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Lyu Y, Wang F, Cheng H, Han J, Dang R, Xia X, Wang H, Zhong J, Lenstra JA, Zhang H, Han J, MacHugh DE, Medugorac I, Upadhyay M, Leonard AS, Ding H, Yang X, Wang MS, Quji S, Zhuzha B, Quzhen P, Wangmu S, Cangjue N, Wa D, Ma W, Liu J, Zhang J, Huang B, Qi X, Li F, Huang Y, Ma Y, Wang Y, Gao Y, Lu W, Lei C, Chen N. Recent selection and introgression facilitated high-altitude adaptation in cattle. Sci Bull (Beijing) 2024:S2095-9273(24)00380-3. [PMID: 38945748 DOI: 10.1016/j.scib.2024.05.030] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2023] [Revised: 05/09/2024] [Accepted: 05/13/2024] [Indexed: 07/02/2024]
Abstract
During the past 3000 years, cattle on the Qinghai-Xizang Plateau have developed adaptive phenotypes under the selective pressure of hypoxia, ultraviolet (UV) radiation, and extreme cold. The genetic mechanism underlying this rapid adaptation is not yet well understood. Here, we present whole-genome resequencing data for 258 cattle from 32 cattle breeds/populations, including 89 Tibetan cattle representing eight populations distributed at altitudes ranging from 3400 m to 4300 m. Our genomic analysis revealed that Tibetan cattle exhibited a continuous phylogeographic cline from the East Asian taurine to the South Asian indicine ancestries. We found that recently selected genes in Tibetan cattle were related to body size (HMGA2 and NCAPG) and energy expenditure (DUOXA2). We identified signals of sympatric introgression from yak into Tibetan cattle at different altitudes, covering 0.64%-3.26% of their genomes, which included introgressed genes responsible for hypoxia response (EGLN1), cold adaptation (LRP11), DNA damage repair (LATS1), and UV radiation resistance (GNPAT). We observed that introgressed yak alleles were associated with noncoding variants, including those in present EGLN1. In Tibetan cattle, three yak introgressed SNPs in the EGLN1 promoter region reduced the expression of EGLN1, suggesting that these genomic variants enhance hypoxia tolerance. Taken together, our results indicated complex adaptation processes in Tibetan cattle, where recently selected genes and introgressed yak alleles jointly facilitated rapid adaptation to high-altitude environments.
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Affiliation(s)
- Yang Lyu
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling 712100, China; Key Laboratory of Animal Production, Product Quality, and Security, Ministry of Education, College of Animal Science and Technology, Jilin Agricultural University, Changchun 130118, China
| | - Fuwen Wang
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling 712100, China
| | - Haijian Cheng
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling 712100, China; Institute of Animal Science and Veterinary Medicine, Shandong Academy of Agricultural Sciences, Shandong Key Lab of Animal Disease Control and Breeding, Jinan 250000, China
| | - Jing Han
- College of Veterinary Medicine, Northwest A&F University, Yangling 712100, China
| | - Ruihua Dang
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling 712100, China
| | - Xiaoting Xia
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling 712100, China
| | - Hui Wang
- Key Laboratory of Qinghai-Tibetan Plateau Animal Genetic Resource Reservation and Utilization, Sichuan Province and Ministry of Education, Southwest Minzu University, Chengdu 610000, China
| | - Jincheng Zhong
- Key Laboratory of Qinghai-Tibetan Plateau Animal Genetic Resource Reservation and Utilization, Sichuan Province and Ministry of Education, Southwest Minzu University, Chengdu 610000, China
| | - Johannes A Lenstra
- Faculty of Veterinary Medicine, Utrecht University, Utrecht 3584 CM, The Netherlands
| | - Hucai Zhang
- Institute for Ecological Research and Pollution Control of Plateau Lakes, School of Ecology and Environmental Science, Yunnan University, Kunming 650500, China; Southwest United Graduate School, Kunming 650500, China
| | - Jianlin Han
- Yazhouwan National Laboratory, Sanya 572024, China; CAAS-ILRI Joint Laboratory on Livestock and Forage Genetic Resources, Institute of Animal Science, Chinese Academy of Agriculture Sciences (CAAS), Beijing 100000, China
| | - David E MacHugh
- Animal Genomics Laboratory, UCD School of Agriculture and Food Science, University College Dublin, Dublin D04 V1W8, Ireland; UCD Conway Institute of Biomolecular and Biomedical Research, University College Dublin, Dublin D04 V1W8, Ireland
| | - Ivica Medugorac
- Population Genomics Group, Department of Veterinary Sciences, LMU Munich, Martinsried 82152, Germany
| | - Maulik Upadhyay
- Population Genomics Group, Department of Veterinary Sciences, LMU Munich, Martinsried 82152, Germany
| | - Alexander S Leonard
- Animal Genomics, ETH Zurich, Universitaetstrasse 2, Zurich 8006, Switzerland
| | - He Ding
- Key Laboratory of Animal Production, Product Quality, and Security, Ministry of Education, College of Animal Science and Technology, Jilin Agricultural University, Changchun 130118, China
| | - Xiaorui Yang
- Key Laboratory of Animal Production, Product Quality, and Security, Ministry of Education, College of Animal Science and Technology, Jilin Agricultural University, Changchun 130118, China
| | - Ming-Shan Wang
- State Key Laboratory of Genetic Resources and Evolution, Yunnan Laboratory of Molecular Biology of Domestic Animals, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming 650223, China
| | - Suolang Quji
- Institute of Animal Husbandry and Veterinary Science, Xizang Autonomous Region Academy of Agricultural and Animal Husbandry Sciences, Lhasa 850000, China
| | - Basang Zhuzha
- Institute of Animal Husbandry and Veterinary Science, Xizang Autonomous Region Academy of Agricultural and Animal Husbandry Sciences, Lhasa 850000, China
| | - Pubu Quzhen
- Shigatse City Kangma County Shaogang Township Agriculture and Animal Husbandry Comprehensive Service Center, Shigatse 857000, China
| | - Silang Wangmu
- Institute of Animal Husbandry and Veterinary Science, Xizang Autonomous Region Academy of Agricultural and Animal Husbandry Sciences, Lhasa 850000, China
| | - Nima Cangjue
- Institute of Animal Husbandry and Veterinary Science, Xizang Autonomous Region Academy of Agricultural and Animal Husbandry Sciences, Lhasa 850000, China
| | - Da Wa
- Institute of Animal Husbandry and Veterinary Science, Xizang Autonomous Region Academy of Agricultural and Animal Husbandry Sciences, Lhasa 850000, China
| | - Weidong Ma
- Shaanxi Province Agriculture & Husbandry Breeding Farm, Fufeng 722203, China
| | - Jianyong Liu
- Yunnan Academy of Grassland and Animal Science, Kunming 650500, China
| | - Jicai Zhang
- Yunnan Academy of Grassland and Animal Science, Kunming 650500, China
| | - Bizhi Huang
- Yunnan Academy of Grassland and Animal Science, Kunming 650500, China
| | - Xingshan Qi
- Animal Husbandry Bureau in Biyang County, Biyang 463700, China
| | - Fuqiang Li
- Hunan Tianhua Industrial Corporation Ltd., Lianyuan 417126, China
| | - Yongzhen Huang
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling 712100, China
| | - Yun Ma
- Key Laboratory of Ruminant Molecular and Cellular Breeding of Ningxia Hui Autonomous Region, School of Agriculture, Ningxia University, Yinchuan 750000, China
| | - Yu Wang
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling 712100, China
| | - Yuanpeng Gao
- College of Veterinary Medicine, Northwest A&F University, Yangling 712100, China.
| | - Wenfa Lu
- Key Laboratory of Animal Production, Product Quality, and Security, Ministry of Education, College of Animal Science and Technology, Jilin Agricultural University, Changchun 130118, China; Yazhouwan National Laboratory, Sanya 572024, China.
| | - Chuzhao Lei
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling 712100, China.
| | - Ningbo Chen
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling 712100, China.
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Saal-Zapata G, Walker M, Cervantes-Medina R, Rodríguez-Varela R. Three-Dimensional Morphometric Analysis of Anterior Cerebral Circulation Aneurysms. Int J Angiol 2024; 33:22-28. [PMID: 38352634 PMCID: PMC10861294 DOI: 10.1055/s-0043-1774740] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/16/2024] Open
Abstract
This article assesses the association between anterior circulation morphometry and the presence of intracranial aneurysm using three-dimensional rotational angiography (3DRA). A retrospective analysis at a Peruvian academic medical center between December 2018 and February 2020 identified 206 patients with unruptured intracranial aneurysms and matched controls who underwent 3DRA. Angiographic images were obtained per standard of care, and measurements of the vasculature were performed using 3DRA vascular automated software. A total of 163 aneurysms and 43 control angiograms were evaluated. Women represented 82.5% of the cases and the mean age was 55.9 years (standard deviation ± 14.2). In multivariate analysis, five specific features were found to be statistically significant predictors for presence of an anterior circulation aneurysm: female sex (odds ratio [OR] = 2.71; p = 0.048), C-shape of the middle cerebral artery (MCA) (OR = 2.73; p = 0.018), distal internal carotid artery (ICA) diameter (OR = 3.42; p = 0.012), ICA bifurcation angle (OR = 1.02; p = 0.036), and length of the carotid siphon (OR = 1.08; p = 0.047). Features detected on 3DRA suggest morphological characteristics of the ICA and MCA may be predictive for intracranial aneurysm. Our findings build from prior reports by demonstrating five specific patient and imaging features associated with anterior circulation aneurysms. While 3DRA is the standard of care in many settings, medical centers with resource limitations may not have access to this technique. The demographic and morphological features identified in our study may have correlates that if detected on contrast computed tomography or magnetic resonance imaging studies, may be used to help screen for a higher level of care in select patients.
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Affiliation(s)
- Giancarlo Saal-Zapata
- Department of Neurosurgery, Endovascular Neurosurgery Service, Hospital Nacional Guillermo Almenara Irigoyen-EsSalud, La Victoria, Lima, Perú
| | - Melanie Walker
- Department of Neurological Surgery, University of Washington, Seattle, Washington
| | - Rosa Cervantes-Medina
- Department of Radiology, Interventional Radiology Service, Hospital Nacional Guillermo Almenara Irigoyen-EsSalud, La Victoria, Lima, Perú
| | - Rodolfo Rodríguez-Varela
- Department of Neurosurgery, Endovascular Neurosurgery Service, Hospital Nacional Guillermo Almenara Irigoyen-EsSalud, La Victoria, Lima, Perú
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Agata A, Ohtsuka S, Noji R, Gotoh H, Ono K, Nomura T. A Neanderthal/Denisovan GLI3 variant contributes to anatomical variations in mice. Front Cell Dev Biol 2023; 11:1247361. [PMID: 38020913 PMCID: PMC10651735 DOI: 10.3389/fcell.2023.1247361] [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: 06/26/2023] [Accepted: 10/12/2023] [Indexed: 12/01/2023] Open
Abstract
Changes in genomic structures underlie phenotypic diversification in organisms. Amino acid-changing mutations affect pleiotropic functions of proteins, although little is known about how mutated proteins are adapted in existing developmental programs. Here we investigate the biological effects of a variant of the GLI3 transcription factor (GLI3R1537C) carried in Neanderthals and Denisovans, which are extinct hominins close to modern humans. R1537C does not compromise protein stability or GLI3 activator-dependent transcriptional activities. In contrast, R1537C affects the regulation of downstream target genes associated with developmental processes. Furthermore, genome-edited mice carrying the Neanderthal/Denisovan GLI3 mutation exhibited various alterations in skeletal morphology. Our data suggest that an extinct hominin-type GLI3 contributes to species-specific anatomical variations, which were tolerated by relaxed constraint in developmental programs during human evolution.
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Affiliation(s)
- Ako Agata
- Developmental Neurobiology, Kyoto Prefectural University of Medicine, Kyoto, Japan
| | - Satoshi Ohtsuka
- Laboratories for Experimental Animals, Kyoto Prefectural University of Medicine, Kyoto, Japan
| | - Ryota Noji
- Developmental Neurobiology, Kyoto Prefectural University of Medicine, Kyoto, Japan
| | - Hitoshi Gotoh
- Developmental Neurobiology, Kyoto Prefectural University of Medicine, Kyoto, Japan
| | - Katsuhiko Ono
- Developmental Neurobiology, Kyoto Prefectural University of Medicine, Kyoto, Japan
| | - Tadashi Nomura
- Developmental Neurobiology, Kyoto Prefectural University of Medicine, Kyoto, Japan
- Applied Biology, Kyoto Institute of Technology, Kyoto, Japan
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4
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Salehi Nowbandegani P, Wohns AW, Ballard JL, Lander ES, Bloemendal A, Neale BM, O'Connor LJ. Extremely sparse models of linkage disequilibrium in ancestrally diverse association studies. Nat Genet 2023; 55:1494-1502. [PMID: 37640881 DOI: 10.1038/s41588-023-01487-8] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2022] [Accepted: 07/24/2023] [Indexed: 08/31/2023]
Abstract
Linkage disequilibrium (LD) is the correlation among nearby genetic variants. In genetic association studies, LD is often modeled using large correlation matrices, but this approach is inefficient, especially in ancestrally diverse studies. In the present study, we introduce LD graphical models (LDGMs), which are an extremely sparse and efficient representation of LD. LDGMs are derived from genome-wide genealogies; statistical relationships among alleles in the LDGM correspond to genealogical relationships among haplotypes. We published LDGMs and ancestry-specific LDGM precision matrices for 18 million common variants (minor allele frequency >1%) in five ancestry groups, validated their accuracy and demonstrated order-of-magnitude improvements in runtime for commonly used LD matrix computations. We implemented an extremely fast multiancestry polygenic prediction method, BLUPx-ldgm, which performs better than a similar method based on the reference LD correlation matrix. LDGMs will enable sophisticated methods that scale to ancestrally diverse genetic association data across millions of variants and individuals.
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Affiliation(s)
- Pouria Salehi Nowbandegani
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA.
- Department of Biomedical Informatics, Harvard Medical School, Boston, MA, USA.
| | - Anthony Wilder Wohns
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA.
- Department of Biomedical Informatics, Harvard Medical School, Boston, MA, USA.
- Stanford University School of Medicine, Stanford, CA, USA.
| | - Jenna L Ballard
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Graduate Group in Genomics and Computational Biology, University of Pennsylvania, Philadelphia, PA, USA
| | - Eric S Lander
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Department of Biology, MIT, Cambridge, MA, USA
- Department of Systems Biology, Harvard Medical School, Boston, MA, USA
| | - Alex Bloemendal
- Analytic and Translational Genetics Unit, Department of Medicine, Massachusetts General Hospital, Boston, MA, USA
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- The Novo Nordisk Foundation Center for Genomic Mechanisms of Disease, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Benjamin M Neale
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Analytic and Translational Genetics Unit, Department of Medicine, Massachusetts General Hospital, Boston, MA, USA
- Stanley Center for Psychiatric Research, Broad Institute of MIT and Harvard, Cambridge, MA, USA
- The Novo Nordisk Foundation Center for Genomic Mechanisms of Disease, Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Luke J O'Connor
- Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA.
- Department of Biomedical Informatics, Harvard Medical School, Boston, MA, USA.
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5
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Rajabli F, Benchek P, Tosto G, Kushch N, Sha J, Bazemore K, Zhu C, Lee WP, Haut J, Hamilton-Nelson KL, Wheeler NR, Zhao Y, Farrell JJ, Grunin MA, Leung YY, Kuksa PP, Li D, Lucio da Fonseca E, Mez JB, Palmer EL, Pillai J, Sherva RM, Song YE, Zhang X, Iqbal T, Pathak O, Valladares O, Kuzma AB, Abner E, Adams PM, Aguirre A, Albert MS, Albin RL, Allen M, Alvarez L, Apostolova LG, Arnold SE, Asthana S, Atwood CS, Ayres G, Baldwin CT, Barber RC, Barnes LL, Barral S, Beach TG, Becker JT, Beecham GW, Beekly D, Benitez BA, Bennett D, Bertelson J, Bird TD, Blacker D, Boeve BF, Bowen JD, Boxer A, Brewer J, Burke JR, Burns JM, Buxbaum JD, Cairns NJ, Cantwell LB, Cao C, Carlson CS, Carlsson CM, Carney RM, Carrasquillo MM, Chasse S, Chesselet MF, Chin NA, Chui HC, Chung J, Craft S, Crane PK, Cribbs DH, Crocco EA, Cruchaga C, Cuccaro ML, Cullum M, Darby E, Davis B, De Jager PL, DeCarli C, DeToledo J, Dick M, Dickson DW, Dombroski BA, Doody RS, Duara R, Ertekin-Taner NI, Evans DA, Faber KM, Fairchild TJ, Fallon KB, Fardo DW, Farlow MR, Fernandez-Hernandez V, Ferris S, Foroud TM, Frosch MP, Fulton-Howard B, Galasko DR, Gamboa A, Gearing M, Geschwind DH, Ghetti B, Gilbert JR, Goate AM, Grabowski TJ, Graff-Radford NR, Green RC, Growdon JH, Hakonarson H, Hall J, Hamilton RL, Harari O, Hardy J, Harrell LE, Head E, Henderson VW, Hernandez M, Hohman T, Honig LS, Huebinger RM, Huentelman MJ, Hulette CM, Hyman BT, Hynan LS, Ibanez L, Jarvik GP, Jayadev S, Jin LW, Johnson K, Johnson L, Kamboh MI, Karydas AM, Katz MJ, Kauwe JS, Kaye JA, Keene CD, Khaleeq A, Kim R, Knebl J, Kowall NW, Kramer JH, Kukull WA, LaFerla FM, Lah JJ, Larson EB, Lerner A, Leverenz JB, Levey AI, Lieberman AP, Lipton RB, Logue M, Lopez OL, Lunetta KL, Lyketsos CG, Mains D, Margaret FE, Marson DC, Martin ERR, Martiniuk F, Mash DC, Masliah E, Massman P, Masurkar A, McCormick WC, McCurry SM, McDavid AN, McDonough S, McKee AC, Mesulam M, Miller BL, Miller CA, Miller JW, Montine TJ, Monuki ES, Morris JC, Mukherjee S, Myers AJ, Nguyen T, O'Bryant S, Olichney JM, Ory M, Palmer R, Parisi JE, Paulson HL, Pavlik V, Paydarfar D, Perez V, Peskind E, Petersen RC, Pierce A, Polk M, Poon WW, Potter H, Qu L, Quiceno M, Quinn JF, Raj A, Raskind M, Reiman EM, Reisberg B, Reisch JS, Ringman JM, Roberson ED, Rodriguear M, Rogaeva E, Rosen HJ, Rosenberg RN, Royall DR, Sager MA, Sano M, Saykin AJ, Schneider JA, Schneider LS, Seeley WW, Slifer SH, Small S, Smith AG, Smith JP, Sonnen JA, Spina S, St George-Hyslop P, Stern RA, Stevens AB, Strittmatter SM, Sultzer D, Swerdlow RH, Tanzi RE, Tilson JL, Trojanowski JQ, Troncoso JC, Tsuang DW, Van Deerlin VM, van Eldik LJ, Vance JM, Vardarajan BN, Vassar R, Vinters HV, Vonsattel JP, Weintraub S, Welsh-Bohmer KA, Whitehead PL, Wijsman EM, Wilhelmsen KC, Williams B, Williamson J, Wilms H, Wingo TS, Wisniewski T, Woltjer RL, Woon M, Wright CB, Wu CK, Younkin SG, Yu CE, Yu L, Zhu X, Kunkle BW, Bush WS, Wang LS, Farrer LA, Haines JL, Mayeux R, Pericak-Vance MA, Schellenberg GD, Jun GR, Reitz C, Naj AC. Multi-ancestry genome-wide meta-analysis of 56,241 individuals identifies LRRC4C, LHX5-AS1 and nominates ancestry-specific loci PTPRK , GRB14 , and KIAA0825 as novel risk loci for Alzheimer's disease: the Alzheimer's Disease Genetics Consortium. MEDRXIV : THE PREPRINT SERVER FOR HEALTH SCIENCES 2023:2023.07.06.23292311. [PMID: 37461624 PMCID: PMC10350126 DOI: 10.1101/2023.07.06.23292311] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/25/2023]
Abstract
Limited ancestral diversity has impaired our ability to detect risk variants more prevalent in non-European ancestry groups in genome-wide association studies (GWAS). We constructed and analyzed a multi-ancestry GWAS dataset in the Alzheimer's Disease (AD) Genetics Consortium (ADGC) to test for novel shared and ancestry-specific AD susceptibility loci and evaluate underlying genetic architecture in 37,382 non-Hispanic White (NHW), 6,728 African American, 8,899 Hispanic (HIS), and 3,232 East Asian individuals, performing within-ancestry fixed-effects meta-analysis followed by a cross-ancestry random-effects meta-analysis. We identified 13 loci with cross-ancestry associations including known loci at/near CR1 , BIN1 , TREM2 , CD2AP , PTK2B , CLU , SHARPIN , MS4A6A , PICALM , ABCA7 , APOE and two novel loci not previously reported at 11p12 ( LRRC4C ) and 12q24.13 ( LHX5-AS1 ). Reflecting the power of diverse ancestry in GWAS, we observed the SHARPIN locus using 7.1% the sample size of the original discovering single-ancestry GWAS (n=788,989). We additionally identified three GWS ancestry-specific loci at/near ( PTPRK ( P =2.4×10 -8 ) and GRB14 ( P =1.7×10 -8 ) in HIS), and KIAA0825 ( P =2.9×10 -8 in NHW). Pathway analysis implicated multiple amyloid regulation pathways (strongest with P adjusted =1.6×10 -4 ) and the classical complement pathway ( P adjusted =1.3×10 -3 ). Genes at/near our novel loci have known roles in neuronal development ( LRRC4C, LHX5-AS1 , and PTPRK ) and insulin receptor activity regulation ( GRB14 ). These findings provide compelling support for using traditionally-underrepresented populations for gene discovery, even with smaller sample sizes.
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Xiao X, Huang Y, Zhang J, Cao Y, Zhang M. Identification of two variants in PAX3 and FBN1 in a Chinese family with Waardenburg and Marfan syndrome via whole exome sequencing. Funct Integr Genomics 2023; 23:114. [PMID: 37000337 DOI: 10.1007/s10142-023-01012-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2022] [Revised: 03/04/2023] [Accepted: 03/06/2023] [Indexed: 04/01/2023]
Abstract
Both Warrensburg (WS) and Marfan syndrome (MFS) can impair the vision. Here, we recruited a Chinese family consisting of two WS affected individuals (II:1 and III:3) and five MFS affected individuals( I:1, II:2, III:1, III:2, and III:5) as well as one suspected MFS individual (II:4). Using whole exome sequencing (WES) and subsequent PCR-Sanger sequencing, we identified one novel heterozygous variant NM_000438 (PAX3) c.208 T > C, (p.Cys70Arg) from individuals with WS and one previous reported variant NM_000138 (FBN1) c.2740 T > A, (p.Cys914Ser) from individuals with MFS and co-segregated with the diseases. Real-time PCR and Western blot assay showed that, compared to their wild-type, both mRNAs and proteins of PAX3 and FBN1 mutants reduced in HKE293T cells. Together, our study identified two disease-causing variants in a same Chinese family with WS and MFS, and confirmed their damaged effects on their genes' expression. Therefore, those findings expand the mutation spectrum of PAX3 and provide a new perspective for the potential therapy.
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Affiliation(s)
- Xiaoqiang Xiao
- Joint Shantou International Eye Center, Shantou University and the Chinese University of Hong Kong, Shantou, China.
| | - Yuqiang Huang
- Joint Shantou International Eye Center, Shantou University and the Chinese University of Hong Kong, Shantou, China
| | - Jianqiang Zhang
- Joint Shantou International Eye Center, Shantou University and the Chinese University of Hong Kong, Shantou, China
- The Third Affiliated Hospital of Sun Yat-sen University, Guangzhou, China
| | - Yingjie Cao
- Joint Shantou International Eye Center, Shantou University and the Chinese University of Hong Kong, Shantou, China
| | - Mingzhi Zhang
- Joint Shantou International Eye Center, Shantou University and the Chinese University of Hong Kong, Shantou, China
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7
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New insights from GWAS on BMI-related growth traits in a longitudinal cohort of admixed children with Native American and European ancestry. iScience 2023; 26:106091. [PMID: 36844456 PMCID: PMC9947275 DOI: 10.1016/j.isci.2023.106091] [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: 10/27/2021] [Revised: 05/04/2022] [Accepted: 01/25/2023] [Indexed: 02/02/2023] Open
Abstract
Body-mass index (BMI) is a hallmark of adiposity. In contrast with adulthood, the genetic architecture of BMI during childhood is poorly understood. The few genome-wide association studies (GWAS) on children have been performed almost exclusively in Europeans and at single ages. We performed cross-sectional and longitudinal GWAS for BMI-related traits on 904 admixed children with mostly Mapuche Native American and European ancestries. We found regulatory variants of the immune gene HLA-DQB3 strongly associated with BMI at 1.5 - 2.5 years old. A variant in the sex-determining gene DMRT1 was associated with the age at adiposity rebound (Age-AR) in girls (P = 9.8 × 10 - 9 ). BMI was significantly higher in Mapuche than in Europeans between 5.5 and 16.5 years old. Finally, Age-AR was significantly lower (P = 0.004 ) by 1.94 years and BMI at AR was significantly higher (P = 0.04 ) by 1.2 kg/ m 2 , in Mapuche children compared with Europeans.
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Lea AJ, Garcia A, Arevalo J, Ayroles JF, Buetow K, Cole SW, Eid Rodriguez D, Gutierrez M, Highland HM, Hooper PL, Justice A, Kraft T, North KE, Stieglitz J, Kaplan H, Trumble BC, Gurven MD. Natural selection of immune and metabolic genes associated with health in two lowland Bolivian populations. Proc Natl Acad Sci U S A 2023; 120:e2207544120. [PMID: 36574663 PMCID: PMC9910614 DOI: 10.1073/pnas.2207544120] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2022] [Accepted: 09/21/2022] [Indexed: 12/28/2022] Open
Abstract
A growing body of work has addressed human adaptations to diverse environments using genomic data, but few studies have connected putatively selected alleles to phenotypes, much less among underrepresented populations such as Amerindians. Studies of natural selection and genotype-phenotype relationships in underrepresented populations hold potential to uncover previously undescribed loci underlying evolutionarily and biomedically relevant traits. Here, we worked with the Tsimane and the Moseten, two Amerindian populations inhabiting the Bolivian lowlands. We focused most intensively on the Tsimane, because long-term anthropological work with this group has shown that they have a high burden of both macro and microparasites, as well as minimal cardiometabolic disease or dementia. We therefore generated genome-wide genotype data for Tsimane individuals to study natural selection, and paired this with blood mRNA-seq as well as cardiometabolic and immune biomarker data generated from a larger sample that included both populations. In the Tsimane, we identified 21 regions that are candidates for selective sweeps, as well as 5 immune traits that show evidence for polygenic selection (e.g., C-reactive protein levels and the response to coronaviruses). Genes overlapping candidate regions were strongly enriched for known involvement in immune-related traits, such as abundance of lymphocytes and eosinophils. Importantly, we were also able to draw on extensive phenotype information for the Tsimane and Moseten and link five regions (containing PSD4, MUC21 and MUC22, TOX2, ANXA6, and ABCA1) with biomarkers of immune and metabolic function. Together, our work highlights the utility of pairing evolutionary analyses with anthropological and biomedical data to gain insight into the genetic basis of health-related traits.
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Affiliation(s)
- Amanda J. Lea
- Department of Biological Sciences, Vanderbilt University, Nashville, TN37235
| | - Angela Garcia
- Center for Evolution and Medicine, Arizona State University, Tempe, AZ85287
| | - Jesusa Arevalo
- Department of Medicine, University of California, Los Angeles, CA90095
| | - Julien F. Ayroles
- Department of Ecology and Evolution, Princeton University, Princeton, NJ08544
- Lewis Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ08544
| | - Kenneth Buetow
- Center for Evolution and Medicine, Arizona State University, Tempe, AZ85287
- School of Life Sciences, Arizona State University, Tempe, AZ85287
| | - Steve W. Cole
- Department of Psychiatry and Biobehavioral Sciences, University of California, Los Angeles, CA90095
- Department of Medicine, University of California, Los Angeles, CA90095
| | | | | | - Heather M. Highland
- Department of Epidemiology, University of North Carolina at Chapel Hill, Chapel Hill, NC27516
| | - Paul L. Hooper
- Economic Science Institute, Chapman University, Orange, CA92866
| | | | - Thomas Kraft
- Department of Anthropology, University of Utah, Salt Lake City, UT84112
| | - Kari E. North
- Department of Epidemiology, University of North Carolina at Chapel Hill, Chapel Hill, NC27516
| | | | - Hillard Kaplan
- Institute for Economics and Society, Chapman University, Orange, CA92866
| | - Benjamin C. Trumble
- Center for Evolution and Medicine, Arizona State University, Tempe, AZ85287
- School of Human Evolution and Social Change, Arizona State University, Tempe, AZ85287
| | - Michael D. Gurven
- Department of Anthropology, University of California, Santa Barbara, CA93106
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9
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Zheng J, Wang X, Feng T, Rehman SU, Yan X, Shan H, Ma X, Zhou W, Xu W, Lu L, Liu J, Luo X, Cui K, Qin C, Chen W, Yu J, Li Z, Ruan J, Liu Q. Molecular mechanisms underlying hematophagia revealed by comparative analyses of leech genomes. Gigascience 2022; 12:giad023. [PMID: 37039117 PMCID: PMC10087013 DOI: 10.1093/gigascience/giad023] [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: 08/04/2022] [Revised: 12/14/2022] [Accepted: 03/22/2023] [Indexed: 04/12/2023] Open
Abstract
BACKGROUND Leeches have been used in traditional Chinese medicine since prehistoric times to treat a spectrum of ailments, but very little is known about their physiological, genetic, and evolutionary characteristics. FINDINGS We sequenced and assembled chromosome-level genomes of 3 leech species (bloodsucking Hirudo nipponia and Hirudinaria manillensis and nonbloodsucking Whitmania pigra). The dynamic population histories and genome-wide expression patterns of the 2 bloodsucking leech species were found to be similar. A combined analysis of the genomic and transcriptional data revealed that the bloodsucking leeches have a presumably enhanced auditory sense for prey location in relatively deep fresh water. The copy number of genes related to anticoagulation, analgesia, and anti-inflammation increased in the bloodsucking leeches, and their gene expressions responded dynamically to the bloodsucking process. Furthermore, the expanded FBN1 gene family may help in rapid body swelling of leeches after bloodsucking, and the expanded GLB3 gene family may be associated with long-term storage of prey blood in a leech's body. CONCLUSIONS The high-quality reference genomes and comprehensive datasets obtained in this study may facilitate innovations in the artificial culture and strain optimization of leeches.
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Affiliation(s)
- Jinghui Zheng
- Guangdong Provincial Key Laboratory of Animal Molecular Design and Precise
Breeding, School of Life Science and Engineering, Foshan University,
Foshan 528225, China
- Department of Cardiology, Ruikang Hospital Affiliated to Guangxi University
of Chinese Medicine, Nanning 530011, China
| | - Xiaobo Wang
- State Key Laboratory for Conservation and Utilization of Subtropical
Agro-bioresources, Guangxi University, Nanning 530004, China
| | - Tong Feng
- State Key Laboratory for Conservation and Utilization of Subtropical
Agro-bioresources, Guangxi University, Nanning 530004, China
- Department of Bioinformatics and Systems Biology, College of Life Science
and Technology, Huazhong University of Science and Technology, Wuhan,
Hubei 430074, China
| | - Saif ur Rehman
- State Key Laboratory for Conservation and Utilization of Subtropical
Agro-bioresources, Guangxi University, Nanning 530004, China
| | - Xiuying Yan
- State Key Laboratory for Conservation and Utilization of Subtropical
Agro-bioresources, Guangxi University, Nanning 530004, China
| | - Huiquan Shan
- State Key Laboratory for Conservation and Utilization of Subtropical
Agro-bioresources, Guangxi University, Nanning 530004, China
| | - Xiaocong Ma
- Department of Cardiology, Ruikang Hospital Affiliated to Guangxi University
of Chinese Medicine, Nanning 530011, China
| | - Weiguan Zhou
- Biological Institute of Guangxi Academy of Sciences, Nanning
530007, China
| | - Wenhua Xu
- Department of Cardiology, Ruikang Hospital Affiliated to Guangxi University
of Chinese Medicine, Nanning 530011, China
| | - Liying Lu
- Department of Cardiology, Ruikang Hospital Affiliated to Guangxi University
of Chinese Medicine, Nanning 530011, China
| | - Jiasheng Liu
- Department of Cardiology, Ruikang Hospital Affiliated to Guangxi University
of Chinese Medicine, Nanning 530011, China
| | - Xier Luo
- Guangdong Provincial Key Laboratory of Animal Molecular Design and Precise
Breeding, School of Life Science and Engineering, Foshan University,
Foshan 528225, China
- Genome Analysis Laboratory of the Ministry of Agriculture, Agricultural
Genomics Institute, Chinese Academy of Agricultural Sciences, Shenzhen,
Guangdong 518120, China
| | - Kuiqing Cui
- Guangdong Provincial Key Laboratory of Animal Molecular Design and Precise
Breeding, School of Life Science and Engineering, Foshan University,
Foshan 528225, China
- State Key Laboratory for Conservation and Utilization of Subtropical
Agro-bioresources, Guangxi University, Nanning 530004, China
| | - Chaobin Qin
- State Key Laboratory for Conservation and Utilization of Subtropical
Agro-bioresources, Guangxi University, Nanning 530004, China
| | - Weihua Chen
- Department of Bioinformatics and Systems Biology, College of Life Science
and Technology, Huazhong University of Science and Technology, Wuhan,
Hubei 430074, China
| | - Jun Yu
- CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of
Genomics, Chinese Academy of Sciences, Beijing 100101, China
| | - Zhipeng Li
- State Key Laboratory for Conservation and Utilization of Subtropical
Agro-bioresources, Guangxi University, Nanning 530004, China
| | - Jue Ruan
- Genome Analysis Laboratory of the Ministry of Agriculture, Agricultural
Genomics Institute, Chinese Academy of Agricultural Sciences, Shenzhen,
Guangdong 518120, China
| | - Qingyou Liu
- Guangdong Provincial Key Laboratory of Animal Molecular Design and Precise
Breeding, School of Life Science and Engineering, Foshan University,
Foshan 528225, China
- State Key Laboratory for Conservation and Utilization of Subtropical
Agro-bioresources, Guangxi University, Nanning 530004, China
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10
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Ishigaki K, Sakaue S, Terao C, Luo Y, Sonehara K, Yamaguchi K, Amariuta T, Too CL, Laufer VA, Scott IC, Viatte S, Takahashi M, Ohmura K, Murasawa A, Hashimoto M, Ito H, Hammoudeh M, Emadi SA, Masri BK, Halabi H, Badsha H, Uthman IW, Wu X, Lin L, Li T, Plant D, Barton A, Orozco G, Verstappen SMM, Bowes J, MacGregor AJ, Honda S, Koido M, Tomizuka K, Kamatani Y, Tanaka H, Tanaka E, Suzuki A, Maeda Y, Yamamoto K, Miyawaki S, Xie G, Zhang J, Amos CI, Keystone E, Wolbink G, van der Horst-Bruinsma I, Cui J, Liao KP, Carroll RJ, Lee HS, Bang SY, Siminovitch KA, de Vries N, Alfredsson L, Rantapää-Dahlqvist S, Karlson EW, Bae SC, Kimberly RP, Edberg JC, Mariette X, Huizinga T, Dieudé P, Schneider M, Kerick M, Denny JC, Matsuda K, Matsuo K, Mimori T, Matsuda F, Fujio K, Tanaka Y, Kumanogoh A, Traylor M, Lewis CM, Eyre S, Xu H, Saxena R, Arayssi T, Kochi Y, Ikari K, Harigai M, Gregersen PK, Yamamoto K, Louis Bridges S, Padyukov L, Martin J, Klareskog L, Okada Y, Raychaudhuri S. Multi-ancestry genome-wide association analyses identify novel genetic mechanisms in rheumatoid arthritis. Nat Genet 2022; 54:1640-1651. [PMID: 36333501 PMCID: PMC10165422 DOI: 10.1038/s41588-022-01213-w] [Citation(s) in RCA: 85] [Impact Index Per Article: 42.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2021] [Accepted: 09/26/2022] [Indexed: 11/06/2022]
Abstract
Rheumatoid arthritis (RA) is a highly heritable complex disease with unknown etiology. Multi-ancestry genetic research of RA promises to improve power to detect genetic signals, fine-mapping resolution and performances of polygenic risk scores (PRS). Here, we present a large-scale genome-wide association study (GWAS) of RA, which includes 276,020 samples from five ancestral groups. We conducted a multi-ancestry meta-analysis and identified 124 loci (P < 5 × 10-8), of which 34 are novel. Candidate genes at the novel loci suggest essential roles of the immune system (for example, TNIP2 and TNFRSF11A) and joint tissues (for example, WISP1) in RA etiology. Multi-ancestry fine-mapping identified putatively causal variants with biological insights (for example, LEF1). Moreover, PRS based on multi-ancestry GWAS outperformed PRS based on single-ancestry GWAS and had comparable performance between populations of European and East Asian ancestries. Our study provides several insights into the etiology of RA and improves the genetic predictability of RA.
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Affiliation(s)
- Kazuyoshi Ishigaki
- Center for Data Sciences, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA
- Division of Genetics, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
- Laboratory for Human Immunogenetics, RIKEN Center for Integrative Medical Sciences, Yokohama, Japan
| | - Saori Sakaue
- Center for Data Sciences, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA
- Division of Genetics, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
- Department of Statistical Genetics, Osaka University Graduate School of Medicine, Suita, Japan
- Program in Medical and Population Genetics, Broad Institute of Harvard and MIT, Cambridge, MA, USA
| | - Chikashi Terao
- Laboratory for Statistical and Translational Genetics, RIKEN Center for Integrative Medical Sciences, Yokohama, Japan
- Clinical Research Center, Shizuoka General Hospital, Shizuoka, Japan
- The Department of Applied Genetics, The School of Pharmaceutical Sciences, University of Shizuoka, Shizuoka, Japan
| | - Yang Luo
- Center for Data Sciences, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA
- Division of Genetics, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
- Program in Medical and Population Genetics, Broad Institute of Harvard and MIT, Cambridge, MA, USA
- Division of Rheumatology, Inflammation, and Immunity, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA
- Department of Biomedical Informatics, Harvard Medical School, Boston, MA, USA
| | - Kyuto Sonehara
- Department of Statistical Genetics, Osaka University Graduate School of Medicine, Suita, Japan
- Integrated Frontier Research for Medical Science Division, Institute for Open and Transdisciplinary Research Initiatives, Osaka University, Suita, Japan
| | - Kensuke Yamaguchi
- Department of Genomic Function and Diversity, Medical Research Institute, Tokyo Medical and Dental University, Tokyo, Japan
- Laboratory for Autoimmune Diseases, RIKEN Center for Integrative Medical Sciences, Yokohama, Japan
| | - Tiffany Amariuta
- Center for Data Sciences, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA
- Division of Genetics, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
- Program in Medical and Population Genetics, Broad Institute of Harvard and MIT, Cambridge, MA, USA
- Department of Biomedical Informatics, Harvard Medical School, Boston, MA, USA
- Department of Epidemiology, Harvard T.H. Chan School of Public Health, Boston, MA, USA
- Halıcıoğlu Data Science Institute, University of California San Diego, La Jolla, CA, USA
- Department of Medicine, University of California San Diego, La Jolla, CA, USA
| | - Chun Lai Too
- Immunogenetics Unit, Allergy and Immunology Research Center, Institute for Medical Research, National Institutes of Health Complex, Ministry of Health, Kuala Lumpur, Malaysia
- Department of Medicine, Division of Rheumatology, Karolinska Institutet and Karolinska University Hospital, Stockholm, Sweden
| | - Vincent A Laufer
- Department of Clinical Immunology and Rheumatology, University of Alabama at Birmingham School of Medicine, Birmingham, AL, USA
- Department of Pathology, Michigan Medicine, Ann Arbor, MI, USA
| | - Ian C Scott
- Haywood Academic Rheumatology Centre, Haywood Hospital, Midlands Partnership NHS Foundation Trust, Burslem, UK
- Primary Care Centre Versus Arthritis, School of Medicine, Keele University, Keele, UK
| | - Sebastien Viatte
- Centre for Genetics and Genomics Versus Arthritis, Division of Musculoskeletal and Dermatological Sciences, School of Biological Sciences, Faculty of Biology, Medicine and Health, The University of Manchester, Manchester Academic Health Science Centre, Manchester, UK
- Lydia Becker Institute of Immunology and Inflammation, Faculty of Biology, Medicine and Health, The University of Manchester, Manchester, UK
- NIHR Manchester Biomedical Research Centre, Manchester University Foundation Trust, Manchester, UK
| | - Meiko Takahashi
- Center for Genomic Medicine, Kyoto University Graduate School of Medicine, Kyoto, Japan
| | - Koichiro Ohmura
- Department of Rheumatology and Clinical immunology, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - Akira Murasawa
- Department of Rheumatology, Niigata Rheumatic Center, Niigata, Japan
| | - Motomu Hashimoto
- Department of Advanced Medicine for Rheumatic Diseases, Kyoto University Graduate School of Medicine, Kyoto, Japan
- Department of Clinical Immunology, Graduate School of Medicine, Osaka City University, Osaka, Japan
| | - Hiromu Ito
- Department of Advanced Medicine for Rheumatic Diseases, Kyoto University Graduate School of Medicine, Kyoto, Japan
- Department of Orthopaedic Surgery, Kurashiki Central Hospital, Kurashiki, Japan
| | - Mohammed Hammoudeh
- Rheumatology Division, Department of Internal Medicine, Hamad Medical Corporation, Doha, Qatar
| | - Samar Al Emadi
- Rheumatology Division, Department of Internal Medicine, Hamad Medical Corporation, Doha, Qatar
| | - Basel K Masri
- Department of Internal Medicine, Jordan Hospital, Amman, Jordan
| | - Hussein Halabi
- Section of Rheumatology, Department of Internal Medicine, King Faisal Specialist Hospital and Research Center, Jeddah, Saudi Arabia
| | - Humeira Badsha
- Dr. Humeira Badsha Medical Center, Emirates Hospital, Dubai, United Arab Emirates
| | - Imad W Uthman
- Department of Rheumatology, American University of Beirut, Beirut, Lebanon
| | - Xin Wu
- Department of Rheumatology and Immunology, Shanghai Changzeng Hospital, The Second Military Medical University, Shanghai, China
| | - Li Lin
- Department of Rheumatology and Immunology, Shanghai Changzeng Hospital, The Second Military Medical University, Shanghai, China
| | - Ting Li
- Department of Rheumatology and Immunology, Shanghai Changzeng Hospital, The Second Military Medical University, Shanghai, China
| | - Darren Plant
- Centre for Genetics and Genomics Versus Arthritis, Division of Musculoskeletal and Dermatological Sciences, School of Biological Sciences, Faculty of Biology, Medicine and Health, The University of Manchester, Manchester Academic Health Science Centre, Manchester, UK
| | - Anne Barton
- Centre for Genetics and Genomics Versus Arthritis, Division of Musculoskeletal and Dermatological Sciences, School of Biological Sciences, Faculty of Biology, Medicine and Health, The University of Manchester, Manchester Academic Health Science Centre, Manchester, UK
- NIHR Manchester Biomedical Research Centre, Manchester University Foundation Trust, Manchester, UK
| | - Gisela Orozco
- Centre for Genetics and Genomics Versus Arthritis, Division of Musculoskeletal and Dermatological Sciences, School of Biological Sciences, Faculty of Biology, Medicine and Health, The University of Manchester, Manchester Academic Health Science Centre, Manchester, UK
- NIHR Manchester Biomedical Research Centre, Manchester University Foundation Trust, Manchester, UK
| | - Suzanne M M Verstappen
- NIHR Manchester Biomedical Research Centre, Manchester University Foundation Trust, Manchester, UK
- Centre for Epidemiology Versus Arthritis, Centre for Musculoskeletal Research, Division of Musculoskeletal and Dermatological Sciences, The University of Manchester, Manchester, UK
| | - John Bowes
- Centre for Genetics and Genomics Versus Arthritis, Division of Musculoskeletal and Dermatological Sciences, School of Biological Sciences, Faculty of Biology, Medicine and Health, The University of Manchester, Manchester Academic Health Science Centre, Manchester, UK
- NIHR Manchester Biomedical Research Centre, Manchester University Foundation Trust, Manchester, UK
| | | | - Suguru Honda
- Institute of Rheumatology, Tokyo Women's Medical University Hospital, Tokyo, Japan
- Department of Rheumatology, Tokyo Women's Medical University School of Medicine, Tokyo, Japan
| | - Masaru Koido
- Laboratory for Statistical and Translational Genetics, RIKEN Center for Integrative Medical Sciences, Yokohama, Japan
| | - Kohei Tomizuka
- Laboratory for Statistical and Translational Genetics, RIKEN Center for Integrative Medical Sciences, Yokohama, Japan
| | - Yoichiro Kamatani
- Laboratory for Statistical and Translational Genetics, RIKEN Center for Integrative Medical Sciences, Yokohama, Japan
- Laboratory of Complex Trait Genomics, Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, The University of Tokyo, Tokyo, Japan
| | - Hiroaki Tanaka
- The First Department of Internal Medicine, School of Medicine, University of Occupational and Environmental Health Japan, Kitakyushu, Japan
| | - Eiichi Tanaka
- Institute of Rheumatology, Tokyo Women's Medical University Hospital, Tokyo, Japan
- Department of Rheumatology, Tokyo Women's Medical University School of Medicine, Tokyo, Japan
| | - Akari Suzuki
- Laboratory for Autoimmune Diseases, RIKEN Center for Integrative Medical Sciences, Yokohama, Japan
| | - Yuichi Maeda
- Integrated Frontier Research for Medical Science Division, Institute for Open and Transdisciplinary Research Initiatives, Osaka University, Suita, Japan
- Department of Respiratory Medicine and Clinical Immunology, Osaka University Graduate School of Medicine, Suita, Japan
- Department of Immunopathology, Immunology Frontier Research Center (WPI-IFReC), Osaka University, Suita, Japan
| | - Kenichi Yamamoto
- Department of Statistical Genetics, Osaka University Graduate School of Medicine, Suita, Japan
- Laboratory of Statistical Immunology, Immunology Frontier Research Center (WPI-IFReC), Osaka University, Suita, Japan
- Department of Pediatrics, Osaka University Graduate School of Medicine, Suita, Japan
| | - Satoru Miyawaki
- Department of Neurosurgery, Faculty of Medicine, the University of Tokyo, Tokyo, Japan
| | - Gang Xie
- Lunenfeld-Tanenbaum Research Institute, Toronto, Ontario, Canada
| | - Jinyi Zhang
- Lunenfeld-Tanenbaum Research Institute, Toronto, Ontario, Canada
- Department of Medicine, University of Toronto, Toronto, Ontario, Canada
| | | | | | - Gertjan Wolbink
- Department of Rheumatology, Amsterdam Rheumatology and Immunology Center (ARC), Reade, Amsterdam, the Netherlands
| | - Irene van der Horst-Bruinsma
- Department of Rheumatology & Clinical Immunology/ARC, Amsterdam Institute for Infection and Immunity, Amsterdam UMC location Vrije Universiteit, Amsterdam, the Netherlands
| | - Jing Cui
- Division of Rheumatology, Inflammation, and Immunity, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA
| | - Katherine P Liao
- Division of Rheumatology, Inflammation, and Immunity, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA
- Department of Biomedical Informatics, Harvard Medical School, Boston, MA, USA
- Massachusetts Veterans Epidemiology Research and Information Center, VA Boston Healthcare System, Boston, MA, USA
| | - Robert J Carroll
- Department of Biomedical Informatics, Vanderbilt University School of Medicine, Nashville, TN, USA
| | - Hye-Soon Lee
- Department of Rheumatology, Hanyang University Hospital for Rheumatic Diseases, Seoul, Korea
- Hanyang University Institute for Rheumatology Research, Seoul, Korea
| | - So-Young Bang
- Department of Rheumatology, Hanyang University Hospital for Rheumatic Diseases, Seoul, Korea
- Hanyang University Institute for Rheumatology Research, Seoul, Korea
| | - Katherine A Siminovitch
- Lunenfeld-Tanenbaum Research Institute, Toronto, Ontario, Canada
- Departments of Medicine and Immunology, University of Toronto, Toronto, Ontario, Canada
| | - Niek de Vries
- Department of Rheumatology & Clinical Immunology/ARC, Amsterdam Institute for Infection and Immunity, Amsterdam UMC location AMC/University of Amsterdam, Amsterdam, the Netherlands
| | - Lars Alfredsson
- Institute of Environmental Medicine, Karolinska Institutet, Stockholm, Sweden
| | | | - Elizabeth W Karlson
- Division of Rheumatology, Inflammation, and Immunity, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA
| | - Sang-Cheol Bae
- Department of Rheumatology, Hanyang University Hospital for Rheumatic Diseases, Seoul, Korea
- Hanyang University Institute for Rheumatology Research, Seoul, Korea
| | - Robert P Kimberly
- Center for Clinical and Translational Science, Division of Clinical Immunology and Rheumatology, Department of Medicine, University of Alabama at Birmingham, Birmingham, AL, USA
| | - Jeffrey C Edberg
- Center for Clinical and Translational Science, Division of Clinical Immunology and Rheumatology, Department of Medicine, University of Alabama at Birmingham, Birmingham, AL, USA
| | - Xavier Mariette
- Department of Rheumatology, Université Paris-Saclay, Assistance Pubique - Hôpitaux de Paris, Hôpital Bicêtre, INSERM UMR1184, Le Kremlin Bicêtre, France
| | - Tom Huizinga
- Leiden University Medical Center, Leiden, the Netherlands
| | - Philippe Dieudé
- University of Paris Cité, Inserm, PHERE, F-75018, Paris, France
- Department of Rheumatology, Hôpital Bichat, APHP, Paris, France
| | - Matthias Schneider
- Department of Rheumatology & Hiller Research Unit Rheumatology, UKD, Heinrich-Heine University, Düsseldorf, Germany
| | - Martin Kerick
- Institute of Parasitology and Biomedicine Lopez-Neyra, CSIC, Granada, Spain
| | - Joshua C Denny
- Department of Biomedical Informatics, Vanderbilt University School of Medicine, Nashville, TN, USA
- All of Us Research Program, Office of the Director, National Institutes of Health, Bethesda, MD, USA
- Department of Medicine, Vanderbilt University School of Medicine, Nashville, TN, USA
| | - Koichi Matsuda
- Laboratory of Genome Technology, Human Genome Center, Institute of Medical Science, The University of Tokyo, Tokyo, Japan
- Laboratory of Clinical Genome Sequencing, Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, The University of Tokyo, Tokyo, Japan
| | - Keitaro Matsuo
- Division of Cancer Epidemiology and Prevention, Department of Preventive Medicine, Aichi Cancer Center Research Institute, Nagoya, Japan
- Department of Cancer Epidemiology, Nagoya University Graduate School of Medicine, Nagoya, Japan
| | - Tsuneyo Mimori
- Department of Rheumatology and Clinical immunology, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - Fumihiko Matsuda
- Center for Genomic Medicine, Kyoto University Graduate School of Medicine, Kyoto, Japan
| | - Keishi Fujio
- Department of Allergy and Rheumatology, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan
| | - Yoshiya Tanaka
- The First Department of Internal Medicine, School of Medicine, University of Occupational and Environmental Health Japan, Kitakyushu, Japan
| | - Atsushi Kumanogoh
- Integrated Frontier Research for Medical Science Division, Institute for Open and Transdisciplinary Research Initiatives, Osaka University, Suita, Japan
- Centre for Genetics and Genomics Versus Arthritis, Division of Musculoskeletal and Dermatological Sciences, School of Biological Sciences, Faculty of Biology, Medicine and Health, The University of Manchester, Manchester Academic Health Science Centre, Manchester, UK
- Department of Respiratory Medicine and Clinical Immunology, Osaka University Graduate School of Medicine, Suita, Japan
- Department of Immunopathology, Immunology Frontier Research Center (WPI-IFReC), Osaka University, Suita, Japan
| | - Matthew Traylor
- Department of Medical & Molecular Genetics, King's College London, London, UK
- Department of Genetics, Novo Nordisk Research Centre Oxford, Oxford, UK
- Clinical Pharmacology, William Harvey Research Institute, Queen Mary University of London, London, UK
| | - Cathryn M Lewis
- Department of Medical & Molecular Genetics, King's College London, London, UK
- Social, Genetic and Developmental Psychiatry Centre, King's College London, London, UK
| | - Stephen Eyre
- Centre for Genetics and Genomics Versus Arthritis, Division of Musculoskeletal and Dermatological Sciences, School of Biological Sciences, Faculty of Biology, Medicine and Health, The University of Manchester, Manchester Academic Health Science Centre, Manchester, UK
- NIHR Manchester Biomedical Research Centre, Manchester University Foundation Trust, Manchester, UK
| | - Huji Xu
- Department of Rheumatology and Immunology, Shanghai Changzeng Hospital, The Second Military Medical University, Shanghai, China
- School of Clinical Medicine Tsinghua University, Beijing, China
- Peking-Tsinghua Center for Life Sciences, Tsinghua University, Beijing, China
| | - Richa Saxena
- Program in Medical and Population Genetics, Broad Institute of Harvard and MIT, Cambridge, MA, USA
| | - Thurayya Arayssi
- Department of Internal Medicine, Weill Cornell Medicine-Qatar, Education City, Doha, Qatar
| | - Yuta Kochi
- Department of Genomic Function and Diversity, Medical Research Institute, Tokyo Medical and Dental University, Tokyo, Japan
- Laboratory for Autoimmune Diseases, RIKEN Center for Integrative Medical Sciences, Yokohama, Japan
| | - Katsunori Ikari
- Institute of Rheumatology, Tokyo Women's Medical University Hospital, Tokyo, Japan
- Department of Orthopedic Surgery, Tokyo Women's Medical University School of Medicine, Tokyo, Japan
- Division of Multidisciplinary Management of Rheumatic Diseases, Tokyo Women's Medical University, Tokyo, Japan
| | - Masayoshi Harigai
- Institute of Rheumatology, Tokyo Women's Medical University Hospital, Tokyo, Japan
- Division of Rheumatology, Department of Internal Medicine, Tokyo Women's Medical University School of Medicine, Tokyo, Japan
| | - Peter K Gregersen
- Robert S. Boas Center for Genomics and Human Genetics, Feinstein Institutes for Medical Research, Northwell Health, Manhasset, NY, USA
| | - Kazuhiko Yamamoto
- Laboratory for Autoimmune Diseases, RIKEN Center for Integrative Medical Sciences, Yokohama, Japan
| | - S Louis Bridges
- Department of Medicine, Hospital for Special Surgery, New York, NY, USA
- Division of Rheumatology, Weill Cornell Medicine, New York, NY, USA
| | - Leonid Padyukov
- Department of Medicine, Division of Rheumatology, Karolinska Institutet and Karolinska University Hospital, Stockholm, Sweden
| | - Javier Martin
- Institute of Parasitology and Biomedicine Lopez-Neyra, CSIC, Granada, Spain
| | - Lars Klareskog
- Department of Medicine, Division of Rheumatology, Karolinska Institutet and Karolinska University Hospital, Stockholm, Sweden
| | - Yukinori Okada
- Department of Statistical Genetics, Osaka University Graduate School of Medicine, Suita, Japan.
- Integrated Frontier Research for Medical Science Division, Institute for Open and Transdisciplinary Research Initiatives, Osaka University, Suita, Japan.
- Laboratory of Statistical Immunology, Immunology Frontier Research Center (WPI-IFReC), Osaka University, Suita, Japan.
- Laboratory for Systems Genetics, RIKEN Center for Integrative Medical Sciences, Yokohama, Japan.
- Center for Infectious Disease Education and Research (CiDER), Osaka University, Suita, Japan.
- Department of Genome Informatics, Graduate School of Medicine, The University of Tokyo, Tokyo, Japan.
| | - Soumya Raychaudhuri
- Center for Data Sciences, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA.
- Division of Genetics, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA.
- Program in Medical and Population Genetics, Broad Institute of Harvard and MIT, Cambridge, MA, USA.
- Division of Rheumatology, Inflammation, and Immunity, Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, MA, USA.
- Department of Biomedical Informatics, Harvard Medical School, Boston, MA, USA.
- Centre for Genetics and Genomics Versus Arthritis, Division of Musculoskeletal and Dermatological Sciences, School of Biological Sciences, Faculty of Biology, Medicine and Health, The University of Manchester, Manchester Academic Health Science Centre, Manchester, UK.
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11
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Hernández-Vásquez A, Azañedo D. The Association between Altitude and Waist-Height Ratio in Peruvian Adults: A Cross-Sectional Data Analysis of a Population-Based Survey. INTERNATIONAL JOURNAL OF ENVIRONMENTAL RESEARCH AND PUBLIC HEALTH 2022; 19:11494. [PMID: 36141764 PMCID: PMC9517344 DOI: 10.3390/ijerph191811494] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/01/2022] [Revised: 09/05/2022] [Accepted: 09/07/2022] [Indexed: 06/16/2023]
Abstract
To evaluate the association between altitude and cardiometabolic risk calculated with the weight-height ratio (WHtR) in the Peruvian adult population via the cross-sectional data analysis of the Peruvian Demographic and Health Survey 2021. A total of 26,117 adults from 18 to 64 years of age were included in the analysis. The dependent variable was cardiometabolic risk, defined as "Yes" if the WHtR was ≥0.5 and "No" if the WHtR was <0.5. Exposure was altitude of residence categorized as: <1500 meters above sea level (masl); 1500 to 2499 masl; 2500 to 3499 masl; and ≥3500 masl. Crude and adjusted Poisson regression models were used to calculate prevalence ratios (PR) with 95% confidence intervals (CI). The mean WHtR in the population was 0.59 (standard deviation: 0.08), and 87.6% (95% CI: 86.9-88.2) were classified as at risk. After adjusting for sex, age, education level, well-being index, and area of residence, living at altitudes between 2500 and 3499 masl (aPR: 0.98; 95% CI: 0.96-1.00) and ≥3500 masl (aPR: 0.95; 95% CI: 0.93-0.97) were associated with lower cardiometabolic risk in comparison with living at <1500 masl. An inverse association was identified between living at a higher altitude and the proportion of cardiometabolic risk in the Peruvian adult population. However, at least 8 out of 10 people were identified as at risk in all categories of altitude.
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Affiliation(s)
- Akram Hernández-Vásquez
- Centro de Excelencia en Investigaciones Económicas y Sociales en Salud, Vicerrectorado de Investigación, Universidad San Ignacio de Loyola, Lima 15024, Peru
| | - Diego Azañedo
- Facultad de Ciencias de la Salud, Universidad Científica del Sur, Lima 15067, Peru
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12
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The schizophrenia-associated missense variant rs13107325 regulates dendritic spine density. Transl Psychiatry 2022; 12:361. [PMID: 36056013 PMCID: PMC9440106 DOI: 10.1038/s41398-022-02137-z] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/25/2021] [Revised: 08/17/2022] [Accepted: 08/23/2022] [Indexed: 11/26/2022] Open
Abstract
The missense variant rs13107325 (C/T, p.Ala391Thr) in SLC39A8 consistently showed robust association with schizophrenia in recent genome-wide association studies (GWASs), suggesting the potential pathogenicity of this non-synonymous risk variant. Nevertheless, how this missense variant confers schizophrenia risk remains unknown. Here we constructed a knock-in mouse model (by introducing a threonine at the 393th amino acid of mouse SLC39A8 (SLC39A8-p.393T), which corresponds to rs13107325 (p.Ala391Thr) of human SLC39A8) to explore the potential roles and biological effects of this missense variant in schizophrenia pathogenesis. We assessed multiple phenotypes and traits (associated with rs13107325) of the knock-in mice, including body and brain weight, concentrations of metal ions (including cadmium, zinc, manganese, and iron) transported by SLC39A8, blood lipids, proliferation and migration of neural stem cells (NSCs), cortical development, behaviors and cognition, transcriptome, dendritic spine density, and synaptic transmission. Many of the tested phenotypes did not show differences in SLC39A8-p.393T knock-in and wild-type mice. However, we found that zinc concentration in brain and blood of SLC39A8-p.393T knock-in mice was dysregulated compared with wild-types, validating the functionality of rs13107325. Further analysis indicated that cortical dendritic spine density of the SLC39A8-p.393T knock-in mice was significantly decreased compared with wild-types, indicating the important role of SLC39A8-p.393T in dendritic spine morphogenesis. These results indicated that SLC39A8-p.393T knock-in resulted in decreased dendritic spine density, thus mimicking the dendritic spine pathology observed in schizophrenia. Our study indicates that rs13107325 might confer schizophrenia risk by regulating zinc concentration and dendritic spine density, a featured characteristic that was frequently reported to be decreased in schizophrenia.
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13
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Ju D, Hui D, Hammond DA, Wonkam A, Tishkoff SA. Importance of Including Non-European Populations in Large Human Genetic Studies to Enhance Precision Medicine. Annu Rev Biomed Data Sci 2022; 5:321-339. [PMID: 35576557 PMCID: PMC9904154 DOI: 10.1146/annurev-biodatasci-122220-112550] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
One goal of genomic medicine is to uncover an individual's genetic risk for disease, which generally requires data connecting genotype to phenotype, as done in genome-wide association studies (GWAS). While there may be clinical promise to employing prediction tools such as polygenic risk scores (PRS), it currently stands that individuals of non-European ancestry may not reap the benefits of genomic medicine because of underrepresentation in large-scale genetics studies. Here, we discuss why this inequity poses a problem for genomic medicine and the reasons for the low transferability of PRS across populations. We also survey the ancestry representation of published GWAS and investigate how estimates of ancestry diversity in GWASparticipants might be biased. We highlight the importance of expanding genetic research in Africa, one of the most underrepresented regions in human genomics research, and discuss issues of ethics, resources, and technology for equitable advancement of genomic medicine.
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Affiliation(s)
- Dan Ju
- Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA;
| | - Daniel Hui
- Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA;
- Graduate Program in Genomics and Computational Biology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Dorothy A Hammond
- Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA;
- Penn Center for Global Genomics & Health Equity, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Ambroise Wonkam
- Division of Human Genetics, Department of Medicine, Faculty of Health Sciences, University of Cape Town, Cape Town, South Africa
- Department of Genetic Medicine, Johns Hopkins School of Medicine, Baltimore, Maryland, USA;
| | - Sarah A Tishkoff
- Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA;
- Department of Biology, School of Arts and Sciences, University of Pennsylvania, Philadelphia, Pennsylvania, USA
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14
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Halldorsson BV, Eggertsson HP, Moore KHS, Hauswedell H, Eiriksson O, Ulfarsson MO, Palsson G, Hardarson MT, Oddsson A, Jensson BO, Kristmundsdottir S, Sigurpalsdottir BD, Stefansson OA, Beyter D, Holley G, Tragante V, Gylfason A, Olason PI, Zink F, Asgeirsdottir M, Sverrisson ST, Sigurdsson B, Gudjonsson SA, Sigurdsson GT, Halldorsson GH, Sveinbjornsson G, Norland K, Styrkarsdottir U, Magnusdottir DN, Snorradottir S, Kristinsson K, Sobech E, Jonsson H, Geirsson AJ, Olafsson I, Jonsson P, Pedersen OB, Erikstrup C, Brunak S, Ostrowski SR, Thorleifsson G, Jonsson F, Melsted P, Jonsdottir I, Rafnar T, Holm H, Stefansson H, Saemundsdottir J, Gudbjartsson DF, Magnusson OT, Masson G, Thorsteinsdottir U, Helgason A, Jonsson H, Sulem P, Stefansson K. The sequences of 150,119 genomes in the UK Biobank. Nature 2022; 607:732-740. [PMID: 35859178 PMCID: PMC9329122 DOI: 10.1038/s41586-022-04965-x] [Citation(s) in RCA: 150] [Impact Index Per Article: 75.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2021] [Accepted: 06/10/2022] [Indexed: 12/25/2022]
Abstract
Detailed knowledge of how diversity in the sequence of the human genome affects phenotypic diversity depends on a comprehensive and reliable characterization of both sequences and phenotypic variation. Over the past decade, insights into this relationship have been obtained from whole-exome sequencing or whole-genome sequencing of large cohorts with rich phenotypic data1,2. Here we describe the analysis of whole-genome sequencing of 150,119 individuals from the UK Biobank3. This constitutes a set of high-quality variants, including 585,040,410 single-nucleotide polymorphisms, representing 7.0% of all possible human single-nucleotide polymorphisms, and 58,707,036 indels. This large set of variants allows us to characterize selection based on sequence variation within a population through a depletion rank score of windows along the genome. Depletion rank analysis shows that coding exons represent a small fraction of regions in the genome subject to strong sequence conservation. We define three cohorts within the UK Biobank: a large British Irish cohort, a smaller African cohort and a South Asian cohort. A haplotype reference panel is provided that allows reliable imputation of most variants carried by three or more sequenced individuals. We identified 895,055 structural variants and 2,536,688 microsatellites, groups of variants typically excluded from large-scale whole-genome sequencing studies. Using this formidable new resource, we provide several examples of trait associations for rare variants with large effects not found previously through studies based on whole-exome sequencing and/or imputation.
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Affiliation(s)
- Bjarni V Halldorsson
- deCODE genetics/Amgen Inc., Reykjavik, Iceland. .,School of Technology, Reykjavik University, Reykjavik, Iceland.
| | | | | | | | | | - Magnus O Ulfarsson
- deCODE genetics/Amgen Inc., Reykjavik, Iceland.,School of Engineering and Natural Sciences, University of Iceland, Reykjavik, Iceland
| | | | - Marteinn T Hardarson
- deCODE genetics/Amgen Inc., Reykjavik, Iceland.,School of Technology, Reykjavik University, Reykjavik, Iceland
| | | | | | - Snaedis Kristmundsdottir
- deCODE genetics/Amgen Inc., Reykjavik, Iceland.,School of Technology, Reykjavik University, Reykjavik, Iceland
| | - Brynja D Sigurpalsdottir
- deCODE genetics/Amgen Inc., Reykjavik, Iceland.,School of Technology, Reykjavik University, Reykjavik, Iceland
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | - Helgi Jonsson
- Landspitali-University Hospital, Reykjavik, Iceland.,Faculty of Medicine, School of Health Sciences, University of Iceland, Reykjavik, Iceland
| | | | | | - Palmi Jonsson
- Landspitali-University Hospital, Reykjavik, Iceland.,Faculty of Medicine, School of Health Sciences, University of Iceland, Reykjavik, Iceland
| | - Ole Birger Pedersen
- Department of Clinical Immunology, Zealand University Hospital, Køge, Denmark
| | - Christian Erikstrup
- Department of Clinical Medicine, Aarhus University, Aarhus, Denmark.,Department of Clinical Immunology, Aarhus University Hospital, Aarhus, Denmark
| | - Søren Brunak
- Novo Nordisk Foundation Center for Protein Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Sisse Rye Ostrowski
- Department of Clinical Immunology, Copenhagen University Hospital (Rigshospitalet), Copenhagen, Denmark.,Department of Clinical Medicine, Faculty of Health and Clinical Sciences, Copenhagen University, Copenhagen, Denmark
| | | | | | | | - Pall Melsted
- deCODE genetics/Amgen Inc., Reykjavik, Iceland.,School of Engineering and Natural Sciences, University of Iceland, Reykjavik, Iceland
| | - Ingileif Jonsdottir
- deCODE genetics/Amgen Inc., Reykjavik, Iceland.,Faculty of Medicine, School of Health Sciences, University of Iceland, Reykjavik, Iceland
| | | | - Hilma Holm
- deCODE genetics/Amgen Inc., Reykjavik, Iceland
| | | | | | - Daniel F Gudbjartsson
- deCODE genetics/Amgen Inc., Reykjavik, Iceland.,School of Engineering and Natural Sciences, University of Iceland, Reykjavik, Iceland
| | | | | | - Unnur Thorsteinsdottir
- deCODE genetics/Amgen Inc., Reykjavik, Iceland.,Faculty of Medicine, School of Health Sciences, University of Iceland, Reykjavik, Iceland
| | - Agnar Helgason
- deCODE genetics/Amgen Inc., Reykjavik, Iceland.,Department of Anthropology, University of Iceland, Reykjavik, Iceland
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15
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Privé F. Using the UK Biobank as a global reference of worldwide populations: application to measuring ancestry diversity from GWAS summary statistics. Bioinformatics 2022; 38:3477-3480. [PMID: 35604078 PMCID: PMC9237724 DOI: 10.1093/bioinformatics/btac348] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2022] [Revised: 05/11/2022] [Accepted: 05/18/2022] [Indexed: 11/13/2022] Open
Abstract
MOTIVATION Measuring genetic diversity is an important problem because increasing genetic diversity is a key to making new genetic discoveries, while also being a major source of confounding to be aware of in genetics studies. RESULTS Using the UK Biobank data, a prospective cohort study with deep genetic and phenotypic data collected on almost 500 000 individuals from across the UK, we carefully define 21 distinct ancestry groups from all four corners of the world. These ancestry groups can serve as a global reference of worldwide populations, with a handful of applications. Here, we develop a method that uses allele frequencies and principal components derived from these ancestry groups to effectively measure ancestry proportions from allele frequencies of any genetic dataset. AVAILABILITY AND IMPLEMENTATION This method is implemented in function snp_ancestry_summary of R package bigsnpr. SUPPLEMENTARY INFORMATION Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- Florian Privé
- National Centre for Register-based Research, Aarhus University, Aarhus 8210, Denmark
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16
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Nieves-Colón MA, Badillo Rivera KM, Sandoval K, Villanueva Dávalos V, Enriquez Lencinas LE, Mendoza-Revilla J, Adhikari K, González-Buenfil R, Chen JW, Zhang ET, Sockell A, Ortiz-Tello P, Hurtado GM, Condori Salas R, Cebrecos R, Manzaneda Choque JC, Manzaneda Choque FP, Yábar Pilco GP, Rawls E, Eng C, Huntsman S, Burchard E, Ruiz-Linares A, González-José R, Bedoya G, Rothhammer F, Bortolini MC, Poletti G, Gallo C, Bustamante CD, Baker JC, Gignoux CR, Wojcik GL, Moreno-Estrada A. Clotting factor genes are associated with preeclampsia in high-altitude pregnant women in the Peruvian Andes. Am J Hum Genet 2022; 109:1117-1139. [PMID: 35588731 PMCID: PMC9247825 DOI: 10.1016/j.ajhg.2022.04.014] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2021] [Accepted: 04/25/2022] [Indexed: 11/20/2022] Open
Abstract
Preeclampsia is a multi-organ complication of pregnancy characterized by sudden hypertension and proteinuria that is among the leading causes of preterm delivery and maternal morbidity and mortality worldwide. The heterogeneity of preeclampsia poses a challenge for understanding its etiology and molecular basis. Intriguingly, risk for the condition increases in high-altitude regions such as the Peruvian Andes. To investigate the genetic basis of preeclampsia in a population living at high altitude, we characterized genome-wide variation in a cohort of preeclamptic and healthy Andean families (n = 883) from Puno, Peru, a city located above 3,800 meters of altitude. Our study collected genomic DNA and medical records from case-control trios and duos in local hospital settings. We generated genotype data for 439,314 SNPs, determined global ancestry patterns, and mapped associations between genetic variants and preeclampsia phenotypes. A transmission disequilibrium test (TDT) revealed variants near genes of biological importance for placental and blood vessel function. The top candidate region was found on chromosome 13 of the fetal genome and contains clotting factor genes PROZ, F7, and F10. These findings provide supporting evidence that common genetic variants within coagulation genes play an important role in preeclampsia. A selection scan revealed a potential adaptive signal around the ADAM12 locus on chromosome 10, implicated in pregnancy disorders. Our discovery of an association in a functional pathway relevant to pregnancy physiology in an understudied population of Native American origin demonstrates the increased power of family-based study design and underscores the importance of conducting genetic research in diverse populations.
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Affiliation(s)
- Maria A Nieves-Colón
- Laboratorio Nacional de Genómica para la Biodiversidad (UGA-LANGEBIO), CINVESTAV, Irapuato, Guanajuato 36821, México; School of Human Evolution and Social Change, Arizona State University, Tempe, AZ 85281, USA; Department of Anthropology, University of Minnesota Twin Cities, Minneapolis, MN 55455, USA.
| | | | - Karla Sandoval
- Laboratorio Nacional de Genómica para la Biodiversidad (UGA-LANGEBIO), CINVESTAV, Irapuato, Guanajuato 36821, México
| | | | | | - Javier Mendoza-Revilla
- Laboratorios de Investigación y Desarrollo, Facultad de Ciencias y Filosofía, Universidad Peruana Cayetano Heredia, Lima 15102, Peru; Human Evolutionary Genetics Unit, Institut Pasteur, UMR 2000, CNRS, Paris 75015, France
| | - Kaustubh Adhikari
- School of Mathematics and Statistics, Faculty of Science, Technology, Engineering and Mathematics, The Open University, Milton Keynes MK7 6AA, UK; Department of Genetics, Evolution and Environment, and UCL Genetics Institute, University College London, WC1E 6BT London, UK
| | - Ram González-Buenfil
- Laboratorio Nacional de Genómica para la Biodiversidad (UGA-LANGEBIO), CINVESTAV, Irapuato, Guanajuato 36821, México
| | - Jessica W Chen
- Department of Genetics, Stanford School of Medicine, Stanford, CA 94305, USA
| | - Elisa T Zhang
- Department of Genetics, Stanford School of Medicine, Stanford, CA 94305, USA
| | - Alexandra Sockell
- Department of Genetics, Stanford School of Medicine, Stanford, CA 94305, USA
| | | | - Gloria Malena Hurtado
- Laboratorios de Investigación y Desarrollo, Facultad de Ciencias y Filosofía, Universidad Peruana Cayetano Heredia, Lima 15102, Peru
| | - Ramiro Condori Salas
- Laboratorios de Investigación y Desarrollo, Facultad de Ciencias y Filosofía, Universidad Peruana Cayetano Heredia, Lima 15102, Peru
| | - Ricardo Cebrecos
- Laboratorios de Investigación y Desarrollo, Facultad de Ciencias y Filosofía, Universidad Peruana Cayetano Heredia, Lima 15102, Peru
| | | | | | | | - Erin Rawls
- School of Human Evolution and Social Change, Arizona State University, Tempe, AZ 85281, USA
| | - Celeste Eng
- Department of Bioengineering and Therapeutic Sciences, University of California San Francisco, San Francisco, CA 94143, USA
| | - Scott Huntsman
- Department of Bioengineering and Therapeutic Sciences, University of California San Francisco, San Francisco, CA 94143, USA
| | - Esteban Burchard
- Department of Bioengineering and Therapeutic Sciences, University of California San Francisco, San Francisco, CA 94143, USA
| | - Andrés Ruiz-Linares
- Department of Genetics, Evolution and Environment, and UCL Genetics Institute, University College London, WC1E 6BT London, UK; Aix-Marseille Université, CNRS, EFS, ADES, 13005 Marseille, France; Ministry of Education Key Laboratory of Contemporary Anthropology and Collaborative Innovation Center of Genetics and Development, School of Life Sciences and Human Phenome Institute, Fudan University, Yangpu District, Shanghai, China
| | - Rolando González-José
- Instituto Patagónico de Ciencias Sociales y Humanas, Centro Nacional Patagónico-CONICET y Programa Nacional de Referencia y Biobanco Genómico de la Población Argentina (PoblAr), Ministerio de Ciencia, Tecnología e Innovación, Puerto Madryn, Chubut, Argentina
| | - Gabriel Bedoya
- Genética Molecular (GENMOL), Universidad de Antioquía, Medellin, Colombia
| | - Francisco Rothhammer
- Instituto de Alta Investigación Universidad de Tarapacá, Tarapacá, Chile; Programa de Genética Humana, ICBM Facultad de Medicina, Universidad de Chile, Santiago, Chile
| | - Maria Cátira Bortolini
- Departamento de Genética, Instituto de Biociências, Universidade Federal do Rio Grande do Sul, Caixa Postal 15053, 91501-970 Porto Alegre, Rio Grande do Sul, Brazil
| | - Giovanni Poletti
- Laboratorios de Investigación y Desarrollo, Facultad de Ciencias y Filosofía, Universidad Peruana Cayetano Heredia, Lima 15102, Peru
| | - Carla Gallo
- Laboratorios de Investigación y Desarrollo, Facultad de Ciencias y Filosofía, Universidad Peruana Cayetano Heredia, Lima 15102, Peru
| | - Carlos D Bustamante
- Department of Genetics, Stanford School of Medicine, Stanford, CA 94305, USA; Department of Biomedical Data Science, Stanford School of Medicine, Stanford, CA 94305, USA
| | - Julie C Baker
- Department of Genetics, Stanford School of Medicine, Stanford, CA 94305, USA
| | | | - Genevieve L Wojcik
- Department of Epidemiology, Bloomberg School of Public Health, John Hopkins University, Baltimore, MD 21205, USA
| | - Andrés Moreno-Estrada
- Laboratorio Nacional de Genómica para la Biodiversidad (UGA-LANGEBIO), CINVESTAV, Irapuato, Guanajuato 36821, México.
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17
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Fernández-Rhodes L, Graff M, Buchanan VL, Justice AE, Highland HM, Guo X, Zhu W, Chen HH, Young KL, Adhikari K, Palmer ND, Below JE, Bradfield J, Pereira AC, Glover L, Kim D, Lilly AG, Shrestha P, Thomas AG, Zhang X, Chen M, Chiang CW, Pulit S, Horimoto A, Krieger JE, Guindo-Martínez M, Preuss M, Schumann C, Smit RA, Torres-Mejía G, Acuña-Alonzo V, Bedoya G, Bortolini MC, Canizales-Quinteros S, Gallo C, González-José R, Poletti G, Rothhammer F, Hakonarson H, Igo R, Adler SG, Iyengar SK, Nicholas SB, Gogarten SM, Isasi CR, Papnicolaou G, Stilp AM, Qi Q, Kho M, Smith JA, Langefeld CD, Wagenknecht L, Mckean-Cowdin R, Gao XR, Nousome D, Conti DV, Feng Y, Allison MA, Arzumanyan Z, Buchanan TA, Ida Chen YD, Genter PM, Goodarzi MO, Hai Y, Hsueh W, Ipp E, Kandeel FR, Lam K, Li X, Nadler JL, Raffel LJ, Roll K, Sandow K, Tan J, Taylor KD, Xiang AH, Yao J, Audirac-Chalifour A, de Jesus Peralta Romero J, Hartwig F, Horta B, Blangero J, Curran JE, Duggirala R, Lehman DE, Puppala S, Fejerman L, John EM, Aguilar-Salinas C, Burtt NP, Florez JC, García-Ortíz H, González-Villalpando C, Mercader J, Orozco L, Tusié-Luna T, Blanco E, Gahagan S, Cox NJ, Hanis C, Butte NF, Cole SA, Comuzzie AG, Voruganti VS, Rohde R, Wang Y, Sofer T, Ziv E, Grant SF, Ruiz-Linares A, Rotter JI, Haiman CA, Parra EJ, Cruz M, Loos RJ, North KE. Ancestral diversity improves discovery and fine-mapping of genetic loci for anthropometric traits-The Hispanic/Latino Anthropometry Consortium. HGG ADVANCES 2022; 3:100099. [PMID: 35399580 PMCID: PMC8990175 DOI: 10.1016/j.xhgg.2022.100099] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2021] [Accepted: 03/06/2022] [Indexed: 02/05/2023] Open
Abstract
Hispanic/Latinos have been underrepresented in genome-wide association studies (GWAS) for anthropometric traits despite their notable anthropometric variability, ancestry proportions, and high burden of growth stunting and overweight/obesity. To address this knowledge gap, we analyzed densely imputed genetic data in a sample of Hispanic/Latino adults to identify and fine-map genetic variants associated with body mass index (BMI), height, and BMI-adjusted waist-to-hip ratio (WHRadjBMI). We conducted a GWAS of 18 studies/consortia as part of the Hispanic/Latino Anthropometry (HISLA) Consortium (stage 1, n = 59,771) and generalized our findings in 9 additional studies (stage 2, n = 10,538). We conducted a trans-ancestral GWAS with summary statistics from HISLA stage 1 and existing consortia of European and African ancestries. In our HISLA stage 1 + 2 analyses, we discovered one BMI locus, as well as two BMI signals and another height signal each within established anthropometric loci. In our trans-ancestral meta-analysis, we discovered three BMI loci, one height locus, and one WHRadjBMI locus. We also identified 3 secondary signals for BMI, 28 for height, and 2 for WHRadjBMI in established loci. We show that 336 known BMI, 1,177 known height, and 143 known WHRadjBMI (combined) SNPs demonstrated suggestive transferability (nominal significance and effect estimate directional consistency) in Hispanic/Latino adults. Of these, 36 BMI, 124 height, and 11 WHRadjBMI SNPs were significant after trait-specific Bonferroni correction. Trans-ancestral meta-analysis of the three ancestries showed a small-to-moderate impact of uncorrected population stratification on the resulting effect size estimates. Our findings demonstrate that future studies may also benefit from leveraging diverse ancestries and differences in linkage disequilibrium patterns to discover novel loci and additional signals with less residual population stratification.
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Affiliation(s)
- Lindsay Fernández-Rhodes
- Department of Biobehavioral Health, Pennsylvania State University, 219 Biobehavioral Health Building, University Park, PA 16802, USA
- Department of Epidemiology, Gillings School of Global Public Health, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Mariaelisa Graff
- Department of Epidemiology, Gillings School of Global Public Health, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Victoria L. Buchanan
- Department of Epidemiology, Gillings School of Global Public Health, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Anne E. Justice
- Department of Epidemiology, Gillings School of Global Public Health, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
- Department of Biomedical and Translational Informatics, Geisinger Health System, Danville, PA 17822, USA
| | - Heather M. Highland
- Department of Epidemiology, Gillings School of Global Public Health, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Xiuqing Guo
- The Institute for Translational Genomics and Population Sciences, Department of Pediatrics, The Lundquist Institute for Biomedical Innovation at Harbor-UCLA Medical Center, Torrance, CA 90502 USA
| | - Wanying Zhu
- Vanderbilt Genetics Institute, Division of Genetic Medicine, Department of Medicine, Vanderbilt University Medical Center, Nashville, TN 37232, USA
| | - Hung-Hsin Chen
- Vanderbilt Genetics Institute, Division of Genetic Medicine, Department of Medicine, Vanderbilt University Medical Center, Nashville, TN 37232, USA
| | - Kristin L. Young
- Department of Epidemiology, Gillings School of Global Public Health, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Kaustubh Adhikari
- School of Mathematics and Statistics, Faculty of Science, Technology, Engineering and Mathematics, The Open University, MK7 6AA Milton Keynes, UK
| | - Nicholette D. Palmer
- Department of Biochemistry, Wake Forest School of Medicine, Winston-Salem, NC 27101, USA
| | - Jennifer E. Below
- Vanderbilt Genetics Institute, Division of Genetic Medicine, Department of Medicine, Vanderbilt University Medical Center, Nashville, TN 37232, USA
| | - Jonathan Bradfield
- Center for Applied Genomics, Division of Human Genetics, Department of Pediatrics, The Children’s Hospital of Philadelphia, Philadelphia, PA 19104, USA
| | - Alexandre C. Pereira
- Laboratory of Genetics and Molecular Cardiology, Heart Institute, University of São Paulo, São Paulo 05508-220, Brazil
| | - LáShauntá Glover
- Department of Epidemiology, Gillings School of Global Public Health, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Daeeun Kim
- Department of Epidemiology, Gillings School of Global Public Health, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Adam G. Lilly
- Department of Sociology, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
- Carolina Population Center, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Poojan Shrestha
- Department of Epidemiology, Gillings School of Global Public Health, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
- Division of Pediatric and Public Health, Adams School of Dentistry, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Alvin G. Thomas
- Department of Epidemiology, Gillings School of Global Public Health, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Xinruo Zhang
- Department of Epidemiology, Gillings School of Global Public Health, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Minhui Chen
- Center for Genetic Epidemiology, Department of Preventive Medicine, Keck School of Medicine, University of Southern California, Los Angeles, CA 90033, USA
| | - Charleston W.K. Chiang
- Center for Genetic Epidemiology, Department of Preventive Medicine, Keck School of Medicine, University of Southern California, Los Angeles, CA 90033, USA
- Department of Quantitative and Computational Biology, University of Southern California, Los Angeles, CA 90007, USA
| | - Sara Pulit
- Vertex Pharmaceuticals, W2 6BD Oxford, UK
| | - Andrea Horimoto
- Laboratory of Genetics and Molecular Cardiology, Heart Institute, University of São Paulo, São Paulo 05508-220, Brazil
| | - Jose E. Krieger
- Laboratory of Genetics and Molecular Cardiology, Heart Institute, University of São Paulo, São Paulo 05508-220, Brazil
| | - Marta Guindo-Martínez
- The Charles Bronfman Institutes for Personalized Medicine, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
- The Novo Nordisk Center for Basic Metabolic Research, University of Copenhagen, 2200 Copenhagen, Denmark
| | - Michael Preuss
- The Charles Bronfman Institutes for Personalized Medicine, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Claudia Schumann
- Hasso Plattner Institute, University of Potsdam, Digital Health Center, 14482 Potsdam, Germany
| | - Roelof A.J. Smit
- The Charles Bronfman Institutes for Personalized Medicine, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
| | - Gabriela Torres-Mejía
- Department of Research in Cardiovascular Diseases, Diabetes Mellitus, and Cancer, Population Health Research Center, National Institute of Public Health, Cuernavaca, Morelos 62100, Mexico
| | | | - Gabriel Bedoya
- Molecular Genetics Investigation Group, University of Antioquia, Medellín 1226, Colombia
| | - Maria-Cátira Bortolini
- Department of Genetics, Federal University of Rio Grande do Sul, Porto Alegre 90040-060, Brazil
| | - Samuel Canizales-Quinteros
- Population Genomics Applied to Health Unit, The National Institute of Genomic Medicine and the Faculty of Chemistry at the National Autonomous University of Mexico, Mexico City 04510, Mexico
| | - Carla Gallo
- Laboratorios de Investigación y Desarrollo, Facultad de Ciencias y Filosofía, Universidad Peruana Cayetano Heredia, Lima 15102, Peru
| | - Rolando González-José
- Patagonian Institute of the Social and Human Sciences, Patagonian National Center, Puerto Madryn U9120, Argentina
| | - Giovanni Poletti
- Laboratorios de Investigación y Desarrollo, Facultad de Ciencias y Filosofía, Universidad Peruana Cayetano Heredia, Lima 15102, Peru
| | | | - Hakon Hakonarson
- Center for Applied Genomics, Division of Human Genetics, Department of Pediatrics, The Children’s Hospital of Philadelphia, Philadelphia, PA 19104, USA
| | - Robert Igo
- Department of Population and Quantitative Health Sciences, Case Western Reserve University, Cleveland, OH 44106, USA
| | - Sharon G. Adler
- Division of Nephrology and Hypertension, Harbor-University of California Los Angeles Medical Center, Torrance, CA 90502, USA
| | - Sudha K. Iyengar
- Department of Population and Quantitative Health Sciences, Case Western Reserve University, Cleveland, OH 44106, USA
| | - Susanne B. Nicholas
- Department of Medicine, David Geffen School of Medicine at University of California, Los Angeles, CA 90095, USA
| | | | - Carmen R. Isasi
- Department of Epidemiology and Population Health, Albert Einstein College of Medicine, Bronx, NY 10461, USA
| | | | - Adrienne M. Stilp
- Department of Biostatistics, University of Washington, Seattle, WA 98195, USA
| | - Qibin Qi
- Department of Epidemiology and Population Health, Albert Einstein College of Medicine, Bronx, NY 10461, USA
| | - Minjung Kho
- Department of Epidemiology, School of Public Health, University of Michigan, Ann Arbor, MI 48109, USA
| | - Jennifer A. Smith
- Department of Epidemiology, School of Public Health, University of Michigan, Ann Arbor, MI 48109, USA
| | - Carl D. Langefeld
- Department of Biostatistics and Data Science, Wake Forest School of Medicine, Winston-Salem, NC 27101, USA
| | - Lynne Wagenknecht
- Division of Public Health Sciences, Wake Forest School of Medicine, Winston-Salem, NC 27101, USA
| | - Roberta Mckean-Cowdin
- Department of Preventive Medicine, Keck School of Medicine, University of Southern California, Los Angeles, CA 90032, USA
| | - Xiaoyi Raymond Gao
- Department of Ophthalmology and Visual Sciences, Department of Biomedical Informatics, Division of Human Genetics, The Ohio State University, Columbus, OH 43210, USA
| | - Darryl Nousome
- Department of Preventive Medicine, Keck School of Medicine, University of Southern California, Los Angeles, CA 90032, USA
| | - David V. Conti
- Center for Genetic Epidemiology, Department of Preventive Medicine, Keck School of Medicine, University of Southern California, Los Angeles, CA 90033, USA
| | - Ye Feng
- Department of Preventive Medicine, Keck School of Medicine, University of Southern California, Los Angeles, CA 90032, USA
| | - Matthew A. Allison
- Department of Family Medicine, University of California, San Diego, CA 92161, USA
| | - Zorayr Arzumanyan
- The Institute for Translational Genomics and Population Sciences, Department of Pediatrics, The Lundquist Institute for Biomedical Innovation at Harbor-UCLA Medical Center, Torrance, CA 90502 USA
| | - Thomas A. Buchanan
- Department of Medicine, Keck School of Medicine, University of Southern California, Los Angeles, CA 90033, USA
| | - Yii-Der Ida Chen
- The Institute for Translational Genomics and Population Sciences, Department of Pediatrics, The Lundquist Institute for Biomedical Innovation at Harbor-UCLA Medical Center, Torrance, CA 90502 USA
| | - Pauline M. Genter
- Department of Medicine, Division of Endocrinology, The Lundquist Institute for Biomedical Innovation at Harbor-UCLA Medical Center, Torrance, CA 90502, USA
| | - Mark O. Goodarzi
- Division of Endocrinology, Diabetes, and Metabolism, Department of Medicine, Cedars-Sinai Medical Center, Los Angeles, CA 90048, USA
| | - Yang Hai
- The Institute for Translational Genomics and Population Sciences, Department of Pediatrics, The Lundquist Institute for Biomedical Innovation at Harbor-UCLA Medical Center, Torrance, CA 90502 USA
| | - Willa Hsueh
- Department of Internal Medicine, The Ohio State University Wexner Medical Center, Columbus, OH 43210, USA
| | - Eli Ipp
- Department of Medicine, David Geffen School of Medicine at University of California, Los Angeles, CA 90095, USA
- Department of Medicine, Division of Endocrinology, The Lundquist Institute for Biomedical Innovation at Harbor-UCLA Medical Center, Torrance, CA 90502, USA
| | - Fouad R. Kandeel
- Department of Translational Research & Cellular Therapeutics, Beckman Research Institute of City of Hope, Duarte, CA 91010, USA
| | - Kelvin Lam
- The Institute for Translational Genomics and Population Sciences, Department of Pediatrics, The Lundquist Institute for Biomedical Innovation at Harbor-UCLA Medical Center, Torrance, CA 90502 USA
| | - Xiaohui Li
- The Institute for Translational Genomics and Population Sciences, Department of Pediatrics, The Lundquist Institute for Biomedical Innovation at Harbor-UCLA Medical Center, Torrance, CA 90502 USA
| | - Jerry L. Nadler
- Department of Pharmacology at New York Medical College School of Medicine, Valhalla, NY 10595, USA
| | - Leslie J. Raffel
- Division of Genetic and Genomic Medicine, Department of Pediatrics, University of California, Irvine, CA 92697, USA
| | - Kathryn Roll
- The Institute for Translational Genomics and Population Sciences, Department of Pediatrics, The Lundquist Institute for Biomedical Innovation at Harbor-UCLA Medical Center, Torrance, CA 90502 USA
| | - Kevin Sandow
- The Institute for Translational Genomics and Population Sciences, Department of Pediatrics, The Lundquist Institute for Biomedical Innovation at Harbor-UCLA Medical Center, Torrance, CA 90502 USA
| | - Jingyi Tan
- The Institute for Translational Genomics and Population Sciences, Department of Pediatrics, The Lundquist Institute for Biomedical Innovation at Harbor-UCLA Medical Center, Torrance, CA 90502 USA
| | - Kent D. Taylor
- The Institute for Translational Genomics and Population Sciences, Department of Pediatrics, The Lundquist Institute for Biomedical Innovation at Harbor-UCLA Medical Center, Torrance, CA 90502 USA
| | - Anny H. Xiang
- Research and Evaluation Branch, Kaiser Permanente of Southern California, Pasadena, CA 91101, USA
| | - Jie Yao
- The Institute for Translational Genomics and Population Sciences, Department of Pediatrics, The Lundquist Institute for Biomedical Innovation at Harbor-UCLA Medical Center, Torrance, CA 90502 USA
| | - Astride Audirac-Chalifour
- Medical Research Unit in Biochemistry, Specialty Hospital, National Medical Center of the Twenty-First Century, Mexican Institute of Social Security, Mexico City 06725, Mexico
| | - Jose de Jesus Peralta Romero
- Medical Research Unit in Biochemistry, Specialty Hospital, National Medical Center of the Twenty-First Century, Mexican Institute of Social Security, Mexico City 06725, Mexico
| | - Fernando Hartwig
- Postgraduate Program in Epidemiology, Federal University of Pelotas, Pelotas 96010-610, Brazil
| | - Bernando Horta
- Postgraduate Program in Epidemiology, Federal University of Pelotas, Pelotas 96010-610, Brazil
| | - John Blangero
- Department of Human Genetics and South Texas Diabetes and Obesity Institute, School of Medicine, University of Texas Rio Grande Valley, Brownsville and Edinburg, TX 78520 and 78539, USA
| | - Joanne E. Curran
- Department of Human Genetics and South Texas Diabetes and Obesity Institute, School of Medicine, University of Texas Rio Grande Valley, Brownsville and Edinburg, TX 78520 and 78539, USA
| | - Ravindranath Duggirala
- Department of Human Genetics and South Texas Diabetes and Obesity Institute, School of Medicine, University of Texas Rio Grande Valley, Brownsville and Edinburg, TX 78520 and 78539, USA
| | - Donna E. Lehman
- Department of Medicine, School of Medicine, University of Texas Health San Antonio, San Antonio, TX 78229, USA
| | - Sobha Puppala
- Department of Internal Medicine, Section of Molecular Medicine, Wake Forest School of Medicine, Winston-Salem, NC 27109, USA
| | - Laura Fejerman
- Department of Public Health Sciences, School of Medicine, and the Comprehensive Cancer Center, University of California Davis, Davis, CA 95616, USA
| | - Esther M. John
- Departments of Epidemiology & Population Health and Medicine-Oncology, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Carlos Aguilar-Salinas
- Division of Nutrition, Salvador Zubirán National Institute of Health Sciences and Nutrition, Mexico City 14080, Mexico
| | - Noël P. Burtt
- Programs in Metabolism and Medical and Population Genetics, Broad Institute of the Massachusetts Institute of Technology and Harvard, Cambridge, MA 02142, USA
| | - Jose C. Florez
- Programs in Metabolism and Medical and Population Genetics, Broad Institute of the Massachusetts Institute of Technology and Harvard, Cambridge, MA 02142, USA
- Department of Medicine, Harvard Medical School, Boston, MA 02115, USA
- Diabetes Unit and Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA 02114, USA
| | - Humberto García-Ortíz
- Laboratory of Immunogenomics and Metabolic Diseases, National Institute of Genomic Medicine, Mexico City 14610, Mexico
| | - Clicerio González-Villalpando
- Center for Diabetes Studies, Research Unit for Diabetes and Cardiovascular Risk, Center for Population Health Studies, National Institute of Public Health, Mexico City 14080, Mexico
| | - Josep Mercader
- Programs in Metabolism and Medical and Population Genetics, Broad Institute of the Massachusetts Institute of Technology and Harvard, Cambridge, MA 02142, USA
- Department of Medicine, Harvard Medical School, Boston, MA 02115, USA
- Diabetes Unit and Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA 02114, USA
| | - Lorena Orozco
- Laboratory of Immunogenomics and Metabolic Diseases, National Institute of Genomic Medicine, Mexico City 14610, Mexico
| | - Teresa Tusié-Luna
- Molecular Biology and Medical Genomics Unity, Institute of Biomedical Research, The National Autonomous University of Mexico and the Salvador Zubirán National Institute of Health Sciences and Nutrition, Mexico City 14080, Mexico
| | - Estela Blanco
- Center for Community Health, Division of Academic General Pediatrics, University of California at San Diego, San Diego, CA 92093, USA
| | - Sheila Gahagan
- Center for Community Health, Division of Academic General Pediatrics, University of California at San Diego, San Diego, CA 92093, USA
| | - Nancy J. Cox
- Vanderbilt Genetics Institute, Division of Genetic Medicine, Department of Medicine, Vanderbilt University Medical Center, Nashville, TN 37232, USA
| | - Craig Hanis
- University of Texas Health Science Center at Houston, Houston, TX 77030, USA
| | - Nancy F. Butte
- United States Department of Agriculture, Agricultural Research Service, The Children’s Nutrition Research Center, and the Department Pediatrics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Shelley A. Cole
- Population Health Program, Texas Biomedical Research Institute, San Antonio, TX 78227, USA
| | | | - V. Saroja Voruganti
- Department of Nutrition and Nutrition Research Institute, University of North Carolina at Chapel Hill, Kannapolis, NC 28081, USA
| | - Rebecca Rohde
- Department of Epidemiology, Gillings School of Global Public Health, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Yujie Wang
- Department of Epidemiology, Gillings School of Global Public Health, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Tamar Sofer
- Diabetes Unit and Center for Genomic Medicine, Massachusetts General Hospital, Boston, MA 02114, USA
- Division of Sleep and Circadian Disorders, Brigham and Women’s Hospital, Boston, MA 02115, USA
| | - Elad Ziv
- Division of General Internal Medicine, Department of Medicine, Helen Diller Family Comprehensive Cancer Center, Institute for Human Genetics, University of California, San Francisco, San Francisco, CA 94115, USA
| | - Struan F.A. Grant
- Center for Applied Genomics, Division of Human Genetics, Department of Pediatrics, The Children’s Hospital of Philadelphia, Philadelphia, PA 19104, USA
| | - Andres Ruiz-Linares
- Ministry of Education Key Laboratory of Contemporary Anthropology and Collaborative Innovation Center of Genetics and Development, School of Life Sciences and Human Phenome Institute, Fudan University, Shanghai 200438, China
- Department of Genetics, Evolution and Environment, and Genetics Institute of the University College London, London WC1E 6BT, UK
- Laboratory of Biocultural Anthropology, Law, Ethics, and Health, Aix-Marseille University, Marseille 13385, France
| | - Jerome I. Rotter
- The Institute for Translational Genomics and Population Sciences, Department of Pediatrics, The Lundquist Institute for Biomedical Innovation at Harbor-UCLA Medical Center, Torrance, CA 90502 USA
| | - Christopher A. Haiman
- Center for Genetic Epidemiology, Department of Preventive Medicine, Keck School of Medicine, University of Southern California, Los Angeles, CA 90033, USA
| | - Esteban J. Parra
- Department of Anthropology, University of Toronto- Mississauga, Mississauga, ON L5L 1C6, Canada
| | - Miguel Cruz
- Medical Research Unit in Biochemistry, Specialty Hospital, National Medical Center of the Twenty-First Century, Mexican Institute of Social Security, Mexico City 06725, Mexico
| | - Ruth J.F. Loos
- The Charles Bronfman Institutes for Personalized Medicine, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA
- Novo Nordisk Foundation Center for Basic Metabolic Research, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Kari E. North
- Department of Epidemiology, Gillings School of Global Public Health, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
- Carolina Center for Genome Sciences, University of North Carolina at Chapel Hill, Chapel Hill, NC 27514, USA
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18
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Balagué-Dobón L, Cáceres A, González JR. Fully exploiting SNP arrays: a systematic review on the tools to extract underlying genomic structure. Brief Bioinform 2022; 23:6535682. [PMID: 35211719 PMCID: PMC8921734 DOI: 10.1093/bib/bbac043] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2021] [Revised: 01/25/2022] [Accepted: 01/28/2022] [Indexed: 12/12/2022] Open
Abstract
Single nucleotide polymorphisms (SNPs) are the most abundant type of genomic variation and the most accessible to genotype in large cohorts. However, they individually explain a small proportion of phenotypic differences between individuals. Ancestry, collective SNP effects, structural variants, somatic mutations or even differences in historic recombination can potentially explain a high percentage of genomic divergence. These genetic differences can be infrequent or laborious to characterize; however, many of them leave distinctive marks on the SNPs across the genome allowing their study in large population samples. Consequently, several methods have been developed over the last decade to detect and analyze different genomic structures using SNP arrays, to complement genome-wide association studies and determine the contribution of these structures to explain the phenotypic differences between individuals. We present an up-to-date collection of available bioinformatics tools that can be used to extract relevant genomic information from SNP array data including population structure and ancestry; polygenic risk scores; identity-by-descent fragments; linkage disequilibrium; heritability and structural variants such as inversions, copy number variants, genetic mosaicisms and recombination histories. From a systematic review of recently published applications of the methods, we describe the main characteristics of R packages, command-line tools and desktop applications, both free and commercial, to help make the most of a large amount of publicly available SNP data.
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19
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Sohail M, Izarraras-Gomez A, Ortega-Del Vecchyo D. Populations, Traits, and Their Spatial Structure in Humans. Genome Biol Evol 2021; 13:evab272. [PMID: 34894236 PMCID: PMC8715524 DOI: 10.1093/gbe/evab272] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 12/06/2021] [Indexed: 11/16/2022] Open
Abstract
The spatial distribution of genetic variants is jointly determined by geography, past demographic processes, natural selection, and its interplay with environmental variation. A fraction of these genetic variants are "causal alleles" that affect the manifestation of a complex trait. The effect exerted by these causal alleles on complex traits can be independent or dependent on the environment. Understanding the evolutionary processes that shape the spatial structure of causal alleles is key to comprehend the spatial distribution of complex traits. Natural selection, past population size changes, range expansions, consanguinity, assortative mating, archaic introgression, admixture, and the environment can alter the frequencies, effect sizes, and heterozygosities of causal alleles. This provides a genetic axis along which complex traits can vary. However, complex traits also vary along biogeographical and sociocultural axes which are often correlated with genetic axes in complex ways. The purpose of this review is to consider these genetic and environmental axes in concert and examine the ways they can help us decipher the variation in complex traits that is visible in humans today. This initiative necessarily implies a discussion of populations, traits, the ability to infer and interpret "genetic" components of complex traits, and how these have been impacted by adaptive events. In this review, we provide a history-aware discussion on these topics using both the recent and more distant past of our academic discipline and its relevant contexts.
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Affiliation(s)
- Mashaal Sohail
- Department of Human Genetics, University of Chicago, USA
- Centro de Ciencias Genómicas (CCG), Universidad Nacional Autónoma de México (UNAM), Cuernavaca, Morelos, México
| | - Alan Izarraras-Gomez
- Laboratorio Internacional de Investigación sobre el Genoma Humano (LIIGH), Universidad Nacional Autónoma de México (UNAM), Juriquilla, Querétaro, México
| | - Diego Ortega-Del Vecchyo
- Laboratorio Internacional de Investigación sobre el Genoma Humano (LIIGH), Universidad Nacional Autónoma de México (UNAM), Juriquilla, Querétaro, México
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20
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Chiang CWK. The Opportunities and Challenges of Integrating Population Histories Into Genetic Studies for Diverse Populations: A Motivating Example From Native Hawaiians. Front Genet 2021; 12:643883. [PMID: 34646295 PMCID: PMC8503554 DOI: 10.3389/fgene.2021.643883] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2020] [Accepted: 08/19/2021] [Indexed: 11/25/2022] Open
Abstract
There is a well-recognized need to include diverse populations in genetic studies, but several obstacles continue to be prohibitive, including (but are not limited to) the difficulty of recruiting individuals from diverse populations in large numbers and the lack of representation in available genomic references. These obstacles notwithstanding, studying multiple diverse populations would provide informative, population-specific insights. Using Native Hawaiians as an example of an understudied population with a unique evolutionary history, I will argue that by developing key genomic resources and integrating evolutionary thinking into genetic epidemiology, we will have the opportunity to efficiently advance our knowledge of the genetic risk factors, ameliorate health disparity, and improve healthcare in this underserved population.
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Affiliation(s)
- Charleston W K Chiang
- Department of Population and Public Health Sciences, Center for Genetic Epidemiology, Keck School of Medicine, University of Southern California, Los Angeles, CA, United States.,Department of Quantitative and Computational Biology, University of Southern California, Los Angeles, CA, United States
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21
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Provenzano A, Farina A, Seidenari A, Azzaroli F, Serra C, Della Gatta A, Zuffardi O, Giglio SR. Prenatal Noninvasive Trio-WES in a Case of Pregnancy-Related Liver Disorder. Diagnostics (Basel) 2021; 11:diagnostics11101904. [PMID: 34679599 PMCID: PMC8534548 DOI: 10.3390/diagnostics11101904] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2021] [Revised: 10/11/2021] [Accepted: 10/13/2021] [Indexed: 01/16/2023] Open
Abstract
Liver disease in pregnancy may present as an acute condition related to the gestational period, characterized by pruritus, jaundice, and abnormal liver function. The disease may be misdiagnosed with other liver diseases, some of which may have consequences for fetal health. It is therefore advisable to implement rapid diagnostic strategies to provide information for the management of pregnancy in these conditions. We report the case of a healthy woman with a twin pregnancy from homologous in vitro fertilization (IVF), who in the third trimester presented jaundice and malaise. Biochemical investigations and liver hyperechogenicity raised the suspicion of acute fatty liver disease of pregnancy (AFLP). Non-invasive prenatal whole-exome sequencing (WES) in the trio identified the Phe305Ile heterozygous variant in the ATP8B1 gene. Considering the twin pregnancy, the percentage of the variant versus the wild allele was of 31%, suggesting heterozygosity present in the mother alone. This analysis showed that the mother was affected by benign recurrent intrahepatic cholestasis of pregnancy (ICP1: # 147480) and indicated the opportunity to anticipate childbirth to avoid worsening of the mother’s health. WES after the birth of the twins confirmed the molecular data.
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Affiliation(s)
- Aldesia Provenzano
- Medical Genetics Unit, Department of Experimental and Clinical Biomedical Sciences “Mario Serio”, University of Florence, 50139 Florence, Italy
- Correspondence:
| | - Antonio Farina
- Division of Obstetrics and Prenatal Medicine, IRCCS Sant’Orsola-Malpighi Hospital, University of Bologna, 40138 Bologna, Italy; (A.F.); (A.S.); (A.D.G.)
| | - Anna Seidenari
- Division of Obstetrics and Prenatal Medicine, IRCCS Sant’Orsola-Malpighi Hospital, University of Bologna, 40138 Bologna, Italy; (A.F.); (A.S.); (A.D.G.)
| | - Francesco Azzaroli
- Division of Internal Medicine, IRCCS, Azienda Ospedaliero-Universitaria di Bologna, 40138 Bologna, Italy;
| | - Carla Serra
- Department of Organ Failure and Transplantation, Sant’Orsola-Malpighi Hospital, Via Massarenti 9, 40138 Bologna, Italy;
| | - Anna Della Gatta
- Division of Obstetrics and Prenatal Medicine, IRCCS Sant’Orsola-Malpighi Hospital, University of Bologna, 40138 Bologna, Italy; (A.F.); (A.S.); (A.D.G.)
| | - Orsetta Zuffardi
- Medical Genetics Unit, Department of Molecular Medicine, University of Pavia, 27100 Pavia, Italy;
| | - Sabrina Rita Giglio
- Medical Genetics Unit, Department of Medical Sciences and Public Health, University of Cagliari, 09126 Cagliari, Italy;
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22
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Gamache I, Legault MA, Grenier JC, Sanchez R, Rhéaume E, Asgari S, Barhdadi A, Zada YF, Trochet H, Luo Y, Lecca L, Murray M, Raychaudhuri S, Tardif JC, Dubé MP, Hussin J. A sex-specific evolutionary interaction between ADCY9 and CETP. eLife 2021; 10:69198. [PMID: 34609279 PMCID: PMC8594919 DOI: 10.7554/elife.69198] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2021] [Accepted: 10/04/2021] [Indexed: 12/14/2022] Open
Abstract
Pharmacogenomic studies have revealed associations between rs1967309 in the adenylyl cyclase type 9 (ADCY9) gene and clinical responses to the cholesteryl ester transfer protein (CETP) modulator dalcetrapib, however, the mechanism behind this interaction is still unknown. Here, we characterized selective signals at the locus associated with the pharmacogenomic response in human populations and we show that rs1967309 region exhibits signatures of positive selection in several human populations. Furthermore, we identified a variant in CETP, rs158477, which is in long-range linkage disequilibrium with rs1967309 in the Peruvian population. The signal is mainly seen in males, a sex-specific result that is replicated in the LIMAA cohort of over 3400 Peruvians. Analyses of RNA-seq data further suggest an epistatic interaction on CETP expression levels between the two SNPs in multiple tissues, which also differs between males and females. We also detected interaction effects of the two SNPs with sex on cardiovascular phenotypes in the UK Biobank, in line with the sex-specific genotype associations found in Peruvians at these loci. We propose that ADCY9 and CETP coevolved during recent human evolution due to sex-specific selection, which points toward a biological link between dalcetrapib’s pharmacogene ADCY9 and its therapeutic target CETP.
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Affiliation(s)
- Isabel Gamache
- Université de Montréal, Montréal, Canada.,Montreal Heart Institute, Montréal, Canada
| | - Marc-André Legault
- Université de Montréal, Montréal, Canada.,Montreal Heart Institute, Montréal, Canada.,Université de Montréal Beaulieu-Saucier Pharmacogenomics Centre, Montréal, Canada
| | | | | | - Eric Rhéaume
- Université de Montréal, Montréal, Canada.,Montreal Heart Institute, Montréal, Canada
| | - Samira Asgari
- Center for Data Sciences, Brigham and Women's Hospital, Harvard Medical School, Boston, United States.,Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, United States
| | - Amina Barhdadi
- Montreal Heart Institute, Montréal, Canada.,Université de Montréal Beaulieu-Saucier Pharmacogenomics Centre, Montréal, Canada
| | - Yassamin Feroz Zada
- Université de Montréal Beaulieu-Saucier Pharmacogenomics Centre, Montréal, Canada
| | - Holly Trochet
- Université de Montréal, Montréal, Canada.,Montreal Heart Institute, Montréal, Canada
| | - Yang Luo
- Center for Data Sciences, Brigham and Women's Hospital, Harvard Medical School, Boston, United States.,Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, United States
| | - Leonid Lecca
- Socios En Salud, Lima, Peru.,Harvard Medical School, Boston, United States
| | - Megan Murray
- Center for Data Sciences, Brigham and Women's Hospital, Harvard Medical School, Boston, United States
| | - Soumya Raychaudhuri
- Center for Data Sciences, Brigham and Women's Hospital, Harvard Medical School, Boston, United States.,Program in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, United States.,Centre for Genetics and Genomics Versus Arthritis, Manchester Academic Health Science Centre, University of Manchester, Manchester, United Kingdom.,Department of Biomedical Informatics, Harvard Medical School, Boston, United States.,Department of Medicine, Brigham and Women's Hospital and Harvard Medical School, Boston, United States
| | - Jean-Claude Tardif
- Université de Montréal, Montréal, Canada.,Montreal Heart Institute, Montréal, Canada
| | - Marie-Pierre Dubé
- Université de Montréal, Montréal, Canada.,Montreal Heart Institute, Montréal, Canada.,Université de Montréal Beaulieu-Saucier Pharmacogenomics Centre, Montréal, Canada
| | - Julie Hussin
- Université de Montréal, Montréal, Canada.,Montreal Heart Institute, Montréal, Canada
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23
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The distribution of common-variant effect sizes. Nat Genet 2021; 53:1243-1249. [PMID: 34326547 DOI: 10.1038/s41588-021-00901-3] [Citation(s) in RCA: 31] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2020] [Accepted: 06/23/2021] [Indexed: 01/08/2023]
Abstract
The genetic effect-size distribution of a disease describes the number of risk variants, the range of their effect sizes and sample sizes that will be required to discover them. Accurate estimation has been a challenge. Here I propose Fourier Mixture Regression (FMR), validating that it accurately estimates real and simulated effect-size distributions. Applied to summary statistics for ten diseases (average [Formula: see text]), FMR estimates that 100,000-1,000,000 cases will be required for genome-wide significant SNPs to explain 50% of SNP heritability. In such large studies, genome-wide significance becomes increasingly conservative, and less stringent thresholds achieve high true positive rates if confounding is controlled. Across traits, polygenicity varies, but the range of their effect sizes is similar. Compared with effect sizes in the top 10% of heritability, including most discovered thus far, those in the bottom 10-50% are orders of magnitude smaller and more numerous, spanning a large fraction of the genome.
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Abrams MB, Dubin CA, AlZaben F, Bravo J, Joubert PM, Weiss CV, Brem RB. Population and comparative genetics of thermotolerance divergence between yeast species. G3 (BETHESDA, MD.) 2021; 11:jkab139. [PMID: 33914073 PMCID: PMC8495929 DOI: 10.1093/g3journal/jkab139] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/21/2021] [Accepted: 04/20/2021] [Indexed: 12/04/2022]
Abstract
Many familiar traits in the natural world-from lions' manes to the longevity of bristlecone pine trees-arose in the distant past, and have long since fixed in their respective species. A key challenge in evolutionary genetics is to figure out how and why species-defining traits have come to be. We used the thermotolerance growth advantage of the yeast Saccharomyces cerevisiae over its sister species Saccharomyces paradoxus as a model for addressing these questions. Analyzing loci at which the S. cerevisiae allele promotes thermotolerance, we detected robust evidence for positive selection, including amino acid divergence between the species and conservation within S. cerevisiae populations. Because such signatures were particularly strong at the chromosome segregation gene ESP1, we used this locus as a case study for focused mechanistic follow-up. Experiments revealed that, in culture at high temperature, the S. paradoxus ESP1 allele conferred a qualitative defect in biomass accumulation and cell division relative to the S. cerevisiae allele. Only genetic divergence in the ESP1 coding region mattered phenotypically, with no functional impact detectable from the promoter. Our data support a model in which an ancient ancestor of S. cerevisiae, under selection to boost viability at high temperature, acquired amino acid variants at ESP1 and many other loci, which have been constrained since then. Complex adaptations of this type hold promise as a paradigm for interspecies genetics, especially in deeply diverged traits that may have taken millions of years to evolve.
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Affiliation(s)
- Melanie B Abrams
- Department of Plant and Microbial Biology, University of California, Berkeley, Berkeley, CA 94720, USA
| | - Claire A Dubin
- Department of Plant and Microbial Biology, University of California, Berkeley, Berkeley, CA 94720, USA
| | - Faisal AlZaben
- Department of Plant and Microbial Biology, University of California, Berkeley, Berkeley, CA 94720, USA
| | - Juan Bravo
- Graduate Program in the Biology of Aging, University of Southern California, Los Angeles, CA 90095, USA
| | - Pierre M Joubert
- Department of Plant and Microbial Biology, University of California, Berkeley, Berkeley, CA 94720, USA
| | - Carly V Weiss
- Department of Plant and Microbial Biology, University of California, Berkeley, Berkeley, CA 94720, USA
- Department of Biology, Stanford University, Palo Alto, CA 94305, USA
| | - Rachel B Brem
- Department of Plant and Microbial Biology, University of California, Berkeley, Berkeley, CA 94720, USA
- Buck Institute for Research on Aging, Novato, CA 94945, USA
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25
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Zhang X, Liu Q, Zhang H, Zhao S, Huang J, Sovannary T, Bunnath L, Aun HS, Samnom H, Su B, Chen H. The distinct morphological phenotypes of Southeast Asian aborigines are shaped by novel mechanisms for adaptation to tropical rainforests. Natl Sci Rev 2021; 9:nwab072. [PMID: 35371514 PMCID: PMC8970429 DOI: 10.1093/nsr/nwab072] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2020] [Revised: 03/09/2021] [Accepted: 03/12/2021] [Indexed: 11/13/2022] Open
Abstract
Southeast Asian aborigines, the hunter-gatherer populations living in tropical rainforests, exhibit distinct morphological phenotypes, including short stature, dark skin, curly hair and a wide and snub nose. The underlying genetic architecture and evolutionary mechanism of these phenotypes remain a long-term mystery. We conducted whole genome deep sequencing of 81 Cambodian aborigines from eight ethnic groups. Through a genome-wide scan of selective sweeps, we discovered key genes harboring Cambodian-enriched mutations that may contribute to their phenotypes, including two hair morphogenesis genes (TCHH and TCHHL1), one nasal morphology gene (PAX3) and a set of genes (such as ENTPD1-AS1) associated with short stature. The identified new genes and novel mutations suggest an independent origin of the distinct phenotypes in Cambodian aborigines through parallel evolution, refuting the long-standing argument on the common ancestry of these phenotypes among the worldwide rainforest hunter-gatherers. Notably, our discovery reveals that various types of molecular mechanisms, including antisense transcription and epigenetic regulation, contribute to human morphogenesis, providing novel insights into the genetics of human environmental adaptation.
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Affiliation(s)
- Xiaoming Zhang
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming 650223, China
- Center for Excellence in Animal Evolution and Genetics, Chinese Academy of Sciences, Kunming 650223, China
| | - Qi Liu
- CAS Key Laboratory of Genomic and Precision Medicine, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100101, China
- China National Center for Bioinformation, Beijing 100101, China
- School of Future Technology and Sino-Danish College, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Hui Zhang
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming 650223, China
- Center for Excellence in Animal Evolution and Genetics, Chinese Academy of Sciences, Kunming 650223, China
| | - Shilei Zhao
- CAS Key Laboratory of Genomic and Precision Medicine, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100101, China
- China National Center for Bioinformation, Beijing 100101, China
- School of Future Technology and Sino-Danish College, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Jiahui Huang
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming 650223, China
- Kunming College of Life Science, University of Chinese Academy of Sciences, Beijing 100101, China
| | - Tuot Sovannary
- Department of Geography and Land Management, Royal University of Phnom Penh, Phnom Penh 12000, Cambodia
| | - Long Bunnath
- Department of Geography and Land Management, Royal University of Phnom Penh, Phnom Penh 12000, Cambodia
| | - Hong Seang Aun
- Department of Geography and Land Management, Royal University of Phnom Penh, Phnom Penh 12000, Cambodia
| | - Ham Samnom
- Capacity Development Facilitator for Handicap International Federation and Freelance Research, Battambang 02358, Cambodia
| | - Bing Su
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming 650223, China
- Center for Excellence in Animal Evolution and Genetics, Chinese Academy of Sciences, Kunming 650223, China
| | - Hua Chen
- CAS Key Laboratory of Genomic and Precision Medicine, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing 100101, China
- China National Center for Bioinformation, Beijing 100101, China
- School of Future Technology and Sino-Danish College, University of Chinese Academy of Sciences, Beijing 100049, China
- Center for Excellence in Animal Evolution and Genetics, Chinese Academy of Sciences, Kunming 650223, China
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26
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Wu Z, Gong H, Zhang M, Tong X, Ai H, Xiao S, Perez-Enciso M, Yang B, Huang L. A worldwide map of swine short tandem repeats and their associations with evolutionary and environmental adaptations. Genet Sel Evol 2021; 53:39. [PMID: 33892623 PMCID: PMC8063339 DOI: 10.1186/s12711-021-00631-4] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2020] [Accepted: 04/09/2021] [Indexed: 11/10/2022] Open
Abstract
Background Short tandem repeats (STRs) are genetic markers with a greater mutation rate than single nucleotide polymorphisms (SNPs) and are widely used in genetic studies and forensics. However, most studies in pigs have focused only on SNPs or on a limited number of STRs. Results This study screened 394 deep-sequenced genomes from 22 domesticated pig breeds/populations worldwide, wild boars from both Europe and Asia, and numerous outgroup Suidaes, and identified a set of 878,967 polymorphic STRs (pSTRs), which represents the largest repository of pSTRs in pigs to date. We found multiple lines of evidence that pSTRs in coding regions were affected by purifying selection. The enrichment of trinucleotide pSTRs in coding sequences (CDS), 5′UTR and H3K4me3 regions suggests that trinucleotide STRs serve as important components in the exons and promoters of the corresponding genes. We demonstrated that, compared to SNPs, pSTRs provide comparable or even greater accuracy in determining the breed identity of individuals. We identified pSTRs that showed significant population differentiation between domestic pigs and wild boars in Asia and Europe. We also observed that some pSTRs were significantly associated with environmental variables, such as average annual temperature or altitude of the originating sites of Chinese indigenous breeds, among which we identified loss-of-function and/or expanded STRs overlapping with genes such as AHR, LAS1L and PDK1. Finally, our results revealed that several pSTRs show stronger signals in domestic pig—wild boar differentiation or association with the analysed environmental variables than the flanking SNPs within a 100-kb window. Conclusions This study provides a genome-wide high-density map of pSTRs in diverse pig populations based on genome sequencing data, enabling a more comprehensive characterization of their roles in evolutionary and environmental adaptation. Supplementary Information The online version contains supplementary material available at 10.1186/s12711-021-00631-4.
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Affiliation(s)
- Zhongzi Wu
- State Key Laboratory for Pig Genetic Improvement and Production Technology, Jiangxi Agricultural University, Nanchang, China
| | - Huanfa Gong
- State Key Laboratory for Pig Genetic Improvement and Production Technology, Jiangxi Agricultural University, Nanchang, China
| | - Mingpeng Zhang
- State Key Laboratory for Pig Genetic Improvement and Production Technology, Jiangxi Agricultural University, Nanchang, China
| | - Xinkai Tong
- State Key Laboratory for Pig Genetic Improvement and Production Technology, Jiangxi Agricultural University, Nanchang, China
| | - Huashui Ai
- State Key Laboratory for Pig Genetic Improvement and Production Technology, Jiangxi Agricultural University, Nanchang, China
| | - Shijun Xiao
- State Key Laboratory for Pig Genetic Improvement and Production Technology, Jiangxi Agricultural University, Nanchang, China
| | - Miguel Perez-Enciso
- Centre for Research in Agricultural Genomics (CRAG), CSIC-IRTA-UAB-UB, Campus UAB, Barcelona, Spain.,ICREA, Passeig de Lluís Companys 23, Barcelona, Spain
| | - Bin Yang
- State Key Laboratory for Pig Genetic Improvement and Production Technology, Jiangxi Agricultural University, Nanchang, China.
| | - Lusheng Huang
- State Key Laboratory for Pig Genetic Improvement and Production Technology, Jiangxi Agricultural University, Nanchang, China.
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Tekola-Ayele F, Ouidir M, Shrestha D, Workalemahu T, Rahman ML, Mendola P, Grantz KL, Hinkle SN, Wu J, Zhang C. Admixture mapping identifies African and Amerindigenous local ancestry loci associated with fetal growth. Hum Genet 2021; 140:985-997. [PMID: 33590300 DOI: 10.1007/s00439-021-02265-4] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2020] [Accepted: 02/04/2021] [Indexed: 12/31/2022]
Abstract
Fetal growth is an important determinant of cardiometabolic disease risk during childhood and adulthood. The genetic architecture of fetal growth remains largely understudied in ancestrally diverse populations. We conducted genome-wide admixture mapping scan and analysis of genetic ancestry among Hispanic American, African American, European American, and Asian American pregnant women to identify genetic loci associated with fetal growth measures across 13-40 weeks gestation. Fetal growth measures were associated with genome-wide average African, European, Amerindigenous and East Asian ancestry proportions (P ranged from10-3 to 4.8 × 10-2). Admixture mapping analysis identified ten African ancestry loci and three Amerindigenous ancestry loci significantly associated with fetal growth measures at Bonferroni-corrected levels of significance (P ranged from 2.18 × 10-8 to 3.71 × 10-6). At the chr2q23.3-24.2 locus in which higher African ancestry was associated with long bone (femur and humerus) lengths, the T allele of rs13030825 (GALNT13) was associated with longer humerus length in African Americans (β = 0.44, P = 6.25 × 10-6 at week 27; β = 0.39, P = 7.72 × 10-5 at week 40). The rs13030825 SNP accounted for most of the admixture association at the chr2q23.3-24.2 locus and has substantial allele frequency difference between African and European reference samples (FST = 0.55, P = 0.03). Regulatory annotation shows that rs13030825 overlaps with the serum response factor (SRF) transcription factor previously implicated in postnatal bone development of mice. Overall, we identified ancestry-related maternal genetic loci that influence fetal growth, shedding light on molecular pathways that regulate fetal growth and potential effects on health across the lifespan.Clinical trials registration ClinicalTrials.gov, NCT00912132.
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Affiliation(s)
- Fasil Tekola-Ayele
- Epidemiology Branch, Division of Intramural Population Health Research, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, 6710B Rockledge Dr, 6710B-3204, Bethesda, MD, 20892-7004, USA.
| | - Marion Ouidir
- Epidemiology Branch, Division of Intramural Population Health Research, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, 6710B Rockledge Dr, 6710B-3204, Bethesda, MD, 20892-7004, USA
| | - Deepika Shrestha
- Epidemiology Branch, Division of Intramural Population Health Research, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, 6710B Rockledge Dr, 6710B-3204, Bethesda, MD, 20892-7004, USA
| | - Tsegaselassie Workalemahu
- Epidemiology Branch, Division of Intramural Population Health Research, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, 6710B Rockledge Dr, 6710B-3204, Bethesda, MD, 20892-7004, USA
| | - Mohammad L Rahman
- Epidemiology Branch, Division of Intramural Population Health Research, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, 6710B Rockledge Dr, 6710B-3204, Bethesda, MD, 20892-7004, USA.,Department of Population Medicine and Harvard Pilgrim Healthcare Institute, Harvard Medical School, Boston, MA, USA
| | - Pauline Mendola
- Epidemiology Branch, Division of Intramural Population Health Research, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, 6710B Rockledge Dr, 6710B-3204, Bethesda, MD, 20892-7004, USA.,Department of Epidemiology and Environmental Health, School of Public Health and Health Professions, University at Buffalo, Buffalo, NY, USA
| | - Katherine L Grantz
- Epidemiology Branch, Division of Intramural Population Health Research, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, 6710B Rockledge Dr, 6710B-3204, Bethesda, MD, 20892-7004, USA
| | - Stefanie N Hinkle
- Epidemiology Branch, Division of Intramural Population Health Research, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, 6710B Rockledge Dr, 6710B-3204, Bethesda, MD, 20892-7004, USA
| | - Jing Wu
- Division of Intramural Population Health Research, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD, USA
| | - Cuilin Zhang
- Epidemiology Branch, Division of Intramural Population Health Research, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, 6710B Rockledge Dr, 6710B-3204, Bethesda, MD, 20892-7004, USA
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Benton ML, Abraham A, LaBella AL, Abbot P, Rokas A, Capra JA. The influence of evolutionary history on human health and disease. Nat Rev Genet 2021; 22:269-283. [PMID: 33408383 PMCID: PMC7787134 DOI: 10.1038/s41576-020-00305-9] [Citation(s) in RCA: 97] [Impact Index Per Article: 32.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 10/26/2020] [Indexed: 01/29/2023]
Abstract
Nearly all genetic variants that influence disease risk have human-specific origins; however, the systems they influence have ancient roots that often trace back to evolutionary events long before the origin of humans. Here, we review how advances in our understanding of the genetic architectures of diseases, recent human evolution and deep evolutionary history can help explain how and why humans in modern environments become ill. Human populations exhibit differences in the prevalence of many common and rare genetic diseases. These differences are largely the result of the diverse environmental, cultural, demographic and genetic histories of modern human populations. Synthesizing our growing knowledge of evolutionary history with genetic medicine, while accounting for environmental and social factors, will help to achieve the promise of personalized genomics and realize the potential hidden in an individual's DNA sequence to guide clinical decisions. In short, precision medicine is fundamentally evolutionary medicine, and integration of evolutionary perspectives into the clinic will support the realization of its full potential.
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Affiliation(s)
- Mary Lauren Benton
- grid.152326.10000 0001 2264 7217Department of Biomedical Informatics, Vanderbilt University School of Medicine, Nashville, TN USA ,grid.252890.40000 0001 2111 2894Department of Computer Science, Baylor University, Waco, TX USA
| | - Abin Abraham
- grid.152326.10000 0001 2264 7217Vanderbilt Genetics Institute, Vanderbilt University, Nashville, TN USA ,grid.152326.10000 0001 2264 7217Vanderbilt University Medical Center, Vanderbilt University, Nashville, TN USA
| | - Abigail L. LaBella
- grid.152326.10000 0001 2264 7217Department of Biological Sciences, Vanderbilt University, Nashville, TN USA
| | - Patrick Abbot
- grid.152326.10000 0001 2264 7217Department of Biological Sciences, Vanderbilt University, Nashville, TN USA
| | - Antonis Rokas
- grid.152326.10000 0001 2264 7217Department of Biomedical Informatics, Vanderbilt University School of Medicine, Nashville, TN USA ,grid.152326.10000 0001 2264 7217Vanderbilt Genetics Institute, Vanderbilt University, Nashville, TN USA ,grid.152326.10000 0001 2264 7217Department of Biological Sciences, Vanderbilt University, Nashville, TN USA
| | - John A. Capra
- grid.152326.10000 0001 2264 7217Department of Biomedical Informatics, Vanderbilt University School of Medicine, Nashville, TN USA ,grid.152326.10000 0001 2264 7217Department of Biological Sciences, Vanderbilt University, Nashville, TN USA ,grid.266102.10000 0001 2297 6811Bakar Computational Health Sciences Institute and Department of Epidemiology and Biostatistics, University of California, San Francisco, CA USA
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29
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Hernández-Vásquez A, Azañedo D, Vargas-Fernández R, Aparco JP, Chaparro RM, Santero M. Cut-off points of anthropometric markers associated with hypertension and diabetes in Peru: Demographic and Health Survey 2018. Public Health Nutr 2020; 24:1-11. [PMID: 33059791 DOI: 10.1017/s1368980020004036] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
OBJECTIVE To determine the optimal anthropometric cut-off points for predicting the likelihood ratios of hypertension and diabetes in the Peruvian population. DESIGN A cross-sectional study was performed to establish cut-off values for body mass index (BMI), waist circumference (WC), waist:height ratio (WHtR) and Conicity index (C-index) associated with increased risk of hypertension and diabetes. Youden's index (YIndex), area under the curve (AUC), sensitivity and specificity were calculated. SETTING Peruvian households. PARTICIPANTS Peruvian population over the age of 18 years. RESULTS A total of 31 553 subjects were included, 57 % being women. Among the women, 53·06 % belonged to the 25- to 44-year-old age group [mean age: 41·66 in men and 40·02 in women]. The mean BMI, WHtR and C-index values were higher in women 27·49, 0·61, 1·30, respectively, while the mean WC value was higher in men 92·12 cm (sd ± 11·28). The best predictors of hypertension in men were the WHtR (AUC = 0·64) and the C-index (AUC = 0·64) with an optimal cut-off point of 0·57 (YIndex = 0·284) and 1·301 (YIndex = 0·284), respectively. Women showed an AUC of 0·63 and 0·61 in the WHtR and C-index, respectively, with an optimal cut-off of 0·61 (YIndex = 0·236) and 1·323 (YIndex = 0·225). The best predictor for diabetes was the C-index: with an AUC = 0·67 and an optimal cut-off of 1·337 (YIndex = 0·346) for men and an AUC = 0·66 and optimal cut-off of 1·313 (YIndex = 0·319) for women. CONCLUSIONS Our findings show that in Peruvian adults, the WHtR and the C-index have the strongest association with hypertension in both sexes. Likewise, the C-index had the strongest association with diabetes.
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Affiliation(s)
- Akram Hernández-Vásquez
- Universidad San Ignacio de Loyola, Vicerrectorado de Investigación, Centro de Excelencia en Investigaciones Económicas y Sociales en Salud, 550 La Fontana Av., La Molina00012, Lima, Peru
| | - Diego Azañedo
- Universidad Católica Los Ángeles de Chimbote, Instituto de Investigación, Chimbote, Peru
| | | | - Juan Pablo Aparco
- Universidad San Ignacio de Loyola, Carrera Nutrición y Dietética, Lima, Peru
- Centro Nacional de Alimentación y Nutrición, Instituto Nacional de Salud, Lima, Peru
| | | | - Marilina Santero
- Universitat Autònoma de Barcelona, Barcelona, Spain
- Iberoamerican Cochrane Centre, Biomedical Research Institute Sant Pau (IIB Sant Pau), Barcelona, Spain
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30
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Stanley S, Balic Z, Hubmacher D. Acromelic dysplasias: how rare musculoskeletal disorders reveal biological functions of extracellular matrix proteins. Ann N Y Acad Sci 2020; 1490:57-76. [PMID: 32880985 DOI: 10.1111/nyas.14465] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2020] [Revised: 07/16/2020] [Accepted: 07/22/2020] [Indexed: 12/15/2022]
Abstract
Acromelic dysplasias are a group of rare musculoskeletal disorders that collectively present with short stature, pseudomuscular build, stiff joints, and tight skin. Acromelic dysplasias are caused by mutations in genes (FBN1, ADAMTSL2, ADAMTS10, ADAMTS17, LTBP2, and LTBP3) that encode secreted extracellular matrix proteins, and in SMAD4, an intracellular coregulator of transforming growth factor-β (TGF-β) signaling. The shared musculoskeletal presentations in acromelic dysplasias suggest that these proteins cooperate in a biological pathway, but also fulfill distinct roles in specific tissues that are affected in individual disorders of the acromelic dysplasia group. In addition, most of the affected proteins directly interact with fibrillin microfibrils in the extracellular matrix and have been linked to the regulation of TGF-β signaling. Together with recently developed knockout mouse models targeting the affected genes, novel insights into molecular mechanisms of how these proteins regulate musculoskeletal development and homeostasis have emerged. Here, we summarize the current knowledge highlighting pathogenic mechanisms of the different disorders that compose acromelic dysplasias and provide an overview of the emerging biological roles of the individual proteins that are compromised. Finally, we develop a conceptual model of how these proteins may interact and form an "acromelic dysplasia complex" on fibrillin microfibrils in connective tissues of the musculoskeletal system.
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Affiliation(s)
- Sarah Stanley
- Leni & Peter W. May Department of Orthopedics, Icahn School of Medicine at Mount Sinai, New York, New York
| | - Zerina Balic
- Leni & Peter W. May Department of Orthopedics, Icahn School of Medicine at Mount Sinai, New York, New York
| | - Dirk Hubmacher
- Leni & Peter W. May Department of Orthopedics, Icahn School of Medicine at Mount Sinai, New York, New York
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