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
Authors: Kowalski Madeline H. , Qian Huijun , Hou Ziyi , Rosen Jonathan D. , Tapia Amanda L. , Shan Yue , Jain Deepti , Argos Maria , Arnett Donna K. , Avery Christy , 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 , Vries Paul S. de , Ellinor Patrick T. , Faraday Nauder , Fornage Myriam , Gabriel Stacey , Ganesh Santhi , Graff Misa , Gupta Namrata , He Jiang , Heckbert Susan R. , Hidalgo Bertha , Hodonsky Chani , Irvin Marguerite R. , Johnson Andrew D. , Jorgenson Eric , Kaplan Robert , Kardia Sharon LR. , Kelly Tanika N. , Kooperberg Charles , 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 N. , Auer Paul L. ,   NHLBI Trans-Omics for Precision Medicine (TOPMed) Consortium,   TOPMed Hematology & Hemostasis Working Group, Raffield Laura M. , Reiner Alexander P. , Li Yun 
Published: July 2019

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 still limited. In addition to the limited inclusion of these populations in genetic studies, these populations have more complex linkage disequilibrium structure that may reduce the number of variants associated with a phenotype. 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 commercial genome-wide genotyping array data. We demonstrate that using TOPMed sequencing data as the imputation reference panel improves genotype imputation quality in these populations, which subsequently enhances 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, respectively. Impressively, even for extremely rare variants with sample 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 ~20,000 self-identified African descent individuals and ~23,000 self-identified Hispanic/Latino individuals identified associations with two rare variants in theHBBgene (rs33930165 with higher WBC (p=8.1×10−12) in African populations, rs11549407 with lower HGB (p=1.59×10−12) and HCT (p=1.13×10−9) 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 TOPMed imputation reference panel for identification of novel associations between rare variants and complex traits not previously detected in similar sized genome-wide studies of under-represented African and Hispanic/Latino populations.

Author summary

Admixed African and Hispanic/Latino populations remain understudied in genome-wide association and fine-mapping studies of complex diseases. These populations have more complex linkage disequilibrium (LD) structure that can impair mapping of variants associated with complex diseases and their risk factors. Genotype imputation represents an approach to improve genome coverage, especially for rare or ancestry-specific variation; however, these understudied populations also have smaller relevant imputation reference panels that need to be expanded to represent their more complex LD patterns. In this study, we leveraged >100,000 phased sequences generated from the multi-ethnic NHLBI TOPMed project to impute in admixed cohorts encompassing ~20,000 individuals of African ancestry (AAs) and ~23,000 Hispanics/Latinos. We demonstrated substantially higher imputation quality for low frequency and rare variants in comparison to the state-of-the-art reference panels (1000 Genomes Project and Haplotype Reference Consortium). Association analyses of ~35 million (AAs) and ~27 million (Hispanics/Latinos) variants passing stringent post-imputation filtering with quantitative hematological traits led to the discovery of associations with two rare variants in theHBBgene; one of these variants was replicated in an independent sample, and the other is known to cause anemia in the homozygous state. By comparison, the sameHBBvariants would not have been genome-wide significant using other state-of-the-art reference panels due to lower imputation quality. Our findings demonstrate the power of the TOPMed whole genome sequencing data for imputation and subsequent association analysis in admixed African and Hispanic/Latino populations.