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Exome Genotyping Identifies Pleiotropic Variants Associated with Red Blood Cell Traits.

TitleExome Genotyping Identifies Pleiotropic Variants Associated with Red Blood Cell Traits.
Publication TypeJournal Article
Year of Publication2016
AuthorsChami, N, Chen, M-H, Slater, AJ, Eicher, JD, Evangelou, E, Tajuddin, SM, Love-Gregory, L, Kacprowski, T, Schick, UM, Nomura, A, Giri, A, Lessard, S, Brody, JA, Schurmann, C, Pankratz, N, Yanek, LR, Manichaikul, A, Pazoki, R, Mihailov, E, W Hill, D, Raffield, LM, Burt, A, Bartz, TM, Becker, DM, Becker, LC, Boerwinkle, E, Bork-Jensen, J, Bottinger, EP, O'Donoghue, ML, Crosslin, DR, de Denus, S, Dube, M-P, Elliott, P, Engström, G, Evans, MK, Floyd, JS, Fornage, M, Gao, H, Greinacher, A, Gudnason, V, Hansen, T, Harris, TB, Hayward, C, Hernesniemi, J, Highland, HM, Hirschhorn, JN, Hofman, A, Irvin, MR, Kähönen, M, Lange, E, Launer, LJ, Lehtimäki, T, Li, J, Liewald, DCM, Linneberg, A, Liu, Y, Lu, Y, Lyytikäinen, L-P, Mägi, R, Mathias, RA, Melander, O, Metspalu, A, Mononen, N, Nalls, MA, Nickerson, DA, Nikus, K, O'Donnell, CJ, Orho-Melander, M, Pedersen, O, Petersmann, A, Polfus, L, Psaty, BM, Raitakari, OT, Raitoharju, E, Richard, M, Rice, KM, Rivadeneira, F, Rotter, JI, Schmidt, F, Smith, AVernon, Starr, JM, Taylor, KD, Teumer, A, Thuesen, BH, Torstenson, ES, Tracy, RP, Tzoulaki, I, Zakai, NA, Vacchi-Suzzi, C, van Duijn, CM, van Rooij, FJA, Cushman, M, Deary, IJ, Edwards, DRVelez, Vergnaud, A-C, Wallentin, L, Waterworth, DM, White, HD, Wilson, JG, Zonderman, AB, Kathiresan, S, Grarup, N, Esko, T, Loos, RJF, Lange, LA, Faraday, N, Abumrad, NA, Edwards, TL, Ganesh, SK, Auer, PL, Johnson, AD, Reiner, AP, Lettre, G
JournalAm J Hum Genet
Volume99
Issue1
Pagination8-21
Date Published2016 Jul 07
ISSN1537-6605
Abstract

Red blood cell (RBC) traits are important heritable clinical biomarkers and modifiers of disease severity. To identify coding genetic variants associated with these traits, we conducted meta-analyses of seven RBC phenotypes in 130,273 multi-ethnic individuals from studies genotyped on an exome array. After conditional analyses and replication in 27,480 independent individuals, we identified 16 new RBC variants. We found low-frequency missense variants in MAP1A (rs55707100, minor allele frequency [MAF] = 3.3%, p = 2 × 10(-10) for hemoglobin [HGB]) and HNF4A (rs1800961, MAF = 2.4%, p < 3 × 10(-8) for hematocrit [HCT] and HGB). In African Americans, we identified a nonsense variant in CD36 associated with higher RBC distribution width (rs3211938, MAF = 8.7%, p = 7 × 10(-11)) and showed that it is associated with lower CD36 expression and strong allelic imbalance in ex vivo differentiated human erythroblasts. We also identified a rare missense variant in ALAS2 (rs201062903, MAF = 0.2%) associated with lower mean corpuscular volume and mean corpuscular hemoglobin (p < 8 × 10(-9)). Mendelian mutations in ALAS2 are a cause of sideroblastic anemia and erythropoietic protoporphyria. Gene-based testing highlighted three rare missense variants in PKLR, a gene mutated in Mendelian non-spherocytic hemolytic anemia, associated with HGB and HCT (SKAT p < 8 × 10(-7)). These rare, low-frequency, and common RBC variants showed pleiotropy, being also associated with platelet, white blood cell, and lipid traits. Our association results and functional annotation suggest the involvement of new genes in human erythropoiesis. We also confirm that rare and low-frequency variants play a role in the architecture of complex human traits, although their phenotypic effect is generally smaller than originally anticipated.

DOI10.1016/j.ajhg.2016.05.007
Alternate JournalAm. J. Hum. Genet.
PubMed ID27346685
PubMed Central IDPMC5005438
Grant ListR01 DK060022 / DK / NIDDK NIH HHS / United States
R01 HL107816 / HL / NHLBI NIH HHS / United States
P30 DK056341 / DK / NIDDK NIH HHS / United States
UL1 TR000124 / TR / NCATS NIH HHS / United States
P30 DK063491 / DK / NIDDK NIH HHS / United States
R01 DK033301 / DK / NIDDK NIH HHS / United States
R21 HL121422 / HL / NHLBI NIH HHS / United States