Harmonizing Genetic Ancestry and Self-identified Race/Ethnicity in Genome-wide Association Studies

Huaying Fang; Qin Hui; Julie Lynch; Jacqueline Honerlaw; Themistocles L Assimes; Jie Huang; Marijana Vujkovic; Scott M Damrauer; Saiju Pyarajan; J Michael Gaziano; Scott L DuVall; Christopher J O'Donnell; Kelly Cho; Kyong-Mi Chang; Peter W F Wilson; Philip S Tsao; Yan V Sun; Hua Tang; VA Million Veteran Program

doi:10.1016/j.ajhg.2019.08.012

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Harmonizing Genetic Ancestry and Self-identified Race/Ethnicity in Genome-wide Association Studies

Journal article

Open access

Peer reviewed

Harmonizing Genetic Ancestry and Self-identified Race/Ethnicity in Genome-wide Association Studies

Huaying Fang, Qin Hui, Julie Lynch, Jacqueline Honerlaw, Themistocles L Assimes, Jie Huang, Marijana Vujkovic, Scott M Damrauer, Saiju Pyarajan, J Michael Gaziano, …

American journal of human genetics, Vol.105(4), pp.763-772

10/03/2019

DOI: 10.1016/j.ajhg.2019.08.012

PMCID: PMC6817526

PMID: 31564439

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https://doi.org/10.1016/j.ajhg.2019.08.012View

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Abstract

Large-scale multi-ethnic cohorts offer unprecedented opportunities to elucidate the genetic factors influencing complex traits related to health and disease among minority populations. At the same time, the genetic diversity in these cohorts presents new challenges for analysis and interpretation. We consider the utility of race and/or ethnicity categories in genome-wide association studies (GWASs) of multi-ethnic cohorts. We demonstrate that race/ethnicity information enhances the ability to understand population-specific genetic architecture. To address the practical issue that self-identified racial/ethnic information may be incomplete, we propose a machine learning algorithm that produces a surrogate variable, termed HARE. We use height as a model trait to demonstrate the utility of HARE and ethnicity-specific GWASs.

Algorithms

Machine Learning

Continental Population Groups - genetics

Ethnic Groups - genetics

Genome-Wide Association Study

Humans

Support Vector Machine

Details

Title: Subtitle: Harmonizing Genetic Ancestry and Self-identified Race/Ethnicity in Genome-wide Association Studies
Creators: Huaying Fang - Stanford University
Qin Hui - Emory University
Julie Lynch - University of Massachusetts Amherst
Jacqueline Honerlaw - VA Boston Healthcare System
Themistocles L Assimes - Stanford University
Jie Huang - VA Boston Healthcare System
Marijana Vujkovic - University of Pennsylvania
Scott M Damrauer - University of Pennsylvania
Saiju Pyarajan - Brigham and Women's Hospital
J Michael Gaziano - Brigham and Women's Hospital
Scott L DuVall - University of Utah
Christopher J O'Donnell - Harvard University
Kelly Cho - Brigham and Women's Hospital
Kyong-Mi Chang - University of Pennsylvania
Peter W F Wilson - Emory University
Philip S Tsao - Stanford University
Yan V Sun - Emory University
Hua Tang - Stanford University
VA Million Veteran Program
Contributors: Zuhair K Ballas (Contributor) - University of Iowa, Immunology
Resource Type: Journal article
Publication Details: American journal of human genetics, Vol.105(4), pp.763-772
DOI: 10.1016/j.ajhg.2019.08.012
PMID: 31564439
PMCID: PMC6817526
ISSN: 0002-9297
eISSN: 1537-6605
Grant note: R35 GM127063 / NIGMS NIH HHS R01 GM073059 / NIGMS NIH HHS R01 NR013520 / NINR NIH HHS
Language: English
Date published: 10/03/2019
Academic Unit: Immunology; Internal Medicine
Record Identifier: 9984359666502771

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