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Randolph HE, Aracena KA, Lin YL, Mu Z, Barreiro LB. Shaping immunity: The influence of natural selection on population immune diversity. Immunol Rev 2024; 323:227-240. [PMID: 38577999 DOI: 10.1111/imr.13329] [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] [Indexed: 04/06/2024]
Abstract
Humans exhibit considerable variability in their immune responses to the same immune challenges. Such variation is widespread and affects individual and population-level susceptibility to infectious diseases and immune disorders. Although the factors influencing immune response diversity are partially understood, what mechanisms lead to the wide range of immune traits in healthy individuals remain largely unexplained. Here, we discuss the role that natural selection has played in driving phenotypic differences in immune responses across populations and present-day susceptibility to immune-related disorders. Further, we touch on future directions in the field of immunogenomics, highlighting the value of expanding this work to human populations globally, the utility of modeling the immune response as a dynamic process, and the importance of considering the potential polygenic nature of natural selection. Identifying loci acted upon by evolution may further pinpoint variants critically involved in disease etiology, and designing studies to capture these effects will enrich our understanding of the genetic contributions to immunity and immune dysregulation.
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Affiliation(s)
- Haley E Randolph
- Committee on Genetics, Genomics, and Systems Biology, University of Chicago, Chicago, Illinois, USA
- Department of Pediatrics, Columbia University Irving Medical Center, New York, New York, USA
| | | | - Yen-Lung Lin
- Section of Genetic Medicine, Department of Medicine, University of Chicago, Chicago, Illinois, USA
| | - Zepeng Mu
- Committee on Genetics, Genomics, and Systems Biology, University of Chicago, Chicago, Illinois, USA
| | - Luis B Barreiro
- Committee on Genetics, Genomics, and Systems Biology, University of Chicago, Chicago, Illinois, USA
- Department of Human Genetics, University of Chicago, Chicago, Illinois, USA
- Section of Genetic Medicine, Department of Medicine, University of Chicago, Chicago, Illinois, USA
- Committee on Immunology, University of Chicago, Chicago, Illinois, USA
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2
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Koenig Z, Yohannes MT, Nkambule LL, Zhao X, Goodrich JK, Kim HA, Wilson MW, Tiao G, Hao SP, Sahakian N, Chao KR, Walker MA, Lyu Y, Rehm HL, Neale BM, Talkowski ME, Daly MJ, Brand H, Karczewski KJ, Atkinson EG, Martin AR. A harmonized public resource of deeply sequenced diverse human genomes. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2023.01.23.525248. [PMID: 36747613 PMCID: PMC9900804 DOI: 10.1101/2023.01.23.525248] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
Abstract
Underrepresented populations are often excluded from genomic studies due in part to a lack of resources supporting their analyses. The 1000 Genomes Project (1kGP) and Human Genome Diversity Project (HGDP), which have recently been sequenced to high coverage, are valuable genomic resources because of the global diversity they capture and their open data sharing policies. Here, we harmonized a high quality set of 4,094 whole genomes from HGDP and 1kGP with data from the Genome Aggregation Database (gnomAD) and identified over 153 million high-quality SNVs, indels, and SVs. We performed a detailed ancestry analysis of this cohort, characterizing population structure and patterns of admixture across populations, analyzing site frequency spectra, and measuring variant counts at global and subcontinental levels. We also demonstrate substantial added value from this dataset compared to the prior versions of the component resources, typically combined via liftover and variant intersection; for example, we catalog millions of new genetic variants, mostly rare, compared to previous releases. In addition to unrestricted individual-level public release, we provide detailed tutorials for conducting many of the most common quality control steps and analyses with these data in a scalable cloud-computing environment and publicly release this new phased joint callset for use as a haplotype resource in phasing and imputation pipelines. This jointly called reference panel will serve as a key resource to support research of diverse ancestry populations.
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Affiliation(s)
- Zan Koenig
- Stanley Center for Psychiatric Research, The Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
- Analytic and Translational Genetics Unit, Massachusetts General Hospital, Boston, MA 02114, USA
| | - Mary T. Yohannes
- Stanley Center for Psychiatric Research, The Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
- Analytic and Translational Genetics Unit, Massachusetts General Hospital, Boston, MA 02114, USA
| | - Lethukuthula L. Nkambule
- Stanley Center for Psychiatric Research, The Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
- Analytic and Translational Genetics Unit, Massachusetts General Hospital, Boston, MA 02114, USA
| | - Xuefang Zhao
- Program in Medical and Population Genetics, The Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
- Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA 02114, USA
- Department of Neurology, Massachusetts General Hospital and Harvard Medical School, Boston, MA 02114, USA
| | - Julia K. Goodrich
- Analytic and Translational Genetics Unit, Massachusetts General Hospital, Boston, MA 02114, USA
- Program in Medical and Population Genetics, The Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Heesu Ally Kim
- Stanley Center for Psychiatric Research, The Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Michael W. Wilson
- Program in Medical and Population Genetics, The Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Grace Tiao
- Program in Medical and Population Genetics, The Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Stephanie P. Hao
- Program in Medical and Population Genetics, The Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
- Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA 02114, USA
- Department of Neurology, Massachusetts General Hospital and Harvard Medical School, Boston, MA 02114, USA
| | - Nareh Sahakian
- Broad Genomics, The Broad Institute of MIT and Harvard, 320 Charles Street, Cambridge, MA, 02141, USA
| | - Katherine R. Chao
- Program in Medical and Population Genetics, The Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Mark A. Walker
- Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA 02114, USA
- Data Sciences Platform, The Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Yunfei Lyu
- Department of Biostatistics, Harvard T.H. Chan School of Public Health, Boston, MA, USA
| | | | - Heidi L. Rehm
- Program in Medical and Population Genetics, The Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
- Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA 02114, USA
| | - Benjamin M. Neale
- Stanley Center for Psychiatric Research, The Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
- Analytic and Translational Genetics Unit, Massachusetts General Hospital, Boston, MA 02114, USA
- Program in Medical and Population Genetics, The Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
| | - Michael E. Talkowski
- Stanley Center for Psychiatric Research, The Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
- Program in Medical and Population Genetics, The Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
- Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA 02114, USA
- Department of Neurology, Massachusetts General Hospital and Harvard Medical School, Boston, MA 02114, USA
| | - Mark J. Daly
- Stanley Center for Psychiatric Research, The Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
- Analytic and Translational Genetics Unit, Massachusetts General Hospital, Boston, MA 02114, USA
- Program in Medical and Population Genetics, The Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
- Institute for Molecular Medicine Finland, Helsinki, Finland
| | - Harrison Brand
- Program in Medical and Population Genetics, The Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
- Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA 02114, USA
- Department of Neurology, Massachusetts General Hospital and Harvard Medical School, Boston, MA 02114, USA
| | - Konrad J. Karczewski
- Stanley Center for Psychiatric Research, The Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
- Analytic and Translational Genetics Unit, Massachusetts General Hospital, Boston, MA 02114, USA
- Program in Medical and Population Genetics, The Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
- Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA 02114, USA
| | - Elizabeth G. Atkinson
- Stanley Center for Psychiatric Research, The Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
- Analytic and Translational Genetics Unit, Massachusetts General Hospital, Boston, MA 02114, USA
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, 77030, USA
| | - Alicia R. Martin
- Stanley Center for Psychiatric Research, The Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
- Analytic and Translational Genetics Unit, Massachusetts General Hospital, Boston, MA 02114, USA
- Program in Medical and Population Genetics, The Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA
- Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA 02114, USA
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3
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Munday RM, Haque R, Wojcik GL, Korpe P, Nayak U, Kirkpatrick BD, Petri WA, Duggal P. Genome-Wide Association Studies of Diarrhea Frequency and Duration in the First Year of Life in Bangladeshi Infants. J Infect Dis 2023; 228:979-989. [PMID: 36967705 PMCID: PMC11007397 DOI: 10.1093/infdis/jiad068] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2022] [Revised: 03/10/2023] [Accepted: 03/23/2023] [Indexed: 08/18/2023] Open
Abstract
BACKGROUND Diarrhea is the second leading cause of death in children under 5 years old worldwide. Known diarrhea risk factors include sanitation, water sources, and pathogens but do not fully explain the heterogeneity in frequency and duration of diarrhea in young children. We evaluated the role of host genetics in diarrhea. METHODS Using 3 well-characterized birth cohorts from an impoverished area of Dhaka, Bangladesh, we compared infants with no diarrhea in the first year of life to those with an abundance, measured by either frequency or duration. We performed a genome-wide association analysis for each cohort under an additive model and then meta-analyzed across the studies. RESULTS For diarrhea frequency, we identified 2 genome-wide significant loci associated with not having any diarrhea, on chromosome 21 within the noncoding RNA AP000959 (C allele odds ratio [OR] = 0.31, P = 4.01 × 10-8), and on chromosome 8 within SAMD12 (T allele OR = 0.35, P = 4.74 × 10-7). For duration of diarrhea, we identified 2 loci associated with no diarrhea, including the same locus on chromosome 21 (C allele OR = 0.31, P = 1.59 × 10-8) and another locus on chromosome 17 near WSCD1 (C allele OR = 0.35, P = 1.09 × 10-7). CONCLUSIONS These loci are in or near genes involved in enteric nervous system development and intestinal inflammation and may be potential targets for diarrhea therapeutics.
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Affiliation(s)
- Rebecca M Munday
- Department of Genetic Medicine, Johns Hopkins School of Medicine, Baltimore, Maryland, USA
| | - Rashidul Haque
- International Centre for Diarrhoeal Disease Research, Bangladesh, Dhaka, Bangladesh
| | - Genevieve L Wojcik
- Department of Epidemiology, Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland, USA
| | - Poonum Korpe
- Department of Epidemiology, Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland, USA
| | - Uma Nayak
- Center for Public Health Genomics, University of Virginia School of Medicine, Charlottesville, Virginia, USA
- Department of Public Health Sciences, University of Virginia School of Medicine, Charlottesville, Virginia, USA
| | - Beth D Kirkpatrick
- Vaccine Testing Center, Larner College of Medicine, University of Vermont, Burlington, Vermont, USA
| | - William A Petri
- Department of Medicine, Infectious Diseases, and International Health, University of Virginia School of Medicine, Charlottesville, Virginia, USA
| | - Priya Duggal
- Department of Epidemiology, Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland, USA
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4
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Di Pietro L, Boroumand M, Lattanzi W, Manconi B, Salvati M, Cabras T, Olianas A, Flore L, Serrao S, Calò CM, Francalacci P, Parolini O, Castagnola M. A Catalog of Coding Sequence Variations in Salivary Proteins' Genes Occurring during Recent Human Evolution. Int J Mol Sci 2023; 24:15010. [PMID: 37834461 PMCID: PMC10573131 DOI: 10.3390/ijms241915010] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2023] [Revised: 10/04/2023] [Accepted: 10/06/2023] [Indexed: 10/15/2023] Open
Abstract
Saliva houses over 2000 proteins and peptides with poorly clarified functions, including proline-rich proteins, statherin, P-B peptides, histatins, cystatins, and amylases. Their genes are poorly conserved across related species, reflecting an evolutionary adaptation. We searched the nucleotide substitutions fixed in these salivary proteins' gene loci in modern humans compared with ancient hominins. We mapped 3472 sequence variants/nucleotide substitutions in coding, noncoding, and 5'-3' untranslated regions. Despite most of the detected variations being within noncoding regions, the frequency of coding variations was far higher than the general rate found throughout the genome. Among the various missense substitutions, specific substitutions detected in PRB1 and PRB2 genes were responsible for the introduction/abrogation of consensus sequences recognized by convertase enzymes that cleave the protein precursors. Overall, these changes that occurred during the recent human evolution might have generated novel functional features and/or different expression ratios among the various components of the salivary proteome. This may have influenced the homeostasis of the oral cavity environment, possibly conditioning the eating habits of modern humans. However, fixed nucleotide changes in modern humans represented only 7.3% of all the substitutions reported in this study, and no signs of evolutionary pressure or adaptative introgression from archaic hominins were found on the tested genes.
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Affiliation(s)
- Lorena Di Pietro
- Dipartimento Scienze della Vita e Sanità Pubblica, Università Cattolica del Sacro Cuore, 00168 Rome, Italy; (L.D.P.)
- Fondazione Policlinico Universitario A. Gemelli IRCCS, 00168 Rome, Italy
| | - Mozhgan Boroumand
- Laboratorio di Proteomica, Centro Europeo di Ricerca sul Cervello, IRCCS Fondazione Santa Lucia, 00179 Rome, Italy
| | - Wanda Lattanzi
- Dipartimento Scienze della Vita e Sanità Pubblica, Università Cattolica del Sacro Cuore, 00168 Rome, Italy; (L.D.P.)
- Fondazione Policlinico Universitario A. Gemelli IRCCS, 00168 Rome, Italy
| | - Barbara Manconi
- Dipartimento di Scienze della Vita e Dell’ambiente, Università di Cagliari, 09042 Monserrato, Italy
| | - Martina Salvati
- Dipartimento Scienze della Vita e Sanità Pubblica, Università Cattolica del Sacro Cuore, 00168 Rome, Italy; (L.D.P.)
| | - Tiziana Cabras
- Dipartimento di Scienze della Vita e Dell’ambiente, Università di Cagliari, 09042 Monserrato, Italy
| | - Alessandra Olianas
- Dipartimento di Scienze della Vita e Dell’ambiente, Università di Cagliari, 09042 Monserrato, Italy
| | - Laura Flore
- Dipartimento di Scienze della Vita e Dell’ambiente, Università di Cagliari, 09042 Monserrato, Italy
| | - Simone Serrao
- Department of Medicine and Surgery, Proteomics and Metabolomics Unit, University of Milano-Bicocca, 20854 Vedano al Lambro, Italy
| | - Carla M. Calò
- Dipartimento di Scienze della Vita e Dell’ambiente, Università di Cagliari, 09042 Monserrato, Italy
| | - Paolo Francalacci
- Dipartimento di Scienze della Vita e Dell’ambiente, Università di Cagliari, 09042 Monserrato, Italy
| | - Ornella Parolini
- Dipartimento Scienze della Vita e Sanità Pubblica, Università Cattolica del Sacro Cuore, 00168 Rome, Italy; (L.D.P.)
- Fondazione Policlinico Universitario A. Gemelli IRCCS, 00168 Rome, Italy
| | - Massimo Castagnola
- Laboratorio di Proteomica, Centro Europeo di Ricerca sul Cervello, IRCCS Fondazione Santa Lucia, 00179 Rome, Italy
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5
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Cheng Z, Cai Y, Zhang K, Zhang J, Gui H, Luo YS, Zhou J, DeVeale B. MAP3K19 regulatory variation in populations with African ancestry may increase COVID-19 severity. iScience 2023; 26:107555. [PMID: 37649700 PMCID: PMC10462844 DOI: 10.1016/j.isci.2023.107555] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2022] [Revised: 05/20/2023] [Accepted: 08/03/2023] [Indexed: 09/01/2023] Open
Abstract
To identify ancestry-linked genetic risk variants associated with COVID-19 hospitalization, we performed an integrative analysis of two genome-wide association studies and resolved four single nucleotide polymorphisms more frequent in COVID-19-hospitalized patients with non-European ancestry. Among them, the COVID-19 risk SNP rs16831827 shows the largest difference in minor allele frequency (MAF) between populations with African and European ancestry and also shows higher MAF in hospitalized COVID-19 patients among cohorts of mixed ancestry (odds ratio [OR] = 1.20, 95% CI: 1.10-1.30) and entirely African ancestry (OR = 1.30, 95% CI: 1.02-1.67). rs16831827 is an expression quantitative trait locus of MAP3K19. MAP3K19 expression is induced during ciliogenesis and most abundant in ciliated tissues including lungs. Single-cell RNA sequencing analyses revealed that MAP3K19 is highly expressed in multiple ciliated cell types. As rs16831827∗T is associated with reduced MAP3K19 expression, it may increase the risk of severe COVID-19 by reducing MAP3K19 expression.
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Affiliation(s)
- Zhongshan Cheng
- Center for Applied Bioinformatics, St Jude Children’s Research Hospital, 262 Danny Thomas Pl, Memphis, TN 38105, USA
| | - Yi Cai
- Guangdong Key Laboratory of Regional Immunity and Diseases, Department of Pathogen Biology, Shenzhen University Medical School, Shenzhen 518000, China
| | - Ke Zhang
- The Key and Characteristic Laboratory of Modern Pathogenicity Biology, School of Basic Medical Sciences, Guizhou Medical University, Guizhou, Guiyang 550025, China
| | - Jingxuan Zhang
- Hubei Key Laboratory of Embryonic Stem Cell Research, School of Basic Medical Sciences, Hubei University of Medicine, Shiyan, Hubei 442000, China
| | - Hongsheng Gui
- Behavioral Health Services and Psychiatry Research, Henry Ford Health, Detroit, MI 48202, USA
| | - Yu-Si Luo
- Department of Emergency, The Affiliated Hospital of Guizhou Medical University, Guizhou, Guiyang 550004, China
| | - Jie Zhou
- Department of Microbiology, The University of Hong Kong, Hong Kong 999077, China
| | - Brian DeVeale
- The Department of Biomedical Sciences, University of Windsor, Windsor, ON N9B 3P4, Canada
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6
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Roca-Umbert A, Garcia-Calleja J, Vogel-González M, Fierro-Villegas A, Ill-Raga G, Herrera-Fernández V, Bosnjak A, Muntané G, Gutiérrez E, Campelo F, Vicente R, Bosch E. Human genetic adaptation related to cellular zinc homeostasis. PLoS Genet 2023; 19:e1010950. [PMID: 37747921 PMCID: PMC10553801 DOI: 10.1371/journal.pgen.1010950] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2023] [Revised: 10/05/2023] [Accepted: 08/31/2023] [Indexed: 09/27/2023] Open
Abstract
SLC30A9 encodes a ubiquitously zinc transporter (ZnT9) and has been consistently suggested as a candidate for positive selection in humans. However, no direct adaptive molecular phenotype has been demonstrated. Our results provide evidence for directional selection operating in two major complementary haplotypes in Africa and East Asia. These haplotypes are associated with differential gene expression but also differ in the Met50Val substitution (rs1047626) in ZnT9, which we show is found in homozygosis in the Denisovan genome and displays accompanying signatures suggestive of archaic introgression. Although we found no significant differences in systemic zinc content between individuals with different rs1047626 genotypes, we demonstrate that the expression of the derived isoform (ZnT9 50Val) in HEK293 cells shows a gain of function when compared with the ancestral (ZnT9 50Met) variant. Notably, the ZnT9 50Val variant was found associated with differences in zinc handling by the mitochondria and endoplasmic reticulum, with an impact on mitochondrial metabolism. Given the essential role of the mitochondria in skeletal muscle and since the derived allele at rs1047626 is known to be associated with greater susceptibility to several neuropsychiatric traits, we propose that adaptation to cold may have driven this selection event, while also impacting predisposition to neuropsychiatric disorders in modern humans.
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Affiliation(s)
- Ana Roca-Umbert
- Institut de Biologia Evolutiva (UPF-CSIC), Departament de Medicina i Ciències de la Vida, Universitat Pompeu Fabra, Parc de Recerca Biomèdica de Barcelona, Barcelona, Spain
| | - Jorge Garcia-Calleja
- Institut de Biologia Evolutiva (UPF-CSIC), Departament de Medicina i Ciències de la Vida, Universitat Pompeu Fabra, Parc de Recerca Biomèdica de Barcelona, Barcelona, Spain
| | - Marina Vogel-González
- Laboratory of Molecular Physiology, Department of Medicine and Life Sciences (MELIS), Universitat Pompeu Fabra, Barcelona, Spain
| | - Alejandro Fierro-Villegas
- Laboratory of Molecular Physiology, Department of Medicine and Life Sciences (MELIS), Universitat Pompeu Fabra, Barcelona, Spain
| | - Gerard Ill-Raga
- Laboratory of Molecular Physiology, Department of Medicine and Life Sciences (MELIS), Universitat Pompeu Fabra, Barcelona, Spain
| | - Víctor Herrera-Fernández
- Laboratory of Molecular Physiology, Department of Medicine and Life Sciences (MELIS), Universitat Pompeu Fabra, Barcelona, Spain
| | - Anja Bosnjak
- Laboratory of Molecular Physiology, Department of Medicine and Life Sciences (MELIS), Universitat Pompeu Fabra, Barcelona, Spain
| | - Gerard Muntané
- Institut de Biologia Evolutiva (UPF-CSIC), Departament de Medicina i Ciències de la Vida, Universitat Pompeu Fabra, Parc de Recerca Biomèdica de Barcelona, Barcelona, Spain
- Hospital Universitari Institut Pere Mata, IISPV, Universitat Rovira i Virgili, Reus, Spain
- Centro de Investigación Biomédica en Red de Salud Mental, Instituto de Salud Carlos III, Madrid, Spain
| | - Esteban Gutiérrez
- Laboratory of Molecular Physiology, Department of Medicine and Life Sciences (MELIS), Universitat Pompeu Fabra, Barcelona, Spain
| | - Felix Campelo
- ICFO-Institut de Ciencies Fotoniques, The Barcelona Institute of Science and Technology, Barcelona, Spain
| | - Rubén Vicente
- Laboratory of Molecular Physiology, Department of Medicine and Life Sciences (MELIS), Universitat Pompeu Fabra, Barcelona, Spain
| | - Elena Bosch
- Institut de Biologia Evolutiva (UPF-CSIC), Departament de Medicina i Ciències de la Vida, Universitat Pompeu Fabra, Parc de Recerca Biomèdica de Barcelona, Barcelona, Spain
- Centro de Investigación Biomédica en Red de Salud Mental, Instituto de Salud Carlos III, Madrid, Spain
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7
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Bagher AM, Hareeri RH. Allele frequency and genotype distribution of the opioid receptor μ-1 (OPRM1) A118G polymorphism in the Western Saudi population. J Appl Biomed 2023; 21:160-165. [PMID: 37747315 DOI: 10.32725/jab.2023.012] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2022] [Accepted: 09/14/2023] [Indexed: 09/26/2023] Open
Abstract
The single nucleotide polymorphism (SNP) A118G (rs1799971) in the Mu Opioid Receptor 1 (OPRM1) gene is associated with significant variations in analgesic doses and adverse effects of opioids. The A118G OPRM1 allele distributions vary significantly between different populations worldwide. The study aimed to assess the allele frequency and genotype distribution of OPRM1 A118G SNP in Saudis. This cross-sectional study included 124 healthy Saudis (62 males and 62 females) visiting the King Abdulaziz University Hospital in Jeddah, Saudi Arabia. The Oragene®-DISCOVER (OGR-600) kits were used to collect saliva samples from the participants. Polymerase chain reaction-restriction fragment length polymorphism was utilized to assess the SNP. Among the tested population, 79.03% (95% C.I. 70.81-85.82) were homozygous wild-type A118A, 16.13% (95% C.I. 10.14-23.80) were heterozygous A118G, and 4.84% (95% C.I. 1.80-10.23) were homozygous mutant G118G. OPRM1 A118G polymorphism allele frequencies were 87% (95% C.I. 79.89-92.44) and 13% (95% C.I. 7.56-20.11) for the 118A and 118G alleles, respectively. A higher frequency of the OPRM1 118G allele was present in females, 21% (95% C.I. 11.66-33.17) compared to males, 5% (95% C.I. 1.01-13.50). Relative to other Asian countries, the Saudi population showed a low prevalence of the OPRM1 A118G polymorphism, with a higher frequency of the 118G allele in females. Our research will contribute to the existing knowledge on the prevalence of OPRM1 A118G polymorphism, which could be considered for the personalized prescribing of opioid analgesics.
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Affiliation(s)
- Amina M Bagher
- King AbdulAziz University, Faculty of Pharmacy, Department of Pharmacology and Toxicology, Jeddah, Saudi Arabia
| | - Rawan H Hareeri
- King AbdulAziz University, Faculty of Pharmacy, Department of Pharmacology and Toxicology, Jeddah, Saudi Arabia
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8
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Pryor Y, Lindo J. Deconstructing Eurocentrism in skin pigmentation research via the incorporation of diverse populations and theoretical perspectives. Evol Anthropol 2023; 32:195-205. [PMID: 37450551 DOI: 10.1002/evan.21993] [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: 12/11/2022] [Revised: 03/29/2023] [Accepted: 06/16/2023] [Indexed: 07/18/2023]
Abstract
The evolution of skin pigmentation has been shaped by numerous biological and cultural shifts throughout human history. Vitamin D is considered a driver of depigmentation evolution in humans, given the deleterious health effects associated with vitamin D deficiency, which is often shaped by cultural factors. New advancements in genomics and epigenomics have opened the door to a deeper exploration of skin pigmentation evolution in both contemporary and ancient populations. Data from ancient Europeans has offered great context to the spread of depigmentation alleles via the evaluation of migration events and cultural shifts that occurred during the Neolithic. However, novel insights can further be gained via the inclusion of diverse ancient and contemporary populations. Here we present on how potential biases and limitations in skin pigmentation research can be overcome with the integration of interdisciplinary data that includes both cultural and biological elements, which have shaped the evolutionary history of skin pigmentation in humans.
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Affiliation(s)
- Yemko Pryor
- Genetics and Molecular Biology, Emory University, Atlanta, Georgia, USA
| | - John Lindo
- Department of Anthropology, Emory University, Atlanta, Georgia, USA
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9
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Jorgensen K, Song D, Weinstein J, Garcia OA, Pearson LN, Inclán M, Rivera-Chira M, León-Velarde F, Kiyamu M, Brutsaert TD, Bigham AW, Lee FS. High-Altitude Andean H194R HIF2A Allele Is a Hypomorphic Allele. Mol Biol Evol 2023; 40:msad162. [PMID: 37463421 PMCID: PMC10370452 DOI: 10.1093/molbev/msad162] [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: 03/09/2023] [Revised: 06/15/2023] [Accepted: 07/03/2023] [Indexed: 07/20/2023] Open
Abstract
For over 10,000 years, Andeans have resided at high altitude where the partial pressure of oxygen challenges human survival. Recent studies have provided evidence for positive selection acting in Andeans on the HIF2A (also known as EPAS1) locus, which encodes for a central transcription factor of the hypoxia-inducible factor pathway. However, the precise mechanism by which this allele might lead to altitude-adaptive phenotypes, if any, is unknown. By analyzing whole genome sequencing data from 46 high-coverage Peruvian Andean genomes, we confirm evidence for positive selection acting on HIF2A and a unique pattern of variation surrounding the Andean-specific single nucleotide variant (SNV), rs570553380, which encodes for an H194R amino acid substitution in HIF-2α. Genotyping the Andean-associated SNV rs570553380 in a group of 299 Peruvian Andeans from Cerro de Pasco, Peru (4,338 m), reveals a positive association with increased fraction of exhaled nitric oxide, a marker of nitric oxide biosynthesis. In vitro assays show that the H194R mutation impairs binding of HIF-2α to its heterodimeric partner, aryl hydrocarbon receptor nuclear translocator. A knockin mouse model bearing the H194R mutation in the Hif2a gene displays decreased levels of hypoxia-induced pulmonary Endothelin-1 transcripts and protection against hypoxia-induced pulmonary hypertension. We conclude the Andean H194R HIF2A allele is a hypomorphic (partial loss of function) allele.
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Affiliation(s)
- Kelsey Jorgensen
- Department of Anthropology, University of California, Los Angeles, CA, USA
| | - Daisheng Song
- Department of Pathology and Laboratory Medicine, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA
| | - Julien Weinstein
- Department of Anthropology, The University of Michigan, Ann Arbor, MI, USA
| | - Obed A Garcia
- Department of Biomedical Data Science, Stanford University, Stanford, CA, USA
| | - Laurel N Pearson
- Department of Anthropology, The Pennsylvania State University, State College, PA, USA
| | - María Inclán
- División de. Estudios Políticos, Centro de Investigación y Docencia Económicas, Mexico City, CDMX, Mexico
| | - Maria Rivera-Chira
- Departamento de Ciencias Biológicas y Fisiológicas, Laboratorios de Investigación y Desarrollo, Facultad de Ciencias y Filosofía, Universidad Peruana Cayetano Heredia, Lima, Lima, Peru
| | - Fabiola León-Velarde
- Departamento de Ciencias Biológicas y Fisiológicas, Laboratorios de Investigación y Desarrollo, Facultad de Ciencias y Filosofía, Universidad Peruana Cayetano Heredia, Lima, Lima, Peru
| | - Melisa Kiyamu
- Departamento de Ciencias Biológicas y Fisiológicas, Laboratorios de Investigación y Desarrollo, Facultad de Ciencias y Filosofía, Universidad Peruana Cayetano Heredia, Lima, Lima, Peru
| | - Tom D Brutsaert
- Department of Exercise Science, Syracuse University, Syracuse, NY, USA
| | - Abigail W Bigham
- Department of Anthropology, University of California, Los Angeles, CA, USA
| | - Frank S Lee
- Department of Pathology and Laboratory Medicine, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA
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10
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Cotter DJ, Hofgard EF, Novembre J, Szpiech ZA, Rosenberg NA. A rarefaction approach for measuring population differences in rare and common variation. Genetics 2023; 224:iyad070. [PMID: 37075098 PMCID: PMC10213490 DOI: 10.1093/genetics/iyad070] [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: 12/20/2022] [Revised: 12/20/2022] [Accepted: 04/07/2023] [Indexed: 04/20/2023] Open
Abstract
In studying allele-frequency variation across populations, it is often convenient to classify an allelic type as "rare," with nonzero frequency less than or equal to a specified threshold, "common," with a frequency above the threshold, or entirely unobserved in a population. When sample sizes differ across populations, however, especially if the threshold separating "rare" and "common" corresponds to a small number of observed copies of an allelic type, discreteness effects can lead a sample from one population to possess substantially more rare allelic types than a sample from another population, even if the two populations have extremely similar underlying allele-frequency distributions across loci. We introduce a rarefaction-based sample-size correction for use in comparing rare and common variation across multiple populations whose sample sizes potentially differ. We use our approach to examine rare and common variation in worldwide human populations, finding that the sample-size correction introduces subtle differences relative to analyses that use the full available sample sizes. We introduce several ways in which the rarefaction approach can be applied: we explore the dependence of allele classifications on subsample sizes, we permit more than two classes of allelic types of nonzero frequency, and we analyze rare and common variation in sliding windows along the genome. The results can assist in clarifying similarities and differences in allele-frequency patterns across populations.
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Affiliation(s)
- Daniel J Cotter
- Department of Genetics, Stanford University, Stanford, CA 94305, USA
| | - Elyssa F Hofgard
- Institute for Computational and Mathematical Engineering, Stanford University, Stanford, CA 94305, USA
| | - John Novembre
- Department of Human Genetics, University of Chicago, Chicago, IL 60637, USA
| | - Zachary A Szpiech
- Department of Biology, Pennsylvania State University, University Park, PA 16802, USA
- Institute for Computational and Data Sciences, Pennsylvania State University, University Park, PA 16802, USA
| | - Noah A Rosenberg
- Department of Biology, Stanford University, Stanford, CA 94305, USA
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11
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Rong S, Neil CR, Welch A, Duan C, Maguire S, Meremikwu IC, Meyerson M, Evans BJ, Fairbrother WG. Large-scale functional screen identifies genetic variants with splicing effects in modern and archaic humans. Proc Natl Acad Sci U S A 2023; 120:e2218308120. [PMID: 37192163 PMCID: PMC10214146 DOI: 10.1073/pnas.2218308120] [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: 11/07/2022] [Accepted: 04/12/2023] [Indexed: 05/18/2023] Open
Abstract
Humans coexisted and interbred with other hominins which later became extinct. These archaic hominins are known to us only through fossil records and for two cases, genome sequences. Here, we engineer Neanderthal and Denisovan sequences into thousands of artificial genes to reconstruct the pre-mRNA processing patterns of these extinct populations. Of the 5,169 alleles tested in this massively parallel splicing reporter assay (MaPSy), we report 962 exonic splicing mutations that correspond to differences in exon recognition between extant and extinct hominins. Using MaPSy splicing variants, predicted splicing variants, and splicing quantitative trait loci, we show that splice-disrupting variants experienced greater purifying selection in anatomically modern humans than that in Neanderthals. Adaptively introgressed variants were enriched for moderate-effect splicing variants, consistent with positive selection for alternative spliced alleles following introgression. As particularly compelling examples, we characterized a unique tissue-specific alternative splicing variant at the adaptively introgressed innate immunity gene TLR1, as well as a unique Neanderthal introgressed alternative splicing variant in the gene HSPG2 that encodes perlecan. We further identified potentially pathogenic splicing variants found only in Neanderthals and Denisovans in genes related to sperm maturation and immunity. Finally, we found splicing variants that may contribute to variation among modern humans in total bilirubin, balding, hemoglobin levels, and lung capacity. Our findings provide unique insights into natural selection acting on splicing in human evolution and demonstrate how functional assays can be used to identify candidate causal variants underlying differences in gene regulation and phenotype.
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Affiliation(s)
- Stephen Rong
- Center for Computational Molecular Biology, Brown University, Providence, RI02912
- Department of Molecular Biology, Cell Biology, and Biochemistry, Brown University, Providence, RI02912
| | - Christopher R. Neil
- Department of Molecular Biology, Cell Biology, and Biochemistry, Brown University, Providence, RI02912
| | - Anastasia Welch
- Department of Molecular Biology, Cell Biology, and Biochemistry, Brown University, Providence, RI02912
| | - Chaorui Duan
- Department of Molecular Biology, Cell Biology, and Biochemistry, Brown University, Providence, RI02912
| | - Samantha Maguire
- Department of Molecular Biology, Cell Biology, and Biochemistry, Brown University, Providence, RI02912
| | - Ijeoma C. Meremikwu
- Department of Molecular Biology, Cell Biology, and Biochemistry, Brown University, Providence, RI02912
| | - Malcolm Meyerson
- Department of Molecular Biology, Cell Biology, and Biochemistry, Brown University, Providence, RI02912
| | - Ben J. Evans
- Department of Biology, McMaster University, Hamilton, ONL8S 4K1, Canada
| | - William G. Fairbrother
- Center for Computational Molecular Biology, Brown University, Providence, RI02912
- Department of Molecular Biology, Cell Biology, and Biochemistry, Brown University, Providence, RI02912
- Hassenfeld Child Health Innovation Institute of Brown University, Providence, RI02912
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12
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Chen HV, Lorenzini MH, Lavalle SN, Sajeev K, Fonseca A, Fiaux PC, Sen A, Luthra I, Ho AJ, Chen AR, Guruvayurappan K, O'Connor C, McVicker G. Deletion mapping of regulatory elements for GATA3 in T cells reveals a distal enhancer involved in allergic diseases. Am J Hum Genet 2023; 110:703-714. [PMID: 36990085 PMCID: PMC10119147 DOI: 10.1016/j.ajhg.2023.03.008] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2022] [Accepted: 03/08/2023] [Indexed: 03/30/2023] Open
Abstract
GATA3 is essential for T cell differentiation and is surrounded by genome-wide association study (GWAS) hits for immune traits. Interpretation of these GWAS hits is challenging because gene expression quantitative trait locus (eQTL) studies lack power to detect variants with small effects on gene expression in specific cell types and the genome region containing GATA3 contains dozens of potential regulatory sequences. To map regulatory sequences for GATA3, we performed a high-throughput tiling deletion screen of a 2 Mb genome region in Jurkat T cells. This revealed 23 candidate regulatory sequences, all but one of which is within the same topological-associating domain (TAD) as GATA3. We then performed a lower-throughput deletion screen to precisely map regulatory sequences in primary T helper 2 (Th2) cells. We tested 25 sequences with ∼100 bp deletions and validated five of the strongest hits with independent deletion experiments. Additionally, we fine-mapped GWAS hits for allergic diseases in a distal regulatory element, 1 Mb downstream of GATA3, and identified 14 candidate causal variants. Small deletions spanning the candidate variant rs725861 decreased GATA3 levels in Th2 cells, and luciferase reporter assays showed regulatory differences between its two alleles, suggesting a causal mechanism for this variant in allergic diseases. Our study demonstrates the power of integrating GWAS signals with deletion mapping and identifies critical regulatory sequences for GATA3.
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Affiliation(s)
- Hsiuyi V Chen
- Integrative Biology Laboratory, Salk Institute for Biological Studies, La Jolla, CA, USA.
| | - Michael H Lorenzini
- Integrative Biology Laboratory, Salk Institute for Biological Studies, La Jolla, CA, USA; Biomedical Sciences Graduate Program, University of California San Diego, La Jolla, CA, USA
| | - Shanna N Lavalle
- Integrative Biology Laboratory, Salk Institute for Biological Studies, La Jolla, CA, USA
| | - Karthyayani Sajeev
- Integrative Biology Laboratory, Salk Institute for Biological Studies, La Jolla, CA, USA; School of Biological Sciences, University of California San Diego, La Jolla, CA, USA
| | - Ariana Fonseca
- Integrative Biology Laboratory, Salk Institute for Biological Studies, La Jolla, CA, USA
| | - Patrick C Fiaux
- Integrative Biology Laboratory, Salk Institute for Biological Studies, La Jolla, CA, USA; Bioinformatics and Systems Biology Graduate Program, University of California San Diego, La Jolla, CA, USA
| | - Arko Sen
- Integrative Biology Laboratory, Salk Institute for Biological Studies, La Jolla, CA, USA
| | - Ishika Luthra
- Integrative Biology Laboratory, Salk Institute for Biological Studies, La Jolla, CA, USA
| | - Aaron J Ho
- Integrative Biology Laboratory, Salk Institute for Biological Studies, La Jolla, CA, USA
| | - Aaron R Chen
- Integrative Biology Laboratory, Salk Institute for Biological Studies, La Jolla, CA, USA
| | - Karthik Guruvayurappan
- Integrative Biology Laboratory, Salk Institute for Biological Studies, La Jolla, CA, USA; School of Biological Sciences, University of California San Diego, La Jolla, CA, USA
| | - Carolyn O'Connor
- Flow Cytometry Core Facility, Salk Institute for Biological Studies, La Jolla, CA, USA
| | - Graham McVicker
- Integrative Biology Laboratory, Salk Institute for Biological Studies, La Jolla, CA, USA.
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13
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Schott BH, Wang L, Zhu X, Harding AT, Ko ER, Bourgeois JS, Washington EJ, Burke TW, Anderson J, Bergstrom E, Gardener Z, Paterson S, Brennan RG, Chiu C, McClain MT, Woods CW, Gregory SG, Heaton NS, Ko DC. Single-cell genome-wide association reveals that a nonsynonymous variant in ERAP1 confers increased susceptibility to influenza virus. CELL GENOMICS 2022; 2:100207. [PMID: 36465279 PMCID: PMC9718543 DOI: 10.1016/j.xgen.2022.100207] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/02/2022] [Revised: 07/26/2022] [Accepted: 10/07/2022] [Indexed: 06/17/2023]
Abstract
During pandemics, individuals exhibit differences in risk and clinical outcomes. Here, we developed single-cell high-throughput human in vitro susceptibility testing (scHi-HOST), a method for rapidly identifying genetic variants that confer resistance and susceptibility. We applied this method to influenza A virus (IAV), the cause of four pandemics since the start of the 20th century. scHi-HOST leverages single-cell RNA sequencing (scRNA-seq) to simultaneously assign genetic identity to cells in mixed infections of cell lines of European, African, and Asian origin, reveal associated genetic variants for viral burden, and identify expression quantitative trait loci. Integration of scHi-HOST with human challenge and experimental validation demonstrated that a missense variant in endoplasmic reticulum aminopeptidase 1 (ERAP1; rs27895) increased IAV burden in cells and human volunteers. rs27895 exhibits population differentiation, likely contributing to greater permissivity of cells from African populations to IAV. scHi-HOST is a broadly applicable method and resource for decoding infectious-disease genetics.
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Affiliation(s)
- Benjamin H Schott
- Department of Molecular Genetics and Microbiology, School of Medicine, Duke University, 0048B CARL Building Box 3053, 213 Research Drive, Durham, NC 27710, USA
- Duke University Program in Genetics and Genomics, Duke University, Durham, NC 27710, USA
- These authors contributed equally
| | - Liuyang Wang
- Department of Molecular Genetics and Microbiology, School of Medicine, Duke University, 0048B CARL Building Box 3053, 213 Research Drive, Durham, NC 27710, USA
- These authors contributed equally
| | - Xinyu Zhu
- Department of Molecular Genetics and Microbiology, School of Medicine, Duke University, 0048B CARL Building Box 3053, 213 Research Drive, Durham, NC 27710, USA
| | - Alfred T Harding
- Department of Molecular Genetics and Microbiology, School of Medicine, Duke University, 0048B CARL Building Box 3053, 213 Research Drive, Durham, NC 27710, USA
| | - Emily R Ko
- Center for Applied Genomics and Precision Medicine, Department of Medicine, Duke University, Durham, NC 27710, USA
- Hospital Medicine, Division of General Internal Medicine, Department of Medicine, Duke Regional Hospital, Durham, NC 27705, USA
| | - Jeffrey S Bourgeois
- Department of Molecular Genetics and Microbiology, School of Medicine, Duke University, 0048B CARL Building Box 3053, 213 Research Drive, Durham, NC 27710, USA
- Duke University Program in Genetics and Genomics, Duke University, Durham, NC 27710, USA
| | - Erica J Washington
- Department of Biochemistry, School of Medicine, Duke University, Durham, NC 27710, USA
| | - Thomas W Burke
- Center for Applied Genomics and Precision Medicine, Department of Medicine, Duke University, Durham, NC 27710, USA
| | - Jack Anderson
- Center for Applied Genomics and Precision Medicine, Department of Medicine, Duke University, Durham, NC 27710, USA
| | - Emma Bergstrom
- Section of Infectious Diseases and Immunity, Imperial College London, London, W12 0NN, UK
| | - Zoe Gardener
- Section of Infectious Diseases and Immunity, Imperial College London, London, W12 0NN, UK
| | - Suzanna Paterson
- Section of Infectious Diseases and Immunity, Imperial College London, London, W12 0NN, UK
| | - Richard G Brennan
- Department of Biochemistry, School of Medicine, Duke University, Durham, NC 27710, USA
| | - Christopher Chiu
- Section of Infectious Diseases and Immunity, Imperial College London, London, W12 0NN, UK
| | - Micah T McClain
- Center for Applied Genomics and Precision Medicine, Department of Medicine, Duke University, Durham, NC 27710, USA
- Durham Veterans Affairs Health Care System, Durham, NC 27705, USA
- Division of Infectious Diseases, Department of Medicine, School of Medicine, Duke University, Durham, NC 27710, USA
| | - Christopher W Woods
- Center for Applied Genomics and Precision Medicine, Department of Medicine, Duke University, Durham, NC 27710, USA
- Durham Veterans Affairs Health Care System, Durham, NC 27705, USA
- Division of Infectious Diseases, Department of Medicine, School of Medicine, Duke University, Durham, NC 27710, USA
| | - Simon G Gregory
- Duke Molecular Physiology Institute, Duke University Medical Center, Durham, NC 27710, USA
| | - Nicholas S Heaton
- Department of Molecular Genetics and Microbiology, School of Medicine, Duke University, 0048B CARL Building Box 3053, 213 Research Drive, Durham, NC 27710, USA
| | - Dennis C Ko
- Department of Molecular Genetics and Microbiology, School of Medicine, Duke University, 0048B CARL Building Box 3053, 213 Research Drive, Durham, NC 27710, USA
- Duke University Program in Genetics and Genomics, Duke University, Durham, NC 27710, USA
- Division of Infectious Diseases, Department of Medicine, School of Medicine, Duke University, Durham, NC 27710, USA
- Lead contact
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14
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Roca-Umbert A, Caro-Consuegra R, Londono-Correa D, Rodriguez-Lozano GF, Vicente R, Bosch E. Understanding signatures of positive natural selection in human zinc transporter genes. Sci Rep 2022; 12:4320. [PMID: 35279701 PMCID: PMC8918337 DOI: 10.1038/s41598-022-08439-y] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2021] [Accepted: 02/25/2022] [Indexed: 12/11/2022] Open
Abstract
Zinc is an essential micronutrient with a tightly regulated systemic and cellular homeostasis. In humans, some zinc transporter genes (ZTGs) have been previously reported as candidates for strong geographically restricted selective sweeps. However, since zinc homeostasis is maintained by the joint action of 24 ZTGs, other more subtle modes of selection could have also facilitated human adaptation to zinc availability. Here, we studied whether the complete set of ZTGs are enriched for signals of positive selection in worldwide populations and population groups from South Asia. ZTGs showed higher levels of genetic differentiation between African and non-African populations than would be randomly expected, as well as other signals of polygenic selection outside Africa. Moreover, in several South Asian population groups, ZTGs were significantly enriched for SNPs with unusually extended haplotypes and displayed SNP genotype-environmental correlations when considering zinc deficiency levels in soil in that geographical area. Our study replicated some well-characterized targets for positive selection in East Asia and sub-Saharan Africa, and proposes new candidates for follow-up in South Asia (SLC39A5) and Africa (SLC39A7). Finally, we identified candidate variants for adaptation in ZTGs that could contribute to different disease susceptibilities and zinc-related human health traits.
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Affiliation(s)
- Ana Roca-Umbert
- Institut de Biologia Evolutiva (UPF-CSIC), Departament de Medicina i Ciències de la Vida, Universitat Pompeu Fabra, Parc de Recerca Biomèdica de Barcelona, 08003, Barcelona, Spain
| | - Rocio Caro-Consuegra
- Institut de Biologia Evolutiva (UPF-CSIC), Departament de Medicina i Ciències de la Vida, Universitat Pompeu Fabra, Parc de Recerca Biomèdica de Barcelona, 08003, Barcelona, Spain
| | - Diego Londono-Correa
- Institut de Biologia Evolutiva (UPF-CSIC), Departament de Medicina i Ciències de la Vida, Universitat Pompeu Fabra, Parc de Recerca Biomèdica de Barcelona, 08003, Barcelona, Spain
| | - Gabriel Felipe Rodriguez-Lozano
- Institut de Biologia Evolutiva (UPF-CSIC), Departament de Medicina i Ciències de la Vida, Universitat Pompeu Fabra, Parc de Recerca Biomèdica de Barcelona, 08003, Barcelona, Spain
| | - Ruben Vicente
- Laboratory of Molecular Physiology, Universitat Pompeu Fabra, Parc de Recerca Biomèdica de Barcelona, 08003, Barcelona, Spain
| | - Elena Bosch
- Institut de Biologia Evolutiva (UPF-CSIC), Departament de Medicina i Ciències de la Vida, Universitat Pompeu Fabra, Parc de Recerca Biomèdica de Barcelona, 08003, Barcelona, Spain. .,Centro de Investigación Biomédica en Red de Salud Mental (CIBERSAM), 43206, Reus, Spain.
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15
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Lee M, Lindo J, Rilling JK. Exploring gene-culture coevolution in humans by inferring neuroendophenotypes: A case study of the oxytocin receptor gene and cultural tightness. GENES, BRAIN, AND BEHAVIOR 2022; 21:e12783. [PMID: 35044077 PMCID: PMC8917075 DOI: 10.1111/gbb.12783] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/27/2021] [Revised: 10/25/2021] [Accepted: 11/15/2021] [Indexed: 01/17/2023]
Abstract
The gene-culture coevolution (GCC) framework has gained increasing prominence in the social and biological sciences. While most studies on human GCC concern the evolution of low-level physiological traits, attempts have also been made to apply GCC to complex human traits, including social behavior and cognition. One major methodological challenge in this endeavor is to reconstruct a specific biological pathway between the implicated genes and their distal phenotypes. Here, we introduce a novel approach that combines data on population genetics and expression quantitative trait loci to infer the specific intermediate phenotypes of genes in the brain. We suggest that such "neuroendophenotypes" will provide more detailed mechanistic insights into the GCC process. We present a case study where we explored a GCC dynamics between the oxytocin receptor gene (OXTR) and cultural tightness-looseness. By combining data from the 1000 Genomes project and the Gene-Tissue-Expression project (GTEx), we estimated and compared OXTR expression in 10 brain regions across five human superpopulations. We found that OXTR expression in the anterior cingulate cortex (ACC) was highly variable across populations, and this variation correlated with cultural tightness and socio-ecological threats worldwide. The mediation models also suggested possible GCC dynamics where the increased OXTR expression in the ACC mediates or emerges from the tight culture and higher socio-ecological threats. Formal selection scans further confirmed that OXTR alleles linked to enhanced receptor expression in the ACC underwent positive selection in East Asian countries with tighter social norms. We discuss the implications of our method in human GCC research.
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Affiliation(s)
- Minwoo Lee
- Department of Anthropology, Emory UniversityAtlantaGeorgiaUSA
| | - John Lindo
- Department of Anthropology, Emory UniversityAtlantaGeorgiaUSA
| | - James K. Rilling
- Department of Anthropology, Emory UniversityAtlantaGeorgiaUSA,Department of Psychiatry and Behavioral Science, Emory UniversityAtlantaGeorgiaUSA,Center for Behavioral Neuroscience, Emory UniversityAtlantaGeorgiaUSA,Yerkes National Primate Research Center, Emory UniversityAtlantaGeorgiaUSA,Center for Translational Social Neuroscience, Emory UniversityAtlantaGeorgiaUSA
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16
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Preston CG, Wright MW, Madhavrao R, Harrison SM, Goldstein JL, Luo X, Wand H, Wulf B, Cheung G, Mandell ME, Tong H, Cheng S, Iacocca MA, Pineda AL, Popejoy AB, Dalton K, Zhen J, Dwight SS, Babb L, DiStefano M, O’Daniel JM, Lee K, Riggs ER, Zastrow DB, Mester JL, Ritter DI, Patel RY, Subramanian SL, Milosavljevic A, Berg JS, Rehm HL, Plon SE, Cherry JM, Bustamante CD, Costa HA. ClinGen Variant Curation Interface: a variant classification platform for the application of evidence criteria from ACMG/AMP guidelines. Genome Med 2022; 14:6. [PMID: 35039090 PMCID: PMC8764818 DOI: 10.1186/s13073-021-01004-8] [Citation(s) in RCA: 23] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2021] [Accepted: 11/12/2021] [Indexed: 12/29/2022] Open
Abstract
BACKGROUND Identification of clinically significant genetic alterations involved in human disease has been dramatically accelerated by developments in next-generation sequencing technologies. However, the infrastructure and accessible comprehensive curation tools necessary for analyzing an individual patient genome and interpreting genetic variants to inform healthcare management have been lacking. RESULTS Here we present the ClinGen Variant Curation Interface (VCI), a global open-source variant classification platform for supporting the application of evidence criteria and classification of variants based on the ACMG/AMP variant classification guidelines. The VCI is among a suite of tools developed by the NIH-funded Clinical Genome Resource (ClinGen) Consortium and supports an FDA-recognized human variant curation process. Essential to this is the ability to enable collaboration and peer review across ClinGen Expert Panels supporting users in comprehensively identifying, annotating, and sharing relevant evidence while making variant pathogenicity assertions. To facilitate evidence-based improvements in human variant classification, the VCI is publicly available to the genomics community. Navigation workflows support users providing guidance to comprehensively apply the ACMG/AMP evidence criteria and document provenance for asserting variant classifications. CONCLUSIONS The VCI offers a central platform for clinical variant classification that fills a gap in the learning healthcare system, facilitates widespread adoption of standards for clinical curation, and is available at https://curation.clinicalgenome.org.
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Affiliation(s)
- Christine G. Preston
- grid.168010.e0000000419368956Department of Pathology, Stanford University School of Medicine, 300 Pasteur Drive, MSOB x313, Stanford, CA 94305 USA
| | - Matt W. Wright
- grid.168010.e0000000419368956Department of Pathology, Stanford University School of Medicine, 300 Pasteur Drive, MSOB x313, Stanford, CA 94305 USA
| | - Rao Madhavrao
- grid.168010.e0000000419368956Department of Pathology, Stanford University School of Medicine, 300 Pasteur Drive, MSOB x313, Stanford, CA 94305 USA
| | - Steven M. Harrison
- grid.66859.340000 0004 0546 1623Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA 02142 USA
| | - Jennifer L. Goldstein
- grid.410711.20000 0001 1034 1720Department of Genetics, University of North Carolina, Chapel Hill, NC 27599 USA
| | - Xi Luo
- grid.39382.330000 0001 2160 926XDepartment of Pediatrics/Hematology-Oncology, Baylor College of Medicine, Houston, TX 77030 USA
| | - Hannah Wand
- grid.490568.60000 0004 5997 482XCenter for Inherited Cardiovascular Disease, Stanford Health Care, Stanford, CA 94305 USA
| | - Bryan Wulf
- grid.168010.e0000000419368956Department of Pathology, Stanford University School of Medicine, 300 Pasteur Drive, MSOB x313, Stanford, CA 94305 USA
| | - Gloria Cheung
- grid.168010.e0000000419368956Department of Pathology, Stanford University School of Medicine, 300 Pasteur Drive, MSOB x313, Stanford, CA 94305 USA
| | - Mark E. Mandell
- grid.168010.e0000000419368956Department of Pathology, Stanford University School of Medicine, 300 Pasteur Drive, MSOB x313, Stanford, CA 94305 USA
| | - Howard Tong
- grid.168010.e0000000419368956Department of Pathology, Stanford University School of Medicine, 300 Pasteur Drive, MSOB x313, Stanford, CA 94305 USA
| | - Shaung Cheng
- grid.168010.e0000000419368956Department of Pathology, Stanford University School of Medicine, 300 Pasteur Drive, MSOB x313, Stanford, CA 94305 USA
| | - Michael A. Iacocca
- grid.168010.e0000000419368956Department of Pathology, Stanford University School of Medicine, 300 Pasteur Drive, MSOB x313, Stanford, CA 94305 USA
| | - Arturo Lopez Pineda
- grid.168010.e0000000419368956Department of Biomedical Data Science, Stanford University School of Medicine, Stanford, CA 94305 USA
| | - Alice B. Popejoy
- grid.168010.e0000000419368956Department of Biomedical Data Science, Stanford University School of Medicine, Stanford, CA 94305 USA
| | - Karen Dalton
- grid.168010.e0000000419368956Department of Medicine, Stanford University School of Medicine, Stanford, CA 94305 USA
| | - Jimmy Zhen
- grid.168010.e0000000419368956Department of Medicine, Stanford University School of Medicine, Stanford, CA 94305 USA
| | | | - Lawrence Babb
- grid.66859.340000 0004 0546 1623Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA 02142 USA
| | - Marina DiStefano
- grid.66859.340000 0004 0546 1623Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA 02142 USA
| | - Julianne M. O’Daniel
- grid.410711.20000 0001 1034 1720Department of Genetics, University of North Carolina, Chapel Hill, NC 27599 USA
| | - Kristy Lee
- grid.410711.20000 0001 1034 1720Department of Genetics, University of North Carolina, Chapel Hill, NC 27599 USA
| | - Erin R. Riggs
- grid.280776.c0000 0004 0394 1447Autism & Developmental Medicine Institute, Geisinger Health System, Lewisburg, PA 17837 USA
| | - Diane B. Zastrow
- grid.416759.80000 0004 0460 3124Sutter Health, Mountain View, CA 94040 USA
| | - Jessica L. Mester
- grid.428467.b0000 0004 0409 2707GeneDx Inc., Gaithersburg, MD 20877 USA
| | - Deborah I. Ritter
- grid.39382.330000 0001 2160 926XDepartment of Pediatrics/Hematology-Oncology, Baylor College of Medicine, Houston, TX 77030 USA
| | - Ronak Y. Patel
- grid.39382.330000 0001 2160 926XDepartment of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030 USA
| | - Sai Lakshmi Subramanian
- grid.39382.330000 0001 2160 926XDepartment of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030 USA
| | - Aleksander Milosavljevic
- grid.39382.330000 0001 2160 926XDepartment of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030 USA
| | - Jonathan S. Berg
- grid.410711.20000 0001 1034 1720Department of Genetics, University of North Carolina, Chapel Hill, NC 27599 USA
| | - Heidi L. Rehm
- grid.66859.340000 0004 0546 1623Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA 02142 USA ,grid.32224.350000 0004 0386 9924Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA 02114 USA
| | - Sharon E. Plon
- grid.39382.330000 0001 2160 926XDepartment of Pediatrics/Hematology-Oncology, Baylor College of Medicine, Houston, TX 77030 USA ,grid.39382.330000 0001 2160 926XDepartment of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030 USA
| | - J. Michael Cherry
- grid.168010.e0000000419368956Department of Genetics, Stanford University School of Medicine, Stanford, CA 94305 USA
| | - Carlos D. Bustamante
- grid.168010.e0000000419368956Department of Biomedical Data Science, Stanford University School of Medicine, Stanford, CA 94305 USA ,grid.168010.e0000000419368956Department of Genetics, Stanford University School of Medicine, Stanford, CA 94305 USA
| | - Helio A. Costa
- grid.168010.e0000000419368956Department of Pathology, Stanford University School of Medicine, 300 Pasteur Drive, MSOB x313, Stanford, CA 94305 USA ,grid.168010.e0000000419368956Department of Biomedical Data Science, Stanford University School of Medicine, Stanford, CA 94305 USA
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17
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Quiver MH, Lachance J. Adaptive eQTLs reveal the evolutionary impacts of pleiotropy and tissue-specificity while contributing to health and disease. HGG ADVANCES 2022; 3:100083. [PMID: 35047867 PMCID: PMC8756519 DOI: 10.1016/j.xhgg.2021.100083] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2021] [Accepted: 12/21/2021] [Indexed: 11/24/2022] Open
Abstract
Large numbers of expression quantitative trait loci (eQTLs) have recently been identified in humans, and many of these regulatory variants have large allele frequency differences between populations. Here, we conducted genome-wide scans of selection to identify adaptive eQTLs (i.e., eQTLs with large population branch statistics). We then tested if tissue pleiotropy affects whether eQTLs are more or less likely to be adaptive and identified tissues that have been key targets of positive selection during the last 100,000 years. Top adaptive eQTL outliers include rs1043809, rs66899053, and rs2814778 (a SNP that is associated with malaria resistance). We found that effect sizes of eQTLs were negatively correlated with population branch statistics and that adaptive eQTLs affect two-thirds as many tissues as do non-adaptive eQTLs. Because the tissue breadth of an eQTL can be viewed as a measure of pleiotropy, these results imply that pleiotropy inhibits adaptation. The proportion of eQTLs that are adaptive varies by tissue, and we found that eQTLs that regulate expression in testis, thyroid, blood, or sun-exposed skin are enriched for signatures of positive selection. By contrast, eQTLs that regulate expression in the cerebrum or female-specific tissues have a relative lack of adaptive outliers. Scans of selections also reveal that many adaptive eQTLs are closely linked to disease-associated loci. Taken together, our results indicate that eQTLs have played an important role in recent human evolution.
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Affiliation(s)
- Melanie H Quiver
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA 30332, USA
| | - Joseph Lachance
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA 30332, USA
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18
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Barnes AB, Keener RM, Schott BH, Wang L, Valdivia RH, Ko DC. Human genetic diversity regulating the TLR10/TLR1/TLR6 locus confers increased cytokines in response to Chlamydia trachomatis. HGG ADVANCES 2022; 3:100071. [PMID: 35047856 PMCID: PMC8756536 DOI: 10.1016/j.xhgg.2021.100071] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2021] [Accepted: 11/15/2021] [Indexed: 12/25/2022] Open
Abstract
Human genetic diversity can have profound effects on health outcomes upon exposure to infectious agents. For infections with Chlamydia trachomatis (C. trachomatis), the wide range of genital and ocular disease manifestations are likely influenced by human genetic differences that regulate interactions between C. trachomatis and host cells. We leveraged this diversity in cellular responses to demonstrate the importance of variation at the Toll-like receptor 1 (TLR1), TLR6, and TLR10 locus to cytokine production in response to C. trachomatis. We determined that a single-nucleotide polymorphism (SNP) (rs1057807), located in a region that forms a loop with the TLR6 promoter, is associated with increased expression of TLR1, TLR6, and TLR10 and secreted levels of ten C. trachomatis-induced cytokines. Production of these C. trachomatis-induced cytokines is primarily dependent on MyD88 and TLR6 based on experiments using inhibitors, blocking antibodies, RNAi, and protein overexpression. Population genetic analyses further demonstrated that the mean IL-6 response of cells from two European populations were higher than the mean response of cells from three African populations and that this difference was partially attributable to variation in rs1057807 allele frequency. In contrast, a SNP associated with a different pro-inflammatory cytokine (rs2869462 associated with the chemokine CXCL10) exhibited an opposite response, underscoring the complexity of how different genetic variants contribute to an individual's immune response. This multidisciplinary study has identified a long-range chromatin interaction and genetic variation that regulates TLR6 to broaden our understanding of how human genetic variation affects the C. trachomatis-induced immune response.
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Affiliation(s)
- Alyson B. Barnes
- Department of Molecular Genetics and Microbiology, School of Medicine, Duke University, Durham, NC 27710, USA
| | - Rachel M. Keener
- Department of Molecular Genetics and Microbiology, School of Medicine, Duke University, Durham, NC 27710, USA
- University Program in Genetics and Genomics, Duke University, Durham, NC 27710, USA
| | - Benjamin H. Schott
- Department of Molecular Genetics and Microbiology, School of Medicine, Duke University, Durham, NC 27710, USA
- University Program in Genetics and Genomics, Duke University, Durham, NC 27710, USA
| | - Liuyang Wang
- Department of Molecular Genetics and Microbiology, School of Medicine, Duke University, Durham, NC 27710, USA
| | - Raphael H. Valdivia
- Department of Molecular Genetics and Microbiology, School of Medicine, Duke University, Durham, NC 27710, USA
| | - Dennis C. Ko
- Department of Molecular Genetics and Microbiology, School of Medicine, Duke University, Durham, NC 27710, USA
- University Program in Genetics and Genomics, Duke University, Durham, NC 27710, USA
- Division of Infectious Diseases, Department of Medicine, School of Medicine, Duke University, Durham, NC 27710, USA
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19
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Carioscia SA, Weaver KJ, Bortvin AN, Pan H, Ariad D, Bell AD, McCoy RC. A method for low-coverage single-gamete sequence analysis demonstrates adherence to Mendel's first law across a large sample of human sperm. eLife 2022; 11:76383. [PMID: 36475543 PMCID: PMC9844984 DOI: 10.7554/elife.76383] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2021] [Accepted: 12/05/2022] [Indexed: 12/12/2022] Open
Abstract
Recently published single-cell sequencing data from individual human sperm (n=41,189; 969-3377 cells from each of 25 donors) offer an opportunity to investigate questions of inheritance with improved statistical power, but require new methods tailored to these extremely low-coverage data (∼0.01× per cell). To this end, we developed a method, named rhapsodi, that leverages sparse gamete genotype data to phase the diploid genomes of the donor individuals, impute missing gamete genotypes, and discover meiotic recombination breakpoints, benchmarking its performance across a wide range of study designs. We then applied rhapsodi to the sperm sequencing data to investigate adherence to Mendel's Law of Segregation, which states that the offspring of a diploid, heterozygous parent will inherit either allele with equal probability. While the vast majority of loci adhere to this rule, research in model and non-model organisms has uncovered numerous exceptions whereby 'selfish' alleles are disproportionately transmitted to the next generation. Evidence of such 'transmission distortion' (TD) in humans remains equivocal in part because scans of human pedigrees have been under-powered to detect small effects. After applying rhapsodi to the sperm data and scanning for evidence of TD, our results exhibited close concordance with binomial expectations under balanced transmission. Together, our work demonstrates that rhapsodi can facilitate novel uses of inferred genotype data and meiotic recombination events, while offering a powerful quantitative framework for testing for TD in other cohorts and study systems.
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Affiliation(s)
- Sara A Carioscia
- Department of Biology, Johns Hopkins UniversityBaltimoreUnited States
| | - Kathryn J Weaver
- Department of Biology, Johns Hopkins UniversityBaltimoreUnited States
| | - Andrew N Bortvin
- Department of Biology, Johns Hopkins UniversityBaltimoreUnited States
| | - Hao Pan
- Department of Biology, Johns Hopkins UniversityBaltimoreUnited States
| | - Daniel Ariad
- Department of Biology, Johns Hopkins UniversityBaltimoreUnited States
| | - Avery Davis Bell
- School of Biological Sciences, Georgia Institute of TechnologyAtlantaUnited States
| | - Rajiv C McCoy
- Department of Biology, Johns Hopkins UniversityBaltimoreUnited States
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20
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Choate LA, Barshad G, McMahon PW, Said I, Rice EJ, Munn PR, Lewis JJ, Danko CG. Multiple stages of evolutionary change in anthrax toxin receptor expression in humans. Nat Commun 2021; 12:6590. [PMID: 34782625 PMCID: PMC8592990 DOI: 10.1038/s41467-021-26854-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2020] [Accepted: 10/18/2021] [Indexed: 11/09/2022] Open
Abstract
The advent of animal husbandry and hunting increased human exposure to zoonotic pathogens. To understand how a zoonotic disease may have influenced human evolution, we study changes in human expression of anthrax toxin receptor 2 (ANTXR2), which encodes a cell surface protein necessary for Bacillus anthracis virulence toxins to cause anthrax disease. In immune cells, ANTXR2 is 8-fold down-regulated in all available human samples compared to non-human primates, indicating regulatory changes early in the evolution of modern humans. We also observe multiple genetic signatures consistent with recent positive selection driving a European-specific decrease in ANTXR2 expression in multiple tissues affected by anthrax toxins. Our observations fit a model in which humans adapted to anthrax disease following early ecological changes associated with hunting and scavenging, as well as a second period of adaptation after the rise of modern agriculture.
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Affiliation(s)
- Lauren A Choate
- Baker Institute for Animal Health, College of Veterinary Medicine, Cornell University, Ithaca, NY, 14853, USA
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY, 14853, USA
| | - Gilad Barshad
- Baker Institute for Animal Health, College of Veterinary Medicine, Cornell University, Ithaca, NY, 14853, USA
| | - Pierce W McMahon
- Baker Institute for Animal Health, College of Veterinary Medicine, Cornell University, Ithaca, NY, 14853, USA
| | - Iskander Said
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY, 14853, USA
| | - Edward J Rice
- Baker Institute for Animal Health, College of Veterinary Medicine, Cornell University, Ithaca, NY, 14853, USA
| | - Paul R Munn
- Baker Institute for Animal Health, College of Veterinary Medicine, Cornell University, Ithaca, NY, 14853, USA
| | - James J Lewis
- Baker Institute for Animal Health, College of Veterinary Medicine, Cornell University, Ithaca, NY, 14853, USA.
| | - Charles G Danko
- Baker Institute for Animal Health, College of Veterinary Medicine, Cornell University, Ithaca, NY, 14853, USA.
- Department of Biomedical Sciences, College of Veterinary Medicine, Cornell University, Ithaca, NY, 14853, USA.
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21
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Yan SM, Sherman RM, Taylor DJ, Nair DR, Bortvin AN, Schatz MC, McCoy RC. Local adaptation and archaic introgression shape global diversity at human structural variant loci. eLife 2021; 10:e67615. [PMID: 34528508 PMCID: PMC8492059 DOI: 10.7554/elife.67615] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2021] [Accepted: 09/14/2021] [Indexed: 12/13/2022] Open
Abstract
Large genomic insertions and deletions are a potent source of functional variation, but are challenging to resolve with short-read sequencing, limiting knowledge of the role of such structural variants (SVs) in human evolution. Here, we used a graph-based method to genotype long-read-discovered SVs in short-read data from diverse human genomes. We then applied an admixture-aware method to identify 220 SVs exhibiting extreme patterns of frequency differentiation - a signature of local adaptation. The top two variants traced to the immunoglobulin heavy chain locus, tagging a haplotype that swept to near fixation in certain southeast Asian populations, but is rare in other global populations. Further investigation revealed evidence that the haplotype traces to gene flow from Neanderthals, corroborating the role of immune-related genes as prominent targets of adaptive introgression. Our study demonstrates how recent technical advances can help resolve signatures of key evolutionary events that remained obscured within technically challenging regions of the genome.
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Affiliation(s)
- Stephanie M Yan
- Department of Biology, Johns Hopkins University, BaltimoreBaltimoreUnited States
| | - Rachel M Sherman
- Department of Computer Science, Johns Hopkins UniversityBaltimoreUnited States
| | - Dylan J Taylor
- Department of Biology, Johns Hopkins University, BaltimoreBaltimoreUnited States
| | - Divya R Nair
- Department of Biology, Johns Hopkins University, BaltimoreBaltimoreUnited States
| | - Andrew N Bortvin
- Department of Biology, Johns Hopkins University, BaltimoreBaltimoreUnited States
| | - Michael C Schatz
- Department of Biology, Johns Hopkins University, BaltimoreBaltimoreUnited States
- Department of Computer Science, Johns Hopkins UniversityBaltimoreUnited States
| | - Rajiv C McCoy
- Department of Biology, Johns Hopkins University, BaltimoreBaltimoreUnited States
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22
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Soveg FW, Schwerk J, Gokhale NS, Cerosaletti K, Smith JR, Pairo-Castineira E, Kell AM, Forero A, Zaver SA, Esser-Nobis K, Roby JA, Hsiang TY, Ozarkar S, Clingan JM, McAnarney ET, Stone AEL, Malhotra U, Speake C, Perez J, Balu C, Allenspach EJ, Hyde JL, Menachery VD, Sarkar SN, Woodward JJ, Stetson DB, Baillie JK, Buckner JH, Gale M, Savan R. Endomembrane targeting of human OAS1 p46 augments antiviral activity. eLife 2021; 10:e71047. [PMID: 34342578 PMCID: PMC8357416 DOI: 10.7554/elife.71047] [Citation(s) in RCA: 36] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2021] [Accepted: 06/11/2021] [Indexed: 12/14/2022] Open
Abstract
Many host RNA sensors are positioned in the cytosol to detect viral RNA during infection. However, most positive-strand RNA viruses replicate within a modified organelle co-opted from intracellular membranes of the endomembrane system, which shields viral products from cellular innate immune sensors. Targeting innate RNA sensors to the endomembrane system may enhance their ability to sense RNA generated by viruses that use these compartments for replication. Here, we reveal that an isoform of oligoadenylate synthetase 1, OAS1 p46, is prenylated and targeted to the endomembrane system. Membrane localization of OAS1 p46 confers enhanced access to viral replication sites and results in increased antiviral activity against a subset of RNA viruses including flaviviruses, picornaviruses, and SARS-CoV-2. Finally, our human genetic analysis shows that the OAS1 splice-site SNP responsible for production of the OAS1 p46 isoform correlates with protection from severe COVID-19. This study highlights the importance of endomembrane targeting for the antiviral specificity of OAS1 and suggests that early control of SARS-CoV-2 replication through OAS1 p46 is an important determinant of COVID-19 severity.
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Affiliation(s)
- Frank W Soveg
- Department of Immunology, School of Medicine, University of WashingtonSeattleUnited States
- Center for Innate Immunity and Immune Disease, University of WashingtonSeattleUnited States
| | - Johannes Schwerk
- Department of Immunology, School of Medicine, University of WashingtonSeattleUnited States
- Center for Innate Immunity and Immune Disease, University of WashingtonSeattleUnited States
| | - Nandan S Gokhale
- Department of Immunology, School of Medicine, University of WashingtonSeattleUnited States
- Center for Innate Immunity and Immune Disease, University of WashingtonSeattleUnited States
| | | | - Julian R Smith
- Department of Immunology, School of Medicine, University of WashingtonSeattleUnited States
- Center for Innate Immunity and Immune Disease, University of WashingtonSeattleUnited States
| | | | - Alison M Kell
- Department of Immunology, School of Medicine, University of WashingtonSeattleUnited States
- Center for Innate Immunity and Immune Disease, University of WashingtonSeattleUnited States
- Department of Molecular Genetics and Microbiology, School of Medicine, University of New MexicoAlbuquerqueUnited States
| | - Adriana Forero
- Department of Immunology, School of Medicine, University of WashingtonSeattleUnited States
- Center for Innate Immunity and Immune Disease, University of WashingtonSeattleUnited States
- Department of Microbial Infection and Immunity, College of Medicine, The Ohio State UniversityColumbusUnited States
| | - Shivam A Zaver
- Department of Microbiology, School of Medicine, University of WashingtonSeattleUnited States
| | - Katharina Esser-Nobis
- Department of Immunology, School of Medicine, University of WashingtonSeattleUnited States
- Center for Innate Immunity and Immune Disease, University of WashingtonSeattleUnited States
| | - Justin A Roby
- Department of Immunology, School of Medicine, University of WashingtonSeattleUnited States
- Center for Innate Immunity and Immune Disease, University of WashingtonSeattleUnited States
| | - Tien-Ying Hsiang
- Department of Immunology, School of Medicine, University of WashingtonSeattleUnited States
- Center for Innate Immunity and Immune Disease, University of WashingtonSeattleUnited States
| | - Snehal Ozarkar
- Department of Immunology, School of Medicine, University of WashingtonSeattleUnited States
- Center for Innate Immunity and Immune Disease, University of WashingtonSeattleUnited States
| | - Jonathan M Clingan
- Department of Immunology, School of Medicine, University of WashingtonSeattleUnited States
- Center for Innate Immunity and Immune Disease, University of WashingtonSeattleUnited States
| | - Eileen T McAnarney
- Department of Microbiology and Immunology, University of Texas Medical CenterGalvestonUnited States
| | - Amy EL Stone
- Department of Immunology, School of Medicine, University of WashingtonSeattleUnited States
- Center for Innate Immunity and Immune Disease, University of WashingtonSeattleUnited States
- Department of Basic Sciences, College of Osteopathic Medicine, Touro University NevadaHendersonUnited States
| | - Uma Malhotra
- Department of Infectious Disease, Virginia Mason Medical CenterSeattleUnited States
- Department of Medicine, Section of Infectious Diseases, University of WashingtonSeattleUnited States
| | - Cate Speake
- Benaroya Research Institute at Virginia MasonSeattleUnited States
| | - Joseph Perez
- Cancer Virology Program, University of Pittsburgh Cancer Institute, University of PittsburghPittsburghUnited States
| | - Chiraag Balu
- Department of Immunology, School of Medicine, University of WashingtonSeattleUnited States
- Center for Innate Immunity and Immune Disease, University of WashingtonSeattleUnited States
| | - Eric J Allenspach
- Center for Immunity and Immunotherapies, Seattle Children's Research InstituteSeattleUnited States
| | - Jennifer L Hyde
- Department of Microbial Infection and Immunity, College of Medicine, The Ohio State UniversityColumbusUnited States
| | - Vineet D Menachery
- Department of Microbiology and Immunology, University of Texas Medical CenterGalvestonUnited States
| | - Saumendra N Sarkar
- Cancer Virology Program, University of Pittsburgh Cancer Institute, University of PittsburghPittsburghUnited States
| | - Joshua J Woodward
- Center for Innate Immunity and Immune Disease, University of WashingtonSeattleUnited States
- Department of Microbiology, School of Medicine, University of WashingtonSeattleUnited States
| | - Daniel B Stetson
- Department of Immunology, School of Medicine, University of WashingtonSeattleUnited States
- Center for Innate Immunity and Immune Disease, University of WashingtonSeattleUnited States
| | - John Kenneth Baillie
- Roslin Institute, University of EdinburghEdinburghUnited Kingdom
- MRC Human Genetics Unit, Institute of Genetics and Molecular Medicine, University of Edinburgh, Western General HospitalEdinburghUnited Kingdom
| | - Jane H Buckner
- Benaroya Research Institute at Virginia MasonSeattleUnited States
| | - Michael Gale
- Department of Immunology, School of Medicine, University of WashingtonSeattleUnited States
- Center for Innate Immunity and Immune Disease, University of WashingtonSeattleUnited States
| | - Ram Savan
- Department of Immunology, School of Medicine, University of WashingtonSeattleUnited States
- Center for Innate Immunity and Immune Disease, University of WashingtonSeattleUnited States
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23
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Rosas-Madrigal S, Villarreal-Molina MT, Flores-Rivera J, Rivas-Alonso V, Macias-Kauffer LR, Ordoñez G, Chima-Galán MDC, Acuña-Alonzo V, Macín-Pérez G, Barquera R, Granados J, Valle-Rios R, Corona T, Carnevale A, Romero-Hidalgo S. Interaction of HLA Class II rs9272219 and TMPO rs17028450 (Arg690Cys) Variants Affects Neuromyelitis Optica Spectrum Disorder Susceptibility in an Admixed Mexican Population. Front Genet 2021; 12:647343. [PMID: 34335680 PMCID: PMC8320513 DOI: 10.3389/fgene.2021.647343] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2020] [Accepted: 06/23/2021] [Indexed: 12/02/2022] Open
Abstract
Neuromyelitis Optica Spectrum Disorder (NMOSD) is a demyelinating autoimmune disease of the central nervous system, more prevalent in individuals of non-European ancestry. Few studies have analyzed genetic risk factors in NMOSD, and HLA class II gene variation has been associated NMOSD risk in various populations including Mexicans. Thymopoietin (TMPO) has not been tested as a candidate gene for NMOSD or other autoimmune disease, however, experimental evidence suggests this gene may be involved in negative selection of autoreactive T cells and autoimmunity. We thus investigated whether the missense TMPO variant rs17028450 (Arg630Cys, frequent in Latin America) is associated with NMOSD, and whether this variant shows an interaction with HLA-class II rs9272219, previously associated with NMOSD risk. A total of 119 Mexican NMOSD patients, 1208 controls and 357 Native Mexican individuals were included. The HLA rs9272219 “T” risk allele frequency ranged from 21 to 68%, while the rs17028450 “T” minor allele frequency was as high as 18% in Native Mexican groups. Both rs9272219 and rs17028450 were significantly associated with NMOSD risk under additive models (OR = 2.48; p = 8 × 10–10 and OR = 1.59; p = 0.0075, respectively), and a significant interaction between both variants was identified with logistic regression models (p = 0.048). Individuals bearing both risk alleles had an estimated 3.9-fold increased risk of NMOSD. To our knowledge, this is the first study reporting an association of TMPO gene variation with an autoimmune disorder and the interaction of specific susceptibility gene variants, that may contribute to the genetic architecture of NMOSD in admixed Latin American populations.
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Affiliation(s)
- Sandra Rosas-Madrigal
- Laboratorio de Enfermedades Mendelianas, Instituto Nacional de Medicina Genómica, Mexico City, Mexico
| | | | - José Flores-Rivera
- Laboratorio Clínico de Enfermedades Neurodegenerativas, Instituto Nacional de Neurología y Neurocirugía "Manuel Velasco Suarez" (INNN), Mexico City, Mexico
| | - Verónica Rivas-Alonso
- Laboratorio Clínico de Enfermedades Neurodegenerativas, Instituto Nacional de Neurología y Neurocirugía "Manuel Velasco Suarez" (INNN), Mexico City, Mexico
| | - Luis Rodrigo Macias-Kauffer
- Unidad de Genómica de Poblaciones Aplicada a La Salud, Facultad de Química, UNAM/INMEGEN, Mexico City, Mexico
| | | | | | | | | | - Rodrigo Barquera
- Department of Archaeogenetics, Max Planck Institute for the Science of Human History, Jena, Germany
| | - Julio Granados
- Departamento de Trasplantes, Instituto Nacional de Ciencias Medicas y Nutrición "Salvador Zubirán", Mexico City, Mexico
| | - Ricardo Valle-Rios
- División de Investigación, Facultad de Medicina, Unidad de Investigación en Inmunología y Proteómica, Hospital Infantil de México Federico Gómez, Universidad Nacional Autónoma de México, Mexico City, Mexico
| | - Teresa Corona
- Laboratorio Clínico de Enfermedades Neurodegenerativas, Instituto Nacional de Neurología y Neurocirugía "Manuel Velasco Suarez" (INNN), Mexico City, Mexico
| | - Alessandra Carnevale
- Laboratorio de Enfermedades Mendelianas, Instituto Nacional de Medicina Genómica, Mexico City, Mexico
| | - Sandra Romero-Hidalgo
- Departamento de Genómica Computacional, Instituto Nacional de Medicina Genómica (INMEGEN), Mexico City, Mexico
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24
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Genome-wide association study of resistance to Mycobacterium tuberculosis infection identifies a locus at 10q26.2 in three distinct populations. PLoS Genet 2021; 17:e1009392. [PMID: 33661925 PMCID: PMC7963100 DOI: 10.1371/journal.pgen.1009392] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2020] [Revised: 03/16/2021] [Accepted: 02/02/2021] [Indexed: 12/19/2022] Open
Abstract
The natural history of tuberculosis (TB) is characterized by a large inter-individual outcome variability after exposure to Mycobacterium tuberculosis. Specifically, some highly exposed individuals remain resistant to M. tuberculosis infection, as inferred by tuberculin skin test (TST) or interferon-gamma release assays (IGRAs). We performed a genome-wide association study of resistance to M. tuberculosis infection in an endemic region of Southern Vietnam. We enrolled household contacts (HHC) of pulmonary TB cases and compared subjects who were negative for both TST and IGRA (n = 185) with infected individuals (n = 353) who were either positive for both TST and IGRA or had a diagnosis of TB. We found a genome-wide significant locus on chromosome 10q26.2 with a cluster of variants associated with strong protection against M. tuberculosis infection (OR = 0.42, 95%CI 0.35–0.49, P = 3.71×10−8, for the genotyped variant rs17155120). The locus was replicated in a French multi-ethnic HHC cohort and a familial admixed cohort from a hyper-endemic area of South Africa, with an overall OR for rs17155120 estimated at 0.50 (95%CI 0.45–0.55, P = 1.26×10−9). The variants are located in intronic regions and upstream of C10orf90, a tumor suppressor gene which encodes an ubiquitin ligase activating the transcription factor p53. In silico analysis showed that the protective alleles were associated with a decreased expression in monocytes of the nearby gene ADAM12 which could lead to an enhanced response of Th17 lymphocytes. Our results reveal a novel locus controlling resistance to M. tuberculosis infection across different populations. There is strong epidemiological evidence that a proportion of highly exposed individuals remain resistant to M. tuberculosis infection, as shown by a negative result for Tuberculin Skin Test (TST) or IFN-γ Release Assays (IGRAs). We performed a genome-wide association study between resistant and infected individuals, which were carefully selected employing a household contact design to maximize exposure by infectious index patients. We employed stringently defined concordant results for both TST and IGRA assays to avoid misclassifications. We discovered a locus at 10q26.2 associated with resistance to M. tuberculosis infection in a Vietnamese discovery cohort. This locus could be replicated in two independent cohorts from different epidemiological settings and of diverse ancestries enrolled in France and South Africa.
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Ding X, Schimenti JC. Strategies to Identify Genetic Variants Causing Infertility. Trends Mol Med 2021; 27:792-806. [PMID: 33431240 DOI: 10.1016/j.molmed.2020.12.008] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2020] [Revised: 11/26/2020] [Accepted: 12/11/2020] [Indexed: 12/19/2022]
Abstract
Genetic causes are thought to underlie about half of infertility cases, but understanding the genetic bases has been a major challenge. Modern genomics tools allow more sophisticated exploration of genetic causes of infertility through population, family-based, and individual studies. Nevertheless, potential therapies based on genetic diagnostics will be limited until there is certainty regarding the causality of genetic variants identified in an individual. Genome modulation and editing technologies have revolutionized our ability to functionally test such variants, and also provide a potential means for clinical correction of infertility variants. This review addresses strategies being used to identify causative variants of infertility.
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Affiliation(s)
- Xinbao Ding
- Cornell University, College of Veterinary Medicine, Department of Biomedical Sciences, Ithaca, NY 14853, USA
| | - John C Schimenti
- Cornell University, College of Veterinary Medicine, Department of Biomedical Sciences, Ithaca, NY 14853, USA.
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Fiorica PN, Schubert R, Morris JD, Abdul Sami M, Wheeler HE. Multi-ethnic transcriptome-wide association study of prostate cancer. PLoS One 2020; 15:e0236209. [PMID: 32986714 PMCID: PMC7521738 DOI: 10.1371/journal.pone.0236209] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2020] [Accepted: 09/11/2020] [Indexed: 12/13/2022] Open
Abstract
The genetic risk for prostate cancer has been governed by a few rare variants with high penetrance and over 150 commonly occurring variants with lower impact on risk; however, most of these variants have been identified in studies containing exclusively European individuals. People of non-European ancestries make up less than 15% of prostate cancer GWAS subjects. Across the globe, incidence of prostate cancer varies with population due to environmental and genetic factors. The discrepancy between disease incidence and representation in genetics highlights the need for more studies of the genetic risk for prostate cancer across diverse populations. To better understand the genetic risk for prostate cancer across diverse populations, we performed PrediXcan and GWAS in a case-control study of 4,769 self-identified African American (2,463 cases and 2,306 controls), 2,199 Japanese American (1,106 cases and 1,093 controls), and 2,147 Latin American (1,081 cases and 1,066 controls) individuals from the Multiethnic Genome-wide Scan of Prostate Cancer. We used prediction models from 46 tissues in GTEx version 8 and five models from monocyte transcriptomes in the Multi-Ethnic Study of Atherosclerosis. Across the three populations, we predicted 19 gene-tissue pairs, including five unique genes, to be significantly (lfsr < 0.05) associated with prostate cancer. One of these genes, NKX3-1, replicated in a larger European study. At the SNP level, 110 SNPs met genome-wide significance in the African American study while 123 SNPs met significance in the Japanese American study. Fine mapping revealed three significant independent loci in the African American study and two significant independent loci in the Japanese American study. These identified loci confirm findings from previous GWAS of prostate cancer in diverse populations while PrediXcan-identified genes suggest potential new directions for prostate cancer research in populations across the globe.
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Affiliation(s)
- Peter N. Fiorica
- Department of Chemistry & Biochemistry, Loyola University Chicago, Chicago, IL, United States of America
- Department of Biology, Loyola University Chicago, Chicago, IL, United States of America
| | - Ryan Schubert
- Department of Biology, Loyola University Chicago, Chicago, IL, United States of America
- Program in Bioinformatics, Loyola University Chicago, Chicago, IL, United States of America
- Department of Statistics, Loyola University Chicago, Chicago, IL, United States of America
| | - John D. Morris
- Department of Biology, Loyola University Chicago, Chicago, IL, United States of America
- Program in Bioinformatics, Loyola University Chicago, Chicago, IL, United States of America
| | - Mohammed Abdul Sami
- Department of Biology, Loyola University Chicago, Chicago, IL, United States of America
| | - Heather E. Wheeler
- Department of Chemistry & Biochemistry, Loyola University Chicago, Chicago, IL, United States of America
- Department of Biology, Loyola University Chicago, Chicago, IL, United States of America
- Program in Bioinformatics, Loyola University Chicago, Chicago, IL, United States of America
- Department of Public Health, Loyola University Chicago, Chicago, IL, United States of America
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Geris JM, Spector LG. Race, ethnicity, and socioeconomic differences in incidence of pediatric embryonal tumors in the United States. Pediatr Blood Cancer 2020; 67:e28582. [PMID: 32672899 PMCID: PMC7674242 DOI: 10.1002/pbc.28582] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/19/2020] [Revised: 06/18/2020] [Accepted: 06/29/2020] [Indexed: 12/16/2022]
Abstract
BACKGROUND The etiology of childhood cancers and its social patterning remains largely unknown. Accounting for socioeconomic status (SES) when exploring the association between race/ethnicity and cancer incidence is necessary to better understand such etiology. We aimed to investigate differences in the incidence of embryonal tumors (ETs) by SES and race/ethnicity in the United States using population-based registries of the Surveillance, Epidemiology, and End Results (SEER) Program. PROCEDURE Children with ETs aged 0-19 years diagnosed between 2000 and 2015 were ascertained from the census tract-level SEER database. SES was measured using a tract-level composite index. Incidence rate ratios (IRRs) with 95% confidence intervals (CIs) by SES quintile and race/ethnicity were estimated using multivariable Poisson regression models. RESULTS The majority of tumors had lower incidence among nonwhite children compared with non-Hispanic (NH) white children, after controlling for SES. NH blacks had a higher incidence of Wilms tumor than NH whites (IRR: 1.26; 95% CI, 1.13-1.39). There was an increasing linear trend (P = 0.0001) across increasing SES quintile for embryonal rhabdomyosarcoma after controlling for race/ethnicity. Effect modification by race/ethnicity of the relationship between SES and tumor incidence was observed for several groups. Hispanics had a significant, linear trend (P = 0.0005) in the incidence of Wilms tumor, while Asian/Pacific Islanders experienced a significant inverse trend (P = 0.0002). CONCLUSIONS Results from this study suggest differences in the incidence of several ETs by race/ethnicity and that these differences may be modified by SES. Investigation of potential risk factors that are socially patterned is warranted.
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Affiliation(s)
- Jennifer M. Geris
- Division of Epidemiology & Clinical Research, Department of Pediatrics, University of Minnesota, Minneapolis MN
| | - Logan G. Spector
- Division of Epidemiology & Clinical Research, Department of Pediatrics, University of Minnesota, Minneapolis MN
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Yao Y, Tan HW, Liang ZL, Wu GQ, Xu YM, Lau ATY. The Impact of Coilin Nonsynonymous SNP Variants E121K and V145I on Cell Growth and Cajal Body Formation: The First Characterization. Genes (Basel) 2020; 11:genes11080895. [PMID: 32764415 PMCID: PMC7463897 DOI: 10.3390/genes11080895] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2020] [Revised: 07/25/2020] [Accepted: 07/27/2020] [Indexed: 02/05/2023] Open
Abstract
Coilin is the main component of Cajal body (CB), a membraneless organelle that is involved in the biogenesis of ribonucleoproteins and telomerase, cell cycle, and cell growth. The disruption of CBs is linked to neurodegenerative diseases and potentially cancers. The coilin gene (COIL) contains two nonsynonymous SNPs: rs116022828 (E121K) and rs61731978 (V145I). Here, we investigated for the first time the functional impacts of these coilin SNPs on CB formation, coilin subcellular localization, microtubule formation, cell growth, and coilin expression and protein structure. We revealed that both E121K and V145I mutants could disrupt CB formation and result in various patterns of subcellular localization with survival motor neuron protein. Noteworthy, many of the E121K cells showed nucleolar coilin accumulation. The microtubule regrowth and cell cycle assays indicated that the E121K cells appeared to be trapped in the S and G2/M phases of cell cycle, resulting in reduced cell proliferation. In silico protein structure prediction suggested that the E121K mutation caused greater destabilization on the coilin structure than the V145I mutation. Additionally, clinical bioinformatic analysis indicated that coilin expression levels could be a risk factor for cancer, depending on the cancer types and races.
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Affiliation(s)
- Yue Yao
- Laboratory of Cancer Biology and Epigenetics, Shantou University Medical College, Shantou 515041, Guangdong, China; (Y.Y.); (H.W.T.); (Z.-L.L.); (G.-Q.W.)
| | - Heng Wee Tan
- Laboratory of Cancer Biology and Epigenetics, Shantou University Medical College, Shantou 515041, Guangdong, China; (Y.Y.); (H.W.T.); (Z.-L.L.); (G.-Q.W.)
| | - Zhan-Ling Liang
- Laboratory of Cancer Biology and Epigenetics, Shantou University Medical College, Shantou 515041, Guangdong, China; (Y.Y.); (H.W.T.); (Z.-L.L.); (G.-Q.W.)
| | - Gao-Qi Wu
- Laboratory of Cancer Biology and Epigenetics, Shantou University Medical College, Shantou 515041, Guangdong, China; (Y.Y.); (H.W.T.); (Z.-L.L.); (G.-Q.W.)
| | - Yan-Ming Xu
- Department of Cell Biology and Genetics, Shantou University Medical College, Shantou 515041, Guangdong, China
- Correspondence: (Y.-M.X.); (A.T.Y.L.); Tel.: +86-754-8890-0437 (Y.-M.X.); +86-754-8853-0052 (A.T.Y.L.)
| | - Andy T. Y. Lau
- Laboratory of Cancer Biology and Epigenetics, Shantou University Medical College, Shantou 515041, Guangdong, China; (Y.Y.); (H.W.T.); (Z.-L.L.); (G.-Q.W.)
- Correspondence: (Y.-M.X.); (A.T.Y.L.); Tel.: +86-754-8890-0437 (Y.-M.X.); +86-754-8853-0052 (A.T.Y.L.)
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Fernandez-Rhodes L, Young KL, Lilly AG, Raffield LM, Highland HM, Wojcik GL, Agler C, M Love SA, Okello S, Petty LE, Graff M, Below JE, Divaris K, North KE. Importance of Genetic Studies of Cardiometabolic Disease in Diverse Populations. Circ Res 2020; 126:1816-1840. [PMID: 32496918 PMCID: PMC7285892 DOI: 10.1161/circresaha.120.315893] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Genome-wide association studies have revolutionized our understanding of the genetic underpinnings of cardiometabolic disease. Yet, the inadequate representation of individuals of diverse ancestral backgrounds in these studies may undercut their ultimate potential for both public health and precision medicine. The goal of this review is to describe the imperativeness of studying the populations who are most affected by cardiometabolic disease, to the aim of better understanding the genetic underpinnings of the disease. We support this premise by describing the current variation in the global burden of cardiometabolic disease and emphasize the importance of building a globally and ancestrally representative genetics evidence base for the identification of population-specific variants, fine-mapping, and polygenic risk score estimation. We discuss the important ethical, legal, and social implications of increasing ancestral diversity in genetic studies of cardiometabolic disease and the challenges that arise from the (1) lack of diversity in current reference populations and available analytic samples and the (2) unequal generation of health-associated genomic data and their prediction accuracies. Despite these challenges, we conclude that additional, unprecedented opportunities lie ahead for public health genomics and the realization of precision medicine, provided that the gap in diversity can be systematically addressed. Achieving this goal will require concerted efforts by social, academic, professional and regulatory stakeholders and communities, and these efforts must be based on principles of equity and social justice.
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Affiliation(s)
- Lindsay Fernandez-Rhodes
- Department of Biobehavioral Health, College of Health and Human Development, Pennsylvania State University, University Park, PA
| | - Kristin L Young
- Department of Epidemiology, Gillings School of Global Public Health, University of North Carolina at Chapel Hill, Chapel Hill, NC
| | - Adam G Lilly
- Department of Sociology, University of North Carolina at Chapel Hill, Chapel Hill, NC
- Carolina Population Center, University of North Carolina at Chapel Hill, Chapel Hill, NC
| | - Laura M Raffield
- Department of Genetics, University of North Carolina at Chapel Hill, Chapel Hill, NC
| | - Heather M Highland
- Department of Epidemiology, Gillings School of Global Public Health, University of North Carolina at Chapel Hill, Chapel Hill, NC
| | - Genevieve L Wojcik
- Department of Epidemiology, Johns Hopkins Bloomberg School of Public Health, Baltimore, MD
| | - Cary Agler
- Department of Epidemiology, Gillings School of Global Public Health, University of North Carolina at Chapel Hill, Chapel Hill, NC
- Department of Pediatric and Public Health, Adams School of Dentistry, University of North Carolina at Chapel Hill, Chapel Hill, NC
| | - Shelly-Ann M Love
- Department of Epidemiology, Gillings School of Global Public Health, University of North Carolina at Chapel Hill, Chapel Hill, NC
| | - Samson Okello
- Department of Internal Medicine, Mbarara University of Science and Technology, Uganda
- University of Virginia, Charlottesville, VA
- Harvard TH Chan School of Public Health, Boston, MA
| | - Lauren E Petty
- Vanderbilt Genetics Institute, Vanderbilt University Medical Center, Vanderbilt, TN
- Department of Genetic Medicine, Vanderbilt University, Vanderbilt, TN
| | - Mariaelisa Graff
- Department of Epidemiology, Gillings School of Global Public Health, University of North Carolina at Chapel Hill, Chapel Hill, NC
| | - Jennifer E Below
- Vanderbilt Genetics Institute, Vanderbilt University Medical Center, Vanderbilt, TN
- Department of Genetic Medicine, Vanderbilt University, Vanderbilt, TN
| | - Kimon Divaris
- Department of Epidemiology, Gillings School of Global Public Health, University of North Carolina at Chapel Hill, Chapel Hill, NC
- Department of Pediatric and Public Health, Adams School of Dentistry, University of North Carolina at Chapel Hill, Chapel Hill, NC
| | - Kari E. North
- Department of Epidemiology, Gillings School of Global Public Health, University of North Carolina at Chapel Hill, Chapel Hill, NC
- Carolina Center for Genome Sciences, Chapel Hill, NC
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30
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Hua J, Wang G, Huang M, Hua S, Yang S. A Visual Approach for the SARS (Severe Acute Respiratory Syndrome) Outbreak Data Analysis. INTERNATIONAL JOURNAL OF ENVIRONMENTAL RESEARCH AND PUBLIC HEALTH 2020; 17:ijerph17113973. [PMID: 32503333 PMCID: PMC7312089 DOI: 10.3390/ijerph17113973] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/23/2020] [Revised: 05/29/2020] [Accepted: 06/02/2020] [Indexed: 12/18/2022]
Abstract
Virus outbreaks are threats to humanity, and coronaviruses are the latest of many epidemics in the last few decades in the world. SARS-CoV (Severe Acute Respiratory Syndrome Associated Coronavirus) is a member of the coronavirus family, so its study is useful for relevant virus data research. In this work, we conduct a proposed approach that is non-medical/clinical, generate graphs from five features of the SARS outbreak data in five countries and regions, and offer insights from a visual analysis perspective. The results show that prevention measures such as quarantine are the most common control policies used, and areas with strict measures did have fewer peak period days; for instance, Hong Kong handled the outbreak better than other areas. Data conflict issues found with this approach are discussed as well. Visual analysis is also proved to be a useful technique to present the SARS outbreak data at this stage; furthermore, we are proceeding to apply a similar methodology with more features to future COVID-19 research from a visual analysis perfective.
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Affiliation(s)
- Jie Hua
- Faculty of Information Engineering, Shaoyang University, Shaoyang 422000, China;
- Correspondence: (J.H.); (G.W.); Tel.: +61-435425678 (J.H.)
| | - Guohua Wang
- School of Software Engineering, South China University of Technology, Guangzhou 510006, China
- Correspondence: (J.H.); (G.W.); Tel.: +61-435425678 (J.H.)
| | - Maolin Huang
- Faculty of Engineering and IT, University of Technology Sydney, Sydney 2007, Australia;
| | - Shuyang Hua
- Faculty of Engineering, University of Sydney, Sydney 2007, Australia;
| | - Shuanghe Yang
- Faculty of Information Engineering, Shaoyang University, Shaoyang 422000, China;
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A positively selected FBN1 missense variant reduces height in Peruvian individuals. Nature 2020; 582:234-239. [PMID: 32499652 PMCID: PMC7410362 DOI: 10.1038/s41586-020-2302-0] [Citation(s) in RCA: 29] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2019] [Accepted: 03/10/2020] [Indexed: 01/21/2023]
Abstract
On average, Peruvian individuals are among the shortest in the world1. Here we show that Native American ancestry is associated with reduced height in an ethnically diverse group of Peruvian individuals, and identify a population-specific, missense variant in the FBN1 gene (E1297G) that is significantly associated with lower height. Each copy of the minor allele (frequency of 4.7%) reduces height by 2.2 cm (4.4 cm in homozygous individuals). To our knowledge, this is the largest effect size known for a common height-associated variant. FBN1 encodes the extracellular matrix protein fibrillin 1, which is a major structural component of microfibrils. We observed less densely packed fibrillin-1-rich microfibrils with irregular edges in the skin of individuals who were homozygous for G1297 compared with individuals who were homozygous for E1297. Moreover, we show that the E1297G locus is under positive selection in non-African populations, and that the E1297 variant shows subtle evidence of positive selection specifically within the Peruvian population. This variant is also significantly more frequent in coastal Peruvian populations than in populations from the Andes or the Amazon, which suggests that short stature might be the result of adaptation to factors that are associated with the coastal environment in Peru.
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32
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Evolutionary and population (epi)genetics of immunity to infection. Hum Genet 2020; 139:723-732. [PMID: 32285198 DOI: 10.1007/s00439-020-02167-x] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2019] [Accepted: 04/07/2020] [Indexed: 12/29/2022]
Abstract
Immune response is one of the functions that have been more strongly targeted by natural selection during human evolution. The evolutionary genetic dissection of the immune system has greatly helped to distinguish genes and functions that are essential, redundant or advantageous for human survival. It is also becoming increasingly clear that admixture between early Eurasians with now-extinct hominins such as Neanderthals or Denisovans, or admixture between modern human populations, can be beneficial for human adaptation to pathogen pressures. In this review, we discuss how the integration of population genetics with functional genomics in diverse human populations can inform about the changes in immune functions related to major lifestyle transitions (e.g., from hunting and gathering to farming), the action of natural selection to the evolution of the immune system, and the history of past epidemics. We also highlight the need of expanding the characterization of the immune system to a larger array of human populations-particularly neglected human groups historically exposed to different pathogen pressures-to fully capture the relative contribution of genetic, epigenetic, and environmental factors to immune response variation in humans.
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O’Neill MB, Laval G, Teixeira JC, Palmenberg AC, Pepperell CS. Genetic susceptibility to severe childhood asthma and rhinovirus-C maintained by balancing selection in humans for 150 000 years. Hum Mol Genet 2020; 29:736-744. [PMID: 31841129 PMCID: PMC7104676 DOI: 10.1093/hmg/ddz304] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2019] [Revised: 11/07/2019] [Accepted: 12/12/2019] [Indexed: 12/18/2022] Open
Abstract
Selective pressures imposed by pathogens have varied among human populations throughout their evolution, leading to marked inter-population differences at some genes mediating susceptibility to infectious and immune-related diseases. Here, we investigated the evolutionary history of a common polymorphism resulting in a Y529 versus C529 change in the cadherin related family member 3 (CDHR3) receptor which underlies variable susceptibility to rhinovirus-C infection and is associated with severe childhood asthma. The protective variant is the derived allele and is found at high frequency worldwide (69-95%). We detected genome-wide significant signatures of natural selection consistent with a rapid increase of the haplotypes carrying the allele, suggesting that non-neutral processes have acted on this locus across all human populations. However, the allele has not fixed in any population despite multiple lines of evidence suggesting that the mutation predates human migrations out of Africa. Using an approximate Bayesian computation method, we estimate the age of the mutation while explicitly accounting for past demography and positive or frequency-dependent balancing selection. Our analyses indicate a single emergence of the mutation in anatomically modern humans ~150 000 years ago and indicate that balancing selection has maintained the beneficial allele at high equilibrium frequencies worldwide. Apart from the well-known cases of the MHC and ABO genes, this study provides the first evidence that negative frequency-dependent selection plausibly acted on a human disease susceptibility locus, a form of balancing selection compatible with typical transmission dynamics of communicable respiratory viruses that might exploit CDHR3.
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Affiliation(s)
- Mary B O’Neill
- Department of Laboratory of Genetics, University of Wisconsin—Madison, Madison, WI 53706, USA
- Department of Medicine, University of Wisconsin—Madison, Madison, WI 53706, USA
- Department of Medical Microbiology and Immunology, University of Wisconsin—Madison, Madison, WI 53706, USA
- Department of Human Evolutionary Genetics Unit, Institut Pasteur, CNRS UMR2000, Paris 75015, France
| | - Guillaume Laval
- Department of Human Evolutionary Genetics Unit, Institut Pasteur, CNRS UMR2000, Paris 75015, France
| | - João C Teixeira
- Department of Human Evolutionary Genetics Unit, Institut Pasteur, CNRS UMR2000, Paris 75015, France
- Department of Australian Centre for Ancient DNA, The University of Adelaide, Adelaide, South Australia 5005, Australia
| | - Ann C Palmenberg
- Department of Biochemistry, Institute for Molecular Virology, University of Wisconsin—Madison, Madison, WI 53706, USA
| | - Caitlin S Pepperell
- Department of Medicine, University of Wisconsin—Madison, Madison, WI 53706, USA
- Department of Medical Microbiology and Immunology, University of Wisconsin—Madison, Madison, WI 53706, USA
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Apata M, Pfeifer SP. Recent population genomic insights into the genetic basis of arsenic tolerance in humans: the difficulties of identifying positively selected loci in strongly bottlenecked populations. Heredity (Edinb) 2020; 124:253-262. [PMID: 31776483 PMCID: PMC6972707 DOI: 10.1038/s41437-019-0285-0] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2019] [Revised: 10/22/2019] [Accepted: 11/13/2019] [Indexed: 02/06/2023] Open
Abstract
Recent advances in genomics have enabled researchers to shed light on the evolutionary processes driving human adaptation, by revealing the genetic architectures underlying traits ranging from lactase persistence, to skin pigmentation, to hypoxic response, to arsenic tolerance. Complicating the identification of targets of positive selection in modern human populations is their complex demographic history, characterized by population bottlenecks and expansions, population structure, migration, and admixture. In particular, founder effects and recent strong population size reductions, such as those experienced by the indigenous peoples of the Americas, have severe impacts on genetic variation that can lead to the accumulation of large allele frequency differences between populations due to genetic drift rather than natural selection. While distinguishing the effects of demographic history from selection remains challenging, neglecting neutral processes can lead to the incorrect identification of candidate loci. We here review the recent population genomic insights into the genetic basis of arsenic tolerance in Andean populations, and utilize this example to highlight both the difficulties pertaining to the identification of local adaptations in strongly bottlenecked populations, as well as the importance of controlling for demographic history in selection scans.
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Affiliation(s)
- Mario Apata
- Center for Evolution & Medicine, School of Life Sciences, Arizona State University, Tempe, AZ, 85821, USA
| | - Susanne P Pfeifer
- Center for Evolution & Medicine, School of Life Sciences, Arizona State University, Tempe, AZ, 85821, USA.
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Alexander TA, Machiela MJ. LDpop: an interactive online tool to calculate and visualize geographic LD patterns. BMC Bioinformatics 2020; 21:14. [PMID: 31924160 PMCID: PMC6954550 DOI: 10.1186/s12859-020-3340-1] [Citation(s) in RCA: 33] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2019] [Accepted: 01/03/2020] [Indexed: 11/10/2022] Open
Abstract
Background Linkage disequilibrium (LD)—the non-random association of alleles at different loci—defines population-specific haplotypes which vary by genomic ancestry. Assessment of allelic frequencies and LD patterns from a variety of ancestral populations enables researchers to better understand population histories as well as improve genetic understanding of diseases in which risk varies by ethnicity. Results We created an interactive web module which allows for quick geographic visualization of linkage disequilibrium (LD) patterns between two user-specified germline variants across geographic populations included in the 1000 Genomes Project. Interactive maps and a downloadable, sortable summary table allow researchers to easily compute and compare allele frequencies and LD statistics of dbSNP catalogued variants. The geographic mapping of each SNP’s allele frequencies by population as well as visualization of LD statistics allows the user to easily trace geographic allelic correlation patterns and examine population-specific differences. Conclusions LDpop is a free and publicly available cross-platform web tool which can be accessed online at https://ldlink.nci.nih.gov/?tab=ldpop
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Affiliation(s)
- T A Alexander
- Center for Bioinformatics and Computational Biology, University of Maryland, College Park, MD, 20740, USA
| | - M J Machiela
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, Rockville, MD, 20892, USA.
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36
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Fuselli S. Beyond drugs: the evolution of genes involved in human response to medications. Proc Biol Sci 2019; 286:20191716. [PMID: 31640517 DOI: 10.1098/rspb.2019.1716] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022] Open
Abstract
The genetic variation of our species reflects human demographic history and adaptation to diverse local environments. Part of this genetic variation affects individual responses to exogenous substances, such as food, pollutants and drugs, and plays an important role in drug efficacy and safety. This review provides a synthesis of the evolution of loci implicated in human pharmacological response and metabolism, interpreted within the theoretical framework of population genetics and molecular evolution. In particular, I review and discuss key evolutionary aspects of different pharmacogenes in humans and other species, such as the relationship between the type of substrates and rate of evolution; the selective pressure exerted by landscape variables or dietary habits; expected and observed patterns of rare genetic variation. Finally, I discuss how this knowledge can be translated directly or after the implementation of specific studies, into practical guidelines.
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Affiliation(s)
- Silvia Fuselli
- Department of Life Sciences and Biotechnology, University of Ferrara, Ferrara, Italy
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37
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Periyasamy S, John S, Padmavati R, Rajendren P, Thirunavukkarasu P, Gratten J, Vinkhuyzen A, McRae A, Holliday EG, Nyholt DR, Nancarrow D, Bakshi A, Hemani G, Nertney D, Smith H, Filippich C, Patel K, Fowdar J, McLean D, Tirupati S, Nagasundaram A, Gundugurti PR, Selvaraj K, Jegadeesan J, Jorde LB, Wray NR, Brown MA, Suetani R, Giacomotto J, Thara R, Mowry BJ. Association of Schizophrenia Risk With Disordered Niacin Metabolism in an Indian Genome-wide Association Study. JAMA Psychiatry 2019; 76:1026-1034. [PMID: 31268507 PMCID: PMC6613304 DOI: 10.1001/jamapsychiatry.2019.1335] [Citation(s) in RCA: 39] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
Importance Genome-wide association studies (GWASs) in European populations have identified more than 100 schizophrenia-associated loci. A schizophrenia GWAS in a unique Indian population offers novel findings. Objective To discover and functionally evaluate genetic loci for schizophrenia in a GWAS of a unique Indian population. Design, Setting, and Participants This GWAS included a sample of affected individuals, family members, and unrelated cases and controls. Three thousand ninety-two individuals were recruited and diagnostically ascertained via medical records, hospitals, clinics, and clinical networks in Chennai and surrounding regions. Affected participants fulfilled DSM-IV diagnostic criteria for schizophrenia. Unrelated control participants had no personal or family history of psychotic disorder. Recruitment, genotyping, and analysis occurred in consecutive phases beginning January 1, 2001. Recruitment was completed on February 28, 2018, and genotyping and analysis are ongoing. Main Outcomes and Measures Associations of single-nucleotide polymorphisms and gene expression with schizophrenia. Results The study population included 1321 participants with schizophrenia, 885 family controls, and 886 unrelated controls. Among participants with schizophrenia, mean (SD) age was 39.1 (11.4) years, and 52.7% were male. This sample demonstrated uniform ethnicity, a degree of inbreeding, and negligible rates of substance abuse. A novel genome-wide significant association was observed between schizophrenia and a chromosome 8q24.3 locus (rs10866912, allele A; odds ratio [OR], 1.27 [95% CI, 1.17-1.38]; P = 4.35 × 10-8) that attracted support in the schizophrenia Psychiatric Genomics Consortium 2 data (rs10866912, allele A; OR, 1.04 [95% CI, 1.02-1.06]; P = 7.56 × 10-4). This locus has undergone natural selection, with the risk allele A declining in frequency from India (approximately 72%) to Europe (approximately 43%). rs10866912 directly modifies the abundance of the nicotinate phosphoribosyltransferase gene (NAPRT1) transcript in brain cortex (normalized effect size, 0.79; 95% CI, 0.6-1.0; P = 5.8 × 10-13). NAPRT1 encodes a key enzyme for niacin metabolism. In Indian lymphoblastoid cell lines, (risk) allele A of rs10866912 was associated with NAPRT1 downregulation (AA: 0.74, n = 21; CC: 1.56, n = 17; P = .004). Preliminary zebrafish data further suggest that partial loss of function of NAPRT1 leads to abnormal brain development. Conclusions and Relevance Bioinformatic analyses and cellular and zebrafish gene expression studies implicate NAPRT1 as a novel susceptibility gene. Given this gene's role in niacin metabolism and the evidence for niacin deficiency provoking schizophrenialike symptoms in neuropsychiatric diseases such as pellagra and Hartnup disease, these results suggest that the rs10866912 genotype and niacin status may have implications for schizophrenia susceptibility and treatment.
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Affiliation(s)
- Sathish Periyasamy
- Queensland Brain Institute, University of Queensland, Brisbane, Australia.,Queensland Centre for Mental Health Research, West Moreton Hospital and Health Service, University of Queensland, Brisbane, Australia
| | - Sujit John
- Schizophrenia Research Foundation, Chennai, India
| | | | | | | | - Jacob Gratten
- Mater Research Institute and University of Queensland, Translational Research Institute, Brisbane, Australia.,Institute for Molecular Bioscience, University of Queensland, Brisbane, Australia
| | - Anna Vinkhuyzen
- Institute for Molecular Bioscience, University of Queensland, Brisbane, Australia
| | - Allan McRae
- Institute for Molecular Bioscience, University of Queensland, Brisbane, Australia
| | | | - Dale R Nyholt
- QIMR Berghofer Medical Research Institute, Brisbane, Australia.,School of Biomedical Sciences and Institute of Health and Biomedical Innovation, Queensland University of Technology, Brisbane, Australia
| | | | - Andrew Bakshi
- Institute for Molecular Bioscience, University of Queensland, Brisbane, Australia
| | - Gibran Hemani
- Queensland Brain Institute, University of Queensland, Brisbane, Australia.,Medical Research Council Integrative Epidemiology Unit, Population Health Sciences, University of Bristol, Bristol, United Kingdom
| | - Deborah Nertney
- Queensland Centre for Mental Health Research, West Moreton Hospital and Health Service, University of Queensland, Brisbane, Australia
| | - Heather Smith
- Queensland Brain Institute, University of Queensland, Brisbane, Australia.,Queensland Centre for Mental Health Research, West Moreton Hospital and Health Service, University of Queensland, Brisbane, Australia
| | - Cheryl Filippich
- Queensland Brain Institute, University of Queensland, Brisbane, Australia.,Queensland Centre for Mental Health Research, West Moreton Hospital and Health Service, University of Queensland, Brisbane, Australia
| | - Kalpana Patel
- Queensland Brain Institute, University of Queensland, Brisbane, Australia.,Queensland Centre for Mental Health Research, West Moreton Hospital and Health Service, University of Queensland, Brisbane, Australia
| | - Javed Fowdar
- Queensland Brain Institute, University of Queensland, Brisbane, Australia
| | - Duncan McLean
- Queensland Brain Institute, University of Queensland, Brisbane, Australia.,Queensland Centre for Mental Health Research, West Moreton Hospital and Health Service, University of Queensland, Brisbane, Australia
| | - Srinivasan Tirupati
- Psychiatric Rehabilitation Service, Hunter New England Mental Health, Newcastle, Australia
| | | | | | | | | | - Lynn B Jorde
- Department of Human Genetics, University of Utah, Salt Lake City
| | - Naomi R Wray
- Queensland Brain Institute, University of Queensland, Brisbane, Australia.,Institute for Molecular Bioscience, University of Queensland, Brisbane, Australia
| | - Matthew A Brown
- Institute of Health and Biomedical Innovation, Translational Research Institute, Princess Alexandra Hospital, Queensland University of Technology, Brisbane, Australia
| | - Rachel Suetani
- Queensland Brain Institute, University of Queensland, Brisbane, Australia.,Queensland Centre for Mental Health Research, West Moreton Hospital and Health Service, University of Queensland, Brisbane, Australia
| | - Jean Giacomotto
- Queensland Brain Institute, University of Queensland, Brisbane, Australia.,Queensland Centre for Mental Health Research, West Moreton Hospital and Health Service, University of Queensland, Brisbane, Australia
| | | | - Bryan J Mowry
- Queensland Brain Institute, University of Queensland, Brisbane, Australia.,Queensland Centre for Mental Health Research, West Moreton Hospital and Health Service, University of Queensland, Brisbane, Australia
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38
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Fiorica PN, Wheeler HE. Transcriptome association studies of neuropsychiatric traits in African Americans implicate PRMT7 in schizophrenia. PeerJ 2019; 7:e7778. [PMID: 31579629 PMCID: PMC6766368 DOI: 10.7717/peerj.7778] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2019] [Accepted: 08/27/2019] [Indexed: 12/23/2022] Open
Abstract
In the past 15 years, genome-wide association studies (GWAS) have provided novel insight into the genetic architecture of various complex traits; however, this insight has been primarily focused on populations of European descent. This emphasis on European populations has led to individuals of recent African descent being grossly underrepresented in the study of genetics. With African Americans making up less than 2% of participants in neuropsychiatric GWAS, this discrepancy is magnified in diseases such as schizophrenia and bipolar disorder. In this study, we performed GWAS and the gene-based association method PrediXcan for schizophrenia (n = 2,256) and bipolar disorder (n = 1,019) in African American cohorts. In our PrediXcan analyses, we identified PRMT7 (P = 5.5 × 10−6, local false sign rate = 0.12) as significantly associated with schizophrenia following an adaptive shrinkage multiple testing adjustment. This association with schizophrenia was confirmed in the much larger, predominantly European, Psychiatric Genomics Consortium. In addition to the PRMT7 association with schizophrenia, we identified rs10168049 (P = 1.0 × 10−6) as a potential candidate locus for bipolar disorder with highly divergent allele frequencies across populations, highlighting the need for diversity in genetic studies.
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Affiliation(s)
- Peter N Fiorica
- Department of Chemistry and Biochemistry, Loyola University Chicago, Chicago, IL, USA.,Department of Biology, Loyola University Chicago, Chicago, IL, USA
| | - Heather E Wheeler
- Department of Biology, Loyola University Chicago, Chicago, IL, USA.,Program in Bioinformatics, Loyola University Chicago, Chicago, IL, USA.,Department of Computer Science, Loyola University Chicago, Chicago, IL, USA.,Department of Public Health Sciences, Loyola University Chicago, Maywood, IL, USA
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39
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Alliey-Rodriguez N, Grey TA, Shafee R, Asif H, Lutz O, Bolo NR, Padmanabhan J, Tandon N, Klinger M, Reis K, Spring J, Coppes L, Zeng V, Hegde RR, Hoang DT, Bannai D, Nawaz U, Henson P, Liu S, Gage D, McCarroll S, Bishop JR, Hill S, Reilly JL, Lencer R, Clementz BA, Buckley P, Glahn DC, Meda SA, Narayanan B, Pearlson G, Keshavan MS, Ivleva EI, Tamminga C, Sweeney JA, Curtis D, Badner JA, Keedy S, Rapoport J, Liu C, Gershon ES. NRXN1 is associated with enlargement of the temporal horns of the lateral ventricles in psychosis. Transl Psychiatry 2019; 9:230. [PMID: 31530798 PMCID: PMC6748921 DOI: 10.1038/s41398-019-0564-9] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/21/2019] [Revised: 07/11/2019] [Accepted: 07/30/2019] [Indexed: 12/19/2022] Open
Abstract
Schizophrenia, Schizoaffective, and Bipolar disorders share behavioral and phenomenological traits, intermediate phenotypes, and some associated genetic loci with pleiotropic effects. Volumetric abnormalities in brain structures are among the intermediate phenotypes consistently reported associated with these disorders. In order to examine the genetic underpinnings of these structural brain modifications, we performed genome-wide association analyses (GWAS) on 60 quantitative structural brain MRI phenotypes in a sample of 777 subjects (483 cases and 294 controls pooled together). Genotyping was performed with the Illumina PsychChip microarray, followed by imputation to the 1000 genomes multiethnic reference panel. Enlargement of the Temporal Horns of Lateral Ventricles (THLV) is associated with an intronic SNP of the gene NRXN1 (rs12467877, P = 6.76E-10), which accounts for 4.5% of the variance in size. Enlarged THLV is associated with psychosis in this sample, and with reduction of the hippocampus and enlargement of the choroid plexus and caudate. Eight other suggestively significant associations (P < 5.5E-8) were identified with THLV and 5 other brain structures. Although rare deletions of NRXN1 have been previously associated with psychosis, this is the first report of a common SNP variant of NRXN1 associated with enlargement of the THLV in psychosis.
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Affiliation(s)
- Ney Alliey-Rodriguez
- University of Chicago, Department of Psychiatry and Behavioral Neurosciences, Chicago, USA.
| | - Tamar A. Grey
- 0000 0001 2341 2786grid.116068.8Massachusetts Institute of Technology, Cambridge, USA
| | - Rebecca Shafee
- 000000041936754Xgrid.38142.3cHarvard Medical School, Department of Genetics, Boston, USA ,grid.66859.34Stanley Center, Broad Institute of MIT and Harvard, Cambridge, USA
| | - Huma Asif
- University of Chicago, Department of Psychiatry and Behavioral Neurosciences, Chicago, USA
| | - Olivia Lutz
- 000000041936754Xgrid.38142.3cHarvard Medical School, Department of Psychiatry, Boston, USA
| | - Nicolas R. Bolo
- 000000041936754Xgrid.38142.3cHarvard Medical School, Department of Psychiatry, Boston, USA
| | - Jaya Padmanabhan
- 000000041936754Xgrid.38142.3cHarvard Medical School, Department of Psychiatry, Boston, USA
| | - Neeraj Tandon
- 000000041936754Xgrid.38142.3cHarvard Medical School, Department of Psychiatry, Boston, USA
| | - Madeline Klinger
- University of Chicago, Department of Psychiatry and Behavioral Neurosciences, Chicago, USA
| | - Katherine Reis
- University of Chicago, Department of Psychiatry and Behavioral Neurosciences, Chicago, USA
| | - Jonathan Spring
- University of Chicago Laboratory for Advanced Computing, Chicago, USA
| | - Lucas Coppes
- University of Chicago, Department of Psychiatry and Behavioral Neurosciences, Chicago, USA
| | - Victor Zeng
- 000000041936754Xgrid.38142.3cHarvard University, Cambridge, USA
| | - Rachal R. Hegde
- 0000 0004 1936 7558grid.189504.1Boston University, Boston, USA
| | - Dung T. Hoang
- 000000041936754Xgrid.38142.3cHarvard University, Cambridge, USA
| | - Deepthi Bannai
- 0000 0004 1936 7558grid.189504.1Boston University, Boston, USA
| | - Uzma Nawaz
- 0000 0004 1936 7558grid.189504.1Boston University, Boston, USA
| | - Philip Henson
- 000000041936754Xgrid.38142.3cHarvard University, Cambridge, USA
| | - Siyuan Liu
- 0000 0001 2297 5165grid.94365.3dChild Psychiatry Branch, National Institutes of Mental Health, National Institutes of Health, Bethesda, MD USA
| | - Diane Gage
- grid.66859.34Broad Institute of MIT and Harvard, Cambridge, USA
| | | | - Jeffrey R. Bishop
- 0000000419368657grid.17635.36University of Minnesota, Department of Experimental and Clinical Pharmacology and Department of Psychiatry, Minneapolis, USA
| | - Scot Hill
- 0000 0004 0388 7807grid.262641.5Rosalind Franklin University, North Chicago, USA
| | - James L. Reilly
- 0000 0001 2299 3507grid.16753.36Northwestern University, Evanston, USA
| | - Rebekka Lencer
- 0000 0001 2172 9288grid.5949.1University of Muenster, Munster, Germany
| | - Brett A. Clementz
- 0000 0000 9564 9822grid.264978.6Department of Psychology, University of Georgia, Athens, Georgia
| | - Peter Buckley
- 0000 0004 0458 8737grid.224260.0Virginia Commonwealth University, Richmond, USA
| | - David C. Glahn
- 0000000419368710grid.47100.32Yale University Departments of Psychiatry & Neuroscience, New Haven, USA
| | - Shashwath A. Meda
- 0000000419368710grid.47100.32Yale University Departments of Psychiatry & Neuroscience, New Haven, USA
| | - Balaji Narayanan
- 0000000419368710grid.47100.32Yale University Departments of Psychiatry & Neuroscience, New Haven, USA
| | - Godfrey Pearlson
- 0000000419368710grid.47100.32Yale University Departments of Psychiatry & Neuroscience, New Haven, USA
| | - Matcheri S. Keshavan
- 000000041936754Xgrid.38142.3cHarvard Medical School, Department of Psychiatry, Boston, USA
| | - Elena I. Ivleva
- 0000 0000 9482 7121grid.267313.2University of Texas Southwestern Medical Center, Department of Psychiatry, Dallas, USA
| | - Carol Tamminga
- 0000 0000 9482 7121grid.267313.2University of Texas Southwestern Medical Center, Department of Psychiatry, Dallas, USA
| | - John A. Sweeney
- 0000 0000 9482 7121grid.267313.2University of Texas Southwestern Medical Center, Department of Psychiatry, Dallas, USA
| | - David Curtis
- 0000 0001 2171 1133grid.4868.2University College London and Centre for Psychiatry, Barts and the London School of Medicine and Dentistry, London, UK
| | - Judith A. Badner
- 0000 0001 0705 3621grid.240684.cRush University Medical Center, Chicago, USA
| | - Sarah Keedy
- University of Chicago, Department of Psychiatry and Behavioral Neurosciences, Chicago, USA
| | - Judith Rapoport
- 0000 0001 2297 5165grid.94365.3dChild Psychiatry Branch, National Institutes of Mental Health, National Institutes of Health, Bethesda, MD USA
| | - Chunyu Liu
- 0000 0000 9159 4457grid.411023.5SUNY Upstate Medical University, Binghamton, USA
| | - Elliot S. Gershon
- University of Chicago, Department of Psychiatry and Behavioral Neurosciences, Chicago, USA ,University of Chicago, Department of Human Genetics, Chicago, USA
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40
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Stern AJ, Wilton PR, Nielsen R. An approximate full-likelihood method for inferring selection and allele frequency trajectories from DNA sequence data. PLoS Genet 2019; 15:e1008384. [PMID: 31518343 PMCID: PMC6760815 DOI: 10.1371/journal.pgen.1008384] [Citation(s) in RCA: 64] [Impact Index Per Article: 12.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2019] [Revised: 09/25/2019] [Accepted: 08/26/2019] [Indexed: 12/24/2022] Open
Abstract
Most current methods for detecting natural selection from DNA sequence data are limited in that they are either based on summary statistics or a composite likelihood, and as a consequence, do not make full use of the information available in DNA sequence data. We here present a new importance sampling approach for approximating the full likelihood function for the selection coefficient. Our method CLUES treats the ancestral recombination graph (ARG) as a latent variable that is integrated out using previously published Markov Chain Monte Carlo (MCMC) methods. The method can be used for detecting selection, estimating selection coefficients, testing models of changes in the strength of selection, estimating the time of the start of a selective sweep, and for inferring the allele frequency trajectory of a selected or neutral allele. We perform extensive simulations to evaluate the method and show that it uniformly improves power to detect selection compared to current popular methods such as nSL and SDS, and can provide reliable inferences of allele frequency trajectories under many conditions. We also explore the potential of our method to detect extremely recent changes in the strength of selection. We use the method to infer the past allele frequency trajectory for a lactase persistence SNP (MCM6) in Europeans. We also infer the trajectory of a SNP (EDAR) in Han Chinese, finding evidence that this allele's age is much older than previously claimed. We also study a set of 11 pigmentation-associated variants. Several genes show evidence of strong selection particularly within the last 5,000 years, including ASIP, KITLG, and TYR. However, selection on OCA2/HERC2 seems to be much older and, in contrast to previous claims, we find no evidence of selection on TYRP1.
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Affiliation(s)
- Aaron J. Stern
- Graduate Group in Computation Biology, University of California, Berkeley, Berkeley, California, United States of America
| | - Peter R. Wilton
- Department of Integrative Biology, University of California, Berkeley, Berkeley, California, United States of America
| | - Rasmus Nielsen
- Department of Integrative Biology, University of California, Berkeley, Berkeley, California, United States of America
- Department of Statistics, University of California, Berkeley, Berkeley, California, United States of America
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41
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Johnston AD, Simões-Pires CA, Thompson TV, Suzuki M, Greally JM. Functional genetic variants can mediate their regulatory effects through alteration of transcription factor binding. Nat Commun 2019; 10:3472. [PMID: 31375681 PMCID: PMC6677801 DOI: 10.1038/s41467-019-11412-5] [Citation(s) in RCA: 28] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2018] [Accepted: 07/10/2019] [Indexed: 12/23/2022] Open
Abstract
Functional variants in the genome are usually identified by their association with local gene expression, DNA methylation or chromatin states. DNA sequence motif analysis and chromatin immunoprecipitation studies have provided indirect support for the hypothesis that functional variants alter transcription factor binding to exert their effects. In this study, we provide direct evidence that functional variants can alter transcription factor binding. We identify a multifunctional variant within the TBC1D4 gene encoding a canonical NFκB binding site, and edited it using CRISPR-Cas9 to remove this site. We show that this editing reduces TBC1D4 expression, local chromatin accessibility and binding of the p65 component of NFκB. We then used CRISPR without genomic editing to guide p65 back to the edited locus, demonstrating that this re-targeting, occurring ~182 kb from the gene promoter, is enough to restore the function of the locus, supporting the central role of transcription factors mediating the effects of functional variants.
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Affiliation(s)
- Andrew D Johnston
- Center for Epigenomics and Department of Genetics (Division of Genomics), Albert Einstein College of Medicine, 1301 Morris Park Avenue, Bronx, NY, 10461, USA
| | - Claudia A Simões-Pires
- Center for Epigenomics and Department of Genetics (Division of Genomics), Albert Einstein College of Medicine, 1301 Morris Park Avenue, Bronx, NY, 10461, USA
| | - Taylor V Thompson
- Center for Epigenomics and Department of Genetics (Division of Genomics), Albert Einstein College of Medicine, 1301 Morris Park Avenue, Bronx, NY, 10461, USA
| | - Masako Suzuki
- Center for Epigenomics and Department of Genetics (Division of Genomics), Albert Einstein College of Medicine, 1301 Morris Park Avenue, Bronx, NY, 10461, USA
| | - John M Greally
- Center for Epigenomics and Department of Genetics (Division of Genomics), Albert Einstein College of Medicine, 1301 Morris Park Avenue, Bronx, NY, 10461, USA.
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42
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Bien SA, Wojcik GL, Hodonsky CJ, Gignoux CR, Cheng I, Matise TC, Peters U, Kenny EE, North KE. The Future of Genomic Studies Must Be Globally Representative: Perspectives from PAGE. Annu Rev Genomics Hum Genet 2019; 20:181-200. [PMID: 30978304 DOI: 10.1146/annurev-genom-091416-035517] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
The past decade has seen a technological revolution in human genetics that has empowered population-level investigations into genetic associations with phenotypes. Although these discoveries rely on genetic variation across individuals, association studies have overwhelmingly been performed in populations of European descent. In this review, we describe limitations faced by single-population studies and provide an overview of strategies to improve global representation in existing data sets and future human genomics research via diversity-focused, multiethnic studies. We highlight the successes of individual studies and meta-analysis consortia that have provided unique knowledge. Additionally, we outline the approach taken by the Population Architecture Using Genomics and Epidemiology (PAGE) study to develop best practices for performing genetic epidemiology in multiethnic contexts. Finally, we discuss how limiting investigations to single populations impairs findings in the clinical domain for both rare-variant identification and genetic risk prediction.
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Affiliation(s)
- Stephanie A Bien
- Department of Public Health Science, Fred Hutchinson Cancer Research Center, Seattle, Washington 98109, USA; ,
| | - Genevieve L Wojcik
- Department of Biomedical Data Science, Stanford University School of Medicine, Stanford, California 94305, USA;
| | - Chani J Hodonsky
- Department of Epidemiology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, USA; ,
| | - Christopher R Gignoux
- Colorado Center for Personalized Medicine, Anschutz Medical Campus, University of Colorado, Aurora, Colorado 80045, USA;
| | - Iona Cheng
- Department of Epidemiology and Biostatistics, University of California, San Francisco, California 94158, USA;
| | - Tara C Matise
- Department of Genetics, Rutgers University, New Brunswick, New Jersey 08554, USA;
| | - Ulrike Peters
- Department of Public Health Science, Fred Hutchinson Cancer Research Center, Seattle, Washington 98109, USA; ,
| | - Eimear E Kenny
- Department of Genetics and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA;
| | - Kari E North
- Department of Epidemiology, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, USA; ,
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43
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Esposito U, Das R, Syed S, Pirooznia M, Elhaik E. Ancient Ancestry Informative Markers for Identifying Fine-Scale Ancient Population Structure in Eurasians. Genes (Basel) 2018; 9:E625. [PMID: 30545160 PMCID: PMC6316245 DOI: 10.3390/genes9120625] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2018] [Revised: 12/05/2018] [Accepted: 12/10/2018] [Indexed: 12/23/2022] Open
Abstract
The rapid accumulation of ancient human genomes from various areas and time periods potentially enables the expansion of studies of biodiversity, biogeography, forensics, population history, and epidemiology into past populations. However, most ancient DNA (aDNA) data were generated through microarrays designed for modern-day populations, which are known to misrepresent the population structure. Past studies addressed these problems by using ancestry informative markers (AIMs). It is, thereby, unclear whether AIMs derived from contemporary human genomes can capture ancient population structures, and whether AIM-finding methods are applicable to aDNA, provided that the high missingness rates in ancient-and oftentimes haploid-DNA can also distort the population structure. Here, we define ancient AIMs (aAIMs) and develop a framework to evaluate established and novel AIM-finding methods in identifying the most informative markers. We show that aAIMs identified by a novel principal component analysis (PCA)-based method outperform all of the competing methods in classifying ancient individuals into populations and identifying admixed individuals. In some cases, predictions made using the aAIMs were more accurate than those made with a complete marker set. We discuss the features of the ancient Eurasian population structure and strategies to identify aAIMs. This work informs the design of single nucleotide polymorphism (SNP) microarrays and the interpretation of aDNA results, which enables a population-wide testing of primordialist theories.
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Affiliation(s)
- Umberto Esposito
- Department of Animal and Plant Sciences, University of Sheffield, Sheffield S10 2TN, UK.
| | - Ranajit Das
- Manipal University, Manipal Centre for Natural Sciences (MCNS), Manipal, Karnataka, 576104, India.
| | - Syakir Syed
- Department of Animal and Plant Sciences, University of Sheffield, Sheffield S10 2TN, UK.
| | - Mehdi Pirooznia
- Bioinformatics and Computational Biology, National Heart Lung and Blood Institute, National Institutes of Health, Bethesda, MD 20892, USA .
| | - Eran Elhaik
- Department of Animal and Plant Sciences, University of Sheffield, Sheffield S10 2TN, UK.
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44
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Brown BC, Bray NL, Pachter L. Expression reflects population structure. PLoS Genet 2018; 14:e1007841. [PMID: 30566439 PMCID: PMC6317812 DOI: 10.1371/journal.pgen.1007841] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2018] [Revised: 01/03/2019] [Accepted: 11/20/2018] [Indexed: 11/19/2022] Open
Abstract
Population structure in genotype data has been extensively studied, and is revealed by looking at the principal components of the genotype matrix. However, no similar analysis of population structure in gene expression data has been conducted, in part because a naïve principal components analysis of the gene expression matrix does not cluster by population. We identify a linear projection that reveals population structure in gene expression data. Our approach relies on the coupling of the principal components of genotype to the principal components of gene expression via canonical correlation analysis. Our method is able to determine the significance of the variance in the canonical correlation projection explained by each gene. We identify 3,571 significant genes, only 837 of which had been previously reported to have an associated eQTL in the GEUVADIS results. We show that our projections are not primarily driven by differences in allele frequency at known cis-eQTLs and that similar projections can be recovered using only several hundred randomly selected genes and SNPs. Finally, we present preliminary work on the consequences for eQTL analysis. We observe that using our projection co-ordinates as covariates results in the discovery of slightly fewer genes with eQTLs, but that these genes replicate in GTEx matched tissue at a slightly higher rate.
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Affiliation(s)
- Brielin C. Brown
- Department of Computer Science, University of California Berkeley, Berkeley, California, United States of America
| | - Nicolas L. Bray
- Institute for Innovative Genomics, University of California Berkeley, Berkeley, California, United States of America
- Department of Molecular & Cell Biology, University of California Berkeley, Berkeley, California, United States of America
| | - Lior Pachter
- Division of Biology and Biological Engineering, California Institute of Technology, Padadena, California, United States of America
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45
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Chiang CWK, Mangul S, Robles C, Sankararaman S. A Comprehensive Map of Genetic Variation in the World's Largest Ethnic Group-Han Chinese. Mol Biol Evol 2018; 35:2736-2750. [PMID: 30169787 PMCID: PMC6693441 DOI: 10.1093/molbev/msy170] [Citation(s) in RCA: 55] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
As are most non-European populations, the Han Chinese are relatively understudied in population and medical genetics studies. From low-coverage whole-genome sequencing of 11,670 Han Chinese women we present a catalog of 25,057,223 variants, including 548,401 novel variants that are seen at least 10 times in our data set. Individuals from this data set came from 24 out of 33 administrative divisions across China (including 19 provinces, 4 municipalities, and 1 autonomous region), thus allowing us to study population structure, genetic ancestry, and local adaptation in Han Chinese. We identified previously unrecognized population structure along the East-West axis of China, demonstrated a general pattern of isolation-by-distance among Han Chinese, and reported unique regional signals of admixture, such as European influences among the Northwestern provinces of China. Furthermore, we identified a number of highly differentiated, putatively adaptive, loci (e.g., MTHFR, ADH7, and FADS, among others) that may be driven by immune response, climate, and diet in the Han Chinese. Finally, we have made available allele frequency estimates stratified by administrative divisions across China in the Geography of Genetic Variant browser for the broader community. By leveraging the largest currently available genetic data set for Han Chinese, we have gained insights into the history and population structure of the world's largest ethnic group.
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Affiliation(s)
- Charleston W K Chiang
- Center for Genetic Epidemiology, Department of Preventive Medicine, Keck School of Medicine, University of Southern California, Los Angeles, CA
- Center for Neurobehavioral Genetics, Semel Institute for Neuroscience and Human Behavior, University of California Los Angeles, Los Angeles, CA
| | - Serghei Mangul
- Department of Computer Science, University of California Los Angeles, Los Angeles, CA
- Institute for Quantitative and Computational Bioscience, University of California Los Angeles, Los Angeles, CA
| | - Christopher Robles
- Department of Human Genetics, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA
| | - Sriram Sankararaman
- Department of Computer Science, University of California Los Angeles, Los Angeles, CA
- Department of Human Genetics, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA
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46
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Lindo J, Haas R, Hofman C, Apata M, Moraga M, Verdugo RA, Watson JT, Viviano Llave C, Witonsky D, Beall C, Warinner C, Novembre J, Aldenderfer M, Di Rienzo A. The genetic prehistory of the Andean highlands 7000 years BP though European contact. SCIENCE ADVANCES 2018; 4:eaau4921. [PMID: 30417096 PMCID: PMC6224175 DOI: 10.1126/sciadv.aau4921] [Citation(s) in RCA: 62] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/15/2018] [Accepted: 10/12/2018] [Indexed: 05/02/2023]
Abstract
The peopling of the Andean highlands above 2500 m in elevation was a complex process that included cultural, biological, and genetic adaptations. Here, we present a time series of ancient whole genomes from the Andes of Peru, dating back to 7000 calendar years before the present (BP), and compare them to 42 new genome-wide genetic variation datasets from both highland and lowland populations. We infer three significant features: a split between low- and high-elevation populations that occurred between 9200 and 8200 BP; a population collapse after European contact that is significantly more severe in South American lowlanders than in highland populations; and evidence for positive selection at genetic loci related to starch digestion and plausibly pathogen resistance after European contact. We do not find selective sweep signals related to known components of the human hypoxia response, which may suggest more complex modes of genetic adaptation to high altitude.
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Affiliation(s)
- John Lindo
- Department of Anthropology, Emory University, Atlanta, GA 30322, USA
- Department of Human Genetics, University of Chicago, Chicago, IL 60637, USA
| | - Randall Haas
- Department of Anthropology, University of California, Davis, CA 95616, USA
| | - Courtney Hofman
- Department of Anthropology, University of Oklahoma, Norman, OK 73019, USA
- Laboratories of Molecular Anthropology and Microbiome Research, University of Oklahoma, Norman, OK 73019, USA
| | - Mario Apata
- Programa de Genética Humana, ICBM, Universidad de Chile, Santiago, Chile
| | - Mauricio Moraga
- Programa de Genética Humana, ICBM, Universidad de Chile, Santiago, Chile
- Departamento de Antropología, Universidad de Chile, Santiago, Chile
| | - Ricardo A. Verdugo
- Programa de Genética Humana, ICBM, Universidad de Chile, Santiago, Chile
- Departamento de Oncología Básico-Clínica, Universidad de Chile, Santiago, Chile
| | - James T. Watson
- Arizona State Museum and School of Anthropology, University of Arizona, Tucson, AZ 85721, USA
| | | | - David Witonsky
- Department of Human Genetics, University of Chicago, Chicago, IL 60637, USA
| | - Cynthia Beall
- Department of Anthropology, Case Western University, Cleveland, OH 44106, USA
| | - Christina Warinner
- Department of Anthropology, University of Oklahoma, Norman, OK 73019, USA
- Laboratories of Molecular Anthropology and Microbiome Research, University of Oklahoma, Norman, OK 73019, USA
- Department of Archaeogenetics, Max Planck Institute for the Science of Human History, Jena 07745, Germany
| | - John Novembre
- Department of Human Genetics, University of Chicago, Chicago, IL 60637, USA
| | - Mark Aldenderfer
- School of Social Sciences, Humanities, and Arts, University of California, Merced, Merced, CA 95343, USA
| | - Anna Di Rienzo
- Department of Human Genetics, University of Chicago, Chicago, IL 60637, USA
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47
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Spear ML, Hu D, Pino-Yanes M, Huntsman S, Eng C, Levin AM, Ortega VE, White MJ, McGarry ME, Thakur N, Galanter J, Mak ACY, Oh SS, Ampleford E, Peters SP, Davis A, Kumar R, Farber HJ, Meade K, Avila PC, Serebrisky D, Lenoir MA, Brigino-Buenaventura E, Cintron WR, Thyne SM, Rodriguez-Santana JR, Ford JG, Chapela R, Estrada AM, Sandoval K, Seibold MA, Winkler CA, Bleecker ER, Myers DA, Williams LK, Hernandez RD, Torgerson DG, Burchard EG. A genome-wide association and admixture mapping study of bronchodilator drug response in African Americans with asthma. THE PHARMACOGENOMICS JOURNAL 2018; 19:249-259. [PMID: 30206298 PMCID: PMC6414286 DOI: 10.1038/s41397-018-0042-4] [Citation(s) in RCA: 38] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/18/2017] [Revised: 06/08/2018] [Accepted: 06/19/2018] [Indexed: 01/15/2023]
Abstract
Short-acting β2-adrenergic receptor agonists (SABAs) are the most commonly prescribed asthma medications worldwide. Response to SABAs is measured as bronchodilator drug response (BDR), which varies among racial/ethnic groups in the U.S1, 2. However, the genetic variation that contributes to BDR is largely undefined in African Americans with asthma3. To identify genetic variants that may contribute to differences in BDR in African Americans with asthma, we performed a genome-wide association study (GWAS) of BDR in 949 African American children with asthma, genotyped with the Axiom World Array 4 (Affymetrix, Santa Clara, CA) followed by imputation using 1000 Genomes phase III genotypes. We used linear regression models adjusting for age, sex, body mass index (BMI) and genetic ancestry to test for an association between BDR and genotype at single nucleotide polymorphisms (SNPs). To increase power and distinguish between shared vs. population-specific associations with BDR in children with asthma, we performed a meta-analysis across 949 African Americans and 1,830 Latinos (Total=2,779). Lastly, we performed genome-wide admixture mapping to identify regions whereby local African or European ancestry is associated with BDR in African Americans. We identified a population-specific association with an intergenic SNP on chromosome 9q21 that was significantly associated with BDR (rs73650726, p=7.69×10−9). A trans-ethnic meta-analysis across African Americans and Latinos identified three additional SNPs within the intron of PRKG1 that were significantly associated with BDR (rs7903366, rs7070958, and rs7081864, p≤5×10−8). Our results failed to replicate in three additional populations of 416 Latinos and 1,615 African Americans. Our findings indicate that both population specific and shared genetic variation contributes to differences in BDR in minority children with asthma, and that the genetic underpinnings of BDR may differ between racial/ethnic groups.
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Affiliation(s)
- Melissa L Spear
- Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, San Francisco, CA, USA
| | - Donglei Hu
- Department of Medicine, University of California, San Francisco, San Francisco, CA, USA
| | - Maria Pino-Yanes
- Research Unit, Hospital Universitario N.S. de Candelaria, Universidad de La Laguna, Tenerife, Spain.,CIBER de Enfermedades Respiratorias, Instituto de Salud Carlos III, Madrid, Spain.,Genomics and Health Group, Department of Biochemistry, Microbiology, Cell Biology and Genetics, Universidad de La Laguna, La Laguna, Tenerife, Spain
| | - Scott Huntsman
- Department of Medicine, University of California, San Francisco, San Francisco, CA, USA
| | - Celeste Eng
- Department of Medicine, University of California, San Francisco, San Francisco, CA, USA
| | - Albert M Levin
- Department of Public Health Sciences, Henry Ford Health System, Detroit, MI, USA
| | - Victor E Ortega
- Department of Internal Medicine, Wake Forest Baptist Medical Center, Winston Salem, NC, USA
| | - Marquitta J White
- Department of Medicine, University of California, San Francisco, San Francisco, CA, USA
| | - Meghan E McGarry
- Department of Pediatrics, University of California, San Francisco, San Francisco, CA, USA
| | - Neeta Thakur
- Department of Medicine, University of California, San Francisco, San Francisco, CA, USA
| | - Joshua Galanter
- Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, San Francisco, CA, USA.,Department of Medicine, University of California, San Francisco, San Francisco, CA, USA.,Department of Epidemiology and Biostatistics, University of California, San Francisco, San Francisco, CA, USA
| | - Angel C Y Mak
- Department of Medicine, University of California, San Francisco, San Francisco, CA, USA
| | - Sam S Oh
- Department of Medicine, University of California, San Francisco, San Francisco, CA, USA
| | - Elizabeth Ampleford
- Department of Internal Medicine, Wake Forest Baptist Medical Center, Winston Salem, NC, USA
| | - Stephen P Peters
- Department of Internal Medicine, Wake Forest Baptist Medical Center, Winston Salem, NC, USA
| | - Adam Davis
- UCSF Benioff Children's Hospital Oakland, Center for Community Health and Engagement, Oakland, CA, USA
| | - Rajesh Kumar
- Ann & Robert H. Lurie Children's Hospital of Chicago, Pediatrics, Chicago, IL, USA
| | - Harold J Farber
- Department of Pediatrics, Section of Pulmonology, Baylor College of Medicine and Texas Children's Hospital, Houston, TX, USA
| | - Kelley Meade
- UCSF Benioff Children's Hospital Oakland, Oakland, CA, USA
| | - Pedro C Avila
- Division of Allergy-Immunology, Northwestern University Feinberg School of Medicine, Chicago, IL, USA
| | - Denise Serebrisky
- Pediatric Pulmonary Division, Jacobi Medical Center, Bronx, NY, USA.,Albert Einstein College of Medicine, Pediatrics, Bronx, NY, USA
| | | | | | | | - Shannon M Thyne
- Department of Pediatrics, David Geffen School of Medicine at ULCA, Olive View-UCLA Medical Center, Sylmar, CA, USA
| | | | | | - Rocio Chapela
- Instituto Nacional de Enfermedades Respiratorias, Mexico City, Mexico
| | - Andrés Moreno Estrada
- National Laboratory of Genomics for Biodiversity (LANGEBIO), CINVESTAV, Irapuato, Guanajuato, Mexico
| | - Karla Sandoval
- National Laboratory of Genomics for Biodiversity (LANGEBIO), CINVESTAV, Irapuato, Guanajuato, Mexico
| | - Max A Seibold
- Department of Pediatrics, National Jewish Health, Denver, CO, USA
| | - Cheryl A Winkler
- Basic Research Laboratory, National Cancer Institute, Leidos Biomedical Research, Frederick National Laboratory, Frederick, MD, USA
| | | | - Deborah A Myers
- Department of Medicine, The University of Arizona, Tucson, AZ, USA
| | - L Keoki Williams
- Center for Health Policy and Health Services Research,, Henry Ford Health System, Detroit, MI, USA.,Department of Internal Medicine, Henry Ford Health System, Detroit, MI, USA
| | - Ryan D Hernandez
- Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, San Francisco, CA, USA.,California Institute for Quantitative Biosciences (QB3), University of California, San Francisco, CA, USA.,Institute for Human Genetics, University of California, San Francisco, CA, USA
| | - Dara G Torgerson
- Department of Medicine, University of California, San Francisco, San Francisco, CA, USA
| | - Esteban G Burchard
- Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, San Francisco, CA, USA. .,Department of Medicine, University of California, San Francisco, San Francisco, CA, USA.
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48
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Wang L, Pittman KJ, Barker JR, Salinas RE, Stanaway IB, Williams GD, Carroll RJ, Balmat T, Ingham A, Gopalakrishnan AM, Gibbs KD, Antonia AL, Heitman J, Lee SC, Jarvik GP, Denny JC, Horner SM, DeLong MR, Valdivia RH, Crosslin DR, Ko DC. An Atlas of Genetic Variation Linking Pathogen-Induced Cellular Traits to Human Disease. Cell Host Microbe 2018; 24:308-323.e6. [PMID: 30092202 PMCID: PMC6093297 DOI: 10.1016/j.chom.2018.07.007] [Citation(s) in RCA: 39] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2018] [Revised: 05/28/2018] [Accepted: 07/05/2018] [Indexed: 12/18/2022]
Abstract
Pathogens have been a strong driving force for natural selection. Therefore, understanding how human genetic differences impact infection-related cellular traits can mechanistically link genetic variation to disease susceptibility. Here we report the Hi-HOST Phenome Project (H2P2): a catalog of cellular genome-wide association studies (GWAS) comprising 79 infection-related phenotypes in response to 8 pathogens in 528 lymphoblastoid cell lines. Seventeen loci surpass genome-wide significance for infection-associated phenotypes ranging from pathogen replication to cytokine production. We combined H2P2 with clinical association data from patients to identify a SNP near CXCL10 as a risk factor for inflammatory bowel disease. A SNP in the transcriptional repressor ZBTB20 demonstrated pleiotropy, likely through suppression of multiple target genes, and was associated with viral hepatitis. These data are available on a web portal to facilitate interpreting human genome variation through the lens of cell biology and should serve as a rich resource for the research community.
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Affiliation(s)
- Liuyang Wang
- Department of Molecular Genetics and Microbiology, School of Medicine, Duke University, Durham, NC 27710, USA
| | - Kelly J Pittman
- Department of Molecular Genetics and Microbiology, School of Medicine, Duke University, Durham, NC 27710, USA
| | - Jeffrey R Barker
- Department of Molecular Genetics and Microbiology, School of Medicine, Duke University, Durham, NC 27710, USA
| | - Raul E Salinas
- Department of Molecular Genetics and Microbiology, School of Medicine, Duke University, Durham, NC 27710, USA
| | - Ian B Stanaway
- Department of Biomedical Informatics and Medical Education, School of Medicine, University of Washington, Seattle, WA 98195, USA
| | - Graham D Williams
- Department of Molecular Genetics and Microbiology, School of Medicine, Duke University, Durham, NC 27710, USA
| | - Robert J Carroll
- Department of Biomedical Informatics, School of Medicine, Vanderbilt University, Nashville, TN 37212, USA
| | - Tom Balmat
- Social Science Research Institute, Duke University, Durham, NC 27710, USA
| | - Andy Ingham
- Duke Research Computing, Duke University, Durham, NC 27710, USA
| | - Anusha M Gopalakrishnan
- Department of Molecular Genetics and Microbiology, School of Medicine, Duke University, Durham, NC 27710, USA
| | - Kyle D Gibbs
- Department of Molecular Genetics and Microbiology, School of Medicine, Duke University, Durham, NC 27710, USA
| | - Alejandro L Antonia
- Department of Molecular Genetics and Microbiology, School of Medicine, Duke University, Durham, NC 27710, USA
| | - Joseph Heitman
- Department of Molecular Genetics and Microbiology, School of Medicine, Duke University, Durham, NC 27710, USA; Division of Infectious Diseases, Department of Medicine, School of Medicine, Duke University, Durham, NC 27710, USA
| | - Soo Chan Lee
- South Texas Center for Emerging Infectious Diseases (STCEID), Department of Biology, College of Sciences, the University of Texas at San Antonio, San Antonio, TX 78249, USA
| | - Gail P Jarvik
- Department of Medicine, Division of Medical Genetics, School of Medicine, University of Washington, Seattle, WA 98195, USA
| | - Joshua C Denny
- Department of Biomedical Informatics, School of Medicine, Vanderbilt University, Nashville, TN 37212, USA
| | - Stacy M Horner
- Department of Molecular Genetics and Microbiology, School of Medicine, Duke University, Durham, NC 27710, USA; Division of Infectious Diseases, Department of Medicine, School of Medicine, Duke University, Durham, NC 27710, USA
| | - Mark R DeLong
- Duke Research Computing, Duke University, Durham, NC 27710, USA
| | - Raphael H Valdivia
- Department of Molecular Genetics and Microbiology, School of Medicine, Duke University, Durham, NC 27710, USA
| | - David R Crosslin
- Department of Biomedical Informatics and Medical Education, School of Medicine, University of Washington, Seattle, WA 98195, USA
| | - Dennis C Ko
- Department of Molecular Genetics and Microbiology, School of Medicine, Duke University, Durham, NC 27710, USA; Division of Infectious Diseases, Department of Medicine, School of Medicine, Duke University, Durham, NC 27710, USA.
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49
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Stein MM, Hrusch CL, Sperling AI, Ober C. Effects of an FcγRIIA polymorphism on leukocyte gene expression and cytokine responses to anti-CD3 and anti-CD28 antibodies. Genes Immun 2018; 20:462-472. [PMID: 29977032 DOI: 10.1038/s41435-018-0038-8] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2017] [Revised: 05/21/2018] [Accepted: 05/23/2018] [Indexed: 02/06/2023]
Abstract
The low affinity Fcγ receptor, FcγRIIA, harbors a common missense mutation, rs1801274 (G>A, Arg131His) that modifies binding affinity to human IgG2 and mouse IgG1 antibodies and is associated with increased risk of autoimmune disease. Despite the important role of the Arg131His variant, little is understood about heterozygous genotype effects on global gene expression and cytokine production during an FcγR-dependent response. To address this gap in knowledge, we treated human whole-blood samples from 130 individuals with mouse IgG1 anti-CD3 and anti-CD28 antibodies and characterized the genome-wide gene expression profiles and cytokine production among individuals stratified by rs1801274 genotype. Our analysis revealed that the levels of four cytokines (IFNγ, IL-12, IL-2, TNFα) and global gene expression patterns differed between all three genotype classes. Surprisingly, the heterozygotes showed suboptimal T cell activation compared to cells from individuals homozygous for the higher-affinity FcγRIIA allele (GG; Arg/Arg). The results of this study demonstrate that IgG response varies among all rs1801274 genotype classes and results in profound differences in both cytokine responses and gene expression patterns in blood leukocytes. Because even heterozygotes showed dampened global responses, our data may provide insight into the heterogeneity of outcomes in cytokine release assays and immunotherapy efficacy.
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Affiliation(s)
- Michelle M Stein
- Department of Human Genetics, University of Chicago, Chicago, IL, 60637, USA.
| | - Cara L Hrusch
- Department of Medicine, Section of Pulmonary and Critical Care Medicine, and the Committee on Immunology, University of Chicago, Chicago, IL, 60637, USA
| | - Anne I Sperling
- Department of Medicine, Section of Pulmonary and Critical Care Medicine, and the Committee on Immunology, University of Chicago, Chicago, IL, 60637, USA
| | - Carole Ober
- Department of Human Genetics, University of Chicago, Chicago, IL, 60637, USA
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50
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Rahman A, Hallgrímsdóttir I, Eisen M, Pachter L. Association mapping from sequencing reads using k-mers. eLife 2018; 7:e32920. [PMID: 29897334 PMCID: PMC6044908 DOI: 10.7554/elife.32920] [Citation(s) in RCA: 52] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2017] [Accepted: 06/08/2018] [Indexed: 01/05/2023] Open
Abstract
Genome wide association studies (GWAS) rely on microarrays, or more recently mapping of sequencing reads, to genotype individuals. The reliance on prior sequencing of a reference genome limits the scope of association studies, and also precludes mapping associations outside of the reference. We present an alignment free method for association studies of categorical phenotypes based on counting [Formula: see text]-mers in whole-genome sequencing reads, testing for associations directly between [Formula: see text]-mers and the trait of interest, and local assembly of the statistically significant [Formula: see text]-mers to identify sequence differences. An analysis of the 1000 genomes data show that sequences identified by our method largely agree with results obtained using the standard approach. However, unlike standard GWAS, our method identifies associations with structural variations and sites not present in the reference genome. We also demonstrate that population stratification can be inferred from [Formula: see text]-mers. Finally, application to an E.coli dataset on ampicillin resistance validates the approach.
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Affiliation(s)
- Atif Rahman
- Department of Electrical Engineering and Computer SciencesUniversity of California, BerkeleyBerkeleyUnited States
| | | | - Michael Eisen
- Department of Molecular and Cell BiologyUniversity of California, BerkeleyBerkeleyUnited States
- Howard Hughes Medical Institute, University of California, BerkeleyBerkeleyUnited States
| | - Lior Pachter
- Department of Electrical Engineering and Computer SciencesUniversity of California, BerkeleyBerkeleyUnited States
- Department of Molecular and Cell BiologyUniversity of California, BerkeleyBerkeleyUnited States
- Department of MathematicsUniversity of California, BerkeleyBerkeleyUnited States
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