Genome-wide association study of red blood cell traits in Hispanics/Latinos: The Hispanic Community Health Study/Study of Latinos

Chani J. Hodonsky, Deepti Jain, Ursula M. Schick, Jean V. Morrison, Lisa Brown, Caitlin P. McHugh, Claudia Schurmann, Diane D. Chen, Yong Mei Liu, Paul L. Auer, Cecilia A. Laurie, Kent D. Taylor, Brian L. Browning, Yun Li, George Papanicolaou, Jerome I. Rotter, Ryo Kurita, Yukio Nakamura, Sharon R. Browning, Ruth J.F. LoosKari E. North, Cathy C. Laurie, Timothy A. Thornton, Nathan Pankratz, Daniel E. Bauer, Tamar Sofer, Alex P. Reiner

Research output: Contribution to journalArticlepeer-review

23 Scopus citations

Abstract

Prior GWAS have identified loci associated with red blood cell (RBC) traits in populations of European, African, and Asian ancestry. These studies have not included individuals with an Amerindian ancestral background, such as Hispanics/Latinos, nor evaluated the full spectrum of genomic variation beyond single nucleotide variants. Using a custom genotyping array enriched for Amerindian ancestral content and 1000 Genomes imputation, we performed GWAS in 12,502 participants of Hispanic Community Health Study and Study of Latinos (HCHS/SOL) for hematocrit, hemoglobin, RBC count, RBC distribution width (RDW), and RBC indices. Approximately 60% of previously reported RBC trait loci generalized to HCHS/SOL Hispanics/Latinos, including African ancestral alpha- and beta-globin gene variants. In addition to the known 3.8kb alpha-globin copy number variant, we identified an Amerindian ancestral association in an alpha-globin regulatory region on chromosome 16p13.3 for mean corpuscular volume and mean corpuscular hemoglobin. We also discovered and replicated three genome-wide significant variants in previously unreported loci for RDW (SLC12A2 rs17764730, PSMB5 rs941718), and hematocrit (PROX1 rs3754140). Among the proxy variants at the SLC12A2 locus we identified rs3812049, located in a bi-directional promoter between SLC12A2 (which encodes a red cell membrane ion-transport protein) and an upstream anti-sense long-noncoding RNA, LINC01184, as the likely causal variant. We further demonstrate that disruption of the regulatory element harboring rs3812049 affects transcription of SLC12A2 and LINC01184 in human erythroid progenitor cells. Together, these results reinforce the importance of genetic study of diverse ancestral populations, in particular Hispanics/Latinos.

Original languageEnglish (US)
Article numbere1006760
JournalPLoS genetics
Volume13
Issue number4
DOIs
StatePublished - Apr 2017

Bibliographical note

Funding Information:
The baseline examination of HCHS/SOL was carried out as a collaborative study supported by contracts from the National Heart, Lung, and Blood Institute (NHLBI) to the University of North Carolina (N01-HC65233), University of Miami (N01-HC65234), Albert Einstein College of Medicine (N01-HC65235), Northwestern University (N01-HC65236), and San Diego State University (N01-HC65237). The Genetic Analysis Center at Washington University was supported by NHLBI and NIDCR contracts (HHSN268201300005C AM03 and MOD03). Additional analysis support was provided by 1R01DK101855-01 and 13GRNT16490017. Genotyping efforts were supported by NHLBI HSN 26220/20054C, NCATS CTSI grant UL1TR000123, and NIDDK Diabetes Research Center (DRC) grant DK063491. This research was supported in part by the SOL (Study of Latinos) Grant?a sub-award issued under the Prime Contract No. HHSB268201200054C between HHS, NIH, National Heart, Lung and Blood Institute and Illumina, Inc. The provision of genotyping data was supported in part by the National Center for Advancing Translational Sciences, CTSI grant UL1TR000124, and the National Institute of Diabetes and Digestive and Kidney Disease Diabetes Research Center (DRC) grant DK063491 to the Southern California Diabetes Endocrinology Research Center. SRB was supported by R01-GM110068. The Mount Sinai BioMe Biobank Program is supported by The Andrea and Charles Bronfman Philanthropies. Analyses of BioMe data was supported in part through the computational resources and staff expertise provided by Scientific Computing at the Icahn School of Medicine at Mount Sinai. DEB is supported by NIDDK (K08DK093705) and the Doris Duke Charitable Foundation, Charles H. Hood Foundation, American Society of Hematology, Burroughs Wellcome Fund, and Cooley?s Anemia Foundation. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript. We thank the participants and staff of the HCHS/SOL study for their contributions to this study. This manuscript has been reviewed by the HCHS/SOL Publications Committee for scientific content and consistency of data interpretation with previous HCHS/SOL publications. We also acknowledge Baransel Kamaz, Brenda Briones, and Mitchel Cole for their contributions to genome-editing experiments.

Publisher Copyright:
© 2017 Public Library of Science. All rights reserved.

Copyright:
Copyright 2017 Elsevier B.V., All rights reserved.

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