
| | - Yoland Aladro Benito
- Department of Immunology, Hospital Universitario Doctor Negrín, Las Palmas de Gran Canaria, Spain
| | - Hakan Thonberg
- Department of Geriatric Medicine, Genetics Unit, Karolinska University Hospital Huddinge, Stockholm, Sweden
- Department of Neurobiology, Care Sciences and Society, KIADRC, Karolinska Institutet, Stockholm, Sweden
| | - Charlotte Forsell
- Department of Geriatric Medicine, Genetics Unit, Karolinska University Hospital Huddinge, Stockholm, Sweden
- Department of Neurobiology, Care Sciences and Society, KIADRC, Karolinska Institutet, Stockholm, Sweden
| | - Lena Lilius
- Department of Geriatric Medicine, Genetics Unit, Karolinska University Hospital Huddinge, Stockholm, Sweden
- Department of Neurobiology, Care Sciences and Society, KIADRC, Karolinska Institutet, Stockholm, Sweden
| | - Anne Kinhult-Stählbom
- Department of Geriatric Medicine, Genetics Unit, Karolinska University Hospital Huddinge, Stockholm, Sweden
- Department of Neurobiology, Care Sciences and Society, KIADRC, Karolinska Institutet, Stockholm, Sweden
| | - Lena Kilander
- Department of Public Health/Geriatrics, Uppsala University, Uppsala, Sweden
| | - RoseMarie Brundin
- Department of Public Health/Geriatrics, Uppsala University, Uppsala, Sweden
| | - Letizia Concari
- Department of Neuroscience, University of Parma, Parma, Italy
- Center for Cognitive Disorders AUSL, Parma, Italy
| | - Seppo Helisalmi
- Department of Neurology, Kuopio University Hospital, Kuopio, Finland
- Institute of Clinical Medicine/Neurology, University of Eastern Finland, Kuopio, Finland
| | - Anne Maria Koivisto
- Department of Neurology, Kuopio University Hospital, Kuopio, Finland
- Institute of Clinical Medicine/Neurology, University of Eastern Finland, Kuopio, Finland
| | - Annakaisa Haapasalo
- Department of Neurology, Kuopio University Hospital, Kuopio, Finland
- Institute of Clinical Medicine/Neurology, University of Eastern Finland, Kuopio, Finland
| | - Vincent Dermecourt
- CHU Lille, Memory Center of Lille (Centre Mémoire de Ressources et de Recherche), Lille, France
| | - Nathalie Fievet
- INSERM, U1167, RID-AGE-Risk Factors and Molecular Determinants of Aging-Related Diseases, Lille, France
- Institut Pasteur de Lille, Lille, France
- University Lille, U1167-Excellence Laboratory LabEx DISTALZ, Lille, France
- University Paris Descartes, EA 4468, AP-HP, Hôpital Broca, Geriatrics Department, Paris, France
| | - Olivier Hanon
- University Paris Descartes, EA 4468, AP-HP, Hôpital Broca, Geriatrics Department, Paris, France
| | - Carole Dufouil
- University of Bordeaux, Neuroepidemiology, Bordeaux, France
- INSERM, Neuroepidemiology, UMR 897, Bordeaux, France
| | - Alexis Brice
- INSERM U1127, CNRS UMR 7225, Sorbonne Universités, UPMC Université Paris 06, UMRS 1127, Institut du Cerveau et de la Moelle Épinière, Paris, France
- AP-HP, Department of Genetics, Pitié-Salpêtrière Hospital, Paris, France
| | - Karen Ritchie
- INSERM U1061, La Colombière Hospital, Montpellier, France
| | - Bruno Dubois
- Institut de la Mémoire et de la Maladie d'Alzheimer (IM2A), Département de Neurologie, Hôpital de la Pitié-Salpêtrière, AP-HP, Paris, France
- Institut des Neurosciences Translationnelles de Paris (IHU-A-ICM), Institut du Cerveau et de la Moelle Épinière (ICM), Paris, France
- INSERM, CNRS, UMRS 975, Institut du Cerveau et de la Moelle Épinière (ICM), Paris, France
- Sorbonne Universités, Université Pierre et Marie Curie, Hôpital de la Pitié-Salpêtrière, AP-HP, Paris, France
| | | | - C Dirk Keene
- Department of Pathology, University of Washington, Seattle, Washington, USA
| | - JoAnn Tschanz
- Department of Mathematics and Statistics, Utah State University, Logan, Utah, USA
| | - Annette L Fitzpatrick
- Department of Epidemiology, University of Washington, Seattle, Washington, USA
- Department of Family Medicine, University of Washington, Seattle, Washington, USA
| | - Walter A Kukull
- Department of Epidemiology, University of Washington, Seattle, Washington, USA
| | - Maria Norton
- Department of Mathematics and Statistics, Utah State University, Logan, Utah, USA
| | - Thor Aspelund
- Icelandic Heart Association, Kopavogur, Iceland
- Centre for Public Health, University of Iceland, Reykjavik, Iceland
| | - Eric B Larson
- Department of Medicine, University of Washington, Seattle, Washington, USA
- Group Health Research Institute, Group Health, Seattle, Washington, USA
| | - Ron Munger
- Department of Mathematics and Statistics, Utah State University, Logan, Utah, USA
| | - Jerome I Rotter
- Institute for Translational Genomics and Population Sciences, Los Angeles BioMedical Research Institute at Harbor-UCLA Medical Center, Torrance, California, USA
| | - Richard B Lipton
- Department of Neurology, Albert Einstein College of Medicine, Bronx, New York, USA
| | - María J Bullido
- Instituto de Investigación Sanitaria Hospital la Paz (IdiPAZ), Madrid, Spain
- Centro de Investigación Biomédica en Red de Enfermedades Neurodegenerativas (CIBERNED), Instituto de Salud Carlos III, Madrid, Spain
- Centro de Biología Molecular Severo Ochoa (CSIC-UAM), Madrid, Spain
| | - Albert Hofman
- Department of Epidemiology, Erasmus Medical Center, Rotterdam, the Netherlands
| | - Thomas J Montine
- Department of Pathology, University of Washington, Seattle, Washington, USA
| | - Eliecer Coto
- Molecular Genetics Laboratory-Hospital, University of Central Asturias, Oviedo, Spain
| | - Eric Boerwinkle
- School of Public Health, Human Genetics Center, University of Texas Health Science Center at Houston, Houston, Texas, USA
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, Texas, USA
| | | | - Victoria Alvarez
- Molecular Genetics Laboratory-Hospital, University of Central Asturias, Oviedo, Spain
| | - Fernando Rivadeneira
- Department of Epidemiology, Erasmus Medical Center, Rotterdam, the Netherlands
- Department of Internal Medicine, Erasmus University Medical Center, Rotterdam, the Netherlands
- Netherlands Consortium on Health Aging and National Genomics Initiative, Leiden, the Netherlands
| | - Eric M Reiman
- Neurogenomics Division, Translational Genomics Research Institute, Phoenix, Arizona, USA
- Arizona Alzheimer's Consortium, Phoenix, Arizona, USA
- Banner Alzheimer's Institute, Phoenix, Arizona, USA
- Department of Psychiatry, University of Arizona, Phoenix, Arizona, USA
| | - Maura Gallo
- Regional Neurogenetic Centre (CRN), ASP Catanzaro, Lamezia Terme, Italy
| | | | - Joan S Reisch
- Department of Clinical Sciences, University of Texas Southwestern Medical Center, Dallas, Texas, USA
| | | | - Donald R Royall
- Departments of Psychiatry, Medicine, and Family and Community Medicine and South Texas Veterans Health Administration Geriatric Research Education and Clinical Center (GRECC), University of Texas Health Science Center at San Antonio, San Antonio, Texas, USA
| | - Martin Dichgans
- Institute for Stroke and Dementia Research, Klinikum der Universität München, Munich, Germany
- German Center for Neurodegenerative Diseases (DZNE), Munich, Germany
| | - Mary Sano
- Department of Psychiatry, Mount Sinai School of Medicine, New York, New York, USA
| | - Daniela Galimberti
- Department of Pathophysiology and Transplantation, University of Milan, Fondazione Ca' Granda, IRCCS Ospedale Policlinico, Milan, Italy
| | - Peter St George-Hyslop
- Tanz Centre for Research in Neurodegenerative Disease, University of Toronto, Toronto, Ontario, Canada
- Cambridge Institute for Medical Research, University of Cambridge, Cambridge, UK
| | - Elio Scarpini
- Department of Pathophysiology and Transplantation, University of Milan, Fondazione Ca' Granda, IRCCS Ospedale Policlinico, Milan, Italy
| | - Debby W Tsuang
- Department of Psychiatry and Behavioral Sciences, University of Washington School of Medicine, Seattle, Washington, USA
- VA Puget Sound Health Care System/GRECC, Seattle, Washington, USA
| | - Michelangelo Mancuso
- Department of Experimental and Clinical Medicine, Neurological Institute, University of Pisa, Pisa, Italy
| | - Ubaldo Bonuccelli
- Department of Experimental and Clinical Medicine, Neurological Institute, University of Pisa, Pisa, Italy
| | - Ashley R Winslow
- PharmaTherapeutics Clinical Research, Pfizer Worldwide Research and Development, Cambridge, Massachusetts, USA
| | - Antonio Daniele
- Institute of Neurology, Catholic University of Sacred Hearth, Rome, Italy
| | - Chuang-Kuo Wu
- Departments of Neurology, Pharmacology, and Neuroscience, Texas Tech University Health Science Center, Lubbock, Texas, USA
| | - Oliver Peters
- Department of Psychiatry, Charité University Medicine, Berlin, Germany
| | - Benedetta Nacmias
- NEUROFARBA (Department of Neuroscience, Psychology, Drug Research and Child Health), University of Florence, Florence, Italy
- IRCCS 'Don Carlo Gnocchi', Florence, Italy
| | | | - Reinhard Heun
- Department of Psychiatry and Psychotherapy, University of Bonn, Bonn, Germany
| | - Carol Brayne
- Institute of Public Health, University of Cambridge, Cambridge, UK
| | - David C Rubinsztein
- Cambridge Institute for Medical Research, University of Cambridge, Cambridge, UK
| | - Jose Bras
- Department of Molecular Neuroscience, UCL, Institute of Neurology, London, UK
- Department of Medical Sciences, Institute of Biomedicine (iBiMED), University of Aveiro, Aveiro, Portugal
| | - Rita Guerreiro
- Department of Molecular Neuroscience, UCL, Institute of Neurology, London, UK
- Department of Medical Sciences, Institute of Biomedicine (iBiMED), University of Aveiro, Aveiro, Portugal
| | - Ammar Al-Chalabi
- Institute of Psychiatry, Psychology and Neuroscience, King's College London, London, UK
| | - Christopher E Shaw
- Institute of Psychiatry, Psychology and Neuroscience, King's College London, London, UK
| | - John Collinge
- Department of Neurodegenerative Disease, MRC Prion Unit, UCL Institute of Neurology, London, UK
| | - David Mann
- Institute of Brain, Behaviour and Mental Health, Clinical and Cognitive Neuroscience Research Group, University of Manchester, Manchester, UK
| | - Magda Tsolaki
- 3rd Department of Neurology, Medical School, Aristotle University of Thessaloniki, Thessaloniki, Greece
| | - Jordi Clarimón
- Centro de Investigación Biomédica en Red de Enfermedades Neurodegenerativas (CIBERNED), Instituto de Salud Carlos III, Madrid, Spain
- Memory Unit, Neurology Department and Sant Pau Biomedical Research Institute, Hospital de la Santa Creu i Sant Pau, Autonomous University of Barcelona, Barcelona, Spain
| | - Rebecca Sussams
- Division of Clinical Neurosciences, School of Medicine, University of Southampton, Southampton, UK
| | | | - Michael C O'Donovan
- Institute of Psychological Medicine and Clinical Neurosciences, MRC Centre for Neuropsychiatric Genetics and Genomics, Cardiff University, Cardiff, UK
| | - Michael J Owen
- Institute of Psychological Medicine and Clinical Neurosciences, MRC Centre for Neuropsychiatric Genetics and Genomics, Cardiff University, Cardiff, UK
| | - Timothy W Behrens
- Immunology Biomarkers Group, Genentech, South San Francisco, California, USA
| | - Simon Mead
- Department of Neurodegenerative Disease, MRC Prion Unit, UCL Institute of Neurology, London, UK
| | - Alison M Goate
- Department of Neuroscience, Mount Sinai School of Medicine, New York, New York, USA
| | - Andre G Uitterlinden
- Department of Epidemiology, Erasmus Medical Center, Rotterdam, the Netherlands
- Department of Neurodegenerative Disease, MRC Prion Unit, UCL Institute of Neurology, London, UK
- Department of Pathophysiology and Transplantation, University of Milan, Fondazione Ca' Granda, IRCCS Ospedale Policlinico, Milan, Italy
| | - Clive Holmes
- VA Puget Sound Health Care System/GRECC, Seattle, Washington, USA
| | - Carlos Cruchaga
- Department of Psychiatry, Washington University School of Medicine, St. Louis, Missouri, USA
- Hope Center Program on Protein Aggregation and Neurodegeneration, Washington University School of Medicine, St. Louis, Missouri, USA
| | - Martin Ingelsson
- Department of Public Health/Geriatrics, Uppsala University, Uppsala, Sweden
| | - David A Bennett
- Department of Neurological Sciences, Rush University Medical Center, Chicago, Illinois, USA
- Rush Alzheimer's Disease Center, Rush University Medical Center, Chicago, Illinois, USA
| | - John Powell
- Department of Basic and Clinical Neuroscience, Institute of Psychiatry, Psychology and Neuroscience, King's College London, London, UK
| | - Todd E Golde
- Center for Translational Research in Neurodegenerative Disease, Department of Neuroscience, University of Florida, Gainesville, Florida, USA
- Florida Alzheimer's Disease Research Center, Gainesville, Florida, USA
| | - Caroline Graff
- Department of Geriatric Medicine, Karolinska University Hospital Huddinge, Stockholm, Sweden
- Department of Neurobiology, Care Sciences and Society, KIADRC, Karolinska Institutet, Stockholm, Sweden
| | - Philip L De Jager
- Center for Translational and Systems Neuroimmunology, Department of Neurology, Columbia University Medical Center, New York, New York, USA
| | - Kevin Morgan
- Institute of Genetics, Queen's Medical Centre, University of Nottingham, Nottingham, UK
| | - Nilufer Ertekin-Taner
- Department of Neuroscience, Mayo Clinic, Jacksonville, Florida, USA
- Department of Neurology, Mayo Clinic, Jacksonville, Florida, USA
| | - Onofre Combarros
- Neurology Service and CIBERNED, 'Marqués de Valdecilla' University Hospital (University of Cantabria and IFIMAV), Santander, Spain
| | - Bruce M Psaty
- Cardiovascular Health Research Unit, Department of Medicine, University of Washington, Seattle, Washington, USA
- Centro de Investigación Biomédica en Red de Enfermedades Neurodegenerativas (CIBERNED), Instituto de Salud Carlos III, Madrid, Spain
- Department of Epidemiology, University of Washington, Seattle, Washington, USA
- Department of Health Services, University of Washington, Seattle, Washington, USA
| | - Peter Passmore
- Centre for Public Health, School of Medicine, Dentistry and Biomedical Sciences, Queen's University, Belfast, UK
| | - Steven G Younkin
- Department of Neuroscience, Mayo Clinic, Jacksonville, Florida, USA
- Department of Neurology, Mayo Clinic, Jacksonville, Florida, USA
| | - Claudine Berr
- Institut de la Mémoire et de la Maladie d'Alzheimer (IM2A), Département de Neurologie, Hôpital de la Pitié-Salpêtrière, AP-HP, Paris, France
- Memory Research and Resources Center, CMRR of Montpellier, Department of Neurology, Hospital Gui de Chauliac, Montpellier, France
- Department of Neurology, Montpellier University, Montpellier, France
| | - Vilmundur Gudnason
- Icelandic Heart Association, Kopavogur, Iceland
- Faculty of Medicine, University of Iceland, Reykjavik, Iceland
| | - Dan Rujescu
- Department of Psychiatry, Martin Luther University Halle-Wittenberg, Halle, Germany
| | - Dennis W Dickson
- Department of Neuroscience, Mayo Clinic, Jacksonville, Florida, USA
| | | | - Anita L DeStefano
- Framingham Heart Study, Framingham, Massachusetts, USA
- Department of Biostatistics, Boston University School of Public Health, Boston, Massachusetts, USA
| | - Sara Ortega-Cubero
- Centro de Investigación Biomédica en Red de Enfermedades Neurodegenerativas (CIBERNED), Instituto de Salud Carlos III, Madrid, Spain
- Neurogenetics Laboratory, Division of Neurosciences, Centre for Applied Medical Research, University of Navarra School of Medicine, Pamplona, Spain
- Department of Neurology, Complejo Asistencial Universitario de Palencia, Palencia, Spain
| | - Hakon Hakonarson
- Center for Applied Genomics, Children's Hospital of Philadelphia, Philadelphia, Pennsylvania, USA
| | - Dominique Campion
- Centre Hospitalier du Rouvray, Sotteville les Rouen, France
- INSERM U1079, Rouen University, IRIB, Normandy University, Rouen, France
| | - Merce Boada
- Research Center and Memory Clinic of Fundació ACE, Institut Català de Neurociències Aplicades, Barcelona, Spain
| | - John Keoni Kauwe
- Departments of Biology and Neuroscience, Brigham Young University, Provo, Utah, USA
| | - Lindsay A Farrer
- Boston University School of Medicine, Boston, Massachusetts, USA
- Department of Medicine (Genetics Program), Boston University, Boston, Massachusetts, USA
- Department of Biostatistics, Boston University, Boston, Massachusetts, USA
- Department of Ophthalmology, Boston University, Boston, Massachusetts, USA
- Department of Neurology, Boston University, Boston, Massachusetts, USA
| | - Christine Van Broeckhoven
- Neurodegenerative Brain Diseases Group, Department of Molecular Genetics, VIB, Antwerp, Belgium
- Institute Born-Bunge, University of Antwerp, Antwerp, Belgium
| | - M Arfan Ikram
- Department of Epidemiology, Erasmus Medical Center, Rotterdam, the Netherlands
- Department of Neurology, Erasmus MC University Medical Center, Rotterdam, the Netherlands
| | - Lesley Jones
- Institute of Psychological Medicine and Clinical Neurosciences, MRC Centre for Neuropsychiatric Genetics and Genomics, Cardiff University, Cardiff, UK
| | - Jonathan L Haines
- Department of Epidemiology and Biostatistics, Case Western Reserve University, Cleveland, Ohio, USA
| | - Christophe Tzourio
- INSERM U1127, CNRS UMR 7225, Sorbonne Universités, UPMC Université Paris 06, UMRS 1127, Institut du Cerveau et de la Moelle Épinière, Paris, France
- University of Bordeaux, Neuroepidemiology, UMR 897, Bordeaux, France
| | - Lenore J Launer
- Laboratory of Epidemiology and Population Sciences, National Institute on Aging, Bethesda, Maryland, USA
| | - Valentina Escott-Price
- Institute of Psychological Medicine and Clinical Neurosciences, MRC Centre for Neuropsychiatric Genetics and Genomics, Cardiff University, Cardiff, UK
| | - Richard Mayeux
- Taub Institute on Alzheimer's Disease and the Aging Brain, Department of Neurology, Columbia University, New York, New York, USA
- Gertrude H. Sergievsky Center, Columbia University, New York, New York, USA
- Department of Neurology, Columbia University, New York, New York, USA
| | | | - Najaf Amin
- Department of Epidemiology, Erasmus Medical Center, Rotterdam, the Netherlands
| | - Peter A Holmans
- Institute of Psychological Medicine and Clinical Neurosciences, MRC Centre for Neuropsychiatric Genetics and Genomics, Cardiff University, Cardiff, UK
| | - Margaret A Pericak-Vance
- John P. Hussman Institute for Human Genomics, University of Miami, Miami, Florida, USA
- Dr. John T. Macdonald Foundation, Department of Human Genetics, University of Miami, Miami, Florida, USA
| | - Philippe Amouyel
- INSERM, U1167, RID-AGE-Risk Factors and Molecular Determinants of Aging-Related Diseases, Lille, France
- Institut Pasteur de Lille, Lille, France
- University Lille, U1167-Excellence Laboratory LabEx DISTALZ, Lille, France
- Centre Hospitalier Universitaire de Lille, Epidemiology and Public Health Department, Lille, France
| | | | - Alfredo Ramirez
- Institute of Human Genetics, University of Bonn, Bonn, Germany
- Department of Psychiatry and Psychotherapy, University of Bonn, Bonn, Germany
- Department of Psychiatry and Psychotherapy, University of Cologne, Cologne, Germany
| | - Li-San Wang
- Penn Neurodegeneration Genomics Center, Department of Pathology and Laboratory Medicine, University of Pennsylvania Perelman School of Medicine, Philadelphia, Pennsylvania, USA
| | - Jean-Charles Lambert
- INSERM, U1167, RID-AGE-Risk Factors and Molecular Determinants of Aging-Related Diseases, Lille, France
- Institut Pasteur de Lille, Lille, France
- University Lille, U1167-Excellence Laboratory LabEx DISTALZ, Lille, France
| | - Sudha Seshadri
- Boston University School of Medicine, Boston, Massachusetts, USA
- Framingham Heart Study, Framingham, Massachusetts, USA
| | - Julie Williams
- Institute of Psychological Medicine and Clinical Neurosciences, MRC Centre for Neuropsychiatric Genetics and Genomics, Cardiff University, Cardiff, UK
| | - Gerard D Schellenberg
- Penn Neurodegeneration Genomics Center, Department of Pathology and Laboratory Medicine, University of Pennsylvania Perelman School of Medicine, Philadelphia, Pennsylvania, USA
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Kan M, Shumyatcher M, Himes BE. Using omics approaches to understand pulmonary diseases. Respir Res 2017; 18:149. [PMID: 28774304 PMCID: PMC5543452 DOI: 10.1186/s12931-017-0631-9] [Citation(s) in RCA: 75] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2017] [Accepted: 07/26/2017] [Indexed: 12/24/2022] Open
Abstract
Omics approaches are high-throughput unbiased technologies that provide snapshots of various aspects of biological systems and include: 1) genomics, the measure of DNA variation; 2) transcriptomics, the measure of RNA expression; 3) epigenomics, the measure of DNA alterations not involving sequence variation that influence RNA expression; 4) proteomics, the measure of protein expression or its chemical modifications; and 5) metabolomics, the measure of metabolite levels. Our understanding of pulmonary diseases has increased as a result of applying these omics approaches to characterize patients, uncover mechanisms underlying drug responsiveness, and identify effects of environmental exposures and interventions. As more tissue- and cell-specific omics data is analyzed and integrated for diverse patients under various conditions, there will be increased identification of key mechanisms that underlie pulmonary biological processes, disease endotypes, and novel therapeutics that are efficacious in select individuals. We provide a synopsis of how omics approaches have advanced our understanding of asthma, chronic obstructive pulmonary disease (COPD), acute respiratory distress syndrome (ARDS), idiopathic pulmonary fibrosis (IPF), and pulmonary arterial hypertension (PAH), and we highlight ongoing work that will facilitate pulmonary disease precision medicine.
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Affiliation(s)
- Mengyuan Kan
- Department of Biostatistics, Epidemiology and Informatics, University of Pennsylvania, 402 Blockley Hall 423 Guardian Drive, Philadelphia, PA 19104 USA
| | - Maya Shumyatcher
- Department of Biostatistics, Epidemiology and Informatics, University of Pennsylvania, 402 Blockley Hall 423 Guardian Drive, Philadelphia, PA 19104 USA
| | - Blanca E. Himes
- Department of Biostatistics, Epidemiology and Informatics, University of Pennsylvania, 402 Blockley Hall 423 Guardian Drive, Philadelphia, PA 19104 USA
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What Ancestry Can Tell Us About the Genetic Origins of Inter-Ethnic Differences in Asthma Expression. Curr Allergy Asthma Rep 2017; 16:53. [PMID: 27393700 DOI: 10.1007/s11882-016-0635-4] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Differences in asthma prevalence have been described across different populations, suggesting that genetic ancestry can play an important role in this disease. In fact, several studies have demonstrated an association between African ancestry with increased asthma susceptibility and severity, higher immunoglobulin E levels, and lower lung function. In contrast, Native American ancestry has been shown to have a protective role for this disease. Genome-wide association studies have allowed the identification of population-specific genetic variants with varying allele frequency among populations. Additionally, the correlation of genetic ancestry at the chromosomal level with asthma and related traits by means of admixture mapping has revealed regions of the genome where ancestry is correlated with the disease. In this review, we discuss the evidence supporting the association of genetic ancestry with asthma susceptibility and asthma-related traits, and highlight the regions of the genome harboring ancestry-specific genetic risk factors.
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Zhu M, Yan C, Ren C, Huang X, Zhu X, Gu H, Wang M, Wang S, Gao Y, Ji Y, Miao X, Yang M, Chen J, Du J, Huang T, Jiang Y, Dai J, Ma H, Zhou J, Wang Z, Hu Z, Ji G, Zhang Z, Shen H, Shi Y, Jin G. Exome Array Analysis Identifies Variants in SPOCD1 and BTN3A2 That Affect Risk for Gastric Cancer. Gastroenterology 2017; 152:2011-2021. [PMID: 28246015 DOI: 10.1053/j.gastro.2017.02.017] [Citation(s) in RCA: 48] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/18/2016] [Revised: 02/16/2017] [Accepted: 02/21/2017] [Indexed: 12/21/2022]
Abstract
BACKGROUND & AIMS Several genetic variants have been associated with gastric cancer risk, although these account for only a fraction of cases of gastric cancer. We aimed to identify low-frequency and other genetic variants that determine gastric cancer susceptibility. METHODS We performed exome array analysis of DNA in blood samples from 1113 patients with gastric cancer, collected at hospitals from 2006 to 2010 in China, and 1848 individuals without cancer (controls) undergoing physical examinations. Among 71,290 variants analyzed (including 25,784 common variants), 24 variants were selected and replicated in an analysis of DNA in blood samples from 4687 additional cases of gastric cancer and 5780 controls. We compared expression of candidate genes in tumor vs normal gastric tissues using data from TCGA and performed functional annotation analyses. An immortalized human gastric epithelial cell line (GES1) and 7 human gastric cancer lines were used to express transgenes, knock down gene expression (with small interfering RNAs), disrupt genes (using the CRISPR/Cas9 system), or assess expression of reporter constructs. We measured cell proliferation, colony formation, invasion, and migration, and assessed growth of xenograft tumors in nude mice. RESULTS A low-frequency missense variant rs112754928 in the SPOC domain containing 1 gene (SPOCD1; encoding p.Arg71Trp), at 1p35.2, was reproducibly associated with reduced risk of gastric cancer (odds ratio, 0.56; P = 3.48 × 10-8). SPOCD1 was overexpressed in gastric tumors, and knockout of SPOCD1 reduced gastric cancer cell proliferation, invasive activity, and migration, as well as growth of xenograft tumors in nude mice. We also associated the variant rs1679709 at 6p22.1 with reduced risk for gastric cancer (odds ratio, 0.80; P = 1.17 × 10-13). The protective allele rs1679709-A correlated with the surrounding haplotype rs2799077-T-rs2799079-C, which reduced the enhancer activity of this site to decrease expression of the butyrophilin subfamily 3 member A2 gene (BTN3A2). BTN3A2 is overexpressed in gastric tumors, and deletion of BTN3A2 inhibited proliferation, migration, and invasion of gastric cancer cells. CONCLUSIONS We have associated variants at 1p35.2 and 6p22.1 with gastric cancer risk, indicating a role for SPOCD1 and BTN3A2 in gastric carcinogenesis.
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Affiliation(s)
- Meng Zhu
- Department of Epidemiology and Biostatistics, Jiangsu Key Lab of Cancer Biomarkers, Prevention and Treatment, Collaborative Innovation Center for Cancer Medicine, School of Public Health, Nanjing Medical University, Nanjing, China; State Key Laboratory of Reproductive Medicine, International Joint Research Center for Environment and Human Health, Nanjing Medical University, Nanjing, China
| | - Caiwang Yan
- Department of Epidemiology and Biostatistics, Jiangsu Key Lab of Cancer Biomarkers, Prevention and Treatment, Collaborative Innovation Center for Cancer Medicine, School of Public Health, Nanjing Medical University, Nanjing, China
| | - Chuanli Ren
- Department of Epidemiology and Biostatistics, Jiangsu Key Lab of Cancer Biomarkers, Prevention and Treatment, Collaborative Innovation Center for Cancer Medicine, School of Public Health, Nanjing Medical University, Nanjing, China; Clinical Medical Testing Laboratory, Northern Jiangsu People's Hospital and Clinical Medical College of Yangzhou University, Yangzhou, China
| | - Xiaodan Huang
- Institute of Digestive Endoscopy and Medical Center for Digestive Diseases, Second Affiliated Hospital of Nanjing Medical University, Nanjing, China
| | - Xun Zhu
- Department of Epidemiology and Biostatistics, Jiangsu Key Lab of Cancer Biomarkers, Prevention and Treatment, Collaborative Innovation Center for Cancer Medicine, School of Public Health, Nanjing Medical University, Nanjing, China
| | - Haiyong Gu
- Department of Cardiothoracic Surgery, Affiliated People's Hospital of Jiangsu University, Zhenjiang, China
| | - Meilin Wang
- Department of Environmental Genomics, Jiangsu Key Laboratory of Cancer Biomarkers, Prevention and Treatment, Collaborative Innovation Center for Cancer Medicine, Nanjing Medical University, Nanjing, China
| | - Shouyu Wang
- Department of Molecular Cell Biology and Toxicology, Jiangsu Key Lab of Cancer Biomarkers, Prevention and Treatment, Collaborative Innovation Center for Cancer Medicine, School of Public Health, Nanjing Medical University, Nanjing, China
| | - Yong Gao
- Department of Medical Oncology, The Affiliated Huai'an First People's Hospital of Nanjing Medical University, Huai'an, China
| | - Yong Ji
- Department of Cardiothoracic Surgery, The Affiliated Wuxi People's Hospital of Nanjing Medical University, Wuxi, China
| | - Xiaoping Miao
- MOE Key Lab of Environment and Health, School of Public Health, Tongji Medical College, Huazhong University of Science & Technology, Wuhan, China
| | - Ming Yang
- Shandong Provincial Key Laboratory of Radiation Oncology, Cancer Research Center, Shandong Cancer Hospital Affiliated to Shandong University, Shandong Academy of Medical Sciences, Jinan, China
| | - Jinfei Chen
- Department of Oncology, Nanjing First Hospital, Nanjing Medical University, Nanjing, China
| | - Jiangbo Du
- Department of Epidemiology and Biostatistics, Jiangsu Key Lab of Cancer Biomarkers, Prevention and Treatment, Collaborative Innovation Center for Cancer Medicine, School of Public Health, Nanjing Medical University, Nanjing, China
| | - Tongtong Huang
- Department of Epidemiology and Biostatistics, Jiangsu Key Lab of Cancer Biomarkers, Prevention and Treatment, Collaborative Innovation Center for Cancer Medicine, School of Public Health, Nanjing Medical University, Nanjing, China
| | - Yue Jiang
- Department of Epidemiology and Biostatistics, Jiangsu Key Lab of Cancer Biomarkers, Prevention and Treatment, Collaborative Innovation Center for Cancer Medicine, School of Public Health, Nanjing Medical University, Nanjing, China
| | - Juncheng Dai
- Department of Epidemiology and Biostatistics, Jiangsu Key Lab of Cancer Biomarkers, Prevention and Treatment, Collaborative Innovation Center for Cancer Medicine, School of Public Health, Nanjing Medical University, Nanjing, China
| | - Hongxia Ma
- Department of Epidemiology and Biostatistics, Jiangsu Key Lab of Cancer Biomarkers, Prevention and Treatment, Collaborative Innovation Center for Cancer Medicine, School of Public Health, Nanjing Medical University, Nanjing, China
| | - Jianwei Zhou
- Department of Molecular Cell Biology and Toxicology, Jiangsu Key Lab of Cancer Biomarkers, Prevention and Treatment, Collaborative Innovation Center for Cancer Medicine, School of Public Health, Nanjing Medical University, Nanjing, China
| | - Zhaoming Wang
- Department of Epidemiology and Biostatistics, Jiangsu Key Lab of Cancer Biomarkers, Prevention and Treatment, Collaborative Innovation Center for Cancer Medicine, School of Public Health, Nanjing Medical University, Nanjing, China
| | - Zhibin Hu
- Department of Epidemiology and Biostatistics, Jiangsu Key Lab of Cancer Biomarkers, Prevention and Treatment, Collaborative Innovation Center for Cancer Medicine, School of Public Health, Nanjing Medical University, Nanjing, China
| | - Guozhong Ji
- Institute of Digestive Endoscopy and Medical Center for Digestive Diseases, Second Affiliated Hospital of Nanjing Medical University, Nanjing, China
| | - Zhengdong Zhang
- Department of Environmental Genomics, Jiangsu Key Laboratory of Cancer Biomarkers, Prevention and Treatment, Collaborative Innovation Center for Cancer Medicine, Nanjing Medical University, Nanjing, China
| | - Hongbing Shen
- Department of Epidemiology and Biostatistics, Jiangsu Key Lab of Cancer Biomarkers, Prevention and Treatment, Collaborative Innovation Center for Cancer Medicine, School of Public Health, Nanjing Medical University, Nanjing, China.
| | - Yongyong Shi
- Key Laboratory for the Genetics of Developmental and Neuropsychiatric Disorders, Ministry of Education, Bio-X Institutes, Shanghai Jiao Tong University, Shanghai, China.
| | - Guangfu Jin
- Department of Epidemiology and Biostatistics, Jiangsu Key Lab of Cancer Biomarkers, Prevention and Treatment, Collaborative Innovation Center for Cancer Medicine, School of Public Health, Nanjing Medical University, Nanjing, China; State Key Laboratory of Reproductive Medicine, International Joint Research Center for Environment and Human Health, Nanjing Medical University, Nanjing, China.
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Zöller B, Pirouzifard M, Memon AA, Sundquist J, Sundquist K. Risk of pulmonary embolism and deep venous thrombosis in patients with asthma: a nationwide case-control study from Sweden. Eur Respir J 2017; 49:49/2/1601014. [PMID: 28202551 DOI: 10.1183/13993003.01014-2016] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2016] [Accepted: 11/11/2016] [Indexed: 01/15/2023]
Abstract
Asthma is associated with an increased risk of pulmonary embolism (PE) but little is known about whether asthma is associated with an increased risk of deep venous thrombosis (DVT). The aim in this study was to determine the risk of the first event of PE, DVT or a combination of PE and DVT in patients with asthma.We conducted this nationwide case-control study using data from Swedish nationwide registries. We included 114 366 Swedish-born patients with a first hospital diagnosis of PE, 76 494 patients with DVT and 6854 patients with both PE and DVT in Sweden between 1981 and 2010. We also included five age-, sex- and education-matched population controls. All previous hospital diagnoses of asthma were identified. Conditional logistic regression was used to compute odds ratios with adjustment for potential confounders.Asthma was associated with an adjusted odds ratio for PE of 1.43 (95% CI 1.37-1.50), for DVT of 1.56 (95% CI 1.47-1.65) and for combined PE and DVT of 1.60 (95% CI 1.32-1.93). Asthma was associated with an increased risk of PE, DVT and combined PE and DVT.Thus, the inflammation conferred by asthma seems to have systemic (and not just local) prothrombotic effects with increased risk of both DVT and PE.
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Affiliation(s)
- Bengt Zöller
- Center for Primary Health Care Research, Lund University, Malmö, Sweden
| | | | - Ashfaque A Memon
- Center for Primary Health Care Research, Lund University, Malmö, Sweden
| | - Jan Sundquist
- Center for Primary Health Care Research, Lund University, Malmö, Sweden
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Zhu M, Geng L, Shen W, Wang Y, Liu J, Cheng Y, Wang C, Dai J, Jin G, Hu Z, Ma H, Shen H. Exome-Wide Association Study Identifies Low-Frequency Coding Variants in 2p23.2 and 7p11.2 Associated with Survival of Non-Small Cell Lung Cancer Patients. J Thorac Oncol 2017; 12:644-656. [PMID: 28104536 DOI: 10.1016/j.jtho.2016.12.025] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2016] [Revised: 11/23/2016] [Accepted: 12/15/2016] [Indexed: 01/10/2023]
Abstract
INTRODUCTION A growing body of evidence has suggested that low-frequency or rare coding variants might have strong effects on the development and prognosis of cancer. Here, we aim to assess the role of low-frequency and rare coding variants in the survival of NSCLC in Chinese populations. METHODS We performed an exome-wide scan of 247,870 variants in 1008 patients with NSCLC and replicated the promising variants by using imputed genotype data of The Cancer Genome Atlas (TCGA) with a Cox regression model. Gene-based and pathway-based analysis were also performed for nonsynonymous or splice site variants. Additionally, analysis of gene expression data in the TCGA was used to increase the reliability of candidate loci and genes. RESULTS A low-frequency missense variant in chaperonin containing TCP1 subunit 6A gene (CCT6A) (rs33922584: adjusted hazard ratio [HRadjusted] = 1.75, p = 6.06 × 10-4) was significantly related to the survival of patients with NSCLC, which was further replicated by the TCGA samples (HRadjusted = 4.19, p = 0.015). Interestingly, the G allele of rs33922584 was significantly associated with high expression of CCT6A (p = 0.019) that might induce the worse survival in the TCGA samples (HRadjusted = 1.15, p = 0.047). Besides, rs117512489 in gene phospholipase B1 gene (PLB1) (HR = 2.02, p = 7.28 × 10-4) was also associated with survival of the patients with NSCLC in our samples, but it was supported only by gene expression analysis in the TCGA (HRadjusted = 1.15, p = 0.023). Gene-based and pathway-based analysis revealed a total of 32 genes, including CCT6A and 34 potential pathways might account for the survival of NSCLC, respectively. CONCLUSION These results provided more evidence for the important role of low-frequency or rare variants in the survival of patients with NSCLC.
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Affiliation(s)
- Meng Zhu
- Department of Epidemiology and Biostatistics, Collaborative Innovation Center For Cancer Personalized Medicine, School of Public Health, Nanjing Medical University, Nanjing, People's Republic of China
| | - Liguo Geng
- Department of Epidemiology and Biostatistics, Collaborative Innovation Center For Cancer Personalized Medicine, School of Public Health, Nanjing Medical University, Nanjing, People's Republic of China
| | - Wei Shen
- Department of Epidemiology and Biostatistics, Collaborative Innovation Center For Cancer Personalized Medicine, School of Public Health, Nanjing Medical University, Nanjing, People's Republic of China
| | - Yuzhuo Wang
- Department of Epidemiology and Biostatistics, Collaborative Innovation Center For Cancer Personalized Medicine, School of Public Health, Nanjing Medical University, Nanjing, People's Republic of China
| | - Jia Liu
- Department of Epidemiology and Biostatistics, Collaborative Innovation Center For Cancer Personalized Medicine, School of Public Health, Nanjing Medical University, Nanjing, People's Republic of China
| | - Yang Cheng
- Department of Epidemiology and Biostatistics, Collaborative Innovation Center For Cancer Personalized Medicine, School of Public Health, Nanjing Medical University, Nanjing, People's Republic of China
| | - Cheng Wang
- Department of Epidemiology and Biostatistics, Collaborative Innovation Center For Cancer Personalized Medicine, School of Public Health, Nanjing Medical University, Nanjing, People's Republic of China
| | - Juncheng Dai
- Department of Epidemiology and Biostatistics, Collaborative Innovation Center For Cancer Personalized Medicine, School of Public Health, Nanjing Medical University, Nanjing, People's Republic of China; Jiangsu Key Lab of Cancer Biomarkers, Prevention and Treatment, Collaborative Innovation Center of Cancer Medicine, Nanjing Medical University, Nanjing, People's Republic of China
| | - Guangfu Jin
- Department of Epidemiology and Biostatistics, Collaborative Innovation Center For Cancer Personalized Medicine, School of Public Health, Nanjing Medical University, Nanjing, People's Republic of China; Jiangsu Key Lab of Cancer Biomarkers, Prevention and Treatment, Collaborative Innovation Center of Cancer Medicine, Nanjing Medical University, Nanjing, People's Republic of China
| | - Zhibin Hu
- Department of Epidemiology and Biostatistics, Collaborative Innovation Center For Cancer Personalized Medicine, School of Public Health, Nanjing Medical University, Nanjing, People's Republic of China; Jiangsu Key Lab of Cancer Biomarkers, Prevention and Treatment, Collaborative Innovation Center of Cancer Medicine, Nanjing Medical University, Nanjing, People's Republic of China
| | - Hongxia Ma
- Department of Epidemiology and Biostatistics, Collaborative Innovation Center For Cancer Personalized Medicine, School of Public Health, Nanjing Medical University, Nanjing, People's Republic of China; Jiangsu Key Lab of Cancer Biomarkers, Prevention and Treatment, Collaborative Innovation Center of Cancer Medicine, Nanjing Medical University, Nanjing, People's Republic of China.
| | - Hongbing Shen
- Department of Epidemiology and Biostatistics, Collaborative Innovation Center For Cancer Personalized Medicine, School of Public Health, Nanjing Medical University, Nanjing, People's Republic of China; Jiangsu Key Lab of Cancer Biomarkers, Prevention and Treatment, Collaborative Innovation Center of Cancer Medicine, Nanjing Medical University, Nanjing, People's Republic of China
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Abstract
Genome-wide association studies (GWAS) of asthma have yielded exciting results and identified novel risk alleles and loci. But, like other common complex diseases, asthma-associated alleles have small effect sizes and account for little of the prevalence of asthma. In this review, I discuss the limitations of GWAS approaches and the major challenges facing geneticists in the post-GWAS era and propose alternative strategies to address these challenges. In particular, I propose that focusing on genetic variations that influences gene expression and using cell models of gene-environment interactions in cell types that are relevant to asthma will allow us to more completely characterize the genetic architecture of asthma.
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Busch R, Qiu W, Lasky-Su J, Morrow J, Criner G, DeMeo D. Differential DNA methylation marks and gene comethylation of COPD in African-Americans with COPD exacerbations. Respir Res 2016; 17:143. [PMID: 27814717 PMCID: PMC5097392 DOI: 10.1186/s12931-016-0459-8] [Citation(s) in RCA: 45] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2016] [Accepted: 10/27/2016] [Indexed: 12/18/2022] Open
Abstract
BACKGROUND Chronic obstructive pulmonary disease (COPD) is the third-leading cause of death worldwide. Identifying COPD-associated DNA methylation marks in African-Americans may contribute to our understanding of racial disparities in COPD susceptibility. We determined differentially methylated genes and co-methylation network modules associated with COPD in African-Americans recruited during exacerbations of COPD and smoking controls from the Pennsylvania Study of Chronic Obstructive Pulmonary Exacerbations (PA-SCOPE) cohort. METHODS We assessed DNA methylation from whole blood samples in 362 African-American smokers in the PA-SCOPE cohort using the Illumina Infinium HumanMethylation27 BeadChip Array. Final analysis included 19302 CpG probes annotated to the nearest gene transcript after quality control. We tested methylation associations with COPD case-control status using mixed linear models. Weighted gene comethylation networks were constructed using weighted gene coexpression network analysis (WGCNA) and network modules were analyzed for association with COPD. RESULTS There were five differentially methylated CpG probes significantly associated with COPD among African-Americans at an FDR less than 5 %, and seven additional probes that approached significance at an FDR less than 10 %. The top ranked gene association was MAML1, which has been shown to affect NOTCH-dependent angiogenesis in murine lung. Network modeling yielded the "yellow" and "blue" comethylation modules which were significantly associated with COPD (p-value 4 × 10-10 and 4 × 10-9, respectively). The yellow module was enriched for gene sets related to inflammatory pathways known to be relevant to COPD. The blue module contained the top ranked genes in the concurrent differential methylation analysis (FXYD1/LGI4, gene significance p-value 1.2 × 10-26; MAML1, p-value 2.0 × 10-26; CD72, p-value 2.1 × 10-25; and LPO, p-value 7.2 × 10-25), and was significantly associated with lung development processes in Gene Ontology gene-set enrichment analysis. CONCLUSION We identified 12 differentially methylated CpG sites associated with COPD that mapped to biologically plausible genes. Network module comethylation patterns have identified candidate genes that may be contributing to racial differences in COPD susceptibility and severity. COPD-associated comethylation modules contained genes previously associated with lung disease and inflammation and recapitulated known COPD-associated genes. The genes implicated by differential methylation and WGCNA analysis may provide mechanistic targets contributing to COPD susceptibility, exacerbations, and outcomes among African-Americans. TRIAL REGISTRATION Trial Registration: NCT00774176 , Registry: ClinicalTrials.gov, URL: www.clinicaltrials.gov , Date of Enrollment of First Participant: June 2004, Date Registered: 04 January 2008 (retrospectively registered).
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Affiliation(s)
- Robert Busch
- Channing Division of Network Medicine, Department of Medicine, Brigham and Women’s Hospital, 181 Longwood Ave, Room 449, Boston, 02111 MA USA
| | - Weiliang Qiu
- Channing Division of Network Medicine, Department of Medicine, Brigham and Women’s Hospital, 181 Longwood Ave, Room 449, Boston, 02111 MA USA
| | - Jessica Lasky-Su
- Channing Division of Network Medicine, Department of Medicine, Brigham and Women’s Hospital, 181 Longwood Ave, Room 449, Boston, 02111 MA USA
| | - Jarrett Morrow
- Channing Division of Network Medicine, Department of Medicine, Brigham and Women’s Hospital, 181 Longwood Ave, Room 449, Boston, 02111 MA USA
| | - Gerard Criner
- Temple Lung Center, Temple University Health System, Philadelphia, PA USA
| | - Dawn DeMeo
- Channing Division of Network Medicine, Department of Medicine, Brigham and Women’s Hospital, 181 Longwood Ave, Room 449, Boston, 02111 MA USA
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Stemmler S, Hoffjan S. Trying to understand the genetics of atopic dermatitis. Mol Cell Probes 2016; 30:374-385. [PMID: 27725295 DOI: 10.1016/j.mcp.2016.10.004] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2016] [Revised: 10/06/2016] [Accepted: 10/06/2016] [Indexed: 02/07/2023]
Abstract
Atopic dermatitis (AD) is a common and complex skin disease associated with both genetic and environmental factors. Loss-of-function mutations in the filaggrin gene, encoding a structural protein with an important role in epidermal barrier function, constitutes a well recognised susceptibility locus for AD. Further, genome-wide association studies (GWAS), including large meta-analyses, have discovered 38 additional susceptibility loci with genome-wide significance. However, the reported variations only explain a fraction of the overall heritability of AD. Here, we summarize the current knowledge of the role of filaggrin and the epidermal differentiation complex as well as the results of GWAS, with an emphasis on novel findings and observations made in the past two years. Additionally, we present first results of exome sequencing for AD and discuss novel therapeutic strategies.
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Affiliation(s)
| | - Sabine Hoffjan
- Department of Human Genetics, Ruhr-University, Bochum, Germany
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Gupta J, Johansson E, Bernstein JA, Chakraborty R, Khurana Hershey GK, Rothenberg ME, Mersha TB. Resolving the etiology of atopic disorders by using genetic analysis of racial ancestry. J Allergy Clin Immunol 2016; 138:676-699. [PMID: 27297995 PMCID: PMC5014679 DOI: 10.1016/j.jaci.2016.02.045] [Citation(s) in RCA: 46] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2015] [Revised: 02/09/2016] [Accepted: 02/25/2016] [Indexed: 12/23/2022]
Abstract
Atopic dermatitis (AD), food allergy, allergic rhinitis, and asthma are common atopic disorders of complex etiology. The frequently observed atopic march from early AD to asthma, allergic rhinitis, or both later in life and the extensive comorbidity of atopic disorders suggest common causal mechanisms in addition to distinct ones. Indeed, both disease-specific and shared genomic regions exist for atopic disorders. Their prevalence also varies among races; for example, AD and asthma have a higher prevalence in African Americans when compared with European Americans. Whether this disparity stems from true genetic or race-specific environmental risk factors or both is unknown. Thus far, the majority of the genetic studies on atopic diseases have used populations of European ancestry, limiting their generalizability. Large-cohort initiatives and new analytic methods, such as admixture mapping, are currently being used to address this knowledge gap. Here we discuss the unique and shared genetic risk factors for atopic disorders in the context of ancestry variations and the promise of high-throughput "-omics"-based systems biology approach in providing greater insight to deconstruct their genetic and nongenetic etiologies. Future research will also focus on deep phenotyping and genotyping of diverse racial ancestry, gene-environment, and gene-gene interactions.
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Affiliation(s)
- Jayanta Gupta
- Division of Asthma Research, Department of Pediatrics, Cincinnati Children's Hospital Medical Center, University of Cincinnati, Cincinnati, Ohio
| | - Elisabet Johansson
- Division of Asthma Research, Department of Pediatrics, Cincinnati Children's Hospital Medical Center, University of Cincinnati, Cincinnati, Ohio
| | - Jonathan A Bernstein
- Division of Immunology/Allergy Section, Department of Internal Medicine, University of Cincinnati, Cincinnati, Ohio
| | - Ranajit Chakraborty
- Center for Computational Genomics, Institute of Applied Genetics, Department of Molecular and Medical Genetics, University of North Texas Health Science Center, Fort Worth, Tex
| | - Gurjit K Khurana Hershey
- Division of Asthma Research, Department of Pediatrics, Cincinnati Children's Hospital Medical Center, University of Cincinnati, Cincinnati, Ohio
| | - Marc E Rothenberg
- Division of Allergy and Immunology, Department of Pediatrics, Cincinnati Children's Hospital Medical Center, University of Cincinnati, Cincinnati, Ohio
| | - Tesfaye B Mersha
- Division of Asthma Research, Department of Pediatrics, Cincinnati Children's Hospital Medical Center, University of Cincinnati, Cincinnati, Ohio.
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Zhou W, Jiang Y, Zhu M, Hang D, Chen J, Zhou J, Dai J, Ma H, Hu Z, Jin G, Sha J, Shen H. Low-frequency nonsynonymous variants inFKBPLandARPC1Bgenes are associated with breast cancer risk in Chinese women. Mol Carcinog 2016; 56:774-780. [DOI: 10.1002/mc.22534] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2016] [Revised: 07/23/2016] [Accepted: 07/29/2016] [Indexed: 12/24/2022]
Affiliation(s)
- Wen Zhou
- State Key Laboratory of Reproductive Medicine; Nanjing Medical University; Nanjing China
- Department of Epidemiology and Biostatistics; School of Public Health; Nanjing Medical University; Nanjing China
| | - Yue Jiang
- State Key Laboratory of Reproductive Medicine; Nanjing Medical University; Nanjing China
- Department of Epidemiology and Biostatistics; School of Public Health; Nanjing Medical University; Nanjing China
| | - Meng Zhu
- Department of Epidemiology and Biostatistics; School of Public Health; Nanjing Medical University; Nanjing China
| | - Dong Hang
- Department of Epidemiology and Biostatistics; School of Public Health; Nanjing Medical University; Nanjing China
| | - Jiaping Chen
- Department of Epidemiology and Biostatistics; School of Public Health; Nanjing Medical University; Nanjing China
| | - Jing Zhou
- Department of Epidemiology and Biostatistics; School of Public Health; Nanjing Medical University; Nanjing China
| | - Juncheng Dai
- Department of Epidemiology and Biostatistics; School of Public Health; Nanjing Medical University; Nanjing China
| | - Hongxia Ma
- Department of Epidemiology and Biostatistics; School of Public Health; Nanjing Medical University; Nanjing China
| | - Zhibin Hu
- State Key Laboratory of Reproductive Medicine; Nanjing Medical University; Nanjing China
- Department of Epidemiology and Biostatistics; School of Public Health; Nanjing Medical University; Nanjing China
- Jiangsu Key Lab of Cancer Biomarkers, Prevention and Treatment; Collaborative Innovation Center for Cancer Medicine; Nanjing Medical University; Nanjing China
| | - Guangfu Jin
- State Key Laboratory of Reproductive Medicine; Nanjing Medical University; Nanjing China
- Department of Epidemiology and Biostatistics; School of Public Health; Nanjing Medical University; Nanjing China
| | - Jiahao Sha
- State Key Laboratory of Reproductive Medicine; Nanjing Medical University; Nanjing China
| | - Hongbing Shen
- State Key Laboratory of Reproductive Medicine; Nanjing Medical University; Nanjing China
- Department of Epidemiology and Biostatistics; School of Public Health; Nanjing Medical University; Nanjing China
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Bønnelykke K, Ober C. Leveraging gene-environment interactions and endotypes for asthma gene discovery. J Allergy Clin Immunol 2016; 137:667-79. [PMID: 26947980 DOI: 10.1016/j.jaci.2016.01.006] [Citation(s) in RCA: 80] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2015] [Revised: 12/30/2015] [Accepted: 01/08/2016] [Indexed: 12/20/2022]
Abstract
Asthma is a heterogeneous clinical syndrome that includes subtypes of disease with different underlying causes and disease mechanisms. Asthma is caused by a complex interaction between genes and environmental exposures; early-life exposures in particular play an important role. Asthma is also heritable, and a number of susceptibility variants have been discovered in genome-wide association studies, although the known risk alleles explain only a small proportion of the heritability. In this review, we present evidence supporting the hypothesis that focusing on more specific asthma phenotypes, such as childhood asthma with severe exacerbations, and on relevant exposures that are involved in gene-environment interactions (GEIs), such as rhinovirus infections, will improve detection of asthma genes and our understanding of the underlying mechanisms. We will discuss the challenges of considering GEIs and the advantages of studying responses to asthma-associated exposures in clinical birth cohorts, as well as in cell models of GEIs, to dissect the context-specific nature of genotypic risks, to prioritize variants in genome-wide association studies, and to identify pathways involved in pathogenesis in subgroups of patients. We propose that such approaches, in spite of their many challenges, present great opportunities for better understanding of asthma pathogenesis and heterogeneity and, ultimately, for improving prevention and treatment of disease.
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Affiliation(s)
- Klaus Bønnelykke
- COPSAC (Copenhagen Prospective Studies on Asthma in Childhood), Herlev and Gentofte Hospital, University of Copenhagen, Copenhagen, Denmark.
| | - Carole Ober
- Department of Human Genetics, University of Chicago, Chicago, Ill.
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Burrows CK, Kosova G, Herman C, Patterson K, Hartmann KE, Velez Edwards DR, Stephenson MD, Lynch VJ, Ober C. Expression Quantitative Trait Locus Mapping Studies in Mid-secretory Phase Endometrial Cells Identifies HLA-F and TAP2 as Fecundability-Associated Genes. PLoS Genet 2016; 12:e1005858. [PMID: 27447835 PMCID: PMC4957750 DOI: 10.1371/journal.pgen.1005858] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2015] [Accepted: 01/20/2016] [Indexed: 12/29/2022] Open
Abstract
Fertility traits in humans are heritable, however, little is known about the genes that influence reproductive outcomes or the genetic variants that contribute to differences in these traits between individuals, particularly women. To address this gap in knowledge, we performed an unbiased genome-wide expression quantitative trait locus (eQTL) mapping study to identify common regulatory (expression) single nucleotide polymorphisms (eSNPs) in mid-secretory endometrium. We identified 423 cis-eQTLs for 132 genes that were significant at a false discovery rate (FDR) of 1%. After pruning for strong LD (r2 >0.95), we tested for associations between eSNPs and fecundability (the ability to get pregnant), measured as the length of the interval to pregnancy, in 117 women. Two eSNPs were associated with fecundability at a FDR of 5%; both were in the HLA region and were eQTLs for the TAP2 gene (P = 1.3x10-4) and the HLA-F gene (P = 4.0x10-4), respectively. The effects of these SNPs on fecundability were replicated in an independent sample. The two eSNPs reside within or near regulatory elements in decidualized human endometrial stromal cells. Our study integrating eQTL mapping in a primary tissue with association studies of a related phenotype revealed novel genes and associated alleles with independent effects on fecundability, and identified a central role for two HLA region genes in human implantation success. Little is known about the genetics of female fertility. In this study, we addressed this gap in knowledge by first searching for genetic variants that regulate gene expression in uterine endometrial cells, and then testing those functional variants for associations with the length of time to pregnancy in fertile women. Two functional genetic variants were associated with time to pregnancy in women after correcting for multiple testing. Those variants were each associated with the expression of genes in the HLA region, HLA-F and TAP2, which are have not previously been implicated female fertility. The association between HLA-F and TAP2 genotypes on the length of time to pregnancy was replicated in an independent cohort of women. Because HLA-F and TAP2 are involved in immune processes, these results suggest their role in specific immune regulation in the endometrium during implantation. Future studies will characterize these molecules in the implantation process and their potential as drug targets for treatment of conditions related to implantation failure.
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Affiliation(s)
- Courtney K. Burrows
- Department of Human Genetics, The University of Chicago, Chicago, Illinois, United States of America
| | - Gülüm Kosova
- Department of Human Genetics, The University of Chicago, Chicago, Illinois, United States of America
| | - Catherine Herman
- Department of Human Genetics, The University of Chicago, Chicago, Illinois, United States of America
| | - Kristen Patterson
- Department of Human Genetics, The University of Chicago, Chicago, Illinois, United States of America
| | - Katherine E. Hartmann
- Institute for Medicine and Public Health, Vanderbilt Epidemiology Center, Vanderbilt University, Nashville, Tennessee, United States of America
- Departments of Obstetrics and Gynecology, Vanderbilt University Medical Center, Nashville, Tennessee, United States of America
- Department of Medicine, Vanderbilt University Medical Center, Nashville, Tennessee, United States of America
| | - Digna R. Velez Edwards
- Institute for Medicine and Public Health, Vanderbilt Epidemiology Center, Vanderbilt University, Nashville, Tennessee, United States of America
- Departments of Obstetrics and Gynecology, Vanderbilt University Medical Center, Nashville, Tennessee, United States of America
- Vanderbilt Genetics Institute, Vanderbilt University, Nashville, Tennessee, United States of America
| | - Mary D. Stephenson
- Department of Obstetrics and Gynecology, The University of Chicago, Chicago, Illinois, United States of America
| | - Vincent J. Lynch
- Department of Human Genetics, The University of Chicago, Chicago, Illinois, United States of America
| | - Carole Ober
- Department of Human Genetics, The University of Chicago, Chicago, Illinois, United States of America
- Department of Obstetrics and Gynecology, The University of Chicago, Chicago, Illinois, United States of America
- * E-mail:
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Fu OY, Chang HW, Lin YD, Chuang LY, Hou MF, Yang CH. Breast cancer-associated high-order SNP-SNP interaction of CXCL12/CXCR4-related genes by an improved multifactor dimensionality reduction (MDR-ER). Oncol Rep 2016; 36:1739-47. [PMID: 27461876 DOI: 10.3892/or.2016.4956] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2016] [Accepted: 03/03/2016] [Indexed: 11/06/2022] Open
Abstract
In association studies, the combined effects of single nucleotide polymorphism (SNP)-SNP interactions and the problem of imbalanced data between cases and controls are frequently ignored. In the present study, we used an improved multifactor dimensionality reduction (MDR) approach namely MDR-ER to detect the high order SNP‑SNP interaction in an imbalanced breast cancer data set containing seven SNPs of chemokine CXCL12/CXCR4 pathway genes. Most individual SNPs were not significantly associated with breast cancer. After MDR‑ER analysis, six significant SNP‑SNP interaction models with seven genes (highest cross‑validation consistency, 10; classification error rates, 41.3‑21.0; and prediction error rates, 47.4‑55.3) were identified. CD4 and VEGFA genes were associated in a 2‑loci interaction model (classification error rate, 41.3; prediction error rate, 47.5; odds ratio (OR), 2.069; 95% bootstrap CI, 1.40‑2.90; P=1.71E‑04) and it also appeared in all the best 2‑7‑loci models. When the loci number increased, the classification error rates and P‑values decreased. The powers in 2‑7‑loci in all models were >0.9. The minimum classification error rate of the MDR‑ER‑generated model was shown with the 7‑loci interaction model (classification error rate, 21.0; OR=15.282; 95% bootstrap CI, 9.54‑23.87; P=4.03E‑31). In the epistasis network analysis, the overall effect with breast cancer susceptibility was identified and the SNP order of impact on breast cancer was identified as follows: CD4 = VEGFA > KITLG > CXCL12 > CCR7 = MMP2 > CXCR4. In conclusion, the MDR‑ER can effectively and correctly identify the best SNP‑SNP interaction models in an imbalanced data set for breast cancer cases.
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Affiliation(s)
- Ou-Yang Fu
- Graduate Institute of Medicine, College of Medicine, Kaohsiung Medical University, Kaohsiung 80708, Taiwan, R.O.C
| | - Hsueh-Wei Chang
- Cancer Center, Kaohsiung Medical University Hospital, Kaohsiung Medical University, Kaohsiung 80708, Taiwan, R.O.C
| | - Yu-Da Lin
- Department of Electronic Engineering, National Kaohsiung University of Applied Sciences, Kaohsiung 80778, Taiwan, R.O.C
| | - Li-Yeh Chuang
- Department of Chemical Engineering and Institute of Biotechnology and Chemical Engineering, I‑Shou University, Kaohsiung 84001, Taiwan, R.O.C
| | - Ming-Feng Hou
- Cancer Center, Kaohsiung Medical University Hospital, Kaohsiung Medical University, Kaohsiung 80708, Taiwan, R.O.C
| | - Cheng-Hong Yang
- Department of Electronic Engineering, National Kaohsiung University of Applied Sciences, Kaohsiung 80778, Taiwan, R.O.C
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50
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Uricchio LH, Zaitlen NA, Ye CJ, Witte JS, Hernandez RD. Selection and explosive growth alter genetic architecture and hamper the detection of causal rare variants. Genome Res 2016; 26:863-73. [PMID: 27197206 PMCID: PMC4937562 DOI: 10.1101/gr.202440.115] [Citation(s) in RCA: 52] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2015] [Accepted: 05/16/2016] [Indexed: 12/20/2022]
Abstract
The role of rare alleles in complex phenotypes has been hotly debated, but most rare variant association tests (RVATs) do not account for the evolutionary forces that affect genetic architecture. Here, we use simulation and numerical algorithms to show that explosive population growth, as experienced by human populations, can dramatically increase the impact of very rare alleles on trait variance. We then assess the ability of RVATs to detect causal loci using simulations and human RNA-seq data. Surprisingly, we find that statistical performance is worst for phenotypes in which genetic variance is due mainly to rare alleles, and explosive population growth decreases power. Although many studies have attempted to identify causal rare variants, few have reported novel associations. This has sometimes been interpreted to mean that rare variants make negligible contributions to complex trait heritability. Our work shows that RVATs are not robust to realistic human evolutionary forces, so general conclusions about the impact of rare variants on complex traits may be premature.
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Affiliation(s)
- Lawrence H Uricchio
- Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, San Francisco, California 94143, USA; Graduate Program in Bioinformatics, University of California, San Francisco, San Francisco, California 94143, USA
| | - Noah A Zaitlen
- Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, San Francisco, California 94143, USA; Institute for Human Genetics, University of California, San Francisco, San Francisco, California 94143, USA; Institute for Quantitative Biosciences (QB3), University of California, San Francisco, San Francisco, California 94143, USA
| | - Chun Jimmie Ye
- Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, San Francisco, California 94143, USA; Institute for Human Genetics, University of California, San Francisco, San Francisco, California 94143, USA; Department of Epidemiology and Biostatistics, University of California, San Francisco, San Francisco, California 94143, USA
| | - John S Witte
- Institute for Human Genetics, University of California, San Francisco, San Francisco, California 94143, USA; Department of Epidemiology and Biostatistics, University of California, San Francisco, San Francisco, California 94143, USA
| | - Ryan D Hernandez
- Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, San Francisco, California 94143, USA; Institute for Human Genetics, University of California, San Francisco, San Francisco, California 94143, USA; Institute for Quantitative Biosciences (QB3), University of California, San Francisco, San Francisco, California 94143, USA
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