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Admixture Mapping Identifies an Amerindian Ancestry Locus

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Admixture Mapping Identifies an Amerindian Ancestry Locus CLINICAL RESEARCH www.jasn.org Admixture Mapping Identifies an Amerindian Ancestry Locus Associated with Albuminuria in Hispanics in the United States † ‡ Lisa A. Brown,* Tamar Sofer,* Adrienne M. Stilp,* Leslie J. Baier, Holly J. Kramer, † † | Ivica Masindova, Daniel Levy,§ Robert L. Hanson, Ashley E. Moncrieft, Susan Redline,¶ †† ‡‡ Sylvia E. Rosas,** James P. Lash, Jianwen Cai, Cathy C. Laurie,* Sharon Browning,* Timothy Thornton,* and Nora Franceschini§§ *Department of Biostatistics, University of Washington School of Public Health, Seattle, Washington; †Epidemiology and Clinical Branch, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Phoenix, Arizona; ‡Department of Public Health Sciences and Medicine, Division of Nephrology and Hypertension, Loyola University Chicago, Maywood, Illinois; §The Framingham Heart Study, Framingham, Massachusetts, and Population Sciences Branch, National Heart, Lung, and Blood Institute, US National Institutes of Health, Bethesda, Maryland; |Department of Psychology, University of Miami, Miami, Florida; ¶Department of Medicine, Brigham and Women’s Hospital and Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, Massachusetts; **Department of Medicine, Division of Nephrology, Beth Israel Deaconess Medical Center, Boston, Massachusetts; ††Department of Medicine, Division of Nephrology and Institute for Minority Health Research, University of Illinois at Chicago, Chicago, Illinois; ‡‡Collaborative Studies Coordinating Center, Department of Biostatistics, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina; and §§Department of Epidemiology, Gillings School of Global Public Health, University of North Carolina, Chapel Hill, North Carolina ABSTRACT Increased urine albumin excretion is highly prevalent in Hispanics/Latinos. Previous studies have found an association between urine albumin excretion and Amerindian ancestry in Hispanic/Latino populations. Admixture between racial/ ethnic groups creates long-range linkage disequilibrium between variants with different allelic frequencies in the founding populations and it can be used to localize genes. Hispanic/Latino genomes are an admixture of European, African, and Amerindian ancestries. We leveraged this admixture to identify associations between urine albumin excretion (urine albumin-to-creatinine ratio [UACR]) and genomic regions harboring variants with highly differentiated allele frequencies among the ancestral populations. Admixture mapping analysis of 12,212 Hispanic Community Health Study/Study of Latinos participants, using a linear mixed model, identified three novel genome-wide significant signals on chromosomes 2, 11, and 16. The admixture mapping signal identified on chromosome 2, spanning q11.2–14.1 and not previously reported for UACR, is driven by a difference between Amerindian ancestry and the other two ancestries 2 (P,5.7 3 10 5). Within this locus, two common variants located at the proapoptotic BCL2L11 gene associated with 2 2 UACR: rs116907128 (allele frequency =0.14; P=1.5 310 7) and rs586283 (C allele frequency =0.35; P=4.2 310 7). In a secondary analysis, rs116907128 accounted for most of the admixture mapping signal observed in the region. The rs116907128 variant is common among full-heritage Pima Indians (A allele frequency =0.54) but is monomorphic in the 1000 Genomes European and African populations. In a replication analysis using a sample of full-heritage Pima Indians, rs116907128 significantly associated with UACR (P=0.01; n=1568). Our findingsprovideevidenceforthepresenceof Amerindian-specificvariantsinfluencing the variation of urine albumin excretion in Hispanics/Latinos. CLINICAL RESEARCH J Am Soc Nephrol 28: 2211–2220, 2017. doi: https://doi.org/10.1681/ASN.2016091010 Received September 20, 2016. Accepted December 29, 2016. Carolina, Gillings School of Global Public Health, 137 E. Franklin St. #306, Chapel Hill, NC. Email: [email protected] Published online ahead of print. Publication date available at www.jasn.org. Copyright © 2017 by the American Society of Nephrology Correspondence: Dr. Nora Franceschini, University of North J Am Soc Nephrol 28: 2211–2220, 2017 ISSN : 1046-6673/2807-2211 2211 CLINICAL RESEARCH www.jasn.org Increased urine albumin excretion is associated with a higher hypertensive-associated CKD, FSGS, and HIV nephropathy in lifetime risk of ESRD and with increased cardiovascular disease blacks.12,15 risk.1,2 Both increased urine albumin excretion and ESRD dif- The HCHS/SOL study reported here used admixture map- fer by racial/ethnic groups in the United States, with the ping analysis in a large population sample of Hispanics/Latinos lowest and highest risks noted in European and Amerindian to identify loci that may harbor variants that increase urine populations, respectively. Using sex-specific cut-points, in- albumin excretion. We identified a new locus at chromosome 2 creased urine albumin excretion prevalence in the United that harbors an Amerindian-specific variant associated with States is 10.3% in whites, 13.6% in blacks, 9.9% in Mexican urine albumin excretion and these findings were replicated in a Americans,3 .20% in American Indians,4 and 12%–14% in cohort of Pima Indians. Hispanics/Latinos of the Hispanic Community Health Study/ Study of Latinos (HCHS/SOL).5 Hispanics/Latinos also have an approximately two-fold higher risk of ESRD than whites.6 RESULTS However, Hispanics/Latinos are a heterogeneous group who show diversity in ancestry background including Amerindian, We analyzed a sample of 12,212 Hispanic/Latino individuals European, and West African.7 The percentages of African from the HCHS/SOL, with mean age of 46 years (SD=14 and Amerindian ancestry have previously been associated years), and with 41% men, 20% of patients with diabetes, with increased urine albumin excretion prevalence in Hispanic/ 28% hypertensive, and 43% with obesity. The UACR was Latino populations.8,9 6.54 mg/dl (interquartile range, 4.49–12.24). Three percent Despite the strong evidence for a role of ancestry in CKD of individuals had an eGFR,60 ml/min per 1.73 m2 and susceptibility, few studies of kidney traits have leveraged the 14.1% had increased UACR ($17 mg/g in men and $25 mg/g known genetic admixture in Hispanic/Latino populations to in women). discover potential chromosomal regions that may harbor var- Local ancestry was estimated as European, African, or iants that confer risk for CKD traits such as urine albumin Amerindian at each of 419,645 genotyped SNPs across the excretion. Among the genome-wide significant loci that have autosomes.16 Admixture mapping consisted of a joint test of been identified and consistently replicated for urine albumin the effects of all three ancestry types on log-transformed excretion, CUBN (chromosome 10) genetic variants are asso- UACR at each of the 419,645 SNP positions (using a linear ciated with urine albumin excretion in individuals of Euro- mixed model with multiple fixed and random effects, as de- pean ancestry and Hispanics/Latinos,10 and the HBB variant scribed in Concise Methods). This analysis identified three 2 related to sickle cell trait (chromosome 11) is African-specific regions with P value(s) ,5.7 3 10 5, indicating genome- and associated with urine albumin excretion in Hispanics/ wide significance (Figure 1A). The most significant peak spans 2 Latinos with African admixture.11 An additional African-specific 2q11.2–q14.1 with a minimum P value achieved (P=5.6 3 10 7) gene associated with increased urine albumin excretion and at 2q13. The second spans 11q13.2–q13.4 with a peak at 2 CKD is APOL1.12,13 Our recent work in the HCHS/SOL has 11q13.3 (P=3.4 3 10 5). The third peak is located in the 2 confirmed a high proportion of Amerindian ancestry among 16p13.3 gene region (P=3.6 3 10 5). Secondary admixture Mainland Hispanics (Mexican, Central, and South American), mapping analyses that tested the effect of each local ancestry who also had a low proportion of African ancestry.14 However, type separately revealed that the 2q13 locus was significantly Mainland Hispanics have similar mean urine albumin excretion associated with local Amerindian ancestry, whereas the 11q13 and frequency of increased urine albumin excretion compared locus was associated with both local Amerindian and local with individuals of Caribbean background (Cuban, Dominican, European ancestries, and the 16p13 locus was associated Puerto-Rican), despite the absence of African-specific risk var- with local African ancestry (Figure 2). The estimates for ad- iants (APOL1 or HBB). This evidence suggests the presence of mixture mapping are shown in the Supplemental Table 1. Amerindian ancestry variants in Hispanics/Latinos influencing Single-variant association analyses performed using imputed urine albumin excretion. genotypes within a 10 Mb window around 2q11.2–q14.1 yielded There is great potential for genetic studies of CKD in Hispanics/ two SNPs significantly associated with UACR: rs116907128 (allele 2 Latinos to provide new insight into population-specific variants frequency for A allele =0.14; P=1.5 3 10 7) and rs586283 (allele 2 that confer risk for CKD traits but have not been uncovered frequency for C allele =0.35; P=4.2 3 10 7)(Figure3A,Supple- through genome-wide association studies (GWAS). Admixture mental Material, Table 1). In analysis excluding diabetic individ- mapping leverages the known genomic heterogeneity of ad- uals, the association of rs116907128 with UACR was unchanged 2 mixed individuals for improved
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