Title | Allelic Heterogeneity at the CRP Locus Identified by Whole-Genome Sequencing in Multi-ancestry Cohorts. |
Publication Type | Journal Article |
Year of Publication | 2020 |
Authors | Raffield, LM, Iyengar, AK, Wang, B, Gaynor, SM, Spracklen, CN, Zhong, X, Kowalski, MH, Salimi, S, Polfus, LM, Benjamin, EJ, Bis, JC, Bowler, R, Cade, BE, Choi, WJung, Comellas, AP, Correa, A, Cruz, P, Doddapaneni, H, Durda, P, Gogarten, SM, Jain, D, Kim, RW, Kral, BG, Lange, LA, Larson, MG, Laurie, C, Lee, J, Lee, S, Lewis, JP, Metcalf, GA, Mitchell, BD, Momin, Z, Muzny, DM, Pankratz, N, Park, CJoo, Rich, SS, Rotter, JI, Ryan, K, Seo, D, Tracy, RP, Viaud-Martinez, KA, Yanek, LR, Zhao, LPing, Lin, X, Li, B, Li, Y, Dupuis, J, Reiner, AP, Mohlke, KL, Auer, PL |
Corporate Authors | TOPMed Inflammation Working Group, NHLBI Trans-Omics for Precision Medicine (TOPMed) Consortium |
Journal | Am J Hum Genet |
Volume | 106 |
Issue | 1 |
Pagination | 112-120 |
Date Published | 2020 Jan 02 |
ISSN | 1537-6605 |
Keywords | Asian People, Black People, C-Reactive Protein, Cohort Studies, Gene Frequency, Genetic Predisposition to Disease, Genome-Wide Association Study, Humans, Linkage Disequilibrium, Polymorphism, Single Nucleotide, White People, Whole Genome Sequencing |
Abstract | Whole-genome sequencing (WGS) can improve assessment of low-frequency and rare variants, particularly in non-European populations that have been underrepresented in existing genomic studies. The genetic determinants of C-reactive protein (CRP), a biomarker of chronic inflammation, have been extensively studied, with existing genome-wide association studies (GWASs) conducted in >200,000 individuals of European ancestry. In order to discover novel loci associated with CRP levels, we examined a multi-ancestry population (n = 23,279) with WGS (∼38× coverage) from the Trans-Omics for Precision Medicine (TOPMed) program. We found evidence for eight distinct associations at the CRP locus, including two variants that have not been identified previously (rs11265259 and rs181704186), both of which are non-coding and more common in individuals of African ancestry (∼10% and ∼1% minor allele frequency, respectively, and rare or monomorphic in 1000 Genomes populations of East Asian, South Asian, and European ancestry). We show that the minor (G) allele of rs181704186 is associated with lower CRP levels and decreased transcriptional activity and protein binding in vitro, providing a plausible molecular mechanism for this African ancestry-specific signal. The individuals homozygous for rs181704186-G have a mean CRP level of 0.23 mg/L, in contrast to individuals heterozygous for rs181704186 with mean CRP of 2.97 mg/L and major allele homozygotes with mean CRP of 4.11 mg/L. This study demonstrates the utility of WGS in multi-ethnic populations to drive discovery of complex trait associations of large effect and to identify functional alleles in noncoding regulatory regions. |
DOI | 10.1016/j.ajhg.2019.12.002 |
Alternate Journal | Am J Hum Genet |
PubMed ID | 31883642 |
PubMed Central ID | PMC7042494 |
Grant List | K01 AG059898 / AG / NIA NIH HHS / United States R01 HG006703 / HG / NHGRI NIH HHS / United States R01 HL137922 / HL / NHLBI NIH HHS / United States R01 HL076784 / HL / NHLBI NIH HHS / United States R01 HL120854 / HL / NHLBI NIH HHS / United States R01 HL128914 / HL / NHLBI NIH HHS / United States T32 HL129982 / HL / NHLBI NIH HHS / United States HHSN268201800013I / MD / NIMHD NIH HHS / United States HHSN268201800011C / HL / NHLBI NIH HHS / United States HHSN268201800010I / HB / NHLBI NIH HHS / United States HHSN268201800011I / HB / NHLBI NIH HHS / United States K01 HL135405 / HL / NHLBI NIH HHS / United States R01 HL132947 / HL / NHLBI NIH HHS / United States R35 CA197449 / CA / NCI NIH HHS / United States HHSN268201800012C / HL / NHLBI NIH HHS / United States HHSN268201500001C / HL / NHLBI NIH HHS / United States P30 ES005605 / ES / NIEHS NIH HHS / United States R01 DK072193 / DK / NIDDK NIH HHS / United States R01 HL129132 / HL / NHLBI NIH HHS / United States HHSN268201500001I / HL / NHLBI NIH HHS / United States HHSN268201800012I / HL / NHLBI NIH HHS / United States N01HC25195 / HL / NHLBI NIH HHS / United States HHSN268201800015I / HB / NHLBI NIH HHS / United States U01 DK105561 / DK / NIDDK NIH HHS / United States U01 HG009086 / HG / NHGRI NIH HHS / United States R01 AG028321 / AG / NIA NIH HHS / United States |
Allelic Heterogeneity at the CRP Locus Identified by Whole-Genome Sequencing in Multi-ancestry Cohorts.
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