%0 Journal Article %J Circ Cardiovasc Genet %D 2010 %T Candidate gene association resource (CARe): design, methods, and proof of concept. %A Musunuru, Kiran %A Lettre, Guillaume %A Young, Taylor %A Farlow, Deborah N %A Pirruccello, James P %A Ejebe, Kenechi G %A Keating, Brendan J %A Yang, Qiong %A Chen, Ming-Huei %A Lapchyk, Nina %A Crenshaw, Andrew %A Ziaugra, Liuda %A Rachupka, Anthony %A Benjamin, Emelia J %A Cupples, L Adrienne %A Fornage, Myriam %A Fox, Ervin R %A Heckbert, Susan R %A Hirschhorn, Joel N %A Newton-Cheh, Christopher %A Nizzari, Marcia M %A Paltoo, Dina N %A Papanicolaou, George J %A Patel, Sanjay R %A Psaty, Bruce M %A Rader, Daniel J %A Redline, Susan %A Rich, Stephen S %A Rotter, Jerome I %A Taylor, Herman A %A Tracy, Russell P %A Vasan, Ramachandran S %A Wilson, James G %A Kathiresan, Sekar %A Fabsitz, Richard R %A Boerwinkle, Eric %A Gabriel, Stacey B %K African Americans %K Cholesterol, HDL %K Cholesterol, LDL %K Cohort Studies %K Databases, Genetic %K European Continental Ancestry Group %K Genetic Association Studies %K Genotype %K Humans %K Phenotype %K Pilot Projects %K Polymorphism, Single Nucleotide %K Research Design %K Triglycerides %X

BACKGROUND: The National Heart, Lung, and Blood Institute's Candidate Gene Association Resource (CARe), a planned cross-cohort analysis of genetic variation in cardiovascular, pulmonary, hematologic, and sleep-related traits, comprises >40,000 participants representing 4 ethnic groups in 9 community-based cohorts. The goals of CARe include the discovery of new variants associated with traits using a candidate gene approach and the discovery of new variants using the genome-wide association mapping approach specifically in African Americans.

METHODS AND RESULTS: CARe has assembled DNA samples for >40,000 individuals self-identified as European American, African American, Hispanic, or Chinese American, with accompanying data on hundreds of phenotypes that have been standardized and deposited in the CARe Phenotype Database. All participants were genotyped for 7 single-nucleotide polymorphisms (SNPs) selected based on prior association evidence. We performed association analyses relating each of these SNPs to lipid traits, stratified by sex and ethnicity, and adjusted for age and age squared. In at least 2 of the ethnic groups, SNPs near CETP, LIPC, and LPL strongly replicated for association with high-density lipoprotein cholesterol concentrations, PCSK9 with low-density lipoprotein cholesterol levels, and LPL and APOA5 with serum triglycerides. Notably, some SNPs showed varying effect sizes and significance of association in different ethnic groups.

CONCLUSIONS: The CARe Pilot Study validates the operational framework for phenotype collection, SNP genotyping, and analytic pipeline of the CARe project and validates the planned candidate gene study of approximately 2000 biological candidate loci in all participants and genome-wide association study in approximately 8000 African American participants. CARe will serve as a valuable resource for the scientific community.

%B Circ Cardiovasc Genet %V 3 %P 267-75 %8 2010 Jun %G eng %N 3 %1 http://www.ncbi.nlm.nih.gov/pubmed/20400780?dopt=Abstract %R 10.1161/CIRCGENETICS.109.882696 %0 Journal Article %J PLoS Genet %D 2011 %T Enhanced statistical tests for GWAS in admixed populations: assessment using African Americans from CARe and a Breast Cancer Consortium. %A Pasaniuc, Bogdan %A Zaitlen, Noah %A Lettre, Guillaume %A Chen, Gary K %A Tandon, Arti %A Kao, W H Linda %A Ruczinski, Ingo %A Fornage, Myriam %A Siscovick, David S %A Zhu, Xiaofeng %A Larkin, Emma %A Lange, Leslie A %A Cupples, L Adrienne %A Yang, Qiong %A Akylbekova, Ermeg L %A Musani, Solomon K %A Divers, Jasmin %A Mychaleckyj, Joe %A Li, Mingyao %A Papanicolaou, George J %A Millikan, Robert C %A Ambrosone, Christine B %A John, Esther M %A Bernstein, Leslie %A Zheng, Wei %A Hu, Jennifer J %A Ziegler, Regina G %A Nyante, Sarah J %A Bandera, Elisa V %A Ingles, Sue A %A Press, Michael F %A Chanock, Stephen J %A Deming, Sandra L %A Rodriguez-Gil, Jorge L %A Palmer, Cameron D %A Buxbaum, Sarah %A Ekunwe, Lynette %A Hirschhorn, Joel N %A Henderson, Brian E %A Myers, Simon %A Haiman, Christopher A %A Reich, David %A Patterson, Nick %A Wilson, James G %A Price, Alkes L %K African Americans %K Algorithms %K Breast Neoplasms %K Chromosome Mapping %K Coronary Disease %K Diabetes Mellitus, Type 2 %K Female %K Gene Frequency %K Genetic Variation %K Genetics, Population %K Genome, Human %K Genome-Wide Association Study %K Genotype %K Humans %K Linkage Disequilibrium %K Male %K Odds Ratio %K Phenotype %K Polymorphism, Single Nucleotide %K Principal Component Analysis %K Receptor, Fibroblast Growth Factor, Type 2 %K Software %X

While genome-wide association studies (GWAS) have primarily examined populations of European ancestry, more recent studies often involve additional populations, including admixed populations such as African Americans and Latinos. In admixed populations, linkage disequilibrium (LD) exists both at a fine scale in ancestral populations and at a coarse scale (admixture-LD) due to chromosomal segments of distinct ancestry. Disease association statistics in admixed populations have previously considered SNP association (LD mapping) or admixture association (mapping by admixture-LD), but not both. Here, we introduce a new statistical framework for combining SNP and admixture association in case-control studies, as well as methods for local ancestry-aware imputation. We illustrate the gain in statistical power achieved by these methods by analyzing data of 6,209 unrelated African Americans from the CARe project genotyped on the Affymetrix 6.0 chip, in conjunction with both simulated and real phenotypes, as well as by analyzing the FGFR2 locus using breast cancer GWAS data from 5,761 African-American women. We show that, at typed SNPs, our method yields an 8% increase in statistical power for finding disease risk loci compared to the power achieved by standard methods in case-control studies. At imputed SNPs, we observe an 11% increase in statistical power for mapping disease loci when our local ancestry-aware imputation framework and the new scoring statistic are jointly employed. Finally, we show that our method increases statistical power in regions harboring the causal SNP in the case when the causal SNP is untyped and cannot be imputed. Our methods and our publicly available software are broadly applicable to GWAS in admixed populations.

%B PLoS Genet %V 7 %P e1001371 %8 2011 Apr %G eng %N 4 %1 http://www.ncbi.nlm.nih.gov/pubmed/21541012?dopt=Abstract %R 10.1371/journal.pgen.1001371 %0 Journal Article %J Atherosclerosis %D 2012 %T Genetic determinants of the ankle-brachial index: a meta-analysis of a cardiovascular candidate gene 50K SNP panel in the candidate gene association resource (CARe) consortium. %A Wassel, Christina L %A Lamina, Claudia %A Nambi, Vijay %A Coassin, Stefan %A Mukamal, Kenneth J %A Ganesh, Santhi K %A Jacobs, David R %A Franceschini, Nora %A Papanicolaou, George J %A Gibson, Quince %A Yanek, Lisa R %A van der Harst, Pim %A Ferguson, Jane F %A Crawford, Dana C %A Waite, Lindsay L %A Allison, Matthew A %A Criqui, Michael H %A McDermott, Mary M %A Mehra, Reena %A Cupples, L Adrienne %A Hwang, Shih-Jen %A Redline, Susan %A Kaplan, Robert C %A Heiss, Gerardo %A Rotter, Jerome I %A Boerwinkle, Eric %A Taylor, Herman A %A Eraso, Luis H %A Haun, Margot %A Li, Mingyao %A Meisinger, Christa %A O'Connell, Jeffrey R %A Shuldiner, Alan R %A Tybjærg-Hansen, Anne %A Frikke-Schmidt, Ruth %A Kollerits, Barbara %A Rantner, Barbara %A Dieplinger, Benjamin %A Stadler, Marietta %A Mueller, Thomas %A Haltmayer, Meinhard %A Klein-Weigel, Peter %A Summerer, Monika %A Wichmann, H-Erich %A Asselbergs, Folkert W %A Navis, Gerjan %A Mateo Leach, Irene %A Brown-Gentry, Kristin %A Goodloe, Robert %A Assimes, Themistocles L %A Becker, Diane M %A Cooke, John P %A Absher, Devin M %A Olin, Jeffrey W %A Mitchell, Braxton D %A Reilly, Muredach P %A Mohler, Emile R %A North, Kari E %A Reiner, Alexander P %A Kronenberg, Florian %A Murabito, Joanne M %K Adult %K African Americans %K Aged %K Ankle Brachial Index %K Aryl Hydrocarbon Hydroxylases %K Cytochrome P-450 CYP2B6 %K European Continental Ancestry Group %K Female %K Humans %K Male %K Middle Aged %K Oxidoreductases, N-Demethylating %K Peripheral Arterial Disease %K Polymorphism, Single Nucleotide %K Risk Factors %K Transcription Factor 7-Like 2 Protein %X

BACKGROUND: Candidate gene association studies for peripheral artery disease (PAD), including subclinical disease assessed with the ankle-brachial index (ABI), have been limited by the modest number of genes examined. We conducted a two stage meta-analysis of ∼50,000 SNPs across ∼2100 candidate genes to identify genetic variants for ABI.

METHODS AND RESULTS: We studied subjects of European ancestry from 8 studies (n=21,547, 55% women, mean age 44-73 years) and African American ancestry from 5 studies (n=7267, 60% women, mean age 41-73 years) involved in the candidate gene association resource (CARe) consortium. In each ethnic group, additive genetic models were used (with each additional copy of the minor allele corresponding to the given beta) to test each SNP for association with continuous ABI (excluding ABI>1.40) and PAD (defined as ABI<0.90) using linear or logistic regression with adjustment for known PAD risk factors and population stratification. We then conducted a fixed-effects inverse-variance weighted meta-analyses considering a p<2×10(-6) to denote statistical significance.

RESULTS: In the European ancestry discovery meta-analyses, rs2171209 in SYTL3 (β=-0.007, p=6.02×10(-7)) and rs290481 in TCF7L2 (β=-0.008, p=7.01×10(-7)) were significantly associated with ABI. None of the SNP associations for PAD were significant, though a SNP in CYP2B6 (p=4.99×10(-5)) was among the strongest associations. These 3 genes are linked to key PAD risk factors (lipoprotein(a), type 2 diabetes, and smoking behavior, respectively). We sought replication in 6 population-based and 3 clinical samples (n=15,440) for rs290481 and rs2171209. However, in the replication stage (rs2171209, p=0.75; rs290481, p=0.19) and in the combined discovery and replication analysis the SNP-ABI associations were no longer significant (rs2171209, p=1.14×10(-3); rs290481, p=8.88×10(-5)). In African Americans, none of the SNP associations for ABI or PAD achieved an experiment-wide level of significance.

CONCLUSIONS: Genetic determinants of ABI and PAD remain elusive. Follow-up of these preliminary findings may uncover important biology given the known gene-risk factor associations. New and more powerful approaches to PAD gene discovery are warranted.

%B Atherosclerosis %V 222 %P 138-47 %8 2012 May %G eng %N 1 %1 http://www.ncbi.nlm.nih.gov/pubmed/22361517?dopt=Abstract %R 10.1016/j.atherosclerosis.2012.01.039 %0 Journal Article %J PLoS One %D 2012 %T Multi-ethnic analysis of lipid-associated loci: the NHLBI CARe project. %A Musunuru, Kiran %A Romaine, Simon P R %A Lettre, Guillaume %A Wilson, James G %A Volcik, Kelly A %A Tsai, Michael Y %A Taylor, Herman A %A Schreiner, Pamela J %A Rotter, Jerome I %A Rich, Stephen S %A Redline, Susan %A Psaty, Bruce M %A Papanicolaou, George J %A Ordovas, Jose M %A Liu, Kiang %A Krauss, Ronald M %A Glazer, Nicole L %A Gabriel, Stacey B %A Fornage, Myriam %A Cupples, L Adrienne %A Buxbaum, Sarah G %A Boerwinkle, Eric %A Ballantyne, Christie M %A Kathiresan, Sekar %A Rader, Daniel J %K African Americans %K Cholesterol, HDL %K Cholesterol, LDL %K European Continental Ancestry Group %K Genetic Association Studies %K Genetic Loci %K Humans %K Polymorphism, Single Nucleotide %K Triglycerides %X

BACKGROUND: Whereas it is well established that plasma lipid levels have substantial heritability within populations, it remains unclear how many of the genetic determinants reported in previous studies (largely performed in European American cohorts) are relevant in different ethnicities.

METHODOLOGY/PRINCIPAL FINDINGS: We tested a set of ∼50,000 polymorphisms from ∼2,000 candidate genes and genetic loci from genome-wide association studies (GWAS) for association with low-density lipoprotein cholesterol (LDL-C), high-density lipoprotein cholesterol (HDL-C), and triglycerides (TG) in 25,000 European Americans and 9,000 African Americans in the National Heart, Lung, and Blood Institute (NHLBI) Candidate Gene Association Resource (CARe). We replicated associations for a number of genes in one or both ethnicities and identified a novel lipid-associated variant in a locus harboring ICAM1. We compared the architecture of genetic loci associated with lipids in both African Americans and European Americans and found that the same genes were relevant across ethnic groups but the specific associated variants at each gene often differed.

CONCLUSIONS/SIGNIFICANCE: We identify or provide further evidence for a number of genetic determinants of plasma lipid levels through population association studies. In many loci the determinants appear to differ substantially between African Americans and European Americans.

%B PLoS One %V 7 %P e36473 %8 2012 %G eng %N 5 %1 http://www.ncbi.nlm.nih.gov/pubmed/22629316?dopt=Abstract %R 10.1371/journal.pone.0036473 %0 Journal Article %J Genetics %D 2012 %T Ultraconserved elements in the human genome: association and transmission analyses of highly constrained single-nucleotide polymorphisms. %A Chiang, Charleston W K %A Liu, Ching-Ti %A Lettre, Guillaume %A Lange, Leslie A %A Jorgensen, Neal W %A Keating, Brendan J %A Vedantam, Sailaja %A Nock, Nora L %A Franceschini, Nora %A Reiner, Alex P %A Demerath, Ellen W %A Boerwinkle, Eric %A Rotter, Jerome I %A Wilson, James G %A North, Kari E %A Papanicolaou, George J %A Cupples, L Adrienne %A Murabito, Joanne M %A Hirschhorn, Joel N %K Alleles %K Animals %K Body Height %K Body Mass Index %K Child %K Conserved Sequence %K Dogs %K Evolution, Molecular %K Female %K Genetic Fitness %K Genetic Variation %K Genome, Human %K Genotype %K Humans %K Inheritance Patterns %K Male %K Mice %K Pedigree %K Phenotype %K Polymorphism, Single Nucleotide %K Rats %K Reproduction %K Young Adult %X

Ultraconserved elements in the human genome likely harbor important biological functions as they are dosage sensitive and are able to direct tissue-specific expression. Because they are under purifying selection, variants in these elements may have a lower frequency in the population but a higher likelihood of association with complex traits. We tested a set of highly constrained SNPs (hcSNPs) distributed genome-wide among ultraconserved and nearly ultraconserved elements for association with seven traits related to reproductive (age at natural menopause, number of children, age at first child, and age at last child) and overall [longevity, body mass index (BMI), and height] fitness. Using up to 24,047 European-American samples from the National Heart, Lung, and Blood Institute Candidate Gene Association Resource (CARe), we observed an excess of associations with BMI and height. In an independent replication panel the most strongly associated SNPs showed an 8.4-fold enrichment of associations at the nominal level, including three variants in previously identified loci and one in a locus (DENND1A) previously shown to be associated with polycystic ovary syndrome. Finally, using 1430 family trios, we showed that the transmissions from heterozygous parents to offspring of the derived alleles of rare (frequency ≤ 0.5%) hcSNPs are not biased, particularly after adjusting for the rates of genotype missingness and error in the data. The lack of transmission bias ruled out an immediately and strongly deleterious effect due to the rare derived alleles, consistent with the observation that mice homozygous for the deletion of ultraconserved elements showed no overt phenotype. Our study also illustrated the importance of carefully modeling potential technical confounders when analyzing genotype data of rare variants.

%B Genetics %V 192 %P 253-66 %8 2012 Sep %G eng %N 1 %1 http://www.ncbi.nlm.nih.gov/pubmed/22714408?dopt=Abstract %R 10.1534/genetics.112.141945 %0 Journal Article %J J Clin Psychopharmacol %D 2013 %T Genetic analysis of a population heavy drinking phenotype identifies risk variants in whites. %A Hamidovic, Ajna %A Goodloe, Robert J %A Young, Taylor R %A Styn, Mindi A %A Mukamal, Kenneth J %A Choquet, Helene %A Kasberger, Jay L %A Buxbaum, Sarah G %A Papanicolaou, George J %A White, Wendy %A Volcik, Kelly %A Spring, Bonnie %A Hitsman, Brian %A Levy, Daniel %A Jorgenson, Eric %K Aged %K Alcohol Drinking %K Alcoholism %K Case-Control Studies %K European Continental Ancestry Group %K Feasibility Studies %K Genetic Association Studies %K Genetic Loci %K Genetic Predisposition to Disease %K Genetic Variation %K Humans %K Incidence %K Male %K Middle Aged %K Phenotype %K Polymorphism, Single Nucleotide %K Risk %X

Genetic association studies thus far have used detailed diagnoses of alcoholism to identify loci associated with risk. This proof-of-concept analysis examined whether population data of lifetime heaviest alcohol consumption may be used to identify genetic loci that modulate risk. We conducted a genetic association study in European Americans between variants in approximately 2100 genes and alcohol consumption as part of the Candidate gene Association Resource project. We defined cases as individuals with a history of drinking 5 or more drinks per day almost every day of the week and controls as current light drinkers (1-5 drinks per week). We cross-validated identified single nucleotide polymorphisms in a meta-analysis of 2 cohorts of unrelated individuals--Atherosclerosis Risk in Communities (ARIC) and Cardiovascular Health Study (CHS)--and in a separate cohort of related individuals--Framingham Heart Study (FHS). The most significant variant in the meta-analysis of ARIC and CHS was rs6933598 in methylenetetrahydrofolate dehydrogenase (P = 7.46 × 10(-05)) with a P value in FHS of 0.042. The top variants in FHS were rs12249562 in cubulin (P = 3.03 × 10(-05)) and rs9839267 near cholecystokinin (P = 3.05 × 10(-05)) with a P value of 0.019 for rs9839267 in CHS. We have here shown feasibility in evaluating lifetime incidence of heavy alcohol drinking from population-based studies for the purpose of conducting genetic association analyses.

%B J Clin Psychopharmacol %V 33 %P 206-10 %8 2013 Apr %G eng %N 2 %1 http://www.ncbi.nlm.nih.gov/pubmed/23422394?dopt=Abstract %& 206 %R 10.1097/JCP.0b013e318287009a %0 Journal Article %J PLoS Genet %D 2013 %T Genome-wide association of body fat distribution in African ancestry populations suggests new loci. %A Liu, Ching-Ti %A Monda, Keri L %A Taylor, Kira C %A Lange, Leslie %A Demerath, Ellen W %A Palmas, Walter %A Wojczynski, Mary K %A Ellis, Jaclyn C %A Vitolins, Mara Z %A Liu, Simin %A Papanicolaou, George J %A Irvin, Marguerite R %A Xue, Luting %A Griffin, Paula J %A Nalls, Michael A %A Adeyemo, Adebowale %A Liu, Jiankang %A Li, Guo %A Ruiz-Narvaez, Edward A %A Chen, Wei-Min %A Chen, Fang %A Henderson, Brian E %A Millikan, Robert C %A Ambrosone, Christine B %A Strom, Sara S %A Guo, Xiuqing %A Andrews, Jeanette S %A Sun, Yan V %A Mosley, Thomas H %A Yanek, Lisa R %A Shriner, Daniel %A Haritunians, Talin %A Rotter, Jerome I %A Speliotes, Elizabeth K %A Smith, Megan %A Rosenberg, Lynn %A Mychaleckyj, Josyf %A Nayak, Uma %A Spruill, Ida %A Garvey, W Timothy %A Pettaway, Curtis %A Nyante, Sarah %A Bandera, Elisa V %A Britton, Angela F %A Zonderman, Alan B %A Rasmussen-Torvik, Laura J %A Chen, Yii-Der Ida %A Ding, Jingzhong %A Lohman, Kurt %A Kritchevsky, Stephen B %A Zhao, Wei %A Peyser, Patricia A %A Kardia, Sharon L R %A Kabagambe, Edmond %A Broeckel, Ulrich %A Chen, Guanjie %A Zhou, Jie %A Wassertheil-Smoller, Sylvia %A Neuhouser, Marian L %A Rampersaud, Evadnie %A Psaty, Bruce %A Kooperberg, Charles %A Manson, JoAnn E %A Kuller, Lewis H %A Ochs-Balcom, Heather M %A Johnson, Karen C %A Sucheston, Lara %A Ordovas, Jose M %A Palmer, Julie R %A Haiman, Christopher A %A McKnight, Barbara %A Howard, Barbara V %A Becker, Diane M %A Bielak, Lawrence F %A Liu, Yongmei %A Allison, Matthew A %A Grant, Struan F A %A Burke, Gregory L %A Patel, Sanjay R %A Schreiner, Pamela J %A Borecki, Ingrid B %A Evans, Michele K %A Taylor, Herman %A Sale, Michèle M %A Howard, Virginia %A Carlson, Christopher S %A Rotimi, Charles N %A Cushman, Mary %A Harris, Tamara B %A Reiner, Alexander P %A Cupples, L Adrienne %A North, Kari E %A Fox, Caroline S %K Adiposity %K African Continental Ancestry Group %K Body Fat Distribution %K European Continental Ancestry Group %K Female %K Genetic Loci %K Genome-Wide Association Study %K Humans %K Male %K Obesity %K Polymorphism, Single Nucleotide %K Waist-Hip Ratio %X

Central obesity, measured by waist circumference (WC) or waist-hip ratio (WHR), is a marker of body fat distribution. Although obesity disproportionately affects minority populations, few studies have conducted genome-wide association study (GWAS) of fat distribution among those of predominantly African ancestry (AA). We performed GWAS of WC and WHR, adjusted and unadjusted for BMI, in up to 33,591 and 27,350 AA individuals, respectively. We identified loci associated with fat distribution in AA individuals using meta-analyses of GWA results for WC and WHR (stage 1). Overall, 25 SNPs with single genomic control (GC)-corrected p-values<5.0 × 10(-6) were followed-up (stage 2) in AA with WC and with WHR. Additionally, we interrogated genomic regions of previously identified European ancestry (EA) WHR loci among AA. In joint analysis of association results including both Stage 1 and 2 cohorts, 2 SNPs demonstrated association, rs2075064 at LHX2, p = 2.24×10(-8) for WC-adjusted-for-BMI, and rs6931262 at RREB1, p = 2.48×10(-8) for WHR-adjusted-for-BMI. However, neither signal was genome-wide significant after double GC-correction (LHX2: p = 6.5 × 10(-8); RREB1: p = 5.7 × 10(-8)). Six of fourteen previously reported loci for waist in EA populations were significant (p<0.05 divided by the number of independent SNPs within the region) in AA studied here (TBX15-WARS2, GRB14, ADAMTS9, LY86, RSPO3, ITPR2-SSPN). Further, we observed associations with metabolic traits: rs13389219 at GRB14 associated with HDL-cholesterol, triglycerides, and fasting insulin, and rs13060013 at ADAMTS9 with HDL-cholesterol and fasting insulin. Finally, we observed nominal evidence for sexual dimorphism, with stronger results in AA women at the GRB14 locus (p for interaction = 0.02). In conclusion, we identified two suggestive loci associated with fat distribution in AA populations in addition to confirming 6 loci previously identified in populations of EA. These findings reinforce the concept that there are fat distribution loci that are independent of generalized adiposity.

%B PLoS Genet %V 9 %P e1003681 %8 2013 %G eng %N 8 %1 http://www.ncbi.nlm.nih.gov/pubmed/23966867?dopt=Abstract %R 10.1371/journal.pgen.1003681 %0 Journal Article %J Nat Genet %D 2013 %T A meta-analysis identifies new loci associated with body mass index in individuals of African ancestry. %A Monda, Keri L %A Chen, Gary K %A Taylor, Kira C %A Palmer, Cameron %A Edwards, Todd L %A Lange, Leslie A %A Ng, Maggie C Y %A Adeyemo, Adebowale A %A Allison, Matthew A %A Bielak, Lawrence F %A Chen, Guanjie %A Graff, Mariaelisa %A Irvin, Marguerite R %A Rhie, Suhn K %A Li, Guo %A Liu, Yongmei %A Liu, Youfang %A Lu, Yingchang %A Nalls, Michael A %A Sun, Yan V %A Wojczynski, Mary K %A Yanek, Lisa R %A Aldrich, Melinda C %A Ademola, Adeyinka %A Amos, Christopher I %A Bandera, Elisa V %A Bock, Cathryn H %A Britton, Angela %A Broeckel, Ulrich %A Cai, Quiyin %A Caporaso, Neil E %A Carlson, Chris S %A Carpten, John %A Casey, Graham %A Chen, Wei-Min %A Chen, Fang %A Chen, Yii-der I %A Chiang, Charleston W K %A Coetzee, Gerhard A %A Demerath, Ellen %A Deming-Halverson, Sandra L %A Driver, Ryan W %A Dubbert, Patricia %A Feitosa, Mary F %A Feng, Ye %A Freedman, Barry I %A Gillanders, Elizabeth M %A Gottesman, Omri %A Guo, Xiuqing %A Haritunians, Talin %A Harris, Tamara %A Harris, Curtis C %A Hennis, Anselm J M %A Hernandez, Dena G %A McNeill, Lorna H %A Howard, Timothy D %A Howard, Barbara V %A Howard, Virginia J %A Johnson, Karen C %A Kang, Sun J %A Keating, Brendan J %A Kolb, Suzanne %A Kuller, Lewis H %A Kutlar, Abdullah %A Langefeld, Carl D %A Lettre, Guillaume %A Lohman, Kurt %A Lotay, Vaneet %A Lyon, Helen %A Manson, JoAnn E %A Maixner, William %A Meng, Yan A %A Monroe, Kristine R %A Morhason-Bello, Imran %A Murphy, Adam B %A Mychaleckyj, Josyf C %A Nadukuru, Rajiv %A Nathanson, Katherine L %A Nayak, Uma %A N'diaye, Amidou %A Nemesure, Barbara %A Wu, Suh-Yuh %A Leske, M Cristina %A Neslund-Dudas, Christine %A Neuhouser, Marian %A Nyante, Sarah %A Ochs-Balcom, Heather %A Ogunniyi, Adesola %A Ogundiran, Temidayo O %A Ojengbede, Oladosu %A Olopade, Olufunmilayo I %A Palmer, Julie R %A Ruiz-Narvaez, Edward A %A Palmer, Nicholette D %A Press, Michael F %A Rampersaud, Evandine %A Rasmussen-Torvik, Laura J %A Rodriguez-Gil, Jorge L %A Salako, Babatunde %A Schadt, Eric E %A Schwartz, Ann G %A Shriner, Daniel A %A Siscovick, David %A Smith, Shad B %A Wassertheil-Smoller, Sylvia %A Speliotes, Elizabeth K %A Spitz, Margaret R %A Sucheston, Lara %A Taylor, Herman %A Tayo, Bamidele O %A Tucker, Margaret A %A Van Den Berg, David J %A Edwards, Digna R Velez %A Wang, Zhaoming %A Wiencke, John K %A Winkler, Thomas W %A Witte, John S %A Wrensch, Margaret %A Wu, Xifeng %A Yang, James J %A Levin, Albert M %A Young, Taylor R %A Zakai, Neil A %A Cushman, Mary %A Zanetti, Krista A %A Zhao, Jing Hua %A Zhao, Wei %A Zheng, Yonglan %A Zhou, Jie %A Ziegler, Regina G %A Zmuda, Joseph M %A Fernandes, Jyotika K %A Gilkeson, Gary S %A Kamen, Diane L %A Hunt, Kelly J %A Spruill, Ida J %A Ambrosone, Christine B %A Ambs, Stefan %A Arnett, Donna K %A Atwood, Larry %A Becker, Diane M %A Berndt, Sonja I %A Bernstein, Leslie %A Blot, William J %A Borecki, Ingrid B %A Bottinger, Erwin P %A Bowden, Donald W %A Burke, Gregory %A Chanock, Stephen J %A Cooper, Richard S %A Ding, Jingzhong %A Duggan, David %A Evans, Michele K %A Fox, Caroline %A Garvey, W Timothy %A Bradfield, Jonathan P %A Hakonarson, Hakon %A Grant, Struan F A %A Hsing, Ann %A Chu, Lisa %A Hu, Jennifer J %A Huo, Dezheng %A Ingles, Sue A %A John, Esther M %A Jordan, Joanne M %A Kabagambe, Edmond K %A Kardia, Sharon L R %A Kittles, Rick A %A Goodman, Phyllis J %A Klein, Eric A %A Kolonel, Laurence N %A Le Marchand, Loïc %A Liu, Simin %A McKnight, Barbara %A Millikan, Robert C %A Mosley, Thomas H %A Padhukasahasram, Badri %A Williams, L Keoki %A Patel, Sanjay R %A Peters, Ulrike %A Pettaway, Curtis A %A Peyser, Patricia A %A Psaty, Bruce M %A Redline, Susan %A Rotimi, Charles N %A Rybicki, Benjamin A %A Sale, Michèle M %A Schreiner, Pamela J %A Signorello, Lisa B %A Singleton, Andrew B %A Stanford, Janet L %A Strom, Sara S %A Thun, Michael J %A Vitolins, Mara %A Zheng, Wei %A Moore, Jason H %A Williams, Scott M %A Ketkar, Shamika %A Zhu, Xiaofeng %A Zonderman, Alan B %A Kooperberg, Charles %A Papanicolaou, George J %A Henderson, Brian E %A Reiner, Alex P %A Hirschhorn, Joel N %A Loos, Ruth J F %A North, Kari E %A Haiman, Christopher A %K African Americans %K Body Mass Index %K Case-Control Studies %K Gene Frequency %K Genetic Loci %K Genetic Predisposition to Disease %K Genome-Wide Association Study %K Humans %K Linkage Disequilibrium %K Obesity %K Polymorphism, Single Nucleotide %X

Genome-wide association studies (GWAS) have identified 36 loci associated with body mass index (BMI), predominantly in populations of European ancestry. We conducted a meta-analysis to examine the association of >3.2 million SNPs with BMI in 39,144 men and women of African ancestry and followed up the most significant associations in an additional 32,268 individuals of African ancestry. We identified one new locus at 5q33 (GALNT10, rs7708584, P = 3.4 × 10(-11)) and another at 7p15 when we included data from the GIANT consortium (MIR148A-NFE2L3, rs10261878, P = 1.2 × 10(-10)). We also found suggestive evidence of an association at a third locus at 6q16 in the African-ancestry sample (KLHL32, rs974417, P = 6.9 × 10(-8)). Thirty-two of the 36 previously established BMI variants showed directionally consistent effect estimates in our GWAS (binomial P = 9.7 × 10(-7)), five of which reached genome-wide significance. These findings provide strong support for shared BMI loci across populations, as well as for the utility of studying ancestrally diverse populations.

%B Nat Genet %V 45 %P 690-6 %8 2013 Jun %G eng %N 6 %1 http://www.ncbi.nlm.nih.gov/pubmed/23583978?dopt=Abstract %R 10.1038/ng.2608 %0 Journal Article %J Hum Genet %D 2014 %T Large multiethnic Candidate Gene Study for C-reactive protein levels: identification of a novel association at CD36 in African Americans. %A Ellis, Jaclyn %A Lange, Ethan M %A Li, Jin %A Dupuis, Josée %A Baumert, Jens %A Walston, Jeremy D %A Keating, Brendan J %A Durda, Peter %A Fox, Ervin R %A Palmer, Cameron D %A Meng, Yan A %A Young, Taylor %A Farlow, Deborah N %A Schnabel, Renate B %A Marzi, Carola S %A Larkin, Emma %A Martin, Lisa W %A Bis, Joshua C %A Auer, Paul %A Ramachandran, Vasan S %A Gabriel, Stacey B %A Willis, Monte S %A Pankow, James S %A Papanicolaou, George J %A Rotter, Jerome I %A Ballantyne, Christie M %A Gross, Myron D %A Lettre, Guillaume %A Wilson, James G %A Peters, Ulrike %A Koenig, Wolfgang %A Tracy, Russell P %A Redline, Susan %A Reiner, Alex P %A Benjamin, Emelia J %A Lange, Leslie A %K Adult %K African Americans %K Aged %K Biomarkers %K C-Reactive Protein %K Cardiovascular Diseases %K CD36 Antigens %K Female %K Genetic Loci %K Genetic Predisposition to Disease %K Genetics, Population %K Genome-Wide Association Study %K Humans %K Meta-Analysis as Topic %K Middle Aged %K Polymorphism, Single Nucleotide %K Risk Factors %X

C-reactive protein (CRP) is a heritable biomarker of systemic inflammation and a predictor of cardiovascular disease (CVD). Large-scale genetic association studies for CRP have largely focused on individuals of European descent. We sought to uncover novel genetic variants for CRP in a multiethnic sample using the ITMAT Broad-CARe (IBC) array, a custom 50,000 SNP gene-centric array having dense coverage of over 2,000 candidate CVD genes. We performed analyses on 7,570 African Americans (AA) from the Candidate gene Association Resource (CARe) study and race-combined meta-analyses that included 29,939 additional individuals of European descent from CARe, the Women's Health Initiative (WHI) and KORA studies. We observed array-wide significance (p < 2.2 × 10(-6)) for four loci in AA, three of which have been reported previously in individuals of European descent (IL6R, p = 2.0 × 10(-6); CRP, p = 4.2 × 10(-71); APOE, p = 1.6 × 10(-6)). The fourth significant locus, CD36 (p = 1.6 × 10(-6)), was observed at a functional variant (rs3211938) that is extremely rare in individuals of European descent. We replicated the CD36 finding (p = 1.8 × 10(-5)) in an independent sample of 8,041 AA women from WHI; a meta-analysis combining the CARe and WHI AA results at rs3211938 reached genome-wide significance (p = 1.5 × 10(-10)). In the race-combined meta-analyses, 13 loci reached significance, including ten (CRP, TOMM40/APOE/APOC1, HNF1A, LEPR, GCKR, IL6R, IL1RN, NLRP3, HNF4A and BAZ1B/BCL7B) previously associated with CRP, and one (ARNTL) previously reported to be nominally associated with CRP. Two novel loci were also detected (RPS6KB1, p = 2.0 × 10(-6); CD36, p = 1.4 × 10(-6)). These results highlight both shared and unique genetic risk factors for CRP in AA compared to populations of European descent.

%B Hum Genet %V 133 %P 985-95 %8 2014 Aug %G eng %N 8 %1 http://www.ncbi.nlm.nih.gov/pubmed/24643644?dopt=Abstract %R 10.1007/s00439-014-1439-z %0 Journal Article %J Nat Genet %D 2016 %T Meta-analysis identifies common and rare variants influencing blood pressure and overlapping with metabolic trait loci. %A Liu, Chunyu %A Kraja, Aldi T %A Smith, Jennifer A %A Brody, Jennifer A %A Franceschini, Nora %A Bis, Joshua C %A Rice, Kenneth %A Morrison, Alanna C %A Lu, Yingchang %A Weiss, Stefan %A Guo, Xiuqing %A Palmas, Walter %A Martin, Lisa W %A Chen, Yii-Der Ida %A Surendran, Praveen %A Drenos, Fotios %A Cook, James P %A Auer, Paul L %A Chu, Audrey Y %A Giri, Ayush %A Zhao, Wei %A Jakobsdottir, Johanna %A Lin, Li-An %A Stafford, Jeanette M %A Amin, Najaf %A Mei, Hao %A Yao, Jie %A Voorman, Arend %A Larson, Martin G %A Grove, Megan L %A Smith, Albert V %A Hwang, Shih-Jen %A Chen, Han %A Huan, Tianxiao %A Kosova, Gulum %A Stitziel, Nathan O %A Kathiresan, Sekar %A Samani, Nilesh %A Schunkert, Heribert %A Deloukas, Panos %A Li, Man %A Fuchsberger, Christian %A Pattaro, Cristian %A Gorski, Mathias %A Kooperberg, Charles %A Papanicolaou, George J %A Rossouw, Jacques E %A Faul, Jessica D %A Kardia, Sharon L R %A Bouchard, Claude %A Raffel, Leslie J %A Uitterlinden, André G %A Franco, Oscar H %A Vasan, Ramachandran S %A O'Donnell, Christopher J %A Taylor, Kent D %A Liu, Kiang %A Bottinger, Erwin P %A Gottesman, Omri %A Daw, E Warwick %A Giulianini, Franco %A Ganesh, Santhi %A Salfati, Elias %A Harris, Tamara B %A Launer, Lenore J %A Dörr, Marcus %A Felix, Stephan B %A Rettig, Rainer %A Völzke, Henry %A Kim, Eric %A Lee, Wen-Jane %A Lee, I-Te %A Sheu, Wayne H-H %A Tsosie, Krystal S %A Edwards, Digna R Velez %A Liu, Yongmei %A Correa, Adolfo %A Weir, David R %A Völker, Uwe %A Ridker, Paul M %A Boerwinkle, Eric %A Gudnason, Vilmundur %A Reiner, Alexander P %A van Duijn, Cornelia M %A Borecki, Ingrid B %A Edwards, Todd L %A Chakravarti, Aravinda %A Rotter, Jerome I %A Psaty, Bruce M %A Loos, Ruth J F %A Fornage, Myriam %A Ehret, Georg B %A Newton-Cheh, Christopher %A Levy, Daniel %A Chasman, Daniel I %X

Meta-analyses of association results for blood pressure using exome-centric single-variant and gene-based tests identified 31 new loci in a discovery stage among 146,562 individuals, with follow-up and meta-analysis in 180,726 additional individuals (total n = 327,288). These blood pressure-associated loci are enriched for known variants for cardiometabolic traits. Associations were also observed for the aggregation of rare and low-frequency missense variants in three genes, NPR1, DBH, and PTPMT1. In addition, blood pressure associations at 39 previously reported loci were confirmed. The identified variants implicate biological pathways related to cardiometabolic traits, vascular function, and development. Several new variants are inferred to have roles in transcription or as hubs in protein-protein interaction networks. Genetic risk scores constructed from the identified variants were strongly associated with coronary disease and myocardial infarction. This large collection of blood pressure-associated loci suggests new therapeutic strategies for hypertension, emphasizing a link with cardiometabolic risk.

%B Nat Genet %V 48 %P 1162-70 %8 2016 Oct %G eng %N 10 %R 10.1038/ng.3660 %0 Journal Article %J Nat Genet %D 2017 %T Analysis commons, a team approach to discovery in a big-data environment for genetic epidemiology. %A Brody, Jennifer A %A Morrison, Alanna C %A Bis, Joshua C %A O'Connell, Jeffrey R %A Brown, Michael R %A Huffman, Jennifer E %A Ames, Darren C %A Carroll, Andrew %A Conomos, Matthew P %A Gabriel, Stacey %A Gibbs, Richard A %A Gogarten, Stephanie M %A Gupta, Namrata %A Jaquish, Cashell E %A Johnson, Andrew D %A Lewis, Joshua P %A Liu, Xiaoming %A Manning, Alisa K %A Papanicolaou, George J %A Pitsillides, Achilleas N %A Rice, Kenneth M %A Salerno, William %A Sitlani, Colleen M %A Smith, Nicholas L %A Heckbert, Susan R %A Laurie, Cathy C %A Mitchell, Braxton D %A Vasan, Ramachandran S %A Rich, Stephen S %A Rotter, Jerome I %A Wilson, James G %A Boerwinkle, Eric %A Psaty, Bruce M %A Cupples, L Adrienne %B Nat Genet %V 49 %P 1560-1563 %8 2017 Oct 27 %G eng %N 11 %R 10.1038/ng.3968 %0 Journal Article %J PLoS Genet %D 2017 %T Single-trait and multi-trait genome-wide association analyses identify novel loci for blood pressure in African-ancestry populations. %A Liang, Jingjing %A Le, Thu H %A Edwards, Digna R Velez %A Tayo, Bamidele O %A Gaulton, Kyle J %A Smith, Jennifer A %A Lu, Yingchang %A Jensen, Richard A %A Chen, Guanjie %A Yanek, Lisa R %A Schwander, Karen %A Tajuddin, Salman M %A Sofer, Tamar %A Kim, Wonji %A Kayima, James %A McKenzie, Colin A %A Fox, Ervin %A Nalls, Michael A %A Young, J Hunter %A Sun, Yan V %A Lane, Jacqueline M %A Cechova, Sylvia %A Zhou, Jie %A Tang, Hua %A Fornage, Myriam %A Musani, Solomon K %A Wang, Heming %A Lee, Juyoung %A Adeyemo, Adebowale %A Dreisbach, Albert W %A Forrester, Terrence %A Chu, Pei-Lun %A Cappola, Anne %A Evans, Michele K %A Morrison, Alanna C %A Martin, Lisa W %A Wiggins, Kerri L %A Hui, Qin %A Zhao, Wei %A Jackson, Rebecca D %A Ware, Erin B %A Faul, Jessica D %A Reiner, Alex P %A Bray, Michael %A Denny, Joshua C %A Mosley, Thomas H %A Palmas, Walter %A Guo, Xiuqing %A Papanicolaou, George J %A Penman, Alan D %A Polak, Joseph F %A Rice, Kenneth %A Taylor, Ken D %A Boerwinkle, Eric %A Bottinger, Erwin P %A Liu, Kiang %A Risch, Neil %A Hunt, Steven C %A Kooperberg, Charles %A Zonderman, Alan B %A Laurie, Cathy C %A Becker, Diane M %A Cai, Jianwen %A Loos, Ruth J F %A Psaty, Bruce M %A Weir, David R %A Kardia, Sharon L R %A Arnett, Donna K %A Won, Sungho %A Edwards, Todd L %A Redline, Susan %A Cooper, Richard S %A Rao, D C %A Rotter, Jerome I %A Rotimi, Charles %A Levy, Daniel %A Chakravarti, Aravinda %A Zhu, Xiaofeng %A Franceschini, Nora %K African Americans %K Animals %K Basic Helix-Loop-Helix Transcription Factors %K Blood Pressure %K Cadherins %K Case-Control Studies %K Female %K Genetic Loci %K Genome-Wide Association Study %K Humans %K Hypertension %K Male %K Membrane Proteins %K Mice %K Multifactorial Inheritance %K Polymorphism, Single Nucleotide %X

Hypertension is a leading cause of global disease, mortality, and disability. While individuals of African descent suffer a disproportionate burden of hypertension and its complications, they have been underrepresented in genetic studies. To identify novel susceptibility loci for blood pressure and hypertension in people of African ancestry, we performed both single and multiple-trait genome-wide association analyses. We analyzed 21 genome-wide association studies comprised of 31,968 individuals of African ancestry, and validated our results with additional 54,395 individuals from multi-ethnic studies. These analyses identified nine loci with eleven independent variants which reached genome-wide significance (P < 1.25×10-8) for either systolic and diastolic blood pressure, hypertension, or for combined traits. Single-trait analyses identified two loci (TARID/TCF21 and LLPH/TMBIM4) and multiple-trait analyses identified one novel locus (FRMD3) for blood pressure. At these three loci, as well as at GRP20/CDH17, associated variants had alleles common only in African-ancestry populations. Functional annotation showed enrichment for genes expressed in immune and kidney cells, as well as in heart and vascular cells/tissues. Experiments driven by these findings and using angiotensin-II induced hypertension in mice showed altered kidney mRNA expression of six genes, suggesting their potential role in hypertension. Our study provides new evidence for genes related to hypertension susceptibility, and the need to study African-ancestry populations in order to identify biologic factors contributing to hypertension.

%B PLoS Genet %V 13 %P e1006728 %8 2017 May %G eng %N 5 %R 10.1371/journal.pgen.1006728 %0 Journal Article %J Am J Respir Cell Mol Biol %D 2018 %T Multiethnic Meta-Analysis Identifies RAI1 as a Possible Obstructive Sleep Apnea-related Quantitative Trait Locus in Men. %A Chen, Han %A Cade, Brian E %A Gleason, Kevin J %A Bjonnes, Andrew C %A Stilp, Adrienne M %A Sofer, Tamar %A Conomos, Matthew P %A Ancoli-Israel, Sonia %A Arens, Raanan %A Azarbarzin, Ali %A Bell, Graeme I %A Below, Jennifer E %A Chun, Sung %A Evans, Daniel S %A Ewert, Ralf %A Frazier-Wood, Alexis C %A Gharib, Sina A %A Haba-Rubio, José %A Hagen, Erika W %A Heinzer, Raphael %A Hillman, David R %A Johnson, W Craig %A Kutalik, Zoltán %A Lane, Jacqueline M %A Larkin, Emma K %A Lee, Seung Ku %A Liang, Jingjing %A Loredo, Jose S %A Mukherjee, Sutapa %A Palmer, Lyle J %A Papanicolaou, George J %A Penzel, Thomas %A Peppard, Paul E %A Post, Wendy S %A Ramos, Alberto R %A Rice, Ken %A Rotter, Jerome I %A Sands, Scott A %A Shah, Neomi A %A Shin, Chol %A Stone, Katie L %A Stubbe, Beate %A Sul, Jae Hoon %A Tafti, Mehdi %A Taylor, Kent D %A Teumer, Alexander %A Thornton, Timothy A %A Tranah, Gregory J %A Wang, Chaolong %A Wang, Heming %A Warby, Simon C %A Wellman, D Andrew %A Zee, Phyllis C %A Hanis, Craig L %A Laurie, Cathy C %A Gottlieb, Daniel J %A Patel, Sanjay R %A Zhu, Xiaofeng %A Sunyaev, Shamil R %A Saxena, Richa %A Lin, Xihong %A Redline, Susan %X

Obstructive sleep apnea (OSA) is a common heritable disorder displaying marked sexual dimorphism in disease prevalence and progression. Previous genetic association studies have identified a few genetic loci associated with OSA and related quantitative traits, but they have only focused on single ethnic groups, and a large proportion of the heritability remains unexplained. The apnea-hypopnea index (AHI) is a commonly used quantitative measure characterizing OSA severity. Because OSA differs by sex, and the pathophysiology of obstructive events differ in rapid eye movement (REM) and non-REM (NREM) sleep, we hypothesized that additional genetic association signals would be identified by analyzing the NREM/REM-specific AHI and by conducting sex-specific analyses in multiethnic samples. We performed genome-wide association tests for up to 19,733 participants of African, Asian, European, and Hispanic/Latino American ancestry in 7 studies. We identified rs12936587 on chromosome 17 as a possible quantitative trait locus for NREM AHI in men (N = 6,737; P = 1.7 × 10) but not in women (P = 0.77). The association with NREM AHI was replicated in a physiological research study (N = 67; P = 0.047). This locus overlapping the RAI1 gene and encompassing genes PEMT1, SREBF1, and RASD1 was previously reported to be associated with coronary artery disease, lipid metabolism, and implicated in Potocki-Lupski syndrome and Smith-Magenis syndrome, which are characterized by abnormal sleep phenotypes. We also identified gene-by-sex interactions in suggestive association regions, suggesting that genetic variants for AHI appear to vary by sex, consistent with the clinical observations of strong sexual dimorphism.

%B Am J Respir Cell Mol Biol %V 58 %P 391-401 %8 2018 Mar %G eng %N 3 %R 10.1165/rcmb.2017-0237OC %0 Journal Article %J Nat Commun %D 2018 %T PR interval genome-wide association meta-analysis identifies 50 loci associated with atrial and atrioventricular electrical activity. %A van Setten, Jessica %A Brody, Jennifer A %A Jamshidi, Yalda %A Swenson, Brenton R %A Butler, Anne M %A Campbell, Harry %A Del Greco, Fabiola M %A Evans, Daniel S %A Gibson, Quince %A Gudbjartsson, Daniel F %A Kerr, Kathleen F %A Krijthe, Bouwe P %A Lyytikäinen, Leo-Pekka %A Müller, Christian %A Müller-Nurasyid, Martina %A Nolte, Ilja M %A Padmanabhan, Sandosh %A Ritchie, Marylyn D %A Robino, Antonietta %A Smith, Albert V %A Steri, Maristella %A Tanaka, Toshiko %A Teumer, Alexander %A Trompet, Stella %A Ulivi, Sheila %A Verweij, Niek %A Yin, Xiaoyan %A Arnar, David O %A Asselbergs, Folkert W %A Bader, Joel S %A Barnard, John %A Bis, Josh %A Blankenberg, Stefan %A Boerwinkle, Eric %A Bradford, Yuki %A Buckley, Brendan M %A Chung, Mina K %A Crawford, Dana %A den Hoed, Marcel %A Denny, Josh C %A Dominiczak, Anna F %A Ehret, Georg B %A Eijgelsheim, Mark %A Ellinor, Patrick T %A Felix, Stephan B %A Franco, Oscar H %A Franke, Lude %A Harris, Tamara B %A Holm, Hilma %A Ilaria, Gandin %A Iorio, Annamaria %A Kähönen, Mika %A Kolcic, Ivana %A Kors, Jan A %A Lakatta, Edward G %A Launer, Lenore J %A Lin, Honghuang %A Lin, Henry J %A Loos, Ruth J F %A Lubitz, Steven A %A Macfarlane, Peter W %A Magnani, Jared W %A Leach, Irene Mateo %A Meitinger, Thomas %A Mitchell, Braxton D %A Münzel, Thomas %A Papanicolaou, George J %A Peters, Annette %A Pfeufer, Arne %A Pramstaller, Peter P %A Raitakari, Olli T %A Rotter, Jerome I %A Rudan, Igor %A Samani, Nilesh J %A Schlessinger, David %A Silva Aldana, Claudia T %A Sinner, Moritz F %A Smith, Jonathan D %A Snieder, Harold %A Soliman, Elsayed Z %A Spector, Timothy D %A Stott, David J %A Strauch, Konstantin %A Tarasov, Kirill V %A Thorsteinsdottir, Unnur %A Uitterlinden, André G %A Van Wagoner, David R %A Völker, Uwe %A Völzke, Henry %A Waldenberger, Melanie %A Jan Westra, Harm %A Wild, Philipp S %A Zeller, Tanja %A Alonso, Alvaro %A Avery, Christy L %A Bandinelli, Stefania %A Benjamin, Emelia J %A Cucca, Francesco %A Dörr, Marcus %A Ferrucci, Luigi %A Gasparini, Paolo %A Gudnason, Vilmundur %A Hayward, Caroline %A Heckbert, Susan R %A Hicks, Andrew A %A Jukema, J Wouter %A Kääb, Stefan %A Lehtimäki, Terho %A Liu, Yongmei %A Munroe, Patricia B %A Parsa, Afshin %A Polasek, Ozren %A Psaty, Bruce M %A Roden, Dan M %A Schnabel, Renate B %A Sinagra, Gianfranco %A Stefansson, Kari %A Stricker, Bruno H %A van der Harst, Pim %A van Duijn, Cornelia M %A Wilson, James F %A Gharib, Sina A %A de Bakker, Paul I W %A Isaacs, Aaron %A Arking, Dan E %A Sotoodehnia, Nona %X

Electrocardiographic PR interval measures atrio-ventricular depolarization and conduction, and abnormal PR interval is a risk factor for atrial fibrillation and heart block. Our genome-wide association study of over 92,000 European-descent individuals identifies 44 PR interval loci (34 novel). Examination of these loci reveals known and previously not-yet-reported biological processes involved in cardiac atrial electrical activity. Genes in these loci are over-represented in cardiac disease processes including heart block and atrial fibrillation. Variants in over half of the 44 loci were associated with atrial or blood transcript expression levels, or were in high linkage disequilibrium with missense variants. Six additional loci were identified either by meta-analysis of ~105,000 African and European-descent individuals and/or by pleiotropic analyses combining PR interval with heart rate, QRS interval, and atrial fibrillation. These findings implicate developmental pathways, and identify transcription factors, ion-channel genes, and cell-junction/cell-signaling proteins in atrio-ventricular conduction, identifying potential targets for drug development.

%B Nat Commun %V 9 %P 2904 %8 2018 Jul 25 %G eng %N 1 %R 10.1038/s41467-018-04766-9 %0 Journal Article %J Nat Commun %D 2020 %T Whole genome sequence analysis of pulmonary function and COPD in 19,996 multi-ethnic participants. %A Zhao, Xutong %A Qiao, Dandi %A Yang, Chaojie %A Kasela, Silva %A Kim, Wonji %A Ma, Yanlin %A Shrine, Nick %A Batini, Chiara %A Sofer, Tamar %A Taliun, Sarah A Gagliano %A Sakornsakolpat, Phuwanat %A Balte, Pallavi P %A Prokopenko, Dmitry %A Yu, Bing %A Lange, Leslie A %A Dupuis, Josée %A Cade, Brian E %A Lee, Jiwon %A Gharib, Sina A %A Daya, Michelle %A Laurie, Cecelia A %A Ruczinski, Ingo %A Cupples, L Adrienne %A Loehr, Laura R %A Bartz, Traci M %A Morrison, Alanna C %A Psaty, Bruce M %A Vasan, Ramachandran S %A Wilson, James G %A Taylor, Kent D %A Durda, Peter %A Johnson, W Craig %A Cornell, Elaine %A Guo, Xiuqing %A Liu, Yongmei %A Tracy, Russell P %A Ardlie, Kristin G %A Aguet, Francois %A VanDenBerg, David J %A Papanicolaou, George J %A Rotter, Jerome I %A Barnes, Kathleen C %A Jain, Deepti %A Nickerson, Deborah A %A Muzny, Donna M %A Metcalf, Ginger A %A Doddapaneni, Harshavardhan %A Dugan-Perez, Shannon %A Gupta, Namrata %A Gabriel, Stacey %A Rich, Stephen S %A O'Connor, George T %A Redline, Susan %A Reed, Robert M %A Laurie, Cathy C %A Daviglus, Martha L %A Preudhomme, Liana K %A Burkart, Kristin M %A Kaplan, Robert C %A Wain, Louise V %A Tobin, Martin D %A London, Stephanie J %A Lappalainen, Tuuli %A Oelsner, Elizabeth C %A Abecasis, Goncalo R %A Silverman, Edwin K %A Barr, R Graham %A Cho, Michael H %A Manichaikul, Ani %K Adult %K African Americans %K Aged %K Aged, 80 and over %K Alpha-Ketoglutarate-Dependent Dioxygenase FTO %K Calcium-Binding Proteins %K Feasibility Studies %K Female %K Follow-Up Studies %K Genetic Loci %K Genetic Predisposition to Disease %K Genome-Wide Association Study %K Humans %K Intracellular Signaling Peptides and Proteins %K Lung %K Male %K Middle Aged %K Polymorphism, Single Nucleotide %K Protein Inhibitors of Activated STAT %K Pulmonary Disease, Chronic Obstructive %K Respiratory Physiological Phenomena %K Small Ubiquitin-Related Modifier Proteins %K Whole Genome Sequencing %X

Chronic obstructive pulmonary disease (COPD), diagnosed by reduced lung function, is a leading cause of morbidity and mortality. We performed whole genome sequence (WGS) analysis of lung function and COPD in a multi-ethnic sample of 11,497 participants from population- and family-based studies, and 8499 individuals from COPD-enriched studies in the NHLBI Trans-Omics for Precision Medicine (TOPMed) Program. We identify at genome-wide significance 10 known GWAS loci and 22 distinct, previously unreported loci, including two common variant signals from stratified analysis of African Americans. Four novel common variants within the regions of PIAS1, RGN (two variants) and FTO show evidence of replication in the UK Biobank (European ancestry n ~ 320,000), while colocalization analyses leveraging multi-omic data from GTEx and TOPMed identify potential molecular mechanisms underlying four of the 22 novel loci. Our study demonstrates the value of performing WGS analyses and multi-omic follow-up in cohorts of diverse ancestry.

%B Nat Commun %V 11 %P 5182 %8 2020 10 14 %G eng %N 1 %R 10.1038/s41467-020-18334-7 %0 Journal Article %J Nature %D 2021 %T Sequencing of 53,831 diverse genomes from the NHLBI TOPMed Program. %A Taliun, Daniel %A Harris, Daniel N %A Kessler, Michael D %A Carlson, Jedidiah %A Szpiech, Zachary A %A Torres, Raul %A Taliun, Sarah A Gagliano %A Corvelo, André %A Gogarten, Stephanie M %A Kang, Hyun Min %A Pitsillides, Achilleas N %A LeFaive, Jonathon %A Lee, Seung-Been %A Tian, Xiaowen %A Browning, Brian L %A Das, Sayantan %A Emde, Anne-Katrin %A Clarke, Wayne E %A Loesch, Douglas P %A Shetty, Amol C %A Blackwell, Thomas W %A Smith, Albert V %A Wong, Quenna %A Liu, Xiaoming %A Conomos, Matthew P %A Bobo, Dean M %A Aguet, Francois %A Albert, Christine %A Alonso, Alvaro %A Ardlie, Kristin G %A Arking, Dan E %A Aslibekyan, Stella %A Auer, Paul L %A Barnard, John %A Barr, R Graham %A Barwick, Lucas %A Becker, Lewis C %A Beer, Rebecca L %A Benjamin, Emelia J %A Bielak, Lawrence F %A Blangero, John %A Boehnke, Michael %A Bowden, Donald W %A Brody, Jennifer A %A Burchard, Esteban G %A Cade, Brian E %A Casella, James F %A Chalazan, Brandon %A Chasman, Daniel I %A Chen, Yii-Der Ida %A Cho, Michael H %A Choi, Seung Hoan %A Chung, Mina K %A Clish, Clary B %A Correa, Adolfo %A Curran, Joanne E %A Custer, Brian %A Darbar, Dawood %A Daya, Michelle %A de Andrade, Mariza %A DeMeo, Dawn L %A Dutcher, Susan K %A Ellinor, Patrick T %A Emery, Leslie S %A Eng, Celeste %A Fatkin, Diane %A Fingerlin, Tasha %A Forer, Lukas %A Fornage, Myriam %A Franceschini, Nora %A Fuchsberger, Christian %A Fullerton, Stephanie M %A Germer, Soren %A Gladwin, Mark T %A Gottlieb, Daniel J %A Guo, Xiuqing %A Hall, Michael E %A He, Jiang %A Heard-Costa, Nancy L %A Heckbert, Susan R %A Irvin, Marguerite R %A Johnsen, Jill M %A Johnson, Andrew D %A Kaplan, Robert %A Kardia, Sharon L R %A Kelly, Tanika %A Kelly, Shannon %A Kenny, Eimear E %A Kiel, Douglas P %A Klemmer, Robert %A Konkle, Barbara A %A Kooperberg, Charles %A Köttgen, Anna %A Lange, Leslie A %A Lasky-Su, Jessica %A Levy, Daniel %A Lin, Xihong %A Lin, Keng-Han %A Liu, Chunyu %A Loos, Ruth J F %A Garman, Lori %A Gerszten, Robert %A Lubitz, Steven A %A Lunetta, Kathryn L %A Mak, Angel C Y %A Manichaikul, Ani %A Manning, Alisa K %A Mathias, Rasika A %A McManus, David D %A McGarvey, Stephen T %A Meigs, James B %A Meyers, Deborah A %A Mikulla, Julie L %A Minear, Mollie A %A Mitchell, Braxton D %A Mohanty, Sanghamitra %A Montasser, May E %A Montgomery, Courtney %A Morrison, Alanna C %A Murabito, Joanne M %A Natale, Andrea %A Natarajan, Pradeep %A Nelson, Sarah C %A North, Kari E %A O'Connell, Jeffrey R %A Palmer, Nicholette D %A Pankratz, Nathan %A Peloso, Gina M %A Peyser, Patricia A %A Pleiness, Jacob %A Post, Wendy S %A Psaty, Bruce M %A Rao, D C %A Redline, Susan %A Reiner, Alexander P %A Roden, Dan %A Rotter, Jerome I %A Ruczinski, Ingo %A Sarnowski, Chloe %A Schoenherr, Sebastian %A Schwartz, David A %A Seo, Jeong-Sun %A Seshadri, Sudha %A Sheehan, Vivien A %A Sheu, Wayne H %A Shoemaker, M Benjamin %A Smith, Nicholas L %A Smith, Jennifer A %A Sotoodehnia, Nona %A Stilp, Adrienne M %A Tang, Weihong %A Taylor, Kent D %A Telen, Marilyn %A Thornton, Timothy A %A Tracy, Russell P %A Van Den Berg, David J %A Vasan, Ramachandran S %A Viaud-Martinez, Karine A %A Vrieze, Scott %A Weeks, Daniel E %A Weir, Bruce S %A Weiss, Scott T %A Weng, Lu-Chen %A Willer, Cristen J %A Zhang, Yingze %A Zhao, Xutong %A Arnett, Donna K %A Ashley-Koch, Allison E %A Barnes, Kathleen C %A Boerwinkle, Eric %A Gabriel, Stacey %A Gibbs, Richard %A Rice, Kenneth M %A Rich, Stephen S %A Silverman, Edwin K %A Qasba, Pankaj %A Gan, Weiniu %A Papanicolaou, George J %A Nickerson, Deborah A %A Browning, Sharon R %A Zody, Michael C %A Zöllner, Sebastian %A Wilson, James G %A Cupples, L Adrienne %A Laurie, Cathy C %A Jaquish, Cashell E %A Hernandez, Ryan D %A O'Connor, Timothy D %A Abecasis, Goncalo R %X

The Trans-Omics for Precision Medicine (TOPMed) programme seeks to elucidate the genetic architecture and biology of heart, lung, blood and sleep disorders, with the ultimate goal of improving diagnosis, treatment and prevention of these diseases. The initial phases of the programme focused on whole-genome sequencing of individuals with rich phenotypic data and diverse backgrounds. Here we describe the TOPMed goals and design as well as the available resources and early insights obtained from the sequence data. The resources include a variant browser, a genotype imputation server, and genomic and phenotypic data that are available through dbGaP (Database of Genotypes and Phenotypes). In the first 53,831 TOPMed samples, we detected more than 400 million single-nucleotide and insertion or deletion variants after alignment with the reference genome. Additional previously undescribed variants were detected through assembly of unmapped reads and customized analysis in highly variable loci. Among the more than 400 million detected variants, 97% have frequencies of less than 1% and 46% are singletons that are present in only one individual (53% among unrelated individuals). These rare variants provide insights into mutational processes and recent human evolutionary history. The extensive catalogue of genetic variation in TOPMed studies provides unique opportunities for exploring the contributions of rare and noncoding sequence variants to phenotypic variation. Furthermore, combining TOPMed haplotypes with modern imputation methods improves the power and reach of genome-wide association studies to include variants down to a frequency of approximately 0.01%.

%B Nature %V 590 %P 290-299 %8 2021 02 %G eng %N 7845 %R 10.1038/s41586-021-03205-y %0 Journal Article %J EBioMedicine %D 2021 %T Whole genome sequence analyses of eGFR in 23,732 people representing multiple ancestries in the NHLBI trans-omics for precision medicine (TOPMed) consortium. %A Lin, Bridget M %A Grinde, Kelsey E %A Brody, Jennifer A %A Breeze, Charles E %A Raffield, Laura M %A Mychaleckyj, Josyf C %A Thornton, Timothy A %A Perry, James A %A Baier, Leslie J %A de Las Fuentes, Lisa %A Guo, Xiuqing %A Heavner, Benjamin D %A Hanson, Robert L %A Hung, Yi-Jen %A Qian, Huijun %A Hsiung, Chao A %A Hwang, Shih-Jen %A Irvin, Margaret R %A Jain, Deepti %A Kelly, Tanika N %A Kobes, Sayuko %A Lange, Leslie %A Lash, James P %A Li, Yun %A Liu, Xiaoming %A Mi, Xuenan %A Musani, Solomon K %A Papanicolaou, George J %A Parsa, Afshin %A Reiner, Alex P %A Salimi, Shabnam %A Sheu, Wayne H-H %A Shuldiner, Alan R %A Taylor, Kent D %A Smith, Albert V %A Smith, Jennifer A %A Tin, Adrienne %A Vaidya, Dhananjay %A Wallace, Robert B %A Yamamoto, Kenichi %A Sakaue, Saori %A Matsuda, Koichi %A Kamatani, Yoichiro %A Momozawa, Yukihide %A Yanek, Lisa R %A Young, Betsi A %A Zhao, Wei %A Okada, Yukinori %A Abecasis, Gonzalo %A Psaty, Bruce M %A Arnett, Donna K %A Boerwinkle, Eric %A Cai, Jianwen %A Yii-Der Chen, Ida %A Correa, Adolfo %A Cupples, L Adrienne %A He, Jiang %A Kardia, Sharon Lr %A Kooperberg, Charles %A Mathias, Rasika A %A Mitchell, Braxton D %A Nickerson, Deborah A %A Turner, Steve T %A Vasan, Ramachandran S %A Rotter, Jerome I %A Levy, Daniel %A Kramer, Holly J %A Köttgen, Anna %A Rich, Stephen S %A Lin, Dan-Yu %A Browning, Sharon R %A Franceschini, Nora %X

BACKGROUND: Genetic factors that influence kidney traits have been understudied for low frequency and ancestry-specific variants.

METHODS: We combined whole genome sequencing (WGS) data from 23,732 participants from 10 NHLBI Trans-Omics for Precision Medicine (TOPMed) Program multi-ethnic studies to identify novel loci for estimated glomerular filtration rate (eGFR). Participants included European, African, East Asian, and Hispanic ancestries. We applied linear mixed models using a genetic relationship matrix estimated from the WGS data and adjusted for age, sex, study, and ethnicity.

FINDINGS: When testing single variants, we identified three novel loci driven by low frequency variants more commonly observed in non-European ancestry (PRKAA2, rs180996919, minor allele frequency [MAF] 0.04%, P = 6.1 × 10; METTL8, rs116951054, MAF 0.09%, P = 4.5 × 10; and MATK, rs539182790, MAF 0.05%, P = 3.4 × 10). We also replicated two known loci for common variants (rs2461702, MAF=0.49, P = 1.2 × 10, nearest gene GATM, and rs71147340, MAF=0.34, P = 3.3 × 10, CDK12). Testing aggregated variants within a gene identified the MAF gene. A statistical approach based on local ancestry helped to identify replication samples for ancestry-specific variants.

INTERPRETATION: This study highlights challenges in studying variants influencing kidney traits that are low frequency in populations and more common in non-European ancestry.

%B EBioMedicine %V 63 %P 103157 %8 2021 Jan %G eng %R 10.1016/j.ebiom.2020.103157