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Use of >100,000 NHLBI Trans-Omics for Precision Medicine (TOPMed) Consortium Whole Genome Sequences Improves Imputation Quality and Detection of Rare Variant Associations in Admixed African and Hispanic/Latino Populations

Citation

Kowalski, Madeline H.; Qian, Huijun; Hou, Ziyi; Rosen, Jonathan D.; Tapia, Amanda L.; Shan, Yue; Jain, Deepti; Argos, Maria; Arnett, Donna K.; & Avery, Christy L., et al. (2019). Use of >100,000 NHLBI Trans-Omics for Precision Medicine (TOPMed) Consortium Whole Genome Sequences Improves Imputation Quality and Detection of Rare Variant Associations in Admixed African and Hispanic/Latino Populations. PLOS Genetics, 15(12), e1008500. PMCID: PMC6953885

Abstract

Most genome-wide association and fine-mapping studies to date have been conducted in individuals of European descent, and genetic studies of populations of Hispanic/Latino and African ancestry are limited. In addition, these populations have more complex linkage disequilibrium structure. In order to better define the genetic architecture of these understudied populations, we leveraged >100,000 phased sequences available from deep-coverage whole genome sequencing through the multi-ethnic NHLBI Trans-Omics for Precision Medicine (TOPMed) program to impute genotypes into admixed African and Hispanic/Latino samples with genome-wide genotyping array data. We demonstrated that using TOPMed sequencing data as the imputation reference panel improves genotype imputation quality in these populations, which subsequently enhanced gene-mapping power for complex traits. For rare variants with minor allele frequency (MAF) < 0.5%, we observed a 2.3- to 6.1-fold increase in the number of well-imputed variants, with 11-34% improvement in average imputation quality, compared to the state-of-the-art 1000 Genomes Project Phase 3 and Haplotype Reference Consortium reference panels. Impressively, even for extremely rare variants with minor allele count <10 (including singletons) in the imputation target samples, average information content rescued was >86%. Subsequent association analyses of TOPMed reference panel-imputed genotype data with hematological traits (hemoglobin (HGB), hematocrit (HCT), and white blood cell count (WBC)) in ~21,600 African-ancestry and ~21,700 Hispanic/Latino individuals identified associations with two rare variants in the HBB gene (rs33930165 with higher WBC [p = 8.8x10-15] in African populations, rs11549407 with lower HGB [p = 1.5x10-12] and HCT [p = 8.8x10-10] in Hispanics/Latinos). By comparison, neither variant would have been genome-wide significant if either 1000 Genomes Project Phase 3 or Haplotype Reference Consortium reference panels had been used for imputation. Our findings highlight the utility of the TOPMed imputation reference panel for identification of novel rare variant associations not previously detected in similarly sized genome-wide studies of under-represented African and Hispanic/Latino populations.

URL

http://dx.doi.org/10.1371/journal.pgen.1008500

Reference Type

Journal Article

Journal Title

PLOS Genetics

Author(s)

Kowalski, Madeline H.
Qian, Huijun
Hou, Ziyi
Rosen, Jonathan D.
Tapia, Amanda L.
Shan, Yue
Jain, Deepti
Argos, Maria
Arnett, Donna K.
Avery, Christy L.
Barnes, Kathleen C.
Becker, Lewis C.
Bien, Stephanie A.
Bis, Joshua C.
Blangero, John
Boerwinkle, Eric
Bowden, Donald W.
Buyske, Steve
Cai, Jianwen
Cho, Michael H.
Choi, Seung Hoan
Choquet, Hélène
Cupples, L. Adrienne
Cushman, Mary
Daya, Michelle
de Vries, Paul S.
Ellinor, Patrick T.
Faraday, Nauder
Fornage, Myriam
Gabriel, Stacey
Ganesh, Santhi K.
Graff, Mariaelisa
Gupta, Namrata
He, Jiang
Heckbert, Susan R.
Hidalgo, Bertha
Hodonsky, Chani J.
Irvin, Marguerite R.
Johnson, Andrew D.
Jorgenson, Eric
Kaplan, Robert
Kardia, Sharon L. R.
Kelly, Tanika N.
Kooperberg, Charles L.
Lasky-Su, Jessica A.
Loos, Ruth J. F.
Lubitz, Steven A.
Mathias, Rasika A.
McHugh, Caitlin P.
Montgomery, Courtney
Moon, Jee-Young
Morrison, Alanna C.
Palmer, Nicholette D.
Pankratz, Nathan
Papanicolaou, George J.
Peralta, Juan M.
Peyser, Patricia A.
Rich, Stephen S.
Rotter, Jerome I.
Silverman, Edwin K.
Smith, Jennifer A.
Smith, Nicholas L.
Taylor, Kent D.
Thornton, Timothy A.
Tiwari, Hemant K.
Tracy, Russell P.
Wang, Tao
Weiss, Scott T.
Weng, Lu-Chen
Wiggins, Kerri L.
Wilson, James G.
Yanek, Lisa R.
Zöllner, Sebastian
North, Kari E.
Auer, Paul L.
Consortium, NHLBI Trans-Omics for Precision Medicine
Hematology, TOPMed
Hemostasis Working, Group
Raffield, Laura M.
Reiner, Alexander P.
Li, Yun

Year Published

2019

Volume Number

15

Issue Number

12

Pages

e1008500

PMCID

PMC6953885

Reference ID

12606