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Duchen D, Vergara C, Thio CL, Kundu P, Chatterjee N, Thomas DL, Wojcik GL, Duggal P. Pathogen exposure misclassification can bias association signals in GWAS of infectious diseases when using population-based common control subjects. Am J Hum Genet 2023; 110:336-348. [PMID: 36649706 PMCID: PMC9943744 DOI: 10.1016/j.ajhg.2022.12.013] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2022] [Accepted: 12/20/2022] [Indexed: 01/18/2023] Open
Abstract
Genome-wide association studies (GWASs) have been performed to identify host genetic factors for a range of phenotypes, including for infectious diseases. The use of population-based common control subjects from biobanks and extensive consortia is a valuable resource to increase sample sizes in the identification of associated loci with minimal additional expense. Non-differential misclassification of the outcome has been reported when the control subjects are not well characterized, which often attenuates the true effect size. However, for infectious diseases the comparison of affected subjects to population-based common control subjects regardless of pathogen exposure can also result in selection bias. Through simulated comparisons of pathogen-exposed cases and population-based common control subjects, we demonstrate that not accounting for pathogen exposure can result in biased effect estimates and spurious genome-wide significant signals. Further, the observed association can be distorted depending upon strength of the association between a locus and pathogen exposure and the prevalence of pathogen exposure. We also used a real data example from the hepatitis C virus (HCV) genetic consortium comparing HCV spontaneous clearance to persistent infection with both well-characterized control subjects and population-based common control subjects from the UK Biobank. We find biased effect estimates for known HCV clearance-associated loci and potentially spurious HCV clearance associations. These findings suggest that the choice of control subjects is especially important for infectious diseases or outcomes that are conditional upon environmental exposures.
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Affiliation(s)
- Dylan Duchen
- Department of Epidemiology, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD 21205, USA
| | - Candelaria Vergara
- Department of Epidemiology, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD 21205, USA
| | - Chloe L Thio
- Division of Infectious Diseases, Johns Hopkins School of Medicine, Baltimore, MD 21205, USA
| | - Prosenjit Kundu
- Department of Biostatistics, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD 21205, USA
| | - Nilanjan Chatterjee
- Department of Biostatistics, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD 21205, USA
| | - David L Thomas
- Division of Infectious Diseases, Johns Hopkins School of Medicine, Baltimore, MD 21205, USA
| | - Genevieve L Wojcik
- Department of Epidemiology, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD 21205, USA
| | - Priya Duggal
- Department of Epidemiology, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD 21205, USA.
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Yu Z, Abdel-Azim S, Duggal P, Vergara C. Identity by descent mapping of HCV spontaneous clearance in populations of diverse ancestry. RESEARCH SQUARE 2023:rs.3.rs-2433454. [PMID: 36712049 PMCID: PMC9882640 DOI: 10.21203/rs.3.rs-2433454/v1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
Abstract
Background Acute infection with hepatitis C virus (HCV) affects millions of individuals worldwide. Host genetics plays a role in spontaneous clearance of the acute infection which occurs in approximately 30% of the individuals. Common variants in GPR158, genes in the interferon lambda (IFNL) cluster, and the MHC region have been associated with HCV clearance in populations of diverse ancestry. Fine mapping of those regions has identified some key variants and amino acids as potential causal variants but the role of rare variants in those regions and in the genome, in general, has not been explored. We aimed to detect haplotypes containing rare variants related to HCV clearance using identity-by-descent (IBD) haplotype sharing between unrelated cases/case pairs and case/controls pairs in 3,608 individuals with European and African ancestry. Results We detected 1,711,832 and 5,678,043 and individual pairs of IBD segments in the European and African ancestry individuals, respectively. As expected, individuals of African descent had more, and shorter segments compared to Europeans. We did not detect any significant IBD signals in the known associated gene regions. Conclusions IBD is based on sharing of haplotypes and is most powerful in populations with a shared founder or recent common ancestor. For the complex trait of HCV clearance, we used two outbred, global populations that limited our power to detect IBD associations. Overall, in this population-based sample we failed to detect rare variations associated with HCV clearance in individuals of European and African ancestry.
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Affiliation(s)
- Zixuan Yu
- Johns Hopkins University, Bloomberg School of Public Health
| | | | - Priya Duggal
- Johns Hopkins University, Bloomberg School of Public Health
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3
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Valencia A, Vergara C, Thio CL, Vince N, Douillard V, Grifoni A, Cox AL, Johnson EO, Kral AH, Goedert JJ, Mangia A, Piazzolla V, Mehta SH, Kirk GD, Kim AY, Lauer GM, Chung RT, Price JC, Khakoo SI, Alric L, Cramp ME, Donfield SM, Edlin BR, Busch MP, Alexander G, Rosen HR, Murphy EL, Wojcik GL, Carrington M, Gourraud PA, Sette A, Thomas DL, Duggal P. Trans-ancestral fine-mapping of MHC reveals key amino acids associated with spontaneous clearance of hepatitis C in HLA-DQβ1. Am J Hum Genet 2022; 109:299-310. [PMID: 35090584 PMCID: PMC8874224 DOI: 10.1016/j.ajhg.2022.01.001] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2021] [Accepted: 12/14/2021] [Indexed: 12/27/2022] Open
Abstract
Spontaneous clearance of acute hepatitis C virus (HCV) infection is associated with single nucleotide polymorphisms (SNPs) on the MHC class II. We fine-mapped the MHC region in European (n = 1,600; 594 HCV clearance/1,006 HCV persistence) and African (n = 1,869; 340 HCV clearance/1,529 HCV persistence) ancestry individuals and evaluated HCV peptide binding affinity of classical alleles. In both populations, HLA-DQβ1Leu26 (p valueMeta = 1.24 × 10-14) located in pocket 4 was negatively associated with HCV spontaneous clearance and HLA-DQβ1Pro55 (p valueMeta = 8.23 × 10-11) located in the peptide binding region was positively associated, independently of HLA-DQβ1Leu26. These two amino acids are not in linkage disequilibrium (r2 < 0.1) and explain the SNPs and classical allele associations represented by rs2647011, rs9274711, HLA-DQB1∗03:01, and HLA-DRB1∗01:01. Additionally, HCV persistence classical alleles tagged by HLA-DQβ1Leu26 had fewer HCV binding epitopes and lower predicted binding affinities compared to clearance alleles (geometric mean of combined IC50 nM of persistence versus clearance; 2,321 nM versus 761.7 nM, p value = 1.35 × 10-38). In summary, MHC class II fine-mapping revealed key amino acids in HLA-DQβ1 explaining allelic and SNP associations with HCV outcomes. This mechanistic advance in understanding of natural recovery and immunogenetics of HCV might set the stage for much needed enhancement and design of vaccine to promote spontaneous clearance of HCV infection.
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Affiliation(s)
- Ana Valencia
- Johns Hopkins University, School of Medicine, Baltimore, MD 21205, USA; Universidad Pontificia Bolivariana, Medellín, Antioquia 050031, Colombia
| | - Candelaria Vergara
- Johns Hopkins University, Bloomberg School of Public Health, Baltimore, MD 21205, USA
| | - Chloe L Thio
- Johns Hopkins University, School of Medicine, Baltimore, MD 21205, USA
| | - Nicolas Vince
- Université de Nantes, CHU Nantes, Inserm, Centre de Recherche en Transplantation et Immunologie, UMR 1064, ITUN, Nantes 44000, France
| | - Venceslas Douillard
- Université de Nantes, CHU Nantes, Inserm, Centre de Recherche en Transplantation et Immunologie, UMR 1064, ITUN, Nantes 44000, France
| | - Alba Grifoni
- Center for infectious Diseases and Vaccine Research, La Jolla Institute for Immunology, La Jolla, CA 92037, USA
| | - Andrea L Cox
- Johns Hopkins University, School of Medicine, Baltimore, MD 21205, USA
| | - Eric O Johnson
- GenOmics, Bioinformatics, and Translational Research Center, RTI International, Research Triangle Park, NC 27709, USA
| | - Alex H Kral
- GenOmics, Bioinformatics, and Translational Research Center, RTI International, Research Triangle Park, NC 27709, USA
| | - James J Goedert
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Alessandra Mangia
- Liver Unit, Medical Sciences Department, Fondazione "Casa Sollievo della Sofferenza" IRCCS, 71013 San Giovanni Rotondo, Italy
| | - Valeria Piazzolla
- Liver Unit, Medical Sciences Department, Fondazione "Casa Sollievo della Sofferenza" IRCCS, 71013 San Giovanni Rotondo, Italy
| | - Shruti H Mehta
- Johns Hopkins University, Bloomberg School of Public Health, Baltimore, MD 21205, USA
| | - Gregory D Kirk
- Johns Hopkins University, School of Medicine, Baltimore, MD 21205, USA; Johns Hopkins University, Bloomberg School of Public Health, Baltimore, MD 21205, USA
| | - Arthur Y Kim
- Division of Infectious Diseases, Department of Medicine, Massachusetts General Hospital and Harvard Medical School, Boston, MA 02114, USA
| | - Georg M Lauer
- Liver Center and Gastrointestinal Division, Department of Medicine, Massachusetts General Hospital and Harvard Medical School, Boston, MA 02114, USA
| | - Raymond T Chung
- Liver Center and Gastrointestinal Division, Department of Medicine, Massachusetts General Hospital and Harvard Medical School, Boston, MA 02114, USA
| | - Jennifer C Price
- Division of Gastroenterology, Department of Medicine, School of Medicine, University of California, San Francisco, CA 94143, USA
| | - Salim I Khakoo
- University of Southampton, Southampton General Hospital, Southampton SO16 6YD, UK
| | - Laurent Alric
- Internal Medicine-Department of Digestive Diseases, Rangueil Hospital, Toulouse University, 1, 31400 Toulouse, France
| | | | | | - Brian R Edlin
- SUNY Downstate College of Medicine, Brooklyn, NY 11203, USA
| | - Michael P Busch
- University of California San Francisco and Vitalant Research Institute, San Francisco, CA 94118, USA
| | - Graeme Alexander
- UCL Institute for Liver and Digestive Health, The Royal Free Hospital, Pond St, Hampstead, London NW3 2QG, UK
| | | | - Edward L Murphy
- University of California San Francisco and Vitalant Research Institute, San Francisco, CA 94118, USA
| | - Genevieve L Wojcik
- Johns Hopkins University, Bloomberg School of Public Health, Baltimore, MD 21205, USA
| | - Mary Carrington
- Basic Science Program, Frederick National Laboratory for Cancer Research, National Cancer Institute, Frederick, MD 21702, USA; Laboratory of Integrative Cancer Immunology, Center for Cancer Research, National Cancer Institute, Bethesda, MD 20892, USA; Ragon Institute of MGH, MIT and Harvard, Cambridge, MA 02139, USA
| | - Pierre-Antoine Gourraud
- Université de Nantes, CHU Nantes, Inserm, Centre de Recherche en Transplantation et Immunologie, UMR 1064, ITUN, Nantes 44000, France
| | - Alessandro Sette
- Center for infectious Diseases and Vaccine Research, La Jolla Institute for Immunology, La Jolla, CA 92037, USA; Department of Medicine, Division of Infectious Diseases and Global Public Health, University of California, San Diego (UCSD), La Jolla, CA 92093, USA
| | - David L Thomas
- Johns Hopkins University, School of Medicine, Baltimore, MD 21205, USA
| | - Priya Duggal
- Johns Hopkins University, Bloomberg School of Public Health, Baltimore, MD 21205, USA.
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4
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Vergara C, Valencia A, Thio CL, Goedert JJ, Mangia A, Piazzolla V, Johnson E, Kral AH, O’Brien TR, Mehta SH, Kirk GD, Kim AY, Lauer GM, Chung RT, Cox AL, Peters MG, Khakoo SI, Alric L, Cramp ME, Donfield SM, Edlin BR, Busch MP, Alexander G, Rosen HR, Murphy EL, Wojcik GL, Taub MA, Thomas DL, Duggal P. A Multiancestry Sex-Stratified Genome-Wide Association Study of Spontaneous Clearance of Hepatitis C Virus. J Infect Dis 2021; 223:2090-2098. [PMID: 33119750 PMCID: PMC8205624 DOI: 10.1093/infdis/jiaa677] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2020] [Accepted: 10/28/2020] [Indexed: 11/14/2022] Open
Abstract
BACKGROUND Spontaneous clearance of acute hepatitis C virus (HCV) infection is more common in women than in men, independent of known risk factors. METHODS To identify sex-specific genetic loci, we studied 4423 HCV-infected individuals (2903 male, 1520 female) of European, African, and Hispanic ancestry. We performed autosomal, and X chromosome sex-stratified and combined association analyses in each ancestry group. RESULTS A male-specific region near the adenosine diphosphate-ribosylation factor-like 5B (ARL5B) gene was identified. Individuals with the C allele of rs76398191 were about 30% more likely to have chronic HCV infection than individuals with the T allele (OR, 0.69; P = 1.98 × 10-07), and this was not seen in females. The ARL5B gene encodes an interferon-stimulated gene that inhibits immune response to double-stranded RNA viruses. We also identified suggestive associations near septin 6 and ribosomal protein L39 genes on the X chromosome. In box sexes, allele G of rs12852885 was associated with a 40% increase in HCV clearance compared with the A allele (OR, 1.4; P = 2.46 × 10-06). Septin 6 facilitates HCV replication via interaction with the HCV NS5b protein, and ribosomal protein L39 acts as an HCV core interactor. CONCLUSIONS These novel gene associations support differential mechanisms of HCV clearance between the sexes and provide biological targets for treatment or vaccine development.
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Affiliation(s)
- Candelaria Vergara
- Johns Hopkins University, Bloomberg School of Public Health, Baltimore, Maryland, USA
| | - Ana Valencia
- Johns Hopkins University, School of Medicine, Baltimore, Maryland, USA
- Universidad Pontificia Bolivariana, Medellín, Colombia
| | - Chloe L Thio
- Johns Hopkins University, School of Medicine, Baltimore, Maryland, USA
| | - James J Goedert
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, Maryland, USA
| | - Alessandra Mangia
- Liver Unit IRCCS “Casa Sollievo della Sofferenza,” San Giovanni Rotondo, Italy
| | - Valeria Piazzolla
- Liver Unit IRCCS “Casa Sollievo della Sofferenza,” San Giovanni Rotondo, Italy
| | - Eric Johnson
- RTI International, Research Triangle Park, North Carolina, USA
| | - Alex H Kral
- RTI International, Research Triangle Park, North Carolina, USA
| | - Thomas R O’Brien
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, Maryland, USA
| | - Shruti H Mehta
- Johns Hopkins University, Bloomberg School of Public Health, Baltimore, Maryland, USA
| | - Gregory D Kirk
- Johns Hopkins University, Bloomberg School of Public Health, Baltimore, Maryland, USA
- Johns Hopkins University, School of Medicine, Baltimore, Maryland, USA
| | - Arthur Y Kim
- Division of Infectious Diseases, Department of Medicine, Massachusetts General Hospital and Harvard Medical School, Boston, Massachusetts, USA
| | - Georg M Lauer
- Liver Center and Gastrointestinal Division, Department of Medicine, Massachusetts General Hospital and Harvard Medical School, Boston, Massachusetts, USA
| | - Raymond T Chung
- Liver Center and Gastrointestinal Division, Department of Medicine, Massachusetts General Hospital and Harvard Medical School, Boston, Massachusetts, USA
| | - Andrea L Cox
- Johns Hopkins University, Bloomberg School of Public Health, Baltimore, Maryland, USA
| | - Marion G Peters
- Division of Gastroenterology, Department of Medicine, School of Medicine, University of California, San Francisco, California, USA
| | - Salim I Khakoo
- University of Southampton, Southampton General Hospital, Southampton, United Kingdom
| | - Laurent Alric
- Department of Internal Medicine and Digestive Diseases, CHU Rangueil, UMR 152 IRD, Toulouse 3 University, France
| | | | | | - Brian R Edlin
- SUNY Downstate College of Medicine, Brooklyn, New York, USA
| | - Michael P Busch
- University of California and Vitalant Research Institute, San Francisco, California, USA
| | - Graeme Alexander
- UCL Institute for Liver and Digestive Health, Royal Free Hospital, Hampstead, London, United Kingdom
| | | | - Edward L Murphy
- University of California and Vitalant Research Institute, San Francisco, California, USA
| | - Genevieve L Wojcik
- Johns Hopkins University, Bloomberg School of Public Health, Baltimore, Maryland, USA
| | - Margaret A Taub
- Johns Hopkins University, Bloomberg School of Public Health, Baltimore, Maryland, USA
| | - David L Thomas
- Johns Hopkins University, School of Medicine, Baltimore, Maryland, USA
| | - Priya Duggal
- Johns Hopkins University, School of Medicine, Baltimore, Maryland, USA
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5
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Vergara C, Duggal P, Thio CL, Valencia A, O'Brien TR, Latanich R, Timp W, Johnson EO, Kral AH, Mangia A, Goedert JJ, Piazzola V, Mehta SH, Kirk GD, Peters MG, Donfield SM, Edlin BR, Busch MP, Alexander G, Murphy EL, Kim AY, Lauer GM, Chung RT, Cramp ME, Cox AL, Khakoo SI, Rosen HR, Alric L, Wheelan SJ, Wojcik GL, Thomas DL, Taub MA. Multi-ancestry fine mapping of interferon lambda and the outcome of acute hepatitis C virus infection. Genes Immun 2020; 21:348-359. [PMID: 33116245 PMCID: PMC7657970 DOI: 10.1038/s41435-020-00115-3] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2019] [Revised: 10/08/2020] [Accepted: 10/12/2020] [Indexed: 02/06/2023]
Abstract
Clearance of acute infection with hepatitis C virus (HCV) is associated with the chr19q13.13 region containing the rs368234815 (TT/ΔG) polymorphism. We fine-mapped this region to detect possible causal variants that may contribute to HCV clearance. First, we performed sequencing of IFNL1-IFNL4 region in 64 individuals sampled according to rs368234815 genotype: TT/clearance (N = 16) and ΔG/persistent (N = 15) (genotype-outcome concordant) or TT/persistent (N = 19) and ΔG/clearance (N = 14) (discordant). 25 SNPs had a difference in counts of alternative allele >5 between clearance and persistence individuals. Then, we evaluated those markers in an association analysis of HCV clearance conditioning on rs368234815 in two groups of European (692 clearance/1 025 persistence) and African ancestry (320 clearance/1 515 persistence) individuals. 10/25 variants were associated (P < 0.05) in the conditioned analysis leaded by rs4803221 (P value = 4.9 × 10-04) and rs8099917 (P value = 5.5 × 10-04). In the European ancestry group, individuals with the haplotype rs368234815ΔG/rs4803221C were 1.7× more likely to clear than those with the rs368234815ΔG/rs4803221G haplotype (P value = 3.6 × 10-05). For another nearby SNP, the haplotype of rs368234815ΔG/rs8099917T was associated with HCV clearance compared to rs368234815ΔG/rs8099917G (OR: 1.6, P value = 1.8 × 10-04). We identified four possible causal variants: rs368234815, rs12982533, rs10612351 and rs4803221. Our results suggest a main signal of association represented by rs368234815, with contributions from rs4803221, and/or nearby SNPs including rs8099917.
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Affiliation(s)
- Candelaria Vergara
- Johns Hopkins University, Bloomberg School of Public Health, Baltimore, MD, USA.
| | - Priya Duggal
- Johns Hopkins University, Bloomberg School of Public Health, Baltimore, MD, USA
| | - Chloe L Thio
- Johns Hopkins University, School of Medicine, Baltimore, MD, USA
| | - Ana Valencia
- Johns Hopkins University, School of Medicine, Baltimore, MD, USA
- Universidad Pontificia Bolivariana, Medellin, Colombia
| | - Thomas R O'Brien
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Rachel Latanich
- Johns Hopkins University, School of Medicine, Baltimore, MD, USA
| | - Winston Timp
- Johns Hopkins University, School of Medicine, Baltimore, MD, USA
| | | | - Alex H Kral
- RTI International, Research Triangle Park, NC, USA
| | - Alessandra Mangia
- Liver Unit IRCCS "Casa Sollievo della Sofferenza", San Giovanni Rotondo, Italy
| | - James J Goedert
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Valeria Piazzola
- Liver Unit IRCCS "Casa Sollievo della Sofferenza", San Giovanni Rotondo, Italy
| | - Shruti H Mehta
- Johns Hopkins University, Bloomberg School of Public Health, Baltimore, MD, USA
| | - Gregory D Kirk
- Johns Hopkins University, Bloomberg School of Public Health, Baltimore, MD, USA
| | - Marion G Peters
- Division of Gastroenterology, Department of Medicine, School of Medicine, University of California, San Francisco, CA, USA
| | | | - Brian R Edlin
- Centers for Disease Control and Prevention, Atlanta, GA, USA
| | - Michael P Busch
- University of California San Francisco and Vitalant Research Institute, San Francisco, CA, USA
| | - Graeme Alexander
- University College London Institute for Liver and Digestive Health, The Royal Free Hospital, London, UK
| | - Edward L Murphy
- University of California San Francisco and Vitalant Research Institute, San Francisco, CA, USA
| | - Arthur Y Kim
- Division of Infectious Diseases, Department of Medicine, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA
| | - Georg M Lauer
- Liver Center and Gastrointestinal Division, Department of Medicine, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA
| | - Raymond T Chung
- Liver Center and Gastrointestinal Division, Department of Medicine, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA
| | | | - Andrea L Cox
- Johns Hopkins University, School of Medicine, Baltimore, MD, USA
| | - Salim I Khakoo
- University of Southampton, Southampton General Hospital, Southampton, UK
| | | | - Laurent Alric
- Department of Internal Medicine and Digestive Diseases, Centre Hospitalier Universitaire Rangueil, UMR 152, Institut de Recherche pour le Développement Toulouse 3 University, Toulouse, France
| | - Sarah J Wheelan
- Johns Hopkins University, Bloomberg School of Public Health, Baltimore, MD, USA
- Johns Hopkins University, School of Medicine, Baltimore, MD, USA
| | - Genevieve L Wojcik
- Johns Hopkins University, Bloomberg School of Public Health, Baltimore, MD, USA
| | - David L Thomas
- Johns Hopkins University, School of Medicine, Baltimore, MD, USA
| | - Margaret A Taub
- Johns Hopkins University, Bloomberg School of Public Health, Baltimore, MD, USA
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6
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Vergara C, Parker MM, Franco L, Cho MH, Valencia-Duarte AV, Beaty TH, Duggal P. Genotype imputation performance of three reference panels using African ancestry individuals. Hum Genet 2018; 137:281-292. [PMID: 29637265 PMCID: PMC6209094 DOI: 10.1007/s00439-018-1881-4] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2018] [Accepted: 03/31/2018] [Indexed: 12/22/2022]
Abstract
Genotype imputation estimates unobserved genotypes from genome-wide makers, to increase genome coverage and power for genome-wide association studies. Imputation has been successful for European ancestry populations in which very large reference panels are available. Smaller subsets of African descent populations are available in 1000 Genomes (1000G), the Consortium on Asthma among African ancestry Populations in the Americas (CAAPA) and the Haplotype Reference Consortium (HRC). We compared the performance of these reference panels when imputing variation in 3747 African Americans (AA) from two cohorts (HCV and COPDGene) genotyped using Illumina Omni microarrays. The haplotypes of 2504 (1000G), 883 (CAAPA) and 32,470 individuals (HRC) were used as reference. We compared the number of variants, imputation quality, imputation accuracy and coverage between panels. In both cohorts, 1000G imputed 1.5-1.6× more variants than CAAPA and 1.2× more than HRC. Similar findings were observed for variants with imputation R2 > 0.5 and for rare, low-frequency, and common variants. When merging imputed variants of the three panels, the total number was 62-63 M with 20 M overlapping variants imputed by all three panels, and a range of 5-15 M variants imputed exclusively with one of them. For overlapping variants, imputation quality was highest for HRC, followed by 1000G, then CAAPA, and improved as the minor allele frequency increased. 1000G, HRC and CAAPA provided high performance and accuracy for imputation of African American individuals, increasing the number of variants available for subsequent analyses. These panels are complementary and would benefit from the development of an integrated African reference panel.
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Affiliation(s)
| | - Margaret M Parker
- Channing Division of Network Medicine, Brigham and Women's Hospital, Boston, MA, USA
| | - Liliana Franco
- National School of Public Health, Universidad de Antioquia, Medellín, Colombia
- School of Medicine, Universidad Pontificia Bolivariana, Medellín, Colombia
| | - Michael H Cho
- Channing Division of Network Medicine, Brigham and Women's Hospital, Boston, MA, USA
- Division of Pulmonary and Critical Care Medicine, Brigham and Women's Hospital, Boston, MA, USA
| | | | - Terri H Beaty
- Johns Hopkins University, Bloomberg School of Public Health, Baltimore, MD, USA
| | - Priya Duggal
- Johns Hopkins University, Bloomberg School of Public Health, Baltimore, MD, USA.
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