ArticleBioinformatics (Oxford, England)2013
Imputation of coding variants in African Americans: better performance using data from the exome sequencing project.
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Article in Bioinformatics (Oxford, England), 2013. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 29 papers.
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29 citing papers in PubMed.
- Identification of a SGCD × Discrimination Interaction Effect on Systolic Blood Pressure in African American Adults in the Jackson Heart Study.American journal of hypertension · 2022Article
- Black and White Adults With CKD Hospitalized With Acute Kidney Injury: Findings From the Chronic Renal Insufficiency Cohort (CRIC) Study.American journal of kidney diseases : the official journal of the National Kidney Foundation · 2022Article
- Recovering High-Quality Host Genomes from Gut Metagenomic Data through Genotype Imputation.Advanced genetics (Hoboken, N.J.) · 2022Article
- Whole Exome Sequencing Enhanced Imputation Identifies 85 Metabolite Associations in the Alpine CHRIS Cohort.Metabolites · 2022Article
- Leveraging TOPMed imputation server and constructing a cohort-specific imputation reference panel to enhance genotype imputation among cystic fibrosis patients.HGG advances · 2022Article
- Association between MTNR1B polymorphisms and obesity in African American: findings from the Jackson Heart Study.BMC medical genomics · 2021Article
- Article
- Association of APOL1 With Heart Failure With Preserved Ejection Fraction in Postmenopausal African American Women.JAMA cardiology · 2018Observational
- Genotype imputation for Han Chinese population using Haplotype Reference Consortium as reference.Human genetics · 2018Article
- Genotype imputation performance of three reference panels using African ancestry individuals.Human genetics · 2018Article
- A multi-stage genome-wide association study of uterine fibroids in African Americans.Human genetics · 2017Article
- A population-specific reference panel empowers genetic studies of Anabaptist populations.Scientific reports · 2017Article
- Circadian CLOCK gene polymorphisms in relation to sleep patterns and obesity in African Americans: findings from the Jackson heart study.BMC genetics · 2017Article
- PreCimp: Pre-collapsing imputation approach increases imputation accuracy of rare variants in terms of collapsed variables.Genetic epidemiology · 2017Article
- Evidence of selection as a cause for racial disparities in fibroproliferative disease.PloS one · 2017Article
- Guidelines for Large-Scale Sequence-Based Complex Trait Association Studies: Lessons Learned from the NHLBI Exome Sequencing Project.American journal of human genetics · 2016Article
- Vitamin D Receptor Gene Polymorphisms Are Associated with Abdominal Visceral Adipose Tissue Volume and Serum Adipokine Concentrations but Not with Body Mass Index or Waist Circumference in African Americans: The Jackson Heart Study.The Journal of nutrition · 2016Article
- Across-Platform Imputation of DNA Methylation Levels Incorporating Nonlocal Information Using Penalized Functional Regression.Genetic epidemiology · 2016Article
- A new strategy for enhancing imputation quality of rare variants from next-generation sequencing data via combining SNP and exome chip data.BMC genomics · 2015Article
- Association of ADIPOQ gene with type 2 diabetes and related phenotypes in African American men and women: the Jackson Heart Study.BMC genetics · 2015Article
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Authors and funding
35 authors.
Qing DuanDepartment of Genetics and Department of Computer Science, University of North Carolina, Chapel Hill, NC 27599, USA, Public Health Sciences Division, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA, Department of Biostatistics, University of North Carolina, Chapel Hill, NC 27599, USA, Department of Biostatistics and Center for Statistical Genetics, School of Public Health, University of Michigan, Ann Arbor, MI 48109, USA, Renaissance Computing Institute, University of North Carolina, Chapel Hill, NC 27599, USA, Department of Statistics and Department of Genetics, Rutgers University, Piscataway, NJ 08854, USA, Department of Epidemiology, University of North Carolina, Chapel Hill, NC 27599, USA, Department of Epidemiology, University of Washington, Seattle, WA 98195, USA, Division of Epidemiology, Graduate School of Public Health, University of Pittsburgh, Pittsburgh, PA 15261, USA, Department of Epidemiology and Medicine, University of Iowa, Iowa City, IA 52242, Division of Cardiology, George Washington University School of Medicine and Health Sciences, Washington, DC 20037, USA, Department of Preventive Medicine, Keck School of Medicine, University of Southern California/Norris Comprehensive Cancer Center, Los Angeles, CA 90033, USA, Epidemiology Program, University of Hawaii Cancer Center, HI 96813, USA, Division of Genomic Medicine, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD 20892, USA, Department of Molecular Physiology and Biophysics, Center for Human Genetics Research, Vanderbilt University, Nashville, TN 37232, USA, Department of Medicine, Stanford University School of Medicine, Stanford, CA 94305, USA, Division of Endocrinology, Diabetes and Metabolism, Ohio State University, Columbus, OH 43210, USA, Department of Physiology and Biophysics, University of Mississippi Medical Center, Jackson, MS 39216, USA and Department of Genome Sciences, University of Washington, Seattle, WA 98195, USA.
Eric Yi Liu
Paul L Auer
Guosheng Zhang
Ethan M Lange
Goo Jun
Chris Bizon
Shuo Jiao
Steven Buyske
Nora Franceschini
Chris S Carlson
Li Hsu
Alex P Reiner
Ulrike Peters
Jeffrey Haessler
Keith Curtis
Christina L Wassel
Jennifer G Robinson
Lisa W Martin
Christopher A Haiman
Loic Le Marchand
Tara C Matise
Lucia A Hindorff
Dana C Crawford
Themistocles L Assimes
Hyun Min Kang
Gerardo Heiss
Rebecca D Jackson
Charles Kooperberg
James G Wilson
Gonçalo R Abecasis
Kari E North
Deborah A Nickerson
Leslie A Lange
Yun Li
Funding
Northwest Genomics CenterRC2HL102926 · NHLBI · UNIVERSITY OF WASHINGTON · PI GREEN, PHILIP P, NICKERSON, DEBORAH A · 2009 to 2009
$11.0MComprehensive Sequencing and Analysis of Variation in NHLBI CohortsRC2HL102925 · NHLBI · BROAD INSTITUTE, INC. · PI ALTSHULER, DAVID, GABRIEL, STACEY · 2009 to 2009
$10.2MEpidemiology of putative genuine genetic variant: The Women's Health IntiativeU01HG004790 · NHGRI · FRED HUTCHINSON CANCER RESEARCH CENTER · PI KOOPERBERG, CHARLES L · 2008 to 2012
$9.9MGenetic Epidemiology of Causal Variants Across the Life CourseU01HG004803 · NHGRI · UNIV OF NORTH CAROLINA CHAPEL HILL · PI NORTH, KARI E. · 2008 to 2012
$9.0MEpidemiologic Architecture for Genes Linked to Environment (EAGLE)U01HG004798 · NHGRI · VANDERBILT UNIVERSITY · PI CRAWFORD, DANA C · 2008 to 2013
$8.8MEpidemiology of Putative Causal Variants in the Multiethnic CohortU01HG004802 · NHGRI · UNIVERSITY OF HAWAII AT MANOA · PI LE MARCHAND, LOIC · 2008 to 2012
$8.4MNHGRI EpiGenVar Coordinating CenterU01HG004801 · NHGRI · RUTGERS, THE STATE UNIV OF N.J. · PI MATISE, TARA C. · 2008 to 2012
$4.4MWomen's Health Initiative Memory Study (WHIMS)N01WH44221 · WH · WAKE FOREST UNIVERSITY HEALTH SCIENCES · 2009 to 2010
$3.1MARRA - NHLBI Lung Cohorts Sequencing ProjectRC2HL102923 · NHLBI · UNIVERSITY OF WASHINGTON · PI BAMSHAD, MICHAEL JOSEPH, BARNES, KATHLEEN C · 2009 to 2009
$2.6MWHI Sequencing Project (WHISP)RC2HL102924 · NHLBI · OHIO STATE UNIVERSITY · PI CARLSON, CHRISTOPHER S, JACKSON, REBECCA D · 2009 to 2009
$2.1MDesign and Analysis of Sequencing-based Studies for Complex Human TraitsR01HG006292 · NHGRI · UNIV OF NORTH CAROLINA CHAPEL HILL · PI LI, YUN · 2011 to 2015
$1.8MVANGUARD CENTER FOR WOMEN'S HEALTH INITIATIVEN01WH032111 · WH · EMORY UNIVERSITY · PI WATTS, NELSON · 1993 to 2001
$1.6MNHGRI NIH HHS R01 HG006292NHGRI NIH HHS R01 HG006703NHGRI NIH HHS U01 HG004790NHGRI NIH HHS U01HG004790NHGRI NIH HHS U01 HG004798NHGRI NIH HHS U01HG004798NHGRI NIH HHS U01 HG004801NHGRI NIH HHS U01HG004801NHGRI NIH HHS U01 HG004802NHGRI NIH HHS U01HG004802NHGRI NIH HHS U01 HG004803NHGRI NIH HHS U01HG004803NHLBI NIH HHS RC2 HL-102923NHLBI NIH HHS RC2 HL102923NHLBI NIH HHS RC2 HL-102924NHLBI NIH HHS RC2 HL102924NHLBI NIH HHS RC2 HL-102925NHLBI NIH HHS RC2 HL102925NHLBI NIH HHS RC2 HL-102926NHLBI NIH HHS RC2 HL102926NHLBI NIH HHS RC2 HL-103010NHLBI NIH HHS RC2 HL103010WHI NIH HHS N01 WH022110WHI NIH HHS N01WH24152WHI NIH HHS N01WH32100-2WHI NIH HHS N01WH32105-6WHI NIH HHS N01WH32108-9WHI NIH HHS N01WH32111-13WHI NIH HHS N01WH32115WHI NIH HHS N01WH32118-32119WHI NIH HHS N01WH32122WHI NIH HHS N01WH42107-26WHI NIH HHS N01WH42129-32WHI NIH HHS N01WH44221
Abstract
summaryAlthough the 1000 Genomes haplotypes are the most commonly used reference panel for imputation, medical sequencing projects are generating large alternate sets of sequenced samples. Imputation in African Americans using 3384 haplotypes from the Exome Sequencing Project, compared with 2184 haplotypes from 1000 Genomes Project, increased effective sample size by 8.3-11.4% for coding variants with minor allele frequency <1%. No loss of imputation quality was observed using a panel built from phenotypic extremes. We recommend using haplotypes from Exome Sequencing Project alone or concatenation of the two panels over quality score-based post-imputation selection or IMPUTE2's two-panel combination. CONTACT: yunli@med.unc.edu. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.
Indexed as
ExomeGenetic VariationBlack or African AmericanGene FrequencyGenome, HumanGenome-Wide Association StudyHaplotypesHumansPhenotypePolymorphism, Single NucleotideSequence Analysis, DNA
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