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Pu Y, Pu S, Chen Y, Kong Q, Liu X, Zhao Q, Xu K, Liu J, Li M, Xu X, Qiao X, Su B, Chen J, Yang Z. Weakened tanning ability is an important mechanism for evolutionary skin lightening in East Asians. J Genet Genomics 2024; 51:703-713. [PMID: 38461943 DOI: 10.1016/j.jgg.2024.03.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2024] [Revised: 03/03/2024] [Accepted: 03/03/2024] [Indexed: 03/12/2024]
Abstract
The evolution of light-skin pigmentation among Eurasians is considered as an adaptation to the high-latitude environments. East Asians are ideal populations for studying skin color evolution because of the complex environment of East Asia. Here, we report a strong selection signal for the pigmentation gene phenylalanine hydroxylase (PAH) in light-skinned Han Chinese individuals. The intron mutation rs10778203 in PAH is enriched in East Asians and is significantly associated with skin color of the back of the hand in Han Chinese males (P < 0.05). In vitro luciferase and transcription factor binding assays show that the ancestral allele of rs10778203 could bind to SMAD2 and has a significant enhancer activity for PAH. However, the derived T allele (the major allele in East Asians) of rs10778203 decreases the binding activity of transcription factors and enhancer activity. Meanwhile, the derived T allele of rs10778203 shows a weaker ultraviolet radiation response in A375 cells and zebrafish embryos. Furthermore, rs10778203 decreases melanin production in transgenic zebrafish embryos after ultraviolet B (UVB) treatment. Collectively, PAH is a potential pigmentation gene that regulates skin tanning ability. Natural selection has enriched the adaptive allele, resulting in weakened tanning ability in East Asians, suggesting a unique genetic mechanism for evolutionary skin lightening in East Asians.
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Affiliation(s)
- Youwei Pu
- Tianjian Laboratory of Advanced Biomedical Sciences, Academy of Medical Science, Zhengzhou University, Zhengzhou, Henan 450052, China
| | - Siyu Pu
- Department of Pediatric Surgery and Laboratory of Pediatric Surgery, West China Hospital, Sichuan University, Chengdu, Sichuan 610041, China
| | - Yanyan Chen
- Tianjian Laboratory of Advanced Biomedical Sciences, Academy of Medical Science, Zhengzhou University, Zhengzhou, Henan 450052, China
| | - Qinghong Kong
- Guizhou Provincial College-based Key Lab for Tumor Prevention and Treatment with Distinctive Medicines, Zunyi Medical University, Zunyi, Guizhou 563000, China
| | - Xuyang Liu
- Tianjian Laboratory of Advanced Biomedical Sciences, Academy of Medical Science, Zhengzhou University, Zhengzhou, Henan 450052, China
| | - Qi Zhao
- Yunnan Key Laboratory of Primate Biomedical Research, Institute of Primate Translational Medicine, Kunming University of Science and Technology, Kunming, Yunnan 650500, China
| | - Ke Xu
- Tianjian Laboratory of Advanced Biomedical Sciences, Academy of Medical Science, Zhengzhou University, Zhengzhou, Henan 450052, China
| | - Jiuming Liu
- Tianjian Laboratory of Advanced Biomedical Sciences, Academy of Medical Science, Zhengzhou University, Zhengzhou, Henan 450052, China
| | - Mengyuan Li
- Tianjian Laboratory of Advanced Biomedical Sciences, Academy of Medical Science, Zhengzhou University, Zhengzhou, Henan 450052, China
| | - Xiaoyu Xu
- Tianjian Laboratory of Advanced Biomedical Sciences, Academy of Medical Science, Zhengzhou University, Zhengzhou, Henan 450052, China
| | - Xiaoyang Qiao
- Tianjian Laboratory of Advanced Biomedical Sciences, Academy of Medical Science, Zhengzhou University, Zhengzhou, Henan 450052, China
| | - Bing Su
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, Yunnan 650223, China; Center for Excellence in Animal Evolution and Genetics, Chinese Academy of Sciences, Kunming, Yunnan 650223, China
| | - Jing Chen
- Department of Pediatric Surgery and Laboratory of Pediatric Surgery, West China Hospital, Sichuan University, Chengdu, Sichuan 610041, China.
| | - Zhaohui Yang
- Tianjian Laboratory of Advanced Biomedical Sciences, Academy of Medical Science, Zhengzhou University, Zhengzhou, Henan 450052, China.
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Chen S, Tang D, Deng L, Xu S. Asian-European differentiation of schizophrenia-associated genes driven by admixture and natural selection. iScience 2024; 27:109560. [PMID: 38638564 PMCID: PMC11024917 DOI: 10.1016/j.isci.2024.109560] [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: 08/22/2023] [Revised: 12/29/2023] [Accepted: 03/22/2024] [Indexed: 04/20/2024] Open
Abstract
The European-centered genome-wide association studies of schizophrenia (SCZ) may not be well applied to non-European populations. We analyzed 1,592 reported SCZ-associated genes using the public genome data and found an overall higher Asian-European differentiation on the SCZ-associated variants than at the genome-wide level. Notable examples included 15 missense variants, a regulatory variant SLC5A10-rs1624825, and a damaging variant TSPAN18-rs1001292. Independent local adaptations in recent 25,000 years, after the Asian-European divergence, could have contributed to such genetic differentiation, as were identified at a missense mutation LTN1-rs57646126-A in Asians, and a non-risk allele ZSWIM6-rs72761442-G in Europeans. Altai-Neanderthal-derived alleles may have opposite effects on SCZ susceptibility between ancestries. Furthermore, adaptive introgression was detected on the non-risk haplotype at 1q21.2 in Europeans, while in Asians it was observed on the SCZ risk haplotype at 3p21.31 which is also potentially ultra-violet protective. This study emphasizes the importance of including more representative Asian samples in future SCZ studies.
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Affiliation(s)
- Sihan Chen
- State Key Laboratory of Genetic Engineering, Human Phenome Institute, Zhangjiang Fudan International Innovation Center, Center for Evolutionary Biology, School of Life Sciences, Department of Liver Surgery and Transplantation Liver Cancer Institute, Zhongshan Hospital, Fudan University, Shanghai 200032, China
| | - Die Tang
- State Key Laboratory of Genetic Engineering, Human Phenome Institute, Zhangjiang Fudan International Innovation Center, Center for Evolutionary Biology, School of Life Sciences, Department of Liver Surgery and Transplantation Liver Cancer Institute, Zhongshan Hospital, Fudan University, Shanghai 200032, China
| | - Lian Deng
- State Key Laboratory of Genetic Engineering, Human Phenome Institute, Zhangjiang Fudan International Innovation Center, Center for Evolutionary Biology, School of Life Sciences, Department of Liver Surgery and Transplantation Liver Cancer Institute, Zhongshan Hospital, Fudan University, Shanghai 200032, China
- Ministry of Education Key Laboratory of Contemporary Anthropology, School of Life Sciences, Fudan University, Shanghai 200438, China
| | - Shuhua Xu
- State Key Laboratory of Genetic Engineering, Human Phenome Institute, Zhangjiang Fudan International Innovation Center, Center for Evolutionary Biology, School of Life Sciences, Department of Liver Surgery and Transplantation Liver Cancer Institute, Zhongshan Hospital, Fudan University, Shanghai 200032, China
- Ministry of Education Key Laboratory of Contemporary Anthropology, School of Life Sciences, Fudan University, Shanghai 200438, China
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Chen Y, Liu S, Ren Z, Wang F, Jiang Y, Dai R, Duan F, Han C, Ning Z, Xia Y, Li M, Yuan K, Qiu W, Yan XX, Dai J, Kopp RF, Huang J, Xu S, Tang B, Gamazon ER, Bigdeli T, Gershon E, Huang H, Ma C, Liu C, Chen C. Brain eQTLs of European, African American, and Asian ancestry improve interpretation of schizophrenia GWAS. MEDRXIV : THE PREPRINT SERVER FOR HEALTH SCIENCES 2024:2024.02.13.24301833. [PMID: 38405973 PMCID: PMC10888997 DOI: 10.1101/2024.02.13.24301833] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/27/2024]
Abstract
Research on brain expression quantitative trait loci (eQTLs) has illuminated the genetic underpinnings of schizophrenia (SCZ). Yet, the majority of these studies have been centered on European populations, leading to a constrained understanding of population diversities and disease risks. To address this gap, we examined genotype and RNA-seq data from African Americans (AA, n=158), Europeans (EUR, n=408), and East Asians (EAS, n=217). When comparing eQTLs between EUR and non-EUR populations, we observed concordant patterns of genetic regulatory effect, particularly in terms of the effect sizes of the eQTLs. However, 343,737 cis-eQTLs (representing ∼17% of all eQTLs pairs) linked to 1,276 genes (about 10% of all eGenes) and 198,769 SNPs (approximately 16% of all eSNPs) were identified only in the non-EUR populations. Over 90% of observed population differences in eQTLs could be traced back to differences in allele frequency. Furthermore, 35% of these eQTLs were notably rare (MAF < 0.05) in the EUR population. Integrating brain eQTLs with SCZ signals from diverse populations, we observed a higher disease heritability enrichment of brain eQTLs in matched populations compared to mismatched ones. Prioritization analysis identified seven new risk genes ( SFXN2 , RP11-282018.3 , CYP17A1 , VPS37B , DENR , FTCDNL1 , and NT5DC2 ), and three potential novel regulatory variants in known risk genes ( CNNM2 , C12orf65 , and MPHOSPH9 ) that were missed in the EUR dataset. Our findings underscore that increasing genetic ancestral diversity is more efficient for power improvement than merely increasing the sample size within single-ancestry eQTLs datasets. Such a strategy will not only improve our understanding of the biological underpinnings of population structures but also pave the way for the identification of novel risk genes in SCZ.
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Sinigaglia B, Escudero J, Biagini SA, Garcia-Calleja J, Moreno J, Dobon B, Acosta S, Mondal M, Walsh S, Aguileta G, Vallès M, Forrow S, Martin-Caballero J, Migliano AB, Bertranpetit J, Muñoz FJ, Bosch E. Exploring Adaptive Phenotypes for the Human Calcium-Sensing Receptor Polymorphism R990G. Mol Biol Evol 2024; 41:msae015. [PMID: 38285634 PMCID: PMC10859840 DOI: 10.1093/molbev/msae015] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2024] [Revised: 01/23/2024] [Accepted: 01/23/2024] [Indexed: 01/31/2024] Open
Abstract
Rainforest hunter-gatherers from Southeast Asia are characterized by specific morphological features including a particularly dark skin color (D), short stature (S), woolly hair (W), and the presence of steatopygia (S)-fat accumulation localized in the hips (DSWS phenotype). Based on previous evidence in the Andamanese population, we first characterized signatures of adaptive natural selection around the calcium-sensing receptor gene in Southeast Asian rainforest groups presenting the DSWS phenotype and identified the R990G substitution (rs1042636) as a putative adaptive variant for experimental follow-up. Although the calcium-sensing receptor has a critical role in calcium homeostasis by directly regulating the parathyroid hormone secretion, it is expressed in different tissues and has been described to be involved in many biological functions. Previous works have also characterized the R990G substitution as an activating polymorphism of the calcium-sensing receptor associated with hypocalcemia. Therefore, we generated a knock-in mouse for this substitution and investigated organismal phenotypes that could have become adaptive in rainforest hunter-gatherers from Southeast Asia. Interestingly, we found that mouse homozygous for the derived allele show not only lower serum calcium concentration but also greater body weight and fat accumulation, probably because of enhanced preadipocyte differentiation and lipolysis impairment resulting from the calcium-sensing receptor activation mediated by R990G. We speculate that such differential features in humans could have facilitated the survival of hunter-gatherer groups during periods of nutritional stress in the challenging conditions of the Southeast Asian tropical rainforests.
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Affiliation(s)
- Barbara Sinigaglia
- Institut de Biologia Evolutiva (UPF-CSIC), Departament de Medicina i Ciències de la Vida, Universitat Pompeu Fabra, Parc de Recerca Biomèdica de Barcelona, Barcelona 08003, Spain
| | - Jorge Escudero
- Institut de Biologia Evolutiva (UPF-CSIC), Departament de Medicina i Ciències de la Vida, Universitat Pompeu Fabra, Parc de Recerca Biomèdica de Barcelona, Barcelona 08003, Spain
| | - Simone A Biagini
- Institut de Biologia Evolutiva (UPF-CSIC), Departament de Medicina i Ciències de la Vida, Universitat Pompeu Fabra, Parc de Recerca Biomèdica de Barcelona, Barcelona 08003, Spain
| | - Jorge Garcia-Calleja
- Institut de Biologia Evolutiva (UPF-CSIC), Departament de Medicina i Ciències de la Vida, Universitat Pompeu Fabra, Parc de Recerca Biomèdica de Barcelona, Barcelona 08003, Spain
| | - Josep Moreno
- PCB-PRBB Animal Facility Alliance, Parc de Recerca Biomèdica de Barcelona, Barcelona 08003, Spain
| | - Begoña Dobon
- Institut de Biologia Evolutiva (UPF-CSIC), Departament de Medicina i Ciències de la Vida, Universitat Pompeu Fabra, Parc de Recerca Biomèdica de Barcelona, Barcelona 08003, Spain
| | - Sandra Acosta
- Institut de Biologia Evolutiva (UPF-CSIC), Departament de Medicina i Ciències de la Vida, Universitat Pompeu Fabra, Parc de Recerca Biomèdica de Barcelona, Barcelona 08003, Spain
- UB Institute of Neuroscience, Department of Pathology and Experimental Therapeutics, Universitat de Barcelona, Barcelona 08007, Spain
| | - Mayukh Mondal
- Institute of Genomics, University of Tartu, Tartu 51010, Estonia
- Institute of Clinical Molecular Biology, Christian-Albrechts-Universität zu Kiel, Kiel 24118, Germany
| | - Sandra Walsh
- Institut de Biologia Evolutiva (UPF-CSIC), Departament de Medicina i Ciències de la Vida, Universitat Pompeu Fabra, Parc de Recerca Biomèdica de Barcelona, Barcelona 08003, Spain
| | - Gabriela Aguileta
- Institut de Biologia Evolutiva (UPF-CSIC), Departament de Medicina i Ciències de la Vida, Universitat Pompeu Fabra, Parc de Recerca Biomèdica de Barcelona, Barcelona 08003, Spain
| | - Mònica Vallès
- Institut de Biologia Evolutiva (UPF-CSIC), Departament de Medicina i Ciències de la Vida, Universitat Pompeu Fabra, Parc de Recerca Biomèdica de Barcelona, Barcelona 08003, Spain
| | - Stephen Forrow
- Mouse Mutant Core Facility, Institute for Research in Biomedicine (IRB), Barcelona 08028, Spain
| | - Juan Martin-Caballero
- PCB-PRBB Animal Facility Alliance, Parc de Recerca Biomèdica de Barcelona, Barcelona 08003, Spain
| | - Andrea Bamberg Migliano
- Human Evolutionary Ecology Group, Department of Evolutionary Anthropology, University of Zurich, Zurich 8057, Switzerland
| | - Jaume Bertranpetit
- Institut de Biologia Evolutiva (UPF-CSIC), Departament de Medicina i Ciències de la Vida, Universitat Pompeu Fabra, Parc de Recerca Biomèdica de Barcelona, Barcelona 08003, Spain
| | - Francisco J Muñoz
- Laboratory of Molecular Physiology, Departament de Medicina i Ciències de la Vida, Universitat Pompeu Fabra, Parc de Recerca Biomèdica de Barcelona, Barcelona 08003, Spain
| | - Elena Bosch
- Institut de Biologia Evolutiva (UPF-CSIC), Departament de Medicina i Ciències de la Vida, Universitat Pompeu Fabra, Parc de Recerca Biomèdica de Barcelona, Barcelona 08003, Spain
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Pranckėnienė L, Urnikytė A, Kučinskas V. Microevolutionary processes analysis in the Lithuanian genome. Sci Rep 2023; 13:11941. [PMID: 37488273 PMCID: PMC10366082 DOI: 10.1038/s41598-023-39249-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2023] [Accepted: 07/21/2023] [Indexed: 07/26/2023] Open
Abstract
Differences in the relative fitness of genomic variants are foundational, without these, neither natural selection nor adaption can exist. This research analyzed two microevolutionary forces, mutations, and positive selection, using whole genome sequencing data from Lithuanians across three generations: newborns (generation I), their parents (generation II), 60 years old Lithuanians, and the root ancestors (generation III). The main objective was to determine the frequency of mutations under selection in modern humans and how allele frequencies change across generations. Our results show that going through all the landscapes of the relative fitness on each chromosome, the general relative fitness background pattern remains the same in analysed generations. However, the tendency of relative fitness to decrease, in general, is noted. We hypothesize that the de novo genome variants or genome variants with a very low frequency that formed in the previous generation did not have time to be as affected by natural selection, thus, in the following generation, the force of natural selection acting on them is greater and their cumulative relative fitness also decreases. The strong natural selection pressure on the genetic regions that encode the NEGR1 and PTPN1/PTNP21 genes were also identified, highlighting the evolution of the Lithuanian population's genome over generations, and possible genomic "deficiencies" for better adaptation.
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Affiliation(s)
- Laura Pranckėnienė
- Department of Human and Medical Genetics, Faculty of Medicine, Biomedical Science Institute, Vilnius University, Santariskiu Street 2, 08661, Vilnius, Lithuania.
| | - Alina Urnikytė
- Department of Human and Medical Genetics, Faculty of Medicine, Biomedical Science Institute, Vilnius University, Santariskiu Street 2, 08661, Vilnius, Lithuania.
| | - Vaidutis Kučinskas
- Department of Human and Medical Genetics, Faculty of Medicine, Biomedical Science Institute, Vilnius University, Santariskiu Street 2, 08661, Vilnius, Lithuania
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Tang J, Zhang H, Zhang H, Zhu H. PopTradeOff: A database for exploring population-specificity of adaptive evolution, disease susceptibility, and drug responsiveness. Comput Struct Biotechnol J 2023; 21:3443-3451. [PMID: 37448726 PMCID: PMC10338148 DOI: 10.1016/j.csbj.2023.06.008] [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: 02/23/2023] [Revised: 05/26/2023] [Accepted: 06/08/2023] [Indexed: 07/15/2023] Open
Abstract
The influence of adaptive evolution on disease susceptibility has drawn attention; however, the extent of the influence, whether favored mutations also influence drug responses, and whether the associations between the three are population-specific remain unknown. Using a reported deep learning network to integrate seven statistical tests for detecting selection signals, we predicted favored mutations in the genomes of 17 human populations and integrated these favored mutations with reported GWAS sites and drug response-related variants into the database PopTradeOff (http://www.gaemons.net/PopFMIntro). The database also contains genome annotation information on the SNP, sequence, gene, and pathway levels. The preliminary data analyses suggest that substantial associations exist between adaptive evolution, disease susceptibility, and drug responses and that the associations are highly population-specific. The database may be valuable for disease studies, drug development, and personalized medicine.
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Affiliation(s)
- Ji Tang
- Bioinformatics Section, School of Basic Medical Sciences, Southern Medical University, Guangzhou 510515, China
| | - Huanlin Zhang
- Bioinformatics Section, School of Basic Medical Sciences, Southern Medical University, Guangzhou 510515, China
| | - Hai Zhang
- Network Center, Southern Medical University, Guangzhou 510515, China
| | - Hao Zhu
- Bioinformatics Section, School of Basic Medical Sciences, Southern Medical University, Guangzhou 510515, China
- Guangdong-Hong Kong-Macao Greater Bay Area Center for Brain Science and Brain-Inspired Intelligence, Southern Medical University, Guangzhou 510515, China
- Guangdong Provincial Key Lab of Single Cell Technology and Application, Southern Medical University, Guangzhou 510515, China
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Kovačević M, Milićević O, Branković M, Janković M, Novaković I, Sokić D, Ristić A, Shamsani J, Vojvodić N. Novel variants in established epilepsy genes in focal epilepsy. Seizure 2023; 110:146-152. [PMID: 37390664 DOI: 10.1016/j.seizure.2023.06.005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2023] [Revised: 05/30/2023] [Accepted: 06/06/2023] [Indexed: 07/02/2023] Open
Abstract
INTRODUCTION Next generation sequencing (NGS) has greatly expanded our understanding of genetic contributors in multiple epilepsy syndromes, including focal epilepsy. Describing the genetic architecture of common syndromes promises to facilitate the diagnostic process as well as aid in the identification of patients who stand to benefit from genetic testing, but most studies to date have been limited to examining children or adults with intellectual disability. Our aim was to determine the yield of targeted sequencing of 5 established epilepsy genes (DEPDC5, LGI1, SCN1A, GRIN2A, and PCHD19) in an extensively phenotyped cohort of focal epilepsy patients with normal intellectual function or mild intellectual disability, as well as describe novel variants and determine the characteristics of variant carriers. PATIENTS AND METHODS Targeted panel sequencing was performed on 96 patients with a strong clinical suspicion of genetic focal epilepsy. Patients had previously gone through a comprehensive diagnostic epilepsy evaluation in The Neurology Clinic, University Clinical Center of Serbia. Variants of interest (VOI) were classified using the American College of Medical Genetics and the Association for Molecular Pathology criteria. RESULTS Six VOI in eight (8/96, 8.3%) patients were found in our cohort. Four likely pathogenic VOI were determined in six (6/96, 6.2%) patients, two DEPDC5 variants in two patients, one SCN1A variant in two patients and one PCDH19 variant in two patients. One variant of unknown significance (VUS) was found in GRIN2A in one (1/96, 1.0%) patient. Only one VOI in GRIN2A was classified as likely benign. No VOI were detected in LGI1. CONCLUSION Sequencing of only five known epilepsy genes yielded a diagnostic result in 6.2% of our cohort and revealed multiple novel variants. Further research is necessary for a better understanding of the genetic basis in common epilepsy syndromes in patients with normal intellectual function or mild intellectual disability.
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Affiliation(s)
- Maša Kovačević
- Neurology Clinic, University Clinical Center of Serbia, Belgrade, Serbia; Faculty of Medicine, University of Belgrade, Belgrade, Serbia.
| | | | | | - Milena Janković
- Neurology Clinic, University Clinical Center of Serbia, Belgrade, Serbia
| | - Ivana Novaković
- Faculty of Medicine, University of Belgrade, Belgrade, Serbia
| | - Dragoslav Sokić
- Neurology Clinic, University Clinical Center of Serbia, Belgrade, Serbia; Faculty of Medicine, University of Belgrade, Belgrade, Serbia
| | - Aleksandar Ristić
- Neurology Clinic, University Clinical Center of Serbia, Belgrade, Serbia; Faculty of Medicine, University of Belgrade, Belgrade, Serbia
| | | | - Nikola Vojvodić
- Neurology Clinic, University Clinical Center of Serbia, Belgrade, Serbia; Faculty of Medicine, University of Belgrade, Belgrade, Serbia
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Hu M, Jiang H, Lai W, Shi L, Yi W, Sun H, Chen C, Yuan B, Yan S, Zhang J. Assessing Genomic Diversity and Signatures of Selection in Chinese Red Steppe Cattle Using High-Density SNP Array. Animals (Basel) 2023; 13:ani13101717. [PMID: 37238146 DOI: 10.3390/ani13101717] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2023] [Revised: 05/13/2023] [Accepted: 05/19/2023] [Indexed: 05/28/2023] Open
Abstract
Chinese Red Steppe Cattle (CRS), a composite cattle breed, is well known for its milk production, high slaughter rate, carcass traits, and meat quality. Nowadays, it is widely bred in Jilin and Hebei Province and the Inner Mongolia Autonomous region. However, the population structure and the genetic basis of prominent characteristics of CRS are still unknown. In this study, we systematically describe their population structure, genetic diversity, and selection signature based on genotyping data from 61 CRS individuals with GGP Bovine 100 K chip. The results showed that CRS cattle had low inbreeding levels and had formed a unique genetic structure feature. Using two complementary methods (including comprehensive haplotype score and complex likelihood ratio), we identified 1291 and 1285 potentially selected genes, respectively. There were 141 genes annotated in common 106 overlapping genomic regions covered 5.62 Mb, including PLAG1, PRKG2, DGAT1, PARP10, TONSL, ADCK5, and BMP3, most of which were enriched in pathways related to muscle growth and differentiation, milk production, and lipid metabolism. This study will contribute to understanding the genetic mechanism behind artificial selection and give an extensive reference for subsequent breeding.
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Affiliation(s)
- Mingyue Hu
- College of Animal Science, Jilin University, Changchun 130062, China
| | - Hao Jiang
- College of Animal Science, Jilin University, Changchun 130062, China
| | - Weining Lai
- College of Animal Science, Jilin University, Changchun 130062, China
| | - Lulu Shi
- College of Animal Science, Jilin University, Changchun 130062, China
| | - Wenfeng Yi
- College of Animal Science, Jilin University, Changchun 130062, China
| | - Hao Sun
- College of Animal Science, Jilin University, Changchun 130062, China
| | - Chengzhen Chen
- College of Animal Science, Jilin University, Changchun 130062, China
| | - Bao Yuan
- College of Animal Science, Jilin University, Changchun 130062, China
| | - Shouqing Yan
- College of Animal Science, Jilin University, Changchun 130062, China
| | - Jiabao Zhang
- College of Animal Science, Jilin University, Changchun 130062, China
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Kovačević M, Janković M, Branković M, Milićević O, Novaković I, Sokić D, Ristić A, Shamsani J, Vojvodić N. Novel GATOR1 variants in focal epilepsy. Epilepsy Behav 2023; 141:109139. [PMID: 36848747 DOI: 10.1016/j.yebeh.2023.109139] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/07/2022] [Revised: 02/03/2023] [Accepted: 02/05/2023] [Indexed: 02/27/2023]
Abstract
INTRODUCTION Variants in GATOR1 genes are well established in focal epilepsy syndromes. A strong association of GATOR1 variants with drug-resistant epilepsy as well as an increased risk of sudden unexplained death in epilepsy warrants developing strategies to facilitate the identification of patients who could potentially benefit from genetic testing and precision medicine. We aimed to determine the yield of GATOR1 gene sequencing in patients with focal epilepsy typically referred for genetic testing, establish novel GATOR1 variants and determine clinical, electroencephalographic, and radiological characteristics of variant carriers. PATIENTS AND METHODS Ninety-six patients with clinical suspicion of genetic focal epilepsy with previous comprehensive diagnostic epilepsy evaluation in The Neurology Clinic, University Clinical Center of Serbia, were included in the study. Sequencing was performed using a custom gene panel encompassing DEPDC5, NPRL2, and NPRL3. Variants of interest (VOI) were classified according to criteria proposed by the American College of Medical Genetics and the Association for Molecular Pathology. RESULTS Four previously unreported VOI in 4/96 (4.2%) patients were found in our cohort. Three likely pathogenic variants were determined in 3/96 (3.1%) patients, one frameshift variant in DEPDC5 in a patient with nonlesional frontal lobe epilepsy, one splicogenic DEPDC5 variant in a patient with nonlesional posterior quadrant epilepsy, and one frameshift variant in NPRL2 in a patient with temporal lobe epilepsy associated with hippocampal sclerosis. Only one VOI, a missense variant in NPRL3, found in 1/96 (1.1%) patients, was classified as a variant of unknown significance. CONCLUSION GATOR1 gene sequencing was diagnostic in 3.1% of our cohort and revealed three novel likely pathogenic variants, including a previously unreported association of temporal lobe epilepsy with hippocampal sclerosis with an NPRL2 variant. Further research is essential for a better understanding of the clinical scope of GATOR1 gene-associated epilepsy.
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Affiliation(s)
- Maša Kovačević
- Neurology Clinic, University Clinical Center of Serbia, Serbia; Faculty of Medicine, University of Belgrade, Serbia.
| | - Milena Janković
- Neurology Clinic, University Clinical Center of Serbia, Serbia
| | | | | | | | - Dragoslav Sokić
- Neurology Clinic, University Clinical Center of Serbia, Serbia; Faculty of Medicine, University of Belgrade, Serbia
| | - Aleksandar Ristić
- Neurology Clinic, University Clinical Center of Serbia, Serbia; Faculty of Medicine, University of Belgrade, Serbia
| | | | - Nikola Vojvodić
- Neurology Clinic, University Clinical Center of Serbia, Serbia; Faculty of Medicine, University of Belgrade, Serbia
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Mörseburg A, Pagani L, Malyarchuk B, Derenko M, Kivisild T. Response to Wyckelsma et al.: Loss of α-actinin-3 during human evolution provides superior cold resilience and muscle heat generation. Am J Hum Genet 2022; 109:967-972. [PMID: 35523147 PMCID: PMC9118108 DOI: 10.1016/j.ajhg.2022.03.014] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2021] [Accepted: 03/18/2022] [Indexed: 11/19/2022] Open
Abstract
The common loss-of-function mutation R577X in the structural muscle protein ACTN3 emerged as a potential target of positive selection from early studies and has been the focus of insightful physiological work suggesting a significant impact on muscle metabolism. Adaptation to cold climates has been proposed as a key adaptive mechanism explaining its global allele frequency patterns. Here, we re-examine this hypothesis analyzing modern (n = 3,626) and ancient (n = 1,651) genomic data by using allele-frequency as well as haplotype homozygosity-based methods. The presented results are more consistent with genetic drift rather than selection in cold climates as the main driver of the ACTN3 R577X frequency distribution in human populations across the world. This Matters Arising paper is in response to Wyckelsma et al. (2021),1 published in The American Journal of Human Genetics. See also the response by Wyckelsma et al. (2022),2 published in this issue.
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Affiliation(s)
- Alexander Mörseburg
- Metabolic Research Laboratories, Wellcome Trust-MRC Institute of Metabolic Science, University of Cambridge, Cambridge CB2 0QQ, UK.
| | - Luca Pagani
- Estonian Biocentre, Institute of Genomics, University of Tartu, Riia 23B, Tartu 51010, Estonia; Department of Biology, University of Padova, 35131 Padova, Italy
| | - Boris Malyarchuk
- Genetics Laboratory, Institute of Biological Problems of the North, Russian Academy of Sciences, Portovaya str. 18, Magadan 685000, Russia
| | - Miroslava Derenko
- Genetics Laboratory, Institute of Biological Problems of the North, Russian Academy of Sciences, Portovaya str. 18, Magadan 685000, Russia
| | - Toomas Kivisild
- Estonian Biocentre, Institute of Genomics, University of Tartu, Riia 23B, Tartu 51010, Estonia; Department of Human Genetics, KU Leuven, Leuven, Herestraat 3000, Belgium.
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11
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Alharbi AF, Sheng N, Nicol K, Strömberg N, Hollox EJ. Balancing selection at the human salivary agglutinin gene (DMBT1) driven by host-microbe interactions. iScience 2022; 25:104189. [PMID: 35494225 PMCID: PMC9038570 DOI: 10.1016/j.isci.2022.104189] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2021] [Revised: 02/07/2022] [Accepted: 03/30/2022] [Indexed: 11/19/2022] Open
Abstract
Discovering loci under balancing selection in humans can identify loci with alleles that affect response to the environment and disease. Genome variation data have identified the 5′ region of the DMBT1 gene as undergoing balancing selection in humans. DMBT1 encodes the pattern-recognition glycoprotein DMBT1, also known as SALSA, gp340, or salivary agglutinin. DMBT1 binds to a variety of pathogens through a tandemly arranged scavenger receptor cysteine-rich (SRCR) domain, with the number of domains polymorphic in humans. We show that the signal of balancing selection is driven by one haplotype usually carrying a shorter SRCR repeat and another usually carrying a longer SRCR repeat. DMBT1 encoded by a shorter SRCR repeat allele does not bind a cariogenic and invasive Streptococcus mutans strain, in contrast to the long SRCR allele that shows binding. Our results suggest that balancing selection at DMBT1 is due to host-microbe interactions of encoded SRCR tandem repeat alleles. Clear evidence from many analyses show balancing selection at DMBT1 Scavenger-receptor cysteine-rich domain array associated with balancing selection Genetic variation, not alternative splicing, responsible for protein isoforms Long, but not short, DMBT1 isoforms bind a cariogenic strain of Streptococcus mutans
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Affiliation(s)
- Adel F. Alharbi
- Department of Genetics and Genome Biology, University of Leicester, Leicester, UK
- Medina Regional Laboratory, General Directorate of Health Affairs, Ministry of Health, Medina, Saudi Arabia
| | - Nongfei Sheng
- Department of Odontology, Umeå University, Umeå, Sweden
| | - Katie Nicol
- Department of Genetics and Genome Biology, University of Leicester, Leicester, UK
| | | | - Edward J. Hollox
- Department of Genetics and Genome Biology, University of Leicester, Leicester, UK
- Corresponding author
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12
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Maceda I, Lao O. Analysis of the Batch Effect Due to Sequencing Center in Population Statistics Quantifying Rare Events in the 1000 Genomes Project. Genes (Basel) 2021; 13:genes13010044. [PMID: 35052384 PMCID: PMC8775088 DOI: 10.3390/genes13010044] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2021] [Revised: 12/19/2021] [Accepted: 12/21/2021] [Indexed: 12/01/2022] Open
Abstract
The 1000 Genomes Project (1000G) is one of the most popular whole genome sequencing datasets used in different genomics fields and has boosting our knowledge in medical and population genomics, among other fields. Recent studies have reported the presence of ghost mutation signals in the 1000G. Furthermore, studies have shown that these mutations can influence the outcomes of follow-up studies based on the genetic variation of 1000G, such as single nucleotide variants (SNV) imputation. While the overall effect of these ghost mutations can be considered negligible for common genetic variants in many populations, the potential bias remains unclear when studying low frequency genetic variants in the population. In this study, we analyze the effect of the sequencing center in predicted loss of function (LoF) alleles, the number of singletons, and the patterns of archaic introgression in the 1000G. Our results support previous studies showing that the sequencing center is associated with LoF and singletons independent of the population that is considered. Furthermore, we observed that patterns of archaic introgression were distorted for some populations depending on the sequencing center. When analyzing the frequency of SNPs showing extreme patterns of genotype differentiation among centers for CEU, YRI, CHB, and JPT, we observed that the magnitude of the sequencing batch effect was stronger at MAF < 0.2 and showed different profiles between CHB and the other populations. All these results suggest that data from 1000G must be interpreted with caution when considering statistics using variants at low frequency.
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Affiliation(s)
- Iago Maceda
- Population Genomics, CNAG-CRG, Centre for Genomic Regulation, 08028 Barcelona, Spain;
- Barcelona Institute of Science and Technology (BIST), 08036 Barcelona, Spain
- Universitat Pompeu Fabra (UPF), 08003 Barcelona, Spain
| | - Oscar Lao
- Population Genomics, CNAG-CRG, Centre for Genomic Regulation, 08028 Barcelona, Spain;
- Barcelona Institute of Science and Technology (BIST), 08036 Barcelona, Spain
- Universitat Pompeu Fabra (UPF), 08003 Barcelona, Spain
- Correspondence:
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13
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Massidda M, Flore L, Kikuchi N, Scorcu M, Piras F, Cugia P, Cięszczyk P, Tocco F, Calò CM. Influence of the MCT1-T1470A polymorphism (rs1049434) on repeated sprint ability and blood lactate accumulation in elite football players: a pilot study. Eur J Appl Physiol 2021; 121:3399-3408. [PMID: 34480633 DOI: 10.1007/s00421-021-04797-z] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2021] [Accepted: 08/17/2021] [Indexed: 10/20/2022]
Abstract
PURPOSE The aim of this study is to investigate the influence of the MCT1 T1470A polymorphism (rs1049434) on repeated sprint ability (RSA) and lactate accumulation after RSA testing. METHODS Twenty-six elite Italian male football players (age: 17.7 ± 0.78 years; height: 179.2 ± 7.40 cm; weight: 72.1 ± 5.38 kg) performed RSA testing (6 × 30-m sprints with an active recovery between sprints), and lactate measurements were obtained at 1, 3, 5, 7, and 10 min post-exercise. Genotyping for the MCT1 T1470A polymorphism was performed using PCR. RESULTS Genotype distributions were in Hardy-Weinberg equilibrium, being 42% wildtype (A/A), 46% heterozygotes (T/A), and 12% mutated homozygotes (T/T). Significant differences between genotypic groups were found in the two final sprint times of the RSA test. Under a dominant model, carriers of the major A-allele (Glu-490) in the dominant model showed a significantly lower sprint time compared to footballers with the T/T (Asp/Asp) genotype (5th Sprint time: A/A + T/A = 4.60 s vs TT = 4.97 s, 95% CI 0.07-0.67, p = 0.022; 6th Sprint: A/A + T/A = 4.56 s vs T/T = 4.87 s, 95% CI 0.05-0.57, p = 0.033). CONCLUSIONS The T1470A (Glu490Asp) polymorphism of MCT1 was associated with RSA. Our findings suggest that the presence of the major A-allele (Glu-490) is favourable for RSA in football players.
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Affiliation(s)
- M Massidda
- Department of Life and Environmental Sciences, University of Cagliari, Cagliari, Italy.
- Italian Federation of Sports Medicine Federation (FMSI), Rome, Italy.
- Faculty of Medicine and Surgery, Sport and Exercise Science Degree Courses, University of Cagliari, Cagliari, Italy.
| | - L Flore
- Department of Life and Environmental Sciences, University of Cagliari, Cagliari, Italy
| | - N Kikuchi
- Graduate School of Health and Sport Science, Nippon Sport Science University, Tokyo, Japan
| | - M Scorcu
- Italian Federation of Sports Medicine Federation (FMSI), Rome, Italy
- Cagliari Calcio Spa, Cagliari, Italy
| | - F Piras
- Italian Federation of Sports Medicine Federation (FMSI), Rome, Italy
- Cagliari Calcio Spa, Cagliari, Italy
| | - P Cugia
- Italian Federation of Sports Medicine Federation (FMSI), Rome, Italy
- Cagliari Calcio Spa, Cagliari, Italy
| | - P Cięszczyk
- Department of Physical Education, University of Physical Education and Sport, Gdańsk, Poland
| | - F Tocco
- Department of Medical Sciences and Public Health, University of Cagliari, Cagliari, Italy
| | - C M Calò
- Department of Life and Environmental Sciences, University of Cagliari, Cagliari, Italy
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14
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Trigila AP, Pisciottano F, Franchini LF. Hearing loss genes reveal patterns of adaptive evolution at the coding and non-coding levels in mammals. BMC Biol 2021; 19:244. [PMID: 34784928 PMCID: PMC8594068 DOI: 10.1186/s12915-021-01170-6] [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: 11/20/2020] [Accepted: 10/21/2021] [Indexed: 11/26/2022] Open
Abstract
Background Mammals possess unique hearing capacities that differ significantly from those of the rest of the amniotes. In order to gain insights into the evolution of the mammalian inner ear, we aim to identify the set of genetic changes and the evolutionary forces that underlie this process. We hypothesize that genes that impair hearing when mutated in humans or in mice (hearing loss (HL) genes) must play important roles in the development and physiology of the inner ear and may have been targets of selective forces across the evolution of mammals. Additionally, we investigated if these HL genes underwent a human-specific evolutionary process that could underlie the evolution of phenotypic traits that characterize human hearing. Results We compiled a dataset of HL genes including non-syndromic deafness genes identified by genetic screenings in humans and mice. We found that many genes including those required for the normal function of the inner ear such as LOXHD1, TMC1, OTOF, CDH23, and PCDH15 show strong signatures of positive selection. We also found numerous noncoding accelerated regions in HL genes, and among them, we identified active transcriptional enhancers through functional enhancer assays in transgenic zebrafish. Conclusions Our results indicate that the key inner ear genes and regulatory regions underwent adaptive evolution in the basal branch of mammals and along the human-specific branch, suggesting that they could have played an important role in the functional remodeling of the cochlea. Altogether, our data suggest that morphological and functional evolution could be attained through molecular changes affecting both coding and noncoding regulatory regions. Supplementary Information The online version contains supplementary material available at 10.1186/s12915-021-01170-6.
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Affiliation(s)
- Anabella P Trigila
- Instituto de Investigaciones en Ingeniería Genética y Biología Molecular (INGEBI), Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), C1428, Buenos Aires, Argentina
| | - Francisco Pisciottano
- Instituto de Investigaciones en Ingeniería Genética y Biología Molecular (INGEBI), Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), C1428, Buenos Aires, Argentina.,Current address: Instituto de Biología y Medicina Experimental (IBYME), Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), C1428, Buenos Aires, Argentina
| | - Lucía F Franchini
- Instituto de Investigaciones en Ingeniería Genética y Biología Molecular (INGEBI), Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), C1428, Buenos Aires, Argentina.
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15
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Choate LA, Barshad G, McMahon PW, Said I, Rice EJ, Munn PR, Lewis JJ, Danko CG. Multiple stages of evolutionary change in anthrax toxin receptor expression in humans. Nat Commun 2021; 12:6590. [PMID: 34782625 PMCID: PMC8592990 DOI: 10.1038/s41467-021-26854-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2020] [Accepted: 10/18/2021] [Indexed: 11/09/2022] Open
Abstract
The advent of animal husbandry and hunting increased human exposure to zoonotic pathogens. To understand how a zoonotic disease may have influenced human evolution, we study changes in human expression of anthrax toxin receptor 2 (ANTXR2), which encodes a cell surface protein necessary for Bacillus anthracis virulence toxins to cause anthrax disease. In immune cells, ANTXR2 is 8-fold down-regulated in all available human samples compared to non-human primates, indicating regulatory changes early in the evolution of modern humans. We also observe multiple genetic signatures consistent with recent positive selection driving a European-specific decrease in ANTXR2 expression in multiple tissues affected by anthrax toxins. Our observations fit a model in which humans adapted to anthrax disease following early ecological changes associated with hunting and scavenging, as well as a second period of adaptation after the rise of modern agriculture.
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Affiliation(s)
- Lauren A Choate
- Baker Institute for Animal Health, College of Veterinary Medicine, Cornell University, Ithaca, NY, 14853, USA
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY, 14853, USA
| | - Gilad Barshad
- Baker Institute for Animal Health, College of Veterinary Medicine, Cornell University, Ithaca, NY, 14853, USA
| | - Pierce W McMahon
- Baker Institute for Animal Health, College of Veterinary Medicine, Cornell University, Ithaca, NY, 14853, USA
| | - Iskander Said
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY, 14853, USA
| | - Edward J Rice
- Baker Institute for Animal Health, College of Veterinary Medicine, Cornell University, Ithaca, NY, 14853, USA
| | - Paul R Munn
- Baker Institute for Animal Health, College of Veterinary Medicine, Cornell University, Ithaca, NY, 14853, USA
| | - James J Lewis
- Baker Institute for Animal Health, College of Veterinary Medicine, Cornell University, Ithaca, NY, 14853, USA.
| | - Charles G Danko
- Baker Institute for Animal Health, College of Veterinary Medicine, Cornell University, Ithaca, NY, 14853, USA.
- Department of Biomedical Sciences, College of Veterinary Medicine, Cornell University, Ithaca, NY, 14853, USA.
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16
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Saitou M, Masuda N, Gokcumen O. Similarity-based analysis of allele frequency distribution among multiple populations identifies adaptive genomic structural variants. Mol Biol Evol 2021; 39:6413645. [PMID: 34718708 PMCID: PMC8896759 DOI: 10.1093/molbev/msab313] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022] Open
Abstract
Structural variants have a considerable impact on human genomic diversity. However, their evolutionary history remains mostly unexplored. Here, we developed a new method to identify potentially adaptive structural variants based on a similarity-based analysis that incorporates genotype frequency data from 26 populations simultaneously. Using this method, we analyzed 57,629 structural variants and identified 576 structural variants that show unusual population differentiation. Of these putatively adaptive structural variants, we further showed that 24 variants are multiallelic and overlap with coding sequences, and 20 variants are significantly associated with GWAS traits. Closer inspection of the haplotypic variation associated with these putatively adaptive and functional structural variants reveals deviations from neutral expectations due to: 1) population differentiation of rapidly evolving multiallelic variants, 2) incomplete sweeps, and 3) recent population-specific negative selection. Overall, our study provides new methodological insights, documents hundreds of putatively adaptive variants, and introduces evolutionary models that may better explain the complex evolution of structural variants.
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Affiliation(s)
- Marie Saitou
- Dept. of Biological Sciences, University at Buffalo, State University of New York, Buffalo, NY 14260-2900, USA.,Currently at the Faculty of Biosciences, Norwegian University of Life Sciences, Universitetstunet 3, 1430 Ås, Norway.,Dept. of Medicine, The University of Chicago. Section of Genetic Medicine, 5841 S. Maryland Ave., Chicago, IL, 60637-1447, USA
| | - Naoki Masuda
- Department of Mathematics, University at Buffalo, State University of New York, Buffalo, NY 14260-2900, USA.,Computational and Data-Enabled Science and Engineering Program, University at Buffalo, State University of New York, Buffalo, NY 14260-5030, USA
| | - Omer Gokcumen
- Dept. of Biological Sciences, University at Buffalo, State University of New York, Buffalo, NY 14260-2900, USA
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17
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Huang D, Zhou Y, Yi X, Fan X, Wang J, Yao H, Sham PC, Hao J, Chen K, Li MJ. VannoPortal: multiscale functional annotation of human genetic variants for interrogating molecular mechanism of traits and diseases. Nucleic Acids Res 2021; 50:D1408-D1416. [PMID: 34570217 PMCID: PMC8728305 DOI: 10.1093/nar/gkab853] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2021] [Revised: 09/05/2021] [Accepted: 09/14/2021] [Indexed: 12/16/2022] Open
Abstract
Interpreting the molecular mechanism of genomic variations and their causal relationship with diseases/traits are important and challenging problems in the human genetic study. To provide comprehensive and context-specific variant annotations for biologists and clinicians, here, by systematically integrating over 4TB genomic/epigenomic profiles and frequently-used annotation databases from various biological domains, we develop a variant annotation database, called VannoPortal. In general, the database has following major features: (i) systematically integrates 40 genome-wide variant annotations and prediction scores regarding allele frequency, linkage disequilibrium, evolutionary signature, disease/trait association, tissue/cell type-specific epigenome, base-wise functional prediction, allelic imbalance and pathogenicity; (ii) equips with our recent novel index system and parallel random-sweep searching algorithms for efficient management of backend databases and information extraction; (iii) greatly expands context-dependent variant annotation to incorporate large-scale epigenomic maps and regulatory profiles (such as EpiMap) across over 33 tissue/cell types; (iv) compiles many genome-scale base-wise prediction scores for regulatory/pathogenic variant classification beyond protein-coding region; (v) enables fast retrieval and direct comparison of functional evidence among linked variants using highly interactive web panel in addition to plain table; (vi) introduces many visualization functions for more efficient identification and interpretation of functional variants in single web page. VannoPortal is freely available at http://mulinlab.org/vportal.
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Affiliation(s)
- Dandan Huang
- Department of Bioinformatics, The Province and Ministry Co-sponsored Collaborative Innovation Center for Medical Epigenetics, School of Basic Medical Sciences, National Clinical Research Center for Cancer, Tianjin Medical University Cancer Institute and Hospital, Tianjin Medical University, Tianjin 300070, China.,Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Tianjin Medical University, Tianjin 300070, China
| | - Yao Zhou
- Department of Bioinformatics, The Province and Ministry Co-sponsored Collaborative Innovation Center for Medical Epigenetics, School of Basic Medical Sciences, National Clinical Research Center for Cancer, Tianjin Medical University Cancer Institute and Hospital, Tianjin Medical University, Tianjin 300070, China.,Department of Pharmacology, School of Basic Medical Sciences, Tianjin Medical University, Tianjin 300070, China
| | - Xianfu Yi
- School of Biomedical Engineering, Tianjin Medical University, Tianjin 300070, China
| | - Xutong Fan
- Department of Bioinformatics, The Province and Ministry Co-sponsored Collaborative Innovation Center for Medical Epigenetics, School of Basic Medical Sciences, National Clinical Research Center for Cancer, Tianjin Medical University Cancer Institute and Hospital, Tianjin Medical University, Tianjin 300070, China.,Department of Pharmacology, School of Basic Medical Sciences, Tianjin Medical University, Tianjin 300070, China
| | - Jianhua Wang
- Department of Bioinformatics, The Province and Ministry Co-sponsored Collaborative Innovation Center for Medical Epigenetics, School of Basic Medical Sciences, National Clinical Research Center for Cancer, Tianjin Medical University Cancer Institute and Hospital, Tianjin Medical University, Tianjin 300070, China.,Department of Pharmacology, School of Basic Medical Sciences, Tianjin Medical University, Tianjin 300070, China
| | - Hongcheng Yao
- Centre for PanorOmic Sciences-Genomics and Bioinformatics Cores, LKS Faculty of Medicine, The University of Hong Kong, Hong Kong SAR 999077, China
| | - Pak Chung Sham
- Centre for PanorOmic Sciences-Genomics and Bioinformatics Cores, LKS Faculty of Medicine, The University of Hong Kong, Hong Kong SAR 999077, China
| | - Jihui Hao
- Department of Pancreatic Cancer, Tianjin Medical University Cancer Institute and Hospital, National Clinical Research Center for Cancer, Key Laboratory of Cancer Prevention and Therapy, Tianjin's Clinical Research Center for Cancer, Tianjin 300060, China
| | - Kexin Chen
- Department of Epidemiology and Biostatistics, Tianjin Key Laboratory of Molecular Cancer Epidemiology, Tianjin Medical University Cancer Institute and Hospital, Tianjin Medical University, Tianjin 300060, China
| | - Mulin Jun Li
- Department of Bioinformatics, The Province and Ministry Co-sponsored Collaborative Innovation Center for Medical Epigenetics, School of Basic Medical Sciences, National Clinical Research Center for Cancer, Tianjin Medical University Cancer Institute and Hospital, Tianjin Medical University, Tianjin 300070, China.,Department of Pharmacology, School of Basic Medical Sciences, Tianjin Medical University, Tianjin 300070, China.,Department of Epidemiology and Biostatistics, Tianjin Key Laboratory of Molecular Cancer Epidemiology, Tianjin Medical University Cancer Institute and Hospital, Tianjin Medical University, Tianjin 300060, China
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18
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Saitou M, Resendez S, Pradhan AJ, Wu F, Lie NC, Hall NJ, Zhu Q, Reinholdt L, Satta Y, Speidel L, Nakagome S, Hanchard NA, Churchill G, Lee C, Atilla-Gokcumen GE, Mu X, Gokcumen O. Sex-specific phenotypic effects and evolutionary history of an ancient polymorphic deletion of the human growth hormone receptor. SCIENCE ADVANCES 2021; 7:eabi4476. [PMID: 34559564 PMCID: PMC8462886 DOI: 10.1126/sciadv.abi4476] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/10/2021] [Accepted: 08/04/2021] [Indexed: 06/13/2023]
Abstract
The common deletion of the third exon of the growth hormone receptor gene (GHRd3) in humans is associated with birth weight, growth after birth, and time of puberty. However, its evolutionary history and the molecular mechanisms through which it affects phenotypes remain unresolved. We present evidence that this deletion was nearly fixed in the ancestral population of anatomically modern humans and Neanderthals but underwent a recent adaptive reduction in frequency in East Asia. We documented that GHRd3 is associated with protection from severe malnutrition. Using a novel mouse model, we found that, under calorie restriction, Ghrd3 leads to the female-like gene expression in male livers and the disappearance of sexual dimorphism in weight. The sex- and diet-dependent effects of GHRd3 in our mouse model are consistent with a model in which the allele frequency of GHRd3 varies throughout human evolution as a response to fluctuations in resource availability.
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Affiliation(s)
- Marie Saitou
- Department of Biological Sciences, University at Buffalo, Buffalo, NY, USA
| | - Skyler Resendez
- Department of Biological Sciences, University at Buffalo, Buffalo, NY, USA
| | | | - Fuguo Wu
- Department of Ophthalmology, Ross Eye Institute, Jacobs School of Medicine and Biological Sciences, University at Buffalo, Buffalo, NY, USA
| | - Natasha C. Lie
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
| | - Nancy J. Hall
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
| | - Qihui Zhu
- The Jackson Laboratory for Genomic Medicine, Farmington, CT, USA
| | | | - Yoko Satta
- Department of Evolutionary Studies of Biosystems, SOKENDAI (Graduate University for Advanced Studies), Kanagawa Prefecture, Japan
| | - Leo Speidel
- University College London, Genetics Institute, London, UK
- The Francis Crick Institute, London, UK
| | | | - Neil A. Hanchard
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX, USA
| | | | - Charles Lee
- The Jackson Laboratory for Genomic Medicine, Farmington, CT, USA
- Precision Medicine Center, The First Affiliated Hospital of Xi’an Jiaotong University, Shaanxi, People’s Republic of China
| | | | - Xiuqian Mu
- Department of Ophthalmology, Ross Eye Institute, Jacobs School of Medicine and Biological Sciences, University at Buffalo, Buffalo, NY, USA
| | - Omer Gokcumen
- Department of Biological Sciences, University at Buffalo, Buffalo, NY, USA
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19
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Goitom S, Gicheha MG, Njonge FK, Kiplangat N. Landscape genomics and selection signatures of local adaptation of Eritrean indigenous cattle along environmental gradients. Trop Anim Health Prod 2021; 53:423. [PMID: 34333713 DOI: 10.1007/s11250-021-02837-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2020] [Accepted: 06/18/2021] [Indexed: 11/29/2022]
Abstract
Most parts of Eritrea are classified as arid and semi-arid land (ASALs) which are characterised by dryness, high ambient temperatures and low precipitation. The country has three different environmental landscapes: highland, Western lowland and Eastern lowland agro-ecological zones (AEZs). The geophysical and biophysical characteristics of the AEZs vary. Indigenous cattle which are mainly kept in extensive production system have to cope with the adverse climatic conditions of these AEZs. They have to adapt to the harsh climate, poor feed quality and endemic diseases and parasites and reproduction challenges in the AEZs. The underlying genetic basis of the indigenous cattle adaption to the specific AEZs in Eritrea is limited. In this study, it is hypothesized that the indigenous cattle have evolved and developed unique adaptive characteristics because of being reared in specific ecological landscapes. This was tested using the landscape genomics and analysis of selection signatures to ascertain the genetic basis of their adaptability to the nutritional and environmental constraints that characterise the AEZ conditions. The study was carried out in three different environmental landscapes: highland, Eastern lowland and Western lowland AEZs. Blood samples were collected from a total of 188 indigenous cattle populations sampled from the three AEZs. DNA was extracted and genotyped using the genotype by sequencing (GBS) method. Analysis revealed the existence of medium to high genetic diversity between and within the indigenous cattle populations. Scanning of selection signatures revealed genomic regions under positive selection. The regions harboured genes (IFNAR2, CASR, AHSG, ATP1B3, AIRE, ROBO2, SCHIP1 and PARS2) of importance for facial morphology, locomotion, mineral homeostasis, immune system and skeletal and muscle system development. Findings pointed out the influence of AEZ landscapes on the genetic differentiation of indigenous cattle appearances probably due to selection driven by diverse climatic and biophysical conditions. The differentiation is orientated towards adaptive characteristics.
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Affiliation(s)
- S Goitom
- Department of Animal Sciences, Hamelmalo Agricultural College, Keren, Eritrea
| | - Mathew G Gicheha
- Department of Animal Sciences, Jomo Kenyatta University of Agriculture & Technology, P.O. Box 62000-00200, Nairobi, Kenya.
| | - Francis K Njonge
- Department of Animal Sciences, Jomo Kenyatta University of Agriculture & Technology, P.O. Box 62000-00200, Nairobi, Kenya
| | - Ngeno Kiplangat
- Department of Animal Sciences, Egerton University, P.O. Box 635, Njoro, Kenya
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20
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Genomic selection signatures in autism spectrum disorder identifies cognitive genomic tradeoff and its relevance in paradoxical phenotypes of deficits versus potentialities. Sci Rep 2021; 11:10245. [PMID: 33986442 PMCID: PMC8119484 DOI: 10.1038/s41598-021-89798-w] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2020] [Accepted: 04/26/2021] [Indexed: 11/18/2022] Open
Abstract
Autism spectrum disorder (ASD) is a heterogeneous neurodevelopmental disorder characterized by paradoxical phenotypes of deficits as well as gain in brain function. To address this a genomic tradeoff hypothesis was tested and followed up with the biological interaction and evolutionary significance of positively selected ASD risk genes. SFARI database was used to retrieve the ASD risk genes while for population datasets 1000 genome data was used. Common risk SNPs were subjected to machine learning as well as independent tests for selection, followed by Bayesian analysis to identify the cumulative effect of selection on risk SNPs. Functional implication of these positively selected risk SNPs was assessed and subjected to ontology analysis, pertaining to their interaction and enrichment of biological and cellular functions. This was followed by comparative analysis with the ancient genomes to identify their evolutionary patterns. Our results identified significant positive selection signals in 18 ASD risk SNPs. Functional and ontology analysis indicate the role of biological and cellular processes associated with various brain functions. The core of the biological interaction network constitutes genes for cognition and learning while genes in the periphery of the network had direct or indirect impact on brain function. Ancient genome analysis identified de novo and conserved evolutionary selection clusters. The de-novo evolutionary cluster represented genes involved in cognitive function. Relative enrichment of the ASD risk SNPs from the respective evolutionary cluster or biological interaction networks may help in addressing the phenotypic diversity in ASD. This cognitive genomic tradeoff signatures impacting the biological networks can explain the paradoxical phenotypes in ASD.
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21
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García A, Nores R, Motti JMB, Pauro M, Luisi P, Bravi CM, Fabra M, Gosling AL, Kardailsky O, Boocock J, Solé-Morata N, Matisoo-Smith EA, Comas D, Demarchi DA. Ancient and modern mitogenomes from Central Argentina: new insights into population continuity, temporal depth and migration in South America. Hum Mol Genet 2021; 30:1200-1217. [PMID: 33856032 DOI: 10.1093/hmg/ddab105] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2020] [Revised: 03/15/2021] [Accepted: 03/31/2021] [Indexed: 12/22/2022] Open
Abstract
The inverted triangle shape of South America places Argentina territory as a geographical crossroads between the two principal peopling streams that followed either the Pacific or the Atlantic coasts, which could have then merged in Central Argentina (CA). Although the genetic diversity from this region is therefore crucial to decipher past population movements in South America, its characterization has been overlooked so far. We report 92 modern and 22 ancient mitogenomes spanning a temporal range of 5000 years, which were compared with a large set of previously reported data. Leveraging this dataset representative of the mitochondrial diversity of the subcontinent, we investigate the maternal history of CA populations within a wider geographical context. We describe a large number of novel clades within the mitochondrial DNA tree, thus providing new phylogenetic interpretations for South America. We also identify several local clades of great temporal depth with continuity until the present time, which stem directly from the founder haplotypes, suggesting that they originated in the region and expanded from there. Moreover, the presence of lineages characteristic of other South American regions reveals the existence of gene flow to CA. Finally, we report some lineages with discontinuous distribution across the Americas, which suggest the persistence of relic lineages likely linked to the first population arrivals. The present study represents to date the most exhaustive attempt to elaborate a Native American genetic map from modern and ancient complete mitochondrial genomes in Argentina and provides relevant information about the general process of settlement in South America.
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Affiliation(s)
- Angelina García
- Departamento de Antropología, Facultad de Filosofía y Humanidades, Universidad Nacional de Córdoba, Córdoba 5000, Argentina.,Instituto de Antropología de Córdoba (IDACOR), CONICET, Universidad Nacional de Córdoba, Córdoba 5000, Argentina
| | - Rodrigo Nores
- Departamento de Antropología, Facultad de Filosofía y Humanidades, Universidad Nacional de Córdoba, Córdoba 5000, Argentina.,Instituto de Antropología de Córdoba (IDACOR), CONICET, Universidad Nacional de Córdoba, Córdoba 5000, Argentina
| | - Josefina M B Motti
- FACSO (NEIPHPA), Universidad Nacional del Centro de la Provincia de Buenos Aires, CONICET, Quequén 7631, Argentina
| | - Maia Pauro
- Departamento de Antropología, Facultad de Filosofía y Humanidades, Universidad Nacional de Córdoba, Córdoba 5000, Argentina.,Instituto de Antropología de Córdoba (IDACOR), CONICET, Universidad Nacional de Córdoba, Córdoba 5000, Argentina
| | - Pierre Luisi
- Departamento de Antropología, Facultad de Filosofía y Humanidades, Universidad Nacional de Córdoba, Córdoba 5000, Argentina
| | - Claudio M Bravi
- Instituto Multidisciplinario de Biología Celular (IMBICE), CCT La Plata CONICET, CICPBA, Universidad Nacional de La Plata, La Plata 1906, Argentina
| | - Mariana Fabra
- Departamento de Antropología, Facultad de Filosofía y Humanidades, Universidad Nacional de Córdoba, Córdoba 5000, Argentina.,Instituto de Antropología de Córdoba (IDACOR), CONICET, Universidad Nacional de Córdoba, Córdoba 5000, Argentina
| | - Anna L Gosling
- Department of Anatomy, University of Otago, Dunedin 9054, New Zealand
| | - Olga Kardailsky
- Department of Anatomy, University of Otago, Dunedin 9054, New Zealand
| | - James Boocock
- Department of Biochemistry, School of Biomedical Sciences, University of Otago, Dunedin 9054, New Zealand.,Department of Human Genetics, David Geffen School of Medicine at UCLA, Los Angeles, CA 90095, USA
| | - Neus Solé-Morata
- Departament de Ciències Experimentals i de la Salut, Institut de Biologia Evolutiva (CSIC-UPF), Universitat Pompeu Fabra, Barcelona 08003, Spain
| | | | - David Comas
- Departament de Ciències Experimentals i de la Salut, Institut de Biologia Evolutiva (CSIC-UPF), Universitat Pompeu Fabra, Barcelona 08003, Spain
| | - Darío A Demarchi
- Departamento de Antropología, Facultad de Filosofía y Humanidades, Universidad Nacional de Córdoba, Córdoba 5000, Argentina.,Instituto de Antropología de Córdoba (IDACOR), CONICET, Universidad Nacional de Córdoba, Córdoba 5000, Argentina
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22
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Wakim V, Abi Khalil E, Salloum AK, Khazen G, Ghassibe-Sabbagh M, Zalloua PA. New susceptibility alleles associated with severe coronary artery stenosis in the Lebanese population. BMC Med Genomics 2021; 14:90. [PMID: 33766035 PMCID: PMC7993530 DOI: 10.1186/s12920-021-00942-x] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2020] [Accepted: 03/16/2021] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Coronary Artery Disease (CAD) is the narrowing or blockage of the coronary arteries. It is closely associated with numerous genetics and environmental factors that have been extensively evaluated in various populations. In recent studies, severe phenotypes have been strongly linked to genetic risk factors. METHODS This study investigated the association of clinical, demographic, and genetic factors with severe coronary artery stenosis phenotypes in our population composed of 1734 individuals with severe coronary stenosis (≥ 50% in coronary vessels) and comparing them to 757 controls with no evidence of stenosis on angiography. We performed generalized linear model (GLM) genome-wide association studies to evaluate three stratification models and their associations to characteristics of the clinical disease. In model 1, patients were not stratified. In model 2, patients were stratified based on presence or absence of CAD family history (FxCAD). In model 3, patients were stratified by young age of CAD onset. RESULTS Eight SNPs (single nucleotide polymorphism) were significantly associated with severe CAD phenotypes in the various models [Formula: see text], four of these SNPs were associated with severe CAD and the four others were specifically significant for young CAD patients. While these SNPs were not previously reported for association with CAD, six of them are present in genes that have already been linked to coronary disease. CONCLUSION In conclusion, this study presents new genetic factors associated with severe stenosis and highlights different risk factors associated with a young age at diagnosis of CAD.
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Affiliation(s)
- Victor Wakim
- School of Medicine, Lebanese American University, Beirut, Lebanon
| | - Elie Abi Khalil
- Department of Natural Sciences, School of Arts and Sciences, Lebanese American University, Beirut, Lebanon
| | | | - Georges Khazen
- Department of Natural Sciences, School of Arts and Sciences, Lebanese American University, Beirut, Lebanon
| | - Michella Ghassibe-Sabbagh
- Department of Natural Sciences, School of Arts and Sciences, Lebanese American University, Beirut, Lebanon.
| | - Pierre A Zalloua
- School of Medicine, Lebanese American University, Beirut, Lebanon.
- Harvard School of Public Health, Boston, MA, 02215, USA.
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Long X, Xue H. Genetic-variant hotspots and hotspot clusters in the human genome facilitating adaptation while increasing instability. Hum Genomics 2021; 15:19. [PMID: 33741065 PMCID: PMC7976700 DOI: 10.1186/s40246-021-00318-3] [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: 10/03/2020] [Accepted: 03/04/2021] [Indexed: 12/25/2022] Open
Abstract
Background Genetic variants, underlining phenotypic diversity, are known to distribute unevenly in the human genome. A comprehensive understanding of the distributions of different genetic variants is important for insights into genetic functions and disorders. Methods Herein, a sliding-window scan of regional densities of eight kinds of germline genetic variants, including single-nucleotide-polymorphisms (SNPs) and four size-classes of copy-number-variations (CNVs) in the human genome has been performed. Results The study has identified 44,379 hotspots with high genetic-variant densities, and 1135 hotspot clusters comprising more than one type of hotspots, accounting for 3.1% and 0.2% of the genome respectively. The hotspots and clusters are found to co-localize with different functional genomic features, as exemplified by the associations of hotspots of middle-size CNVs with histone-modification sites, work with balancing and positive selections to meet the need for diversity in immune proteins, and facilitate the development of sensory-perception and neuroactive ligand-receptor interaction pathways in the function-sparse late-replicating genomic sequences. Genetic variants of different lengths co-localize with retrotransposons of different ages on a “long-with-young” and “short-with-all” basis. Hotspots and clusters are highly associated with tumor suppressor genes and oncogenes (p < 10−10), and enriched with somatic tumor CNVs and the trait- and disease-associated SNPs identified by genome-wise association studies, exceeding tenfold enrichment in clusters comprising SNPs and extra-long CNVs. Conclusions In conclusion, the genetic-variant hotspots and clusters represent two-edged swords that spearhead both positive and negative genomic changes. Their strong associations with complex traits and diseases also open up a potential “Common Disease-Hotspot Variant” approach to the missing heritability problem. Supplementary Information The online version contains supplementary material available at 10.1186/s40246-021-00318-3.
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Affiliation(s)
- Xi Long
- Division of Life Science and Applied Genomics Centre, Hong Kong University of Science and Technology, Clear Water Bay, Hong Kong, China.,HKUST Shenzhen Research Institute, 9 Yuexing First Road, Nanshan, Shenzhen, China
| | - Hong Xue
- Division of Life Science and Applied Genomics Centre, Hong Kong University of Science and Technology, Clear Water Bay, Hong Kong, China. .,HKUST Shenzhen Research Institute, 9 Yuexing First Road, Nanshan, Shenzhen, China. .,Centre for Cancer Genomics, School of Basic Medicine and Clinical Pharmacy, China Pharmaceutical University, Nanjing, Jiangsu, China.
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24
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Calò CM, Onali F, Robledo R, Flore L, Massidda M, Francalacci P. Worldwide variation of the COL14A1 gene is shaped by genetic drift rather than selective pressure. Mol Genet Genomic Med 2021; 9:e1629. [PMID: 33650783 PMCID: PMC8123734 DOI: 10.1002/mgg3.1629] [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: 06/03/2020] [Revised: 07/30/2020] [Accepted: 02/10/2021] [Indexed: 11/17/2022] Open
Abstract
Background The aim of this study is to analyze the worldwide distribution of SNP rs4870723 in COL14A1 gene to check if there are significant genetic differences among different populations and to test if the gene is a trait under selection. Methods Genomic DNA was extracted from 69 unrelated individuals from Sardinia and genotyped for SNP rs4870723. Data were compared with 26 different populations, clustered in 5 super‐populations, from the public 1000 genomes database. Allele frequency and heterozygosity were calculated with Genepop. The Hardy–Weinberg equilibrium and pairwise population differentiation through analysis of molecular variance (AMOVA FST) were determined with Arlequin. Results Allele frequencies of COL14A1 rs4870723 were compared in 27 populations clustered in 5 super‐populations. All populations were in the Hardy–Weinberg equilibrium. In almost all populations, allele C was the most frequent allele, reaching the highest values in East Asia. The 27 populations showed an appreciable structure, with significant differences observed between European, African, and Asian populations. Conclusion Significant differences were observed in the rs4870723 SNP distribution among the populations studied. However, we found no evidence for a selective pressure. Rather, the differentiation among the populations is likely the result of founder effect, genetic drift, and cultural factors, all events known to establish and maintain genetic diversity between populations.
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Affiliation(s)
- Carla M Calò
- Department of Life and Environment Sciences, University of Cagliari, Cagliari, Italy
| | - Federico Onali
- Department of Life and Environment Sciences, University of Cagliari, Cagliari, Italy
| | - Renato Robledo
- Department of Biomedical Sciences, University of Cagliari, Cagliari, Italy
| | - Laura Flore
- Department of Life and Environment Sciences, University of Cagliari, Cagliari, Italy
| | - Myosotis Massidda
- Department of Life and Environment Sciences, University of Cagliari, Cagliari, Italy
| | - Paolo Francalacci
- Department of Life and Environment Sciences, University of Cagliari, Cagliari, Italy
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25
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Nye J, Mondal M, Bertranpetit J, Laayouni H. A fully integrated machine learning scan of selection in the chimpanzee genome. NAR Genom Bioinform 2021; 2:lqaa061. [PMID: 33575612 PMCID: PMC7671310 DOI: 10.1093/nargab/lqaa061] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2019] [Revised: 06/11/2020] [Accepted: 07/31/2020] [Indexed: 11/13/2022] Open
Abstract
After diverging, each chimpanzee subspecies has been the target of unique selective pressures. Here, we employ a machine learning approach to classify regions as under positive selection or neutrality genome-wide. The regions determined to be under selection reflect the unique demographic and adaptive history of each subspecies. The results indicate that effective population size is important for determining the proportion of the genome under positive selection. The chimpanzee subspecies share signals of selection in genes associated with immunity and gene regulation. With these results, we have created a selection map for each population that can be displayed in a genome browser (www.hsb.upf.edu/chimp_browser). This study is the first to use a detailed demographic history and machine learning to map selection genome-wide in chimpanzee. The chimpanzee selection map will improve our understanding of the impact of selection on closely related subspecies and will empower future studies of chimpanzee.
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Affiliation(s)
- Jessica Nye
- Institut de Biologia Evolutiva (UPF-CSIC), Universitat Pompeu Fabra, Doctor Aiguader 88, 08003 Barcelona, Catalonia, Spain
| | - Mayukh Mondal
- Institut de Biologia Evolutiva (UPF-CSIC), Universitat Pompeu Fabra, Doctor Aiguader 88, 08003 Barcelona, Catalonia, Spain
| | - Jaume Bertranpetit
- Institut de Biologia Evolutiva (UPF-CSIC), Universitat Pompeu Fabra, Doctor Aiguader 88, 08003 Barcelona, Catalonia, Spain
| | - Hafid Laayouni
- Institut de Biologia Evolutiva (UPF-CSIC), Universitat Pompeu Fabra, Doctor Aiguader 88, 08003 Barcelona, Catalonia, Spain
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26
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Bhutani K, Stansifer K, Ticau S, Bojic L, Villani AC, Slisz J, Cremers CM, Roy C, Donovan J, Fiske B, Friedman RC. Widespread haploid-biased gene expression enables sperm-level natural selection. Science 2021; 371:science.abb1723. [PMID: 33446482 DOI: 10.1126/science.abb1723] [Citation(s) in RCA: 25] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2020] [Accepted: 12/18/2020] [Indexed: 12/16/2022]
Abstract
Sperm are haploid but must be functionally equivalent to distribute alleles equally among progeny. Accordingly, gene products are shared through spermatid cytoplasmic bridges that erase phenotypic differences between individual haploid sperm. Here, we show that a large class of mammalian genes are not completely shared across these bridges. We call these genes "genoinformative markers" (GIMs) and show that a subset can act as selfish genetic elements that spread alleles unevenly through murine, bovine, and human populations. We identify evolutionary pressure to avoid conflict between sperm and somatic function as GIMs are enriched for testis-specific gene expression, paralogs, and isoforms. Therefore, GIMs and sperm-level natural selection may help to explain why testis gene expression patterns are an outlier relative to all other tissues.
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Affiliation(s)
| | | | | | | | - Alexandra-Chloé Villani
- Center for Immunology and Inflammatory Diseases, Center for Cancer Research, Department of Medicine, Massachusetts General Hospital and Harvard Medical School, Boston, MA, USA.,Broad Institute of Massachusetts Institute of Technology and Harvard, Cambridge, MA, USA
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27
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Abstract
MicroRNA target sites are often conserved during evolution and purifying selection to maintain such sites is expected. On the other hand, comparative analyses identified a paucity of microRNA target sites in coexpressed transcripts, and novel target sites can potentially be deleterious. We proposed that selection against novel target sites pervasive. The analysis of derived allele frequencies revealed that, when the derived allele is a target site, the proportion of nontarget sites is higher than expected, particularly for highly expressed microRNAs. Thus, new alleles generating novel microRNA target sites can be deleterious and selected against. When we analyzed ancestral target sites, the derived (nontarget) allele frequency does not show statistical support for microRNA target allele conservation. We investigated the joint effects of microRNA conservation and expression and found that selection against microRNA target sites depends mostly on the expression level of the microRNA. We identified microRNA target sites with relatively high levels of population differentiation. However, when we analyze separately target sites in which the target allele is ancestral to the population, the proportion of single-nucleotide polymorphisms with high Fst significantly increases. These findings support that population differentiation is more likely in target sites that are lost than in the gain of new target sites. Our results indicate that selection against novel microRNA target sites is prevalent and, although individual sites may have a weak selective pressure, the overall effect across untranslated regions is not negligible and should be accounted when studying the evolution of genomic sequences.
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Affiliation(s)
- Andrea Hatlen
- School of Life Sciences, University of Essex, Colchester, United Kingdom
| | - Antonio Marco
- School of Life Sciences, University of Essex, Colchester, United Kingdom
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28
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Siddiqui SS, Vaill M, Do R, Khan N, Verhagen AL, Zhang W, Lenz HJ, Johnson-Pais TL, Leach RJ, Fraser G, Wang C, Feng GS, Varki N, Varki A. Human-specific polymorphic pseudogenization of SIGLEC12 protects against advanced cancer progression. FASEB Bioadv 2020; 3:69-82. [PMID: 33615152 PMCID: PMC7876704 DOI: 10.1096/fba.2020-00092] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2020] [Revised: 10/08/2020] [Accepted: 10/09/2020] [Indexed: 12/22/2022] Open
Abstract
Compared with our closest living evolutionary cousins, humans appear unusually prone to develop carcinomas (cancers arising from epithelia). The SIGLEC12 gene, which encodes the Siglec-XII protein expressed on epithelial cells, has several uniquely human features: a fixed homozygous missense mutation inactivating its natural ligand recognition property; a polymorphic frameshift mutation eliminating full-length protein expression in ~60%-70% of worldwide human populations; and, genomic features suggesting a negative selective sweep favoring the pseudogene state. Despite the loss of canonical sialic acid binding, Siglec-XII still recruits Shp2 and accelerates tumor growth in a mouse model. We hypothesized that dysfunctional Siglec-XII facilitates human carcinoma progression, correlating with known tumorigenic signatures of Shp2-dependent cancers. Immunohistochemistry was used to detect Siglec-XII expression on tissue microarrays. PC-3 prostate cancer cells were transfected with Siglec-XII and transcription of genes enriched with Siglec-XII was determined. Genomic SIGLEC12 status was determined for four different cancer cohorts. Finally, a dot blot analysis of human urinary epithelial cells was established to determine the Siglec-XII expressors versus non-expressors. Forced expression in a SIGLEC12 null carcinoma cell line enriched transcription of genes associated with cancer progression. While Siglec-XII was detected as expected in ~30%-40% of normal epithelia, ~80% of advanced carcinomas showed strong expression. Notably, >80% of late-stage colorectal cancers had a functional SIGLEC12 allele, correlating with overall increased mortality. Thus, advanced carcinomas are much more likely to occur in individuals whose genomes have an intact SIGLEC12 gene, likely because the encoded Siglec-XII protein recruits Shp2-related oncogenic pathways. The finding has prognostic, diagnostic, and therapeutic implications.
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Affiliation(s)
- Shoib S Siddiqui
- Departments of Medicine, Cellular and Molecular Medicine, and Pathology, Glycobiology Research and Training Cente and Center for Academic Research and Training in Anthropogeny University of California San Diego CA USA.,Present address: Department of Biotechnology American University of Ras Al Khaimah (AURAK American University of Ras Al Khaimah Road Al Burairat Area Ras Al Khaimah UAE
| | - Michael Vaill
- Departments of Medicine, Cellular and Molecular Medicine, and Pathology, Glycobiology Research and Training Cente and Center for Academic Research and Training in Anthropogeny University of California San Diego CA USA
| | - Raymond Do
- Departments of Medicine, Cellular and Molecular Medicine, and Pathology, Glycobiology Research and Training Cente and Center for Academic Research and Training in Anthropogeny University of California San Diego CA USA
| | - Naazneen Khan
- Departments of Medicine, Cellular and Molecular Medicine, and Pathology, Glycobiology Research and Training Cente and Center for Academic Research and Training in Anthropogeny University of California San Diego CA USA
| | - Andrea L Verhagen
- Departments of Medicine, Cellular and Molecular Medicine, and Pathology, Glycobiology Research and Training Cente and Center for Academic Research and Training in Anthropogeny University of California San Diego CA USA
| | - Wu Zhang
- University of Southern California Norris Comprehensive Cancer Center Los Angeles CA USA
| | - Heinz-Josef Lenz
- University of Southern California Norris Comprehensive Cancer Center Los Angeles CA USA
| | | | - Robin J Leach
- Department of Urology University of TX Health Science Center San Antonio TX USA.,Departments of Cell Systems and Anatomy University of TX Health Science Center San Antonio TX USA
| | - Gary Fraser
- School of Public Health Loma Linda University Loma Linda CA USA
| | - Charles Wang
- School of Public Health Loma Linda University Loma Linda CA USA
| | - Gen-Sheng Feng
- Departments of Medicine, Cellular and Molecular Medicine, and Pathology, Glycobiology Research and Training Cente and Center for Academic Research and Training in Anthropogeny University of California San Diego CA USA
| | - Nissi Varki
- Departments of Medicine, Cellular and Molecular Medicine, and Pathology, Glycobiology Research and Training Cente and Center for Academic Research and Training in Anthropogeny University of California San Diego CA USA
| | - Ajit Varki
- Departments of Medicine, Cellular and Molecular Medicine, and Pathology, Glycobiology Research and Training Cente and Center for Academic Research and Training in Anthropogeny University of California San Diego CA USA
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29
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Ohsawa S, Umemura T, Terada T, Muto Y. Network and Evolutionary Analysis of Human Epigenetic Regulators to Unravel Disease Associations. Genes (Basel) 2020; 11:genes11121457. [PMID: 33291839 PMCID: PMC7761991 DOI: 10.3390/genes11121457] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2020] [Revised: 11/29/2020] [Accepted: 11/30/2020] [Indexed: 12/15/2022] Open
Abstract
We carried out a system-level analysis of epigenetic regulators (ERs) and detailed the protein–protein interaction (PPI) network characteristics of disease-associated ERs. We found that most diseases associated with ERs can be clustered into two large groups, cancer diseases and developmental diseases. ER genes formed a highly interconnected PPI subnetwork, indicating a high tendency to interact and agglomerate with one another. We used the disease module detection (DIAMOnD) algorithm to expand the PPI subnetworks into a comprehensive cancer disease ER network (CDEN) and developmental disease ER network (DDEN). Using the transcriptome from early mouse developmental stages, we identified the gene co-expression modules significantly enriched for the CDEN and DDEN gene sets, which indicated the stage-dependent roles of ER-related disease genes during early embryonic development. The evolutionary rate and phylogenetic age distribution analysis indicated that the evolution of CDEN and DDEN genes was mostly constrained, and these genes exhibited older evolutionary age. Our analysis of human polymorphism data revealed that genes belonging to DDEN and Seed-DDEN were more likely to show signs of recent positive selection in human history. This finding suggests a potential association between positive selection of ERs and risk of developmental diseases through the mechanism of antagonistic pleiotropy.
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Affiliation(s)
- Shinji Ohsawa
- United Graduate School of Drug Discovery and Medical Information Sciences, Gifu University, 1-1, Yanagido, Gifu 501-1193, Japan; (S.O.); (T.T.)
- Department of Nursing, Ogaki Women’s College, 1-109, Nishinokawa-cho, Ogaki 503-8554, Japan
| | - Toshiaki Umemura
- Graduate School of Medicine and Pharmaceutical Sciences, University of Toyama, 2630, Sugitani, Toyama 930-0194, Japan;
| | - Tomoyoshi Terada
- United Graduate School of Drug Discovery and Medical Information Sciences, Gifu University, 1-1, Yanagido, Gifu 501-1193, Japan; (S.O.); (T.T.)
- Department of Functional Bioscience, Gifu University School of Medicine, 1-1, Yanagido, Gifu 501-1193, Japan
| | - Yoshinori Muto
- United Graduate School of Drug Discovery and Medical Information Sciences, Gifu University, 1-1, Yanagido, Gifu 501-1193, Japan; (S.O.); (T.T.)
- Department of Functional Bioscience, Gifu University School of Medicine, 1-1, Yanagido, Gifu 501-1193, Japan
- Correspondence: ; Tel.: +81-58-293-3241
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30
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Choudhury A, Aron S, Botigué LR, Sengupta D, Botha G, Bensellak T, Wells G, Kumuthini J, Shriner D, Fakim YJ, Ghoorah AW, Dareng E, Odia T, Falola O, Adebiyi E, Hazelhurst S, Mazandu G, Nyangiri OA, Mbiyavanga M, Benkahla A, Kassim SK, Mulder N, Adebamowo SN, Chimusa ER, Muzny D, Metcalf G, Gibbs RA, Rotimi C, Ramsay M, Adeyemo AA, Lombard Z, Hanchard NA. High-depth African genomes inform human migration and health. Nature 2020; 586:741-748. [PMID: 33116287 PMCID: PMC7759466 DOI: 10.1038/s41586-020-2859-7] [Citation(s) in RCA: 168] [Impact Index Per Article: 42.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2019] [Accepted: 08/07/2020] [Indexed: 01/05/2023]
Abstract
The African continent is regarded as the cradle of modern humans and African genomes contain more genetic variation than those from any other continent, yet only a fraction of the genetic diversity among African individuals has been surveyed1. Here we performed whole-genome sequencing analyses of 426 individuals-comprising 50 ethnolinguistic groups, including previously unsampled populations-to explore the breadth of genomic diversity across Africa. We uncovered more than 3 million previously undescribed variants, most of which were found among individuals from newly sampled ethnolinguistic groups, as well as 62 previously unreported loci that are under strong selection, which were predominantly found in genes that are involved in viral immunity, DNA repair and metabolism. We observed complex patterns of ancestral admixture and putative-damaging and novel variation, both within and between populations, alongside evidence that Zambia was a likely intermediate site along the routes of expansion of Bantu-speaking populations. Pathogenic variants in genes that are currently characterized as medically relevant were uncommon-but in other genes, variants denoted as 'likely pathogenic' in the ClinVar database were commonly observed. Collectively, these findings refine our current understanding of continental migration, identify gene flow and the response to human disease as strong drivers of genome-level population variation, and underscore the scientific imperative for a broader characterization of the genomic diversity of African individuals to understand human ancestry and improve health.
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Affiliation(s)
- Ananyo Choudhury
- Sydney Brenner Institute for Molecular Bioscience, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Shaun Aron
- Sydney Brenner Institute for Molecular Bioscience, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Laura R Botigué
- Center for Research in Agricultural Genomics (CRAG), Plant and Animal Genomics Program, CSIC-IRTA-UAB-UB, Barcelona, Spain
| | - Dhriti Sengupta
- Sydney Brenner Institute for Molecular Bioscience, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Gerrit Botha
- Computational Biology Division and H3ABioNet, Department of Integrative Biomedical Sciences, IDM, University of Cape Town, Cape Town, South Africa
| | - Taoufik Bensellak
- System and Data Engineering Team, Abdelmalek Essaadi University, ENSA, Tangier, Morocco
| | - Gordon Wells
- Centre for Proteomic and Genomic Research (CPGR), Cape Town, South Africa.,South African National Bioinformatics Institute, University of the Western Cape, Bellville, South Africa.,Africa Health Research Institute, Durban, South Africa
| | - Judit Kumuthini
- Centre for Proteomic and Genomic Research (CPGR), Cape Town, South Africa.,South African National Bioinformatics Institute, University of the Western Cape, Bellville, South Africa
| | - Daniel Shriner
- Center for Research on Genomics and Global Health, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, USA
| | - Yasmina J Fakim
- Department of Agriculture and Food Science, Faculty of Agriculture, University of Mauritius, Reduit, Mauritius.,Department of Digital Technologies,Faculty of Information, Communication & Digital Technologies, University of Mauritius, Reduit, Mauritius
| | - Anisah W Ghoorah
- Department of Digital Technologies,Faculty of Information, Communication & Digital Technologies, University of Mauritius, Reduit, Mauritius
| | - Eileen Dareng
- Department of Public Health and Primary Care, University of Cambridge, Cambridge, UK.,Institute of Human Virology Nigeria, Abuja, Nigeria
| | - Trust Odia
- Covenant University Bioinformatics Research (CUBRe), Covenant University, Ota, Nigeria
| | - Oluwadamilare Falola
- Covenant University Bioinformatics Research (CUBRe), Covenant University, Ota, Nigeria
| | - Ezekiel Adebiyi
- Covenant University Bioinformatics Research (CUBRe), Covenant University, Ota, Nigeria.,Department of Computer and Information Sciences, Covenant University, Ota, Nigeria
| | - Scott Hazelhurst
- Sydney Brenner Institute for Molecular Bioscience, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa.,School of Electrical and Information Engineering, University of the Witwatersrand, Johannesburg, South Africa
| | - Gaston Mazandu
- Computational Biology Division and H3ABioNet, Department of Integrative Biomedical Sciences, IDM, University of Cape Town, Cape Town, South Africa
| | - Oscar A Nyangiri
- College of Veterinary Medicine, Animal Resources and Biosecurity, Makerere University, Kampala, Uganda
| | - Mamana Mbiyavanga
- Computational Biology Division and H3ABioNet, Department of Integrative Biomedical Sciences, IDM, University of Cape Town, Cape Town, South Africa
| | - Alia Benkahla
- Laboratory of Bioinformatics, Biomathematics and Biostatistics (BIMS), Institute Pasteur of Tunis, Tunis, Tunisia
| | - Samar K Kassim
- Medical Biochemistry and Molecular Biology Department, Faculty of Medicine, Ain Shams University, Abbaseya, Cairo, Egypt
| | - Nicola Mulder
- Computational Biology Division and H3ABioNet, Department of Integrative Biomedical Sciences, IDM, University of Cape Town, Cape Town, South Africa
| | - Sally N Adebamowo
- Department of Epidemiology and Public Health, University of Maryland School of Medicine, University of Maryland Baltimore, Baltimore, MD, USA.,University of Maryland Greenebaum Comprehensive Cancer Center, University of Maryland School of Medicine, University of Maryland Baltimore, Baltimore, MD, USA
| | - Emile R Chimusa
- Division of Human Genetics, Department of Pathology, Faculty of Health Sciences, Institute for Infectious, Disease and Molecular Medicine, University of Cape Town, Cape Town, South Africa
| | - Donna Muzny
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX, USA
| | - Ginger Metcalf
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX, USA
| | - Richard A Gibbs
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX, USA.,Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, USA
| | | | - Charles Rotimi
- Center for Research on Genomics and Global Health, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, USA
| | - Michèle Ramsay
- Sydney Brenner Institute for Molecular Bioscience, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa.,Division of Human Genetics, National Health Laboratory Service, and School of Pathology, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | | | - Adebowale A Adeyemo
- Center for Research on Genomics and Global Health, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD, USA.
| | - Zané Lombard
- Division of Human Genetics, National Health Laboratory Service, and School of Pathology, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa.
| | - Neil A Hanchard
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, USA.
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31
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Salnikova LE, Khadzhieva MB, Kolobkov DS, Gracheva AS, Kuzovlev AN, Abilev SK. Cytokines mapping for tissue-specific expression, eQTLs and GWAS traits. Sci Rep 2020; 10:14740. [PMID: 32895400 PMCID: PMC7477549 DOI: 10.1038/s41598-020-71018-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2020] [Accepted: 07/28/2020] [Indexed: 12/02/2022] Open
Abstract
Dysregulation in cytokine production has been linked to the pathogenesis of various immune-mediated traits, in which genetic variability contributes to the etiopathogenesis. GWA studies have identified many genetic variants in or near cytokine genes, nonetheless, the translation of these findings into knowledge of functional determinants of complex traits remains a fundamental challenge. In this study we aimed at collection, analysis and interpretation of data on cytokines focused on their tissue-specific expression, eQTLs and GWAS traits. Using GO annotations, we generated a list of 314 cytokines and analyzed them with the GTEx resource. Cytokines were highly tissue-specific, 82.3% of cytokines had Tau expression metrics ≥ 0.8. In total, 3077 associations for 1760 unique SNPs in or near 244 cytokines were mapped in the NHGRI-EBI GWAS Catalog. According to the Experimental Factor Ontology resource, the largest numbers of disease associations were related to 'Inflammatory disease', 'Immune system disease' and 'Asthma'. The GTEx-based analysis revealed that among GWAS SNPs, 1142 SNPs had eQTL effects and influenced expression levels of 999 eGenes, among them 178 cytokines. Several types of enrichment analysis showed that it was cytokines expression variability that fundamentally contributed to the molecular origins of considered immune-mediated conditions.
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Affiliation(s)
- Lyubov E Salnikova
- Laboratory of Ecological Genetics, N.I. Vavilov Institute of General Genetics, Russian Academy of Sciences, 3 Gubkin Street, Moscow, Russia, 117971.
- Laboratory of Clinical Pathophysiology of Critical Conditions, Federal Research and Clinical Center of Intensive Care Medicine and Rehabilitology, Petrovka str, 25, b.2, Moscow, Russia, 107031.
| | - Maryam B Khadzhieva
- Laboratory of Ecological Genetics, N.I. Vavilov Institute of General Genetics, Russian Academy of Sciences, 3 Gubkin Street, Moscow, Russia, 117971
- Laboratory of Clinical Pathophysiology of Critical Conditions, Federal Research and Clinical Center of Intensive Care Medicine and Rehabilitology, Petrovka str, 25, b.2, Moscow, Russia, 107031
| | - Dmitry S Kolobkov
- Laboratory of Ecological Genetics, N.I. Vavilov Institute of General Genetics, Russian Academy of Sciences, 3 Gubkin Street, Moscow, Russia, 117971
- Department of Computer Science and Applied Mathematics, Weizmann Institute of Science, 234 Herzl St., PO Box 26, 7610001, Rehovot, Israel
- Department of Molecular Cell Biology, Weizmann Institute of Science, 234 Herzl St., PO Box 26, 7610001, Rehovot, Israel
| | - Alesya S Gracheva
- Laboratory of Ecological Genetics, N.I. Vavilov Institute of General Genetics, Russian Academy of Sciences, 3 Gubkin Street, Moscow, Russia, 117971
- Laboratory of Clinical Pathophysiology of Critical Conditions, Federal Research and Clinical Center of Intensive Care Medicine and Rehabilitology, Petrovka str, 25, b.2, Moscow, Russia, 107031
| | - Artem N Kuzovlev
- Laboratory of Clinical Pathophysiology of Critical Conditions, Federal Research and Clinical Center of Intensive Care Medicine and Rehabilitology, Petrovka str, 25, b.2, Moscow, Russia, 107031
| | - Serikbay K Abilev
- Laboratory of Ecological Genetics, N.I. Vavilov Institute of General Genetics, Russian Academy of Sciences, 3 Gubkin Street, Moscow, Russia, 117971
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32
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Association between MCT1 T1470A polymorphism and climbing status in Polish and Japanese climbers. Biol Sport 2020; 38:229-234. [PMID: 34079167 PMCID: PMC8139354 DOI: 10.5114/biolsport.2020.98624] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2020] [Revised: 06/13/2020] [Accepted: 08/04/2020] [Indexed: 01/07/2023] Open
Abstract
Sport climbing will become an official event at the 2020 Tokyo Olympics; it is a popular wilderness sport among athletes and amateurs. Our previous study suggested that the T1470A polymorphism (rs1049434) of the monocarboxylate transporter 1 (MCT1) gene is associated with athletic performance and physiological phenotypes. The purpose of this study was to investigate the frequency of MCT1 T1470A polymorphism in Polish and Japanese climbers using a case-control study. Our sample consisted of 226 climbers (Japanese: n = 100, 64 male and 36 female; Polish: n = 126, 97 male and 29 female) and 1028 non-athletic controls (Japanese, n = 407; Polish = 621) who were genotyped for the MCT1 T1470A polymorphism (rs1049434) using the TaqMan SNP genotyping assay or restriction enzyme. The frequency of the TT genotype and T allele was significantly higher in climbers than in controls among the Polish subjects (genotype: p = 0.030, allele: p = 0.010); however, there were no significant differences in the genotype and allelic frequencies between the Japanese climbers and controls (genotype: p = 0.968; allele: p = 0.803). Our results suggested that the frequency of the T allele (TT+TA genotype) in the MCT1 T1470A polymorphism is over-represented in Polish climbers but not in Japanese climbers. In addition, the frequency of the T allele and TT genotype in Polish lead climbers is higher than that in controls.
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33
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LaBella AL, Abraham A, Pichkar Y, Fong SL, Zhang G, Muglia LJ, Abbot P, Rokas A, Capra JA. Accounting for diverse evolutionary forces reveals mosaic patterns of selection on human preterm birth loci. Nat Commun 2020; 11:3731. [PMID: 32709900 PMCID: PMC7382462 DOI: 10.1038/s41467-020-17258-6] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2019] [Accepted: 06/19/2020] [Indexed: 02/02/2023] Open
Abstract
Currently, there is no comprehensive framework to evaluate the evolutionary forces acting on genomic regions associated with human complex traits and contextualize the relationship between evolution and molecular function. Here, we develop an approach to test for signatures of diverse evolutionary forces on trait-associated genomic regions. We apply our method to regions associated with spontaneous preterm birth (sPTB), a complex disorder of global health concern. We find that sPTB-associated regions harbor diverse evolutionary signatures including conservation, excess population differentiation, accelerated evolution, and balanced polymorphism. Furthermore, we integrate evolutionary context with molecular evidence to hypothesize how these regions contribute to sPTB risk. Finally, we observe enrichment in signatures of diverse evolutionary forces in sPTB-associated regions compared to genomic background. By quantifying multiple evolutionary forces acting on sPTB-associated regions, our approach improves understanding of both functional roles and the mosaic of evolutionary forces acting on loci. Our work provides a blueprint for investigating evolutionary pressures on complex traits.
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Affiliation(s)
- Abigail L LaBella
- Department of Biological Sciences, Vanderbilt University, Nashville, TN, 37235, USA
| | - Abin Abraham
- Vanderbilt Genetics Institute, Vanderbilt University, Nashville, TN, 37235, USA
- Vanderbilt University Medical Center, Vanderbilt University, Nashville, TN, 37232, USA
| | - Yakov Pichkar
- Department of Biological Sciences, Vanderbilt University, Nashville, TN, 37235, USA
| | - Sarah L Fong
- Vanderbilt Genetics Institute, Vanderbilt University, Nashville, TN, 37235, USA
| | - Ge Zhang
- Division of Human Genetics, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, 45229, USA
- The Center for Prevention of Preterm Birth, Perinatal Institute, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, 45229, USA
- March of Dimes Prematurity Research Center Ohio Collaborative, Cincinnati, OH, 45267, USA
- Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, OH, 45267, USA
| | - Louis J Muglia
- Division of Human Genetics, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, 45229, USA
- The Center for Prevention of Preterm Birth, Perinatal Institute, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, 45229, USA
- March of Dimes Prematurity Research Center Ohio Collaborative, Cincinnati, OH, 45267, USA
- Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, OH, 45267, USA
| | - Patrick Abbot
- Department of Biological Sciences, Vanderbilt University, Nashville, TN, 37235, USA
| | - Antonis Rokas
- Department of Biological Sciences, Vanderbilt University, Nashville, TN, 37235, USA.
- Department of Biomedical Informatics, Vanderbilt University School of Medicine, Nashville, TN, 37235, USA.
| | - John A Capra
- Department of Biological Sciences, Vanderbilt University, Nashville, TN, 37235, USA.
- Departments of Biomedical Informatics and Computer Science, Vanderbilt Genetics Institute, Center for Structural Biology, Vanderbilt University, Nashville, TN, 37235, USA.
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34
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Jallow MW, Cerami C, Clark TG, Prentice AM, Campino S. Differences in the frequency of genetic variants associated with iron imbalance among global populations. PLoS One 2020; 15:e0235141. [PMID: 32609760 PMCID: PMC7329092 DOI: 10.1371/journal.pone.0235141] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2020] [Accepted: 06/09/2020] [Indexed: 02/08/2023] Open
Abstract
Iron deficiency anaemia is a major health problem affecting approximately 1.2 billion people worldwide. Young children, women of reproductive age and pregnant women living in sub-Saharan Africa are the most vulnerable. It is estimated that iron deficiency accounts for half of anaemia cases. Apart from nutritional deficiency, infection, inflammation and genetic factors are the major drivers of anaemia. However, the role of genetic risk factors has not been thoroughly investigated. This is particularly relevant in African populations, as they carry high genetic diversity and have a high prevalence of anaemia. Multiple genetic variations in iron regulatory genes have been linked to impaired iron status. Here we conducted a literature review to identify genetic variants associated with iron imbalance among global populations. We compare their allele frequencies and risk scores and we investigated population-specific selection among populations of varying geographic origin using data from the Keneba Biobank representing individuals in rural Gambia and the 1000 Genomes Project. We identified a significant lack of data on the genetic determinants of iron status in sub-Saharan Africa. Most of the studies on genetic determinants of iron status have been conducted in Europeans. Also, we identified population differences in allele frequencies in candidate putative genetic risk factors. Given the disproportionately high genetic diversity in African populations coupled with their high prevalence of iron deficiency, there is need to investigate the genetic influences of low iron status in Sub-Saharan Africa. The resulting insights may inform the future implementation of iron intervention strategies.
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Affiliation(s)
- Momodou W. Jallow
- Nutrition Theme, MRC Unit The Gambia at London School of Hygiene & Tropical Medicine, Banjul, The Gambia
- Faculty of Infectious and Tropical Diseases, London School of Hygiene & Tropical Medicine, London, United Kingdom
- * E-mail: (SC); (MWJ)
| | - Carla Cerami
- Nutrition Theme, MRC Unit The Gambia at London School of Hygiene & Tropical Medicine, Banjul, The Gambia
| | - Taane G. Clark
- Faculty of Infectious and Tropical Diseases, London School of Hygiene & Tropical Medicine, London, United Kingdom
- Faculty of Epidemiology and Population Health, London School of Hygiene & Tropical Medicine, London, United Kingdom
| | - Andrew M. Prentice
- Nutrition Theme, MRC Unit The Gambia at London School of Hygiene & Tropical Medicine, Banjul, The Gambia
| | - Susana Campino
- Faculty of Infectious and Tropical Diseases, London School of Hygiene & Tropical Medicine, London, United Kingdom
- * E-mail: (SC); (MWJ)
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35
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Murga-Moreno J, Coronado-Zamora M, Bodelón A, Barbadilla A, Casillas S. PopHumanScan: the online catalog of human genome adaptation. Nucleic Acids Res 2020; 47:D1080-D1089. [PMID: 30335169 PMCID: PMC6323894 DOI: 10.1093/nar/gky959] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2018] [Accepted: 10/04/2018] [Indexed: 12/20/2022] Open
Abstract
Since the migrations that led humans to colonize Earth, our species has faced frequent adaptive challenges that have left signatures in the landscape of genetic variation and that we can identify in our today’s genomes. Here, we (i) perform an outlier approach on eight different population genetic statistics for 22 non-admixed human populations of the Phase III of the 1000 Genomes Project to detect selective sweeps at different historical ages, as well as events of recurrent positive selection in the human lineage; and (ii) create PopHumanScan, an online catalog that compiles and annotates all candidate regions under selection to facilitate their validation and thoroughly analysis. Well-known examples of human genetic adaptation published elsewhere are included in the catalog, as well as hundreds of other attractive candidates that will require further investigation. Designed as a collaborative database, PopHumanScan aims to become a central repository to share information, guide future studies and help advance our understanding of how selection has modeled our genomes as a response to changes in the environment or lifestyle of human populations. PopHumanScan is open and freely available at https://pophumanscan.uab.cat.
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Affiliation(s)
- Jesús Murga-Moreno
- Institut de Biotecnologia i de Biomedicina and Departament de Genètica i de Microbiologia, Universitat Autònoma de Barcelona, 08193 Bellaterra, Barcelona, Spain
| | - Marta Coronado-Zamora
- Institut de Biotecnologia i de Biomedicina and Departament de Genètica i de Microbiologia, Universitat Autònoma de Barcelona, 08193 Bellaterra, Barcelona, Spain
| | - Alejandra Bodelón
- Institut de Biotecnologia i de Biomedicina and Departament de Genètica i de Microbiologia, Universitat Autònoma de Barcelona, 08193 Bellaterra, Barcelona, Spain
| | - Antonio Barbadilla
- Institut de Biotecnologia i de Biomedicina and Departament de Genètica i de Microbiologia, Universitat Autònoma de Barcelona, 08193 Bellaterra, Barcelona, Spain
| | - Sònia Casillas
- Institut de Biotecnologia i de Biomedicina and Departament de Genètica i de Microbiologia, Universitat Autònoma de Barcelona, 08193 Bellaterra, Barcelona, Spain
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36
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Harris AM, DeGiorgio M. Identifying and Classifying Shared Selective Sweeps from Multilocus Data. Genetics 2020; 215:143-171. [PMID: 32152048 PMCID: PMC7198270 DOI: 10.1534/genetics.120.303137] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2019] [Accepted: 02/29/2020] [Indexed: 11/18/2022] Open
Abstract
Positive selection causes beneficial alleles to rise to high frequency, resulting in a selective sweep of the diversity surrounding the selected sites. Accordingly, the signature of a selective sweep in an ancestral population may still remain in its descendants. Identifying signatures of selection in the ancestor that are shared among its descendants is important to contextualize the timing of a sweep, but few methods exist for this purpose. We introduce the statistic SS-H12, which can identify genomic regions under shared positive selection across populations and is based on the theory of the expected haplotype homozygosity statistic H12, which detects recent hard and soft sweeps from the presence of high-frequency haplotypes. SS-H12 is distinct from comparable statistics because it requires a minimum of only two populations, and properly identifies and differentiates between independent convergent sweeps and true ancestral sweeps, with high power and robustness to a variety of demographic models. Furthermore, we can apply SS-H12 in conjunction with the ratio of statistics we term [Formula: see text] and [Formula: see text] to further classify identified shared sweeps as hard or soft. Finally, we identified both previously reported and novel shared sweep candidates from human whole-genome sequences. Previously reported candidates include the well-characterized ancestral sweeps at LCT and SLC24A5 in Indo-Europeans, as well as GPHN worldwide. Novel candidates include an ancestral sweep at RGS18 in sub-Saharan Africans involved in regulating the platelet response and implicated in sudden cardiac death, and a convergent sweep at C2CD5 between European and East Asian populations that may explain their different insulin responses.
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Affiliation(s)
- Alexandre M Harris
- Department of Biology, Pennsylvania State University, University Park, Pennsylvania 16802
- Molecular, Cellular, and Integrative Biosciences at the Huck Institutes of the Life Sciences, Pennsylvania State University, University Park, Pennsylvania 16802
| | - Michael DeGiorgio
- Department of Computer and Electrical Engineering and Computer Science, Florida Atlantic University, Boca Raton, Florida 33431
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37
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Hysi PG, Choquet H, Khawaja AP, Wojciechowski R, Tedja MS, Yin J, Simcoe MJ, Patasova K, Mahroo OA, Thai KK, Cumberland PM, Melles RB, Verhoeven VJM, Vitart V, Segre A, Stone RA, Wareham N, Hewitt AW, Mackey DA, Klaver CCW, MacGregor S, Khaw PT, Foster PJ, Guggenheim JA, Rahi JS, Jorgenson E, Hammond CJ. Meta-analysis of 542,934 subjects of European ancestry identifies new genes and mechanisms predisposing to refractive error and myopia. Nat Genet 2020; 52:401-407. [PMID: 32231278 PMCID: PMC7145443 DOI: 10.1038/s41588-020-0599-0] [Citation(s) in RCA: 157] [Impact Index Per Article: 39.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2019] [Accepted: 02/24/2020] [Indexed: 01/10/2023]
Abstract
Refractive errors, in particular myopia, are a leading cause of morbidity and disability worldwide. Genetic investigation can improve understanding of the molecular mechanisms that underlie abnormal eye development and impaired vision. We conducted a meta-analysis of genome-wide association studies (GWAS) that involved 542,934 European participants and identified 336 novel genetic loci associated with refractive error. Collectively, all associated genetic variants explain 18.4% of heritability and improve the accuracy of myopia prediction (area under the curve (AUC) = 0.75). Our results suggest that refractive error is genetically heterogeneous, driven by genes that participate in the development of every anatomical component of the eye. In addition, our analyses suggest that genetic factors controlling circadian rhythm and pigmentation are also involved in the development of myopia and refractive error. These results may enable the prediction of refractive error and the development of personalized myopia prevention strategies in the future.
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Affiliation(s)
- Pirro G Hysi
- Section of Ophthalmology, School of Life Course Sciences, King's College London, London, UK. .,Department of Twin Research and Genetic Epidemiology, King's College London, London, UK. .,UCL Great Ormond Street Institute of Child Health, University College London, London, UK.
| | - Hélène Choquet
- Division of Research, Kaiser Permanente Northern California, Oakland, CA, USA
| | - Anthony P Khawaja
- NIHR Biomedical Research Centre, Moorfields Eye Hospital NHS Foundation Trust and UCL Institute of Ophthalmology, London, UK.,Department of Public Health and Primary Care, Institute of Public Health, University of Cambridge School of Clinical Medicine, Cambridge, UK
| | - Robert Wojciechowski
- Department of Biophysics, Johns Hopkins University, Baltimore, MD, USA.,Wilmer Eye Institute, Johns Hopkins School of Medicine, Baltimore, MD, USA
| | - Milly S Tedja
- Department of Ophthalmology, Erasmus Medical Center, Rotterdam, the Netherlands.,Department of Epidemiology, Erasmus Medical Center, Rotterdam, the Netherlands
| | - Jie Yin
- Division of Research, Kaiser Permanente Northern California, Oakland, CA, USA
| | - Mark J Simcoe
- Department of Twin Research and Genetic Epidemiology, King's College London, London, UK
| | - Karina Patasova
- Section of Ophthalmology, School of Life Course Sciences, King's College London, London, UK
| | - Omar A Mahroo
- Section of Ophthalmology, School of Life Course Sciences, King's College London, London, UK.,NIHR Biomedical Research Centre, Moorfields Eye Hospital NHS Foundation Trust and UCL Institute of Ophthalmology, London, UK
| | - Khanh K Thai
- Division of Research, Kaiser Permanente Northern California, Oakland, CA, USA
| | - Phillippa M Cumberland
- UCL Great Ormond Street Institute of Child Health, University College London, London, UK.,Ulverscroft Vision Research Group, UCL Great Ormond Street Institute of Child Health, University College London, London, UK
| | - Ronald B Melles
- Department of Ophthalmology Kaiser Permanente Northern California, Redwood City, CA, USA
| | - Virginie J M Verhoeven
- Department of Ophthalmology, Erasmus Medical Center, Rotterdam, the Netherlands.,Department of Epidemiology, Erasmus Medical Center, Rotterdam, the Netherlands.,Department of Clinical Genetics, Erasmus Medical Center, Rotterdam, the Netherlands
| | - Veronique Vitart
- MRC Human Genetics Unit, MRC Institute of Genetics and Molecular Medicine, The University of Edinburgh, Edinburgh, UK
| | - Ayellet Segre
- Department of Ophthalmology, Harvard Medical School, Massachusetts Eye and Ear, Boston, MA, USA
| | - Richard A Stone
- Department of Ophthalmology, University of Pennsylvania Perelman School of Medicine, Philadelphia, PA, USA
| | - Nick Wareham
- Department of Public Health and Primary Care, Institute of Public Health, University of Cambridge School of Clinical Medicine, Cambridge, UK
| | - Alex W Hewitt
- Department of Ophthalmology, Royal Hobart Hospital, Hobart, Tasmania, Australia
| | - David A Mackey
- Department of Ophthalmology, Royal Hobart Hospital, Hobart, Tasmania, Australia.,Centre for Ophthalmology and Visual Science, University of Western Australia, Lions Eye Institute, Perth, Western Australia, Australia
| | - Caroline C W Klaver
- Department of Ophthalmology, Erasmus Medical Center, Rotterdam, the Netherlands.,Department of Epidemiology, Erasmus Medical Center, Rotterdam, the Netherlands.,Department of Ophthalmology, Radboud University Medical Center, Rotterdam, the Netherlands.,Institute of Molecular and Clinical Ophthalmology Basel, Basel, Switzerland
| | - Stuart MacGregor
- QIMR Berghofer Medical Research Institute, Brisbane, Queensland, Australia
| | | | - Peng T Khaw
- NIHR Biomedical Research Centre, Moorfields Eye Hospital NHS Foundation Trust and UCL Institute of Ophthalmology, London, UK
| | - Paul J Foster
- NIHR Biomedical Research Centre, Moorfields Eye Hospital NHS Foundation Trust and UCL Institute of Ophthalmology, London, UK.,Division of Genetics and Epidemiology, UCL Institute of Ophthalmology, London, UK
| | | | | | | | - Jugnoo S Rahi
- UCL Great Ormond Street Institute of Child Health, University College London, London, UK.,NIHR Biomedical Research Centre, Moorfields Eye Hospital NHS Foundation Trust and UCL Institute of Ophthalmology, London, UK.,Ulverscroft Vision Research Group, UCL Great Ormond Street Institute of Child Health, University College London, London, UK.,Department of Ophthalmology and NIHR, Biomedical Research Centre, Great Ormond Street Hospital NHS Foundation Trust, London, UK
| | - Eric Jorgenson
- Division of Research, Kaiser Permanente Northern California, Oakland, CA, USA
| | - Christopher J Hammond
- Section of Ophthalmology, School of Life Course Sciences, King's College London, London, UK.,Department of Twin Research and Genetic Epidemiology, King's College London, London, UK
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38
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Perdomo-Sabogal Á, Nowick K. Genetic Variation in Human Gene Regulatory Factors Uncovers Regulatory Roles in Local Adaptation and Disease. Genome Biol Evol 2019; 11:2178-2193. [PMID: 31228201 PMCID: PMC6685493 DOI: 10.1093/gbe/evz131] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/18/2019] [Indexed: 01/13/2023] Open
Abstract
Differences in gene regulation have been suggested to play essential roles in the evolution of phenotypic changes. Although DNA changes in cis-regulatory elements affect only the regulation of its corresponding gene, variations in gene regulatory factors (trans) can have a broader effect, because the expression of many target genes might be affected. Aiming to better understand how natural selection may have shaped the diversity of gene regulatory factors in human, we assembled a catalog of all proteins involved in controlling gene expression. We found that at least five DNA-binding transcription factor classes are enriched among genes located in candidate regions for selection, suggesting that they might be relevant for understanding regulatory mechanisms involved in human local adaptation. The class of KRAB-ZNFs, zinc-finger (ZNF) genes with a Krüppel-associated box, stands out by first, having the most genes located on candidate regions for positive selection. Second, displaying most nonsynonymous single nucleotide polymorphisms (SNPs) with high genetic differentiation between populations within these regions. Third, having 27 KRAB-ZNF gene clusters with high extended haplotype homozygosity. Our further characterization of nonsynonymous SNPs in ZNF genes located within candidate regions for selection, suggests regulatory modifications that might influence the expression of target genes at population level. Our detailed investigation of three candidate regions revealed possible explanations for how SNPs may influence the prevalence of schizophrenia, eye development, and fertility in humans, among other phenotypes. The genetic variation we characterized here may be responsible for subtle to rough regulatory changes that could be important for understanding human adaptation.
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Affiliation(s)
- Álvaro Perdomo-Sabogal
- Human Biology Group, Department of Biology, Chemistry and Pharmacy, Institute for Zoology, Freie Universität Berlin, Germany
| | - Katja Nowick
- Human Biology Group, Department of Biology, Chemistry and Pharmacy, Institute for Zoology, Freie Universität Berlin, Germany
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Casillas S, Mulet R, Villegas-Mirón P, Hervas S, Sanz E, Velasco D, Bertranpetit J, Laayouni H, Barbadilla A. PopHuman: the human population genomics browser. Nucleic Acids Res 2019; 46:D1003-D1010. [PMID: 29059408 PMCID: PMC5753332 DOI: 10.1093/nar/gkx943] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2017] [Accepted: 10/04/2017] [Indexed: 12/17/2022] Open
Abstract
The 1000 Genomes Project (1000GP) represents the most comprehensive world-wide nucleotide variation data set so far in humans, providing the sequencing and analysis of 2504 genomes from 26 populations and reporting >84 million variants. The availability of this sequence data provides the human lineage with an invaluable resource for population genomics studies, allowing the testing of molecular population genetics hypotheses and eventually the understanding of the evolutionary dynamics of genetic variation in human populations. Here we present PopHuman, a new population genomics-oriented genome browser based on JBrowse that allows the interactive visualization and retrieval of an extensive inventory of population genetics metrics. Efficient and reliable parameter estimates have been computed using a novel pipeline that faces the unique features and limitations of the 1000GP data, and include a battery of nucleotide variation measures, divergence and linkage disequilibrium parameters, as well as different tests of neutrality, estimated in non-overlapping windows along the chromosomes and in annotated genes for all 26 populations of the 1000GP. PopHuman is open and freely available at http://pophuman.uab.cat.
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Affiliation(s)
- Sònia Casillas
- Institut de Biotecnologia i de Biomedicina and Department de Genètica i de Microbiologia, Universitat Autònoma de Barcelona, 08193 Bellaterra, Barcelona, Spain
- To whom correspondence should be addressed. Sònia Casillas. Tel: +34 93 5868958; Fax: +34 93 5812011; . Correspondence may also be addressed to Antonio Barbadilla.
| | - Roger Mulet
- Institut de Biotecnologia i de Biomedicina and Department de Genètica i de Microbiologia, Universitat Autònoma de Barcelona, 08193 Bellaterra, Barcelona, Spain
| | - Pablo Villegas-Mirón
- Institute of Evolutionary Biology (UPF-CSIC), Universitat Pompeu Fabra, Doctor Aiguader 88 (PRBB), 08003 Barcelona, Catalonia, Spain
| | - Sergi Hervas
- Institut de Biotecnologia i de Biomedicina and Department de Genètica i de Microbiologia, Universitat Autònoma de Barcelona, 08193 Bellaterra, Barcelona, Spain
| | - Esteve Sanz
- Servei de Genòmica i Bioinformàtica, Universitat Autònoma de Barcelona, 08193 Bellaterra, Barcelona, Spain
| | - Daniel Velasco
- Institut de Biotecnologia i de Biomedicina and Department de Genètica i de Microbiologia, Universitat Autònoma de Barcelona, 08193 Bellaterra, Barcelona, Spain
| | - Jaume Bertranpetit
- Institute of Evolutionary Biology (UPF-CSIC), Universitat Pompeu Fabra, Doctor Aiguader 88 (PRBB), 08003 Barcelona, Catalonia, Spain
| | - Hafid Laayouni
- Institute of Evolutionary Biology (UPF-CSIC), Universitat Pompeu Fabra, Doctor Aiguader 88 (PRBB), 08003 Barcelona, Catalonia, Spain
- Bioinformatics Studies, ESCI-UPF, Pg. Pujades 1, 08003 Barcelona, Spain
| | - Antonio Barbadilla
- Institut de Biotecnologia i de Biomedicina and Department de Genètica i de Microbiologia, Universitat Autònoma de Barcelona, 08193 Bellaterra, Barcelona, Spain
- Servei de Genòmica i Bioinformàtica, Universitat Autònoma de Barcelona, 08193 Bellaterra, Barcelona, Spain
- To whom correspondence should be addressed. Sònia Casillas. Tel: +34 93 5868958; Fax: +34 93 5812011; . Correspondence may also be addressed to Antonio Barbadilla.
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Development of precision medicine approaches based on inter-individual variability of BCRP/ ABCG2. Acta Pharm Sin B 2019; 9:659-674. [PMID: 31384528 PMCID: PMC6664102 DOI: 10.1016/j.apsb.2019.01.007] [Citation(s) in RCA: 44] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2018] [Revised: 12/11/2018] [Accepted: 12/12/2018] [Indexed: 12/15/2022] Open
Abstract
Precision medicine is a rapidly-developing modality of medicine in human healthcare. Based on each patient׳s unique characteristics, more accurate dosages and drug selection can be made to achieve better therapeutic efficacy and less adverse reactions in precision medicine. A patient׳s individual parameters that affect drug transporter action can be used to develop a precision medicine guidance, due to the fact that therapeutic efficacy and adverse reactions of drugs can both be affected by expression and function of drug transporters on the cell membrane surface. The purpose of this review is to summarize unique characteristics of human breast cancer resistant protein (BCRP) and the genetic variability in the BCRP encoded gene ABCG2 in the development of precision medicine. Inter-individual variability of BCRP/ABCG2 can impact choices and outcomes of drug treatment for several diseases, including cancer chemotherapy. Several factors have been implicated in expression and function of BCRP, including genetic, epigenetic, physiologic, pathologic, and environmental factors. Understanding the roles of these factors in controlling expression and function of BCRP is critical for the development of precision medicine based on BCRP-mediated drug transport.
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Key Words
- 3′-UTR, 3′-untranslated region
- 5-aza-C, 5-aza-2′-deoxycytidine
- ABCG2, ATP-binding cassette subfamily G member 2
- ALL, acute lymphocytic leukemia
- AML, acute myeloid leukemia
- AUC, area under curve
- BCRP
- BCRP, breast cancer resistant protein
- Epigenetics
- FTC, fumitremorgin C
- Gene polymorphisms
- H3K4me3, histone H3 lysine 4 trimethylation
- H3K9me3, histone H3 lysine 9 trimethylation
- H3S10P, histone H3 serine 10 phosphorylation
- HDAC, histone deacetylase
- HIF-1α, hypoxia inducible factor 1 subunit alpha
- HIV-1, human immunodeficiency virus type-1
- HMG-CoA, β-hydroxy-β-methyl-glutaryl-coenzyme A
- MDR, multidrug resistance
- MDR1, multidrug resistance 1
- NBD, nucleotide binding domain
- P-gp, P-glycoprotein
- Physiologic factors
- Precision medicine
- RISC, RNA-induced silencing complex
- SNP, Single nucleotide polymorphism
- TKI, tyrosine kinase inhibitor
- Tat, transactivator protein
- miRNA, microRNA
- siRNA, small RNA interference
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Helmy M, Hatlen A, Marco A. The Impact of Population Variation in the Analysis of microRNA Target Sites. Noncoding RNA 2019; 5:E42. [PMID: 31234531 PMCID: PMC6630466 DOI: 10.3390/ncrna5020042] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2019] [Revised: 06/11/2019] [Accepted: 06/20/2019] [Indexed: 02/07/2023] Open
Abstract
The impact of population variation in the analysis of regulatory interactions is an underdeveloped area. MicroRNA target recognition occurs via pairwise complementarity. Consequently, a number of computational prediction tools have been developed to identify potential target sites that can be further validated experimentally. However, as microRNA target predictions are done mostly considering a reference genome sequence, target sites showing variation among populations are neglected. Here, we studied the variation at microRNA target sites in human populations and quantified their impact in microRNA target prediction. We found that African populations carry a significant number of potential microRNA target sites that are not detectable in the current human reference genome sequence. Some of these targets are conserved in primates and only lost in Out-of-Africa populations. Indeed, we identified experimentally validated microRNA/transcript interactions that are not detected in standard microRNA target prediction programs, yet they have segregating target alleles abundant in non-European populations. In conclusion, we show that ignoring population diversity may leave out regulatory elements essential to understand disease and gene expression, particularly neglecting populations of African origin.
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Affiliation(s)
- Mohab Helmy
- School of Biological Sciences, University of Essex, Colchester CO4 3SQ, UK.
| | - Andrea Hatlen
- School of Biological Sciences, University of Essex, Colchester CO4 3SQ, UK.
| | - Antonio Marco
- School of Biological Sciences, University of Essex, Colchester CO4 3SQ, UK.
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Saitou M, Gokcumen O. Resolving the Insertion Sites of Polymorphic Duplications Reveals a HERC2 Haplotype under Selection. Genome Biol Evol 2019; 11:1679-1690. [PMID: 31124564 PMCID: PMC6587411 DOI: 10.1093/gbe/evz107] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/19/2019] [Indexed: 12/18/2022] Open
Abstract
Polymorphic duplications in humans have been shown to contribute to phenotypic diversity. However, the evolutionary forces that maintain variable duplications across the human genome are largely unexplored. We developed a linkage-disequilibrium based method to detect insertion sites of polymorphic duplications not represented in reference genomes. This method also allows resolution of haplotypes harboring the duplications. Using this approach, we conducted genome-wide analyses and identified the insertion sites of 22 common polymorphic duplications. We found that the majority of these duplications is intrachromosomal and only one of them is an interchromosomal insertion. Further characterization of these duplications revealed significant associations to blood and skin phenotypes. On the basis of population genetics analyses, we found that the duplication of a well-characterized pigmentation-related region, including the HERC2 gene, may be selected against in European populations. We further demonstrated that the haplotype harboring this duplication significantly affects the expression of the HERC2P9 gene in multiple tissues. Our study sheds light onto the evolutionary impact of understudied polymorphic duplications in human populations and presents methodological insights for future studies.
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Affiliation(s)
- Marie Saitou
- Department of Biological Sciences, SUNY at Buffalo
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Wang Z, Ma H, Xu L, Zhu B, Liu Y, Bordbar F, Chen Y, Zhang L, Gao X, Gao H, Zhang S, Xu L, Li J. Genome-Wide Scan Identifies Selection Signatures in Chinese Wagyu Cattle Using a High-Density SNP Array. Animals (Basel) 2019; 9:ani9060296. [PMID: 31151238 PMCID: PMC6617538 DOI: 10.3390/ani9060296] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2019] [Revised: 05/23/2019] [Accepted: 05/24/2019] [Indexed: 12/31/2022] Open
Abstract
Selective breeding can lead to genetic diversity and diverse phenotypes in farm animals. Analysis of the genomic regions under selection can provide important insights into the genetic basis of complex traits. In this study, a high-density SNP array was used for analysis of genome selection signatures in Chinese Wagyu cattle. In total, we obtained 478,903 SNPs and 24,820 no-overlap regions for |iHS| (integrated haplotype score) estimations. Under the threshold of the top 1%, 239 regions were finally identified as candidate selected regions and 162 candidate genes were found based on the UMD3.1 genome assembly. These genes were reported to be associated with fatty acids, such as Bos taurus nitric oxide synthase 1 adaptor protein (NOS1AP), Bos taurus hydroxysteroid 17-beta dehydrogenase 7 (HSD17B7), Bos taurus WD repeat domain 7 (WDR7), Bos taurus ELOVL fatty acid elongase 2 (ELOVL2), Bos taurus calpain 1 (CAPN1), Bos taurus parkin RBR E3 ubiquitin protein ligase (PRKN, also known as PARK2), Bos taurus mitogen-activated protein kinase kinase 6 (MAP2K6), meat quality, including Bos taurus ADAM metallopeptidase domain 12 (ADAM12), Bos taurus 5'-aminolevulinate synthase 1 (ALAS1), Bos taurus small integral membrane protein 13 (SMIM13) and Bos taurus potassium two pore domain channel subfamily K member 2 (KCNK2), growth, and developmental traits, such as Bos taurus insulin like growth factor 2 receptor (IGF2R), Bos taurus RAR related orphan receptor A (RORA), Bos taurus fibroblast growth factor 14 (FGF14), Bos taurus paired box 6 (PAX6) and Bos taurus LIM homeobox 6 (LHX6). In addition, we identified several genes that are associated with body size and weight, including Bos taurus sorting nexin 29 (SNX29), Bos taurus zinc finger imprinted 2 (ZIM2), Bos taurus family with sequence similarity 110 member A (FAM110A), immune system, including Bos taurus toll like receptor 9 (TLR9), Bos taurus TAFA chemokine like family member 1 (TAFA1), Bos taurus glutathione peroxidase 8 (putative) (GPX8), Bos taurus interleukin 5 (IL5), Bos taurus PR domain containing 9 (PRDM9), Bos taurus glutamate ionotropic receptor kainate type subunit 2 (GRIK2) and feed intake efficiency, Bos taurus sodium voltage-gated channel alpha subunit 9 (SCN9A), Bos taurus relaxin family peptide/INSL5 receptor 4 (RXFP4), Bos taurus RNA polymerase II associated protein 3 (RPAP3). Moreover, four GO terms of biological regulation (GO:0009987, GO:0008152) and metabolic process (GO:0003824, GO:0005488) were found based on these genes. In addition, we found that 232 candidate regions (~18 Mb) overlapped with the Quantitative trait loci (QTL)regions extracted from cattle QTLdb. Our findings imply that many genes were selected for important traits in Chinese Wagyu cattle. Moreover, these results can contribute to the understanding of the genetic basis of the studied traits during the formation of this population.
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Affiliation(s)
- Zezhao Wang
- Laboratory of Molecular Biology and Bovine Breeding, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing 100193, China.
- National Engineering Laboratory for Animal Breeding, Key Laboratory of Animal Genetics, Breeding and Reproduction, Ministry of Agriculture, College of Animal Science and Technology, China Agricultural University, Beijing 100193, China.
| | - Haoran Ma
- College of Animal Science and Technology, Huazhong Agricultural University, Wuhan 430070, China.
| | - Lei Xu
- Laboratory of Molecular Biology and Bovine Breeding, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing 100193, China.
- National Engineering Laboratory for Animal Breeding, Key Laboratory of Animal Genetics, Breeding and Reproduction, Ministry of Agriculture, College of Animal Science and Technology, China Agricultural University, Beijing 100193, China.
- Institute of Animal Husbandry and Veterinary Research, Anhui Academy of Agricultural Sciences, Hefei 230031, China.
| | - Bo Zhu
- Laboratory of Molecular Biology and Bovine Breeding, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing 100193, China.
| | - Ying Liu
- Laboratory of Molecular Biology and Bovine Breeding, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing 100193, China.
| | - Farhad Bordbar
- Laboratory of Molecular Biology and Bovine Breeding, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing 100193, China.
| | - Yan Chen
- Laboratory of Molecular Biology and Bovine Breeding, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing 100193, China.
| | - Lupei Zhang
- Laboratory of Molecular Biology and Bovine Breeding, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing 100193, China.
| | - Xue Gao
- Laboratory of Molecular Biology and Bovine Breeding, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing 100193, China.
| | - Huijiang Gao
- Laboratory of Molecular Biology and Bovine Breeding, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing 100193, China.
| | - Shengli Zhang
- National Engineering Laboratory for Animal Breeding, Key Laboratory of Animal Genetics, Breeding and Reproduction, Ministry of Agriculture, College of Animal Science and Technology, China Agricultural University, Beijing 100193, China.
| | - Lingyang Xu
- Laboratory of Molecular Biology and Bovine Breeding, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing 100193, China.
| | - Junya Li
- Laboratory of Molecular Biology and Bovine Breeding, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing 100193, China.
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Ham E, Underdown SJ, Houldcroft CJ. The relative roles of maternal survival and inter-personal violence as selection pressures on the persistence of Neanderthal hypercoagulability alleles in modern Europeans. Ann Hum Biol 2019; 46:99-108. [PMID: 31113254 DOI: 10.1080/03014460.2019.1622038] [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: 10/26/2022]
Abstract
Background: Simonti et al. reported variation in the frequency of Neanderthal alleles found in modern humans and argued that they may have provided an evolutionary advantage. One such allele is SNP rs3917862, associated with hypercoagulability. rs3917862 can be deleterious, but can also help prevent blood loss. Aim: To investigate two possible selective pressure hypotheses for rs3917862 surviving to higher frequencies: deaths from interpersonal violent trauma and childbirth. Subjects and methods: Mortality data from modern hunter-gatherers models the living conditions and causes of death of humans and Neanderthals at the point of admixture. Results: National census data indicates a positive correlation between the presence of rs3917862 and decreased maternal mortality ratios. When the maternal mortality ratio is modelled using GDP, births attended by skilled assistants and the presence of rs3917862, women are 0.1% more likely to die in childbirth in populations lacking rs3917862. Deaths due to violence show no correlation with rs3917862. Conclusion: These findings challenge the idea that Neanderthal admixture has negatively impacted the overall health of modern humans. Maternal survival may have acted as a selective pressure for the persistence of hypercoagulability alleles in modern Europeans. Understanding the role of hypercoagulability in childbirth, and the role of rs3917862, could help to reduce maternal mortality ratios.
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Affiliation(s)
- Ellen Ham
- a Division of Biological Anthropology, Department of Archaeology , University of Cambridge , Cambridge , UK
| | - Simon J Underdown
- b Human Origins and Palaeo-Environments Research Group , Oxford Brookes University , Oxford , UK
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Novillo A, Gaibar M, Romero-Lorca A, Chaabani H, Amir N, Moral P, Esteban ME, Fernández-Santander A. UDP-glucuronosyltransferase genetic variation in North African populations: a comparison with African and European data. Ann Hum Biol 2019; 45:516-523. [PMID: 30616396 DOI: 10.1080/03014460.2018.1559354] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
Abstract
BACKGROUND Genetic variation in glucuronosyltransferases (UGT) is crucial in drug metabolism and risk of some diseases. AIM To examine genetic variation in UGT in North African populations. SUBJECTS AND METHODS Allele frequencies of SNPs UGT1A424Thr, UGT1A448Val, UGT2B1585Tyr, UGT2B15523Thr and UGT2B17 CNV deletion from Morocco, Algeria, Tunisia and Libya were compared to European and Sub-Saharan populations. RESULTS North Africans are the group with the highest genetic heterogeneity given by internal differences in the occurrence of UGT2B17 deletion, UGT1A448Val and UGT1A4 haplotypes. UGT2B15 SNPs differentiate Sub-Saharans from the rest of the populations. CONCLUSION North African populations show a high frequency of carriers of UGT2B15523Thr, a variant linked to an increased risk of prostate cancer. High Atlas Moroccans and Algerians show low frequency of UGT2B17del, a variant associated with high concentrations of testosterone and oestradiol.
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Affiliation(s)
- Apolonia Novillo
- a Basic Biomedical Sciences Department , Universidad Europea de Madrid , Madrid , Spain
| | - María Gaibar
- a Basic Biomedical Sciences Department , Universidad Europea de Madrid , Madrid , Spain
| | - Alicia Romero-Lorca
- a Basic Biomedical Sciences Department , Universidad Europea de Madrid , Madrid , Spain
| | - Hassen Chaabani
- b Faculty of Pharmacy , University of Monastir , Monastir , Tunisia
| | - Nadir Amir
- c Laboratoire de Biochimie Appliquée, 5 Faculté des Sciences de la Nature et de la Vie , Université de Bejaia , Bejaia , Algeria
| | - Pedro Moral
- d Section of Zoology and Biological Anthropology, Department of Evolutionary Biology, Ecology and Environmental Sciences, Faculty of Biology , Universitat de Barcelona , Barcelona , Spain.,e Institut de Recerca de la Biodiversitat (IRBio), Universitat de Barcelona , Barcelona , Spain
| | - M Esther Esteban
- d Section of Zoology and Biological Anthropology, Department of Evolutionary Biology, Ecology and Environmental Sciences, Faculty of Biology , Universitat de Barcelona , Barcelona , Spain.,e Institut de Recerca de la Biodiversitat (IRBio), Universitat de Barcelona , Barcelona , Spain
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NCBoost classifies pathogenic non-coding variants in Mendelian diseases through supervised learning on purifying selection signals in humans. Genome Biol 2019; 20:32. [PMID: 30744685 PMCID: PMC6371618 DOI: 10.1186/s13059-019-1634-2] [Citation(s) in RCA: 39] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2018] [Accepted: 01/17/2019] [Indexed: 02/07/2023] Open
Abstract
State-of-the-art methods assessing pathogenic non-coding variants have mostly been characterized on common disease-associated polymorphisms, yet with modest accuracy and strong positional biases. In this study, we curated 737 high-confidence pathogenic non-coding variants associated with monogenic Mendelian diseases. In addition to interspecies conservation, a comprehensive set of recent and ongoing purifying selection signals in humans is explored, accounting for lineage-specific regulatory elements. Supervised learning using gradient tree boosting on such features achieves a high predictive performance and overcomes positional bias. NCBoost performs consistently across diverse learning and independent testing data sets and outperforms other existing reference methods.
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Dobon B, Rossell C, Walsh S, Bertranpetit J. Is there adaptation in the human genome for taste perception and phase I biotransformation? BMC Evol Biol 2019; 19:39. [PMID: 30704392 PMCID: PMC6357387 DOI: 10.1186/s12862-019-1366-7] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2018] [Accepted: 01/17/2019] [Indexed: 12/19/2022] Open
Abstract
Background During the modern human expansion, new environmental pressures may have driven adaptation, especially in genes related to the perception of ingested substances and their detoxification. Consequently, positive (adaptive) selection may have occurred in genes related to taste, and in those related to the CYP450 system due to its role in biotransformation of potentially toxic compounds. A total of 91 genes (taste receptors and CYP450 superfamily) have been studied using Hierarchical Boosting, a powerful combination of different selection tests, to detect signatures of recent positive selection in three continental human populations: Northern Europeans (CEU), East Asians (CHB) and Africans (YRI). Analyses have been refined with selection analyses of the 26 populations of 1000 Genomes Project Phase 3. Results Genes related to taste perception have not been positively selected in the three continental human populations. This finding suggests that, contrary to results of previous studies, different allele frequencies among populations in genes such as TAS2R38 and TAS2R16 are not due to positive selection but to genetic drift. CYP1 and CYP2 genes, also previously considered to be under positive selection, did not show signatures of selective sweeps. However, three genes belonging to the CYP450 system have been identified by the Hierarchical Boosting as positively selected: CYP3A4 and CYP3A43 in CEU, and CYP27A1 in CHB. Conclusions No main adaptive differences are found in known taste receptor genes among the three continental human populations studied. However, there are important genetic adaptations in the cytochrome P450 system related to the Out of Africa expansion of modern humans. We confirmed that CYP3A4 and CYP3A43 are under selection in CEU, and we report for the first time CYP27A1 to be under positive selection in CHB. Electronic supplementary material The online version of this article (10.1186/s12862-019-1366-7) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Begoña Dobon
- Institut de Biologia Evolutiva (UPF-CSIC), Universitat Pompeu Fabra, Dr. Aiguader, 88. 08003, Barcelona, Catalonia, Spain
| | - Carla Rossell
- Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Tomtebodavägen 23a, 17165, Stockholm, Solna, Sweden
| | - Sandra Walsh
- Institut de Biologia Evolutiva (UPF-CSIC), Universitat Pompeu Fabra, Dr. Aiguader, 88. 08003, Barcelona, Catalonia, Spain
| | - Jaume Bertranpetit
- Institut de Biologia Evolutiva (UPF-CSIC), Universitat Pompeu Fabra, Dr. Aiguader, 88. 08003, Barcelona, Catalonia, Spain.
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Hatlen A, Helmy M, Marco A. PopTargs: a database for studying population evolutionary genetics of human microRNA target sites. Database (Oxford) 2019; 2019:baz102. [PMID: 31608947 PMCID: PMC6790967 DOI: 10.1093/database/baz102] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2019] [Revised: 06/07/2019] [Accepted: 08/01/2019] [Indexed: 01/03/2023]
Abstract
There is an increasing interest in the study of polymorphic variants at gene regulatory motifs, including microRNA target sites. Understanding the effects of selective forces at specific microRNA target sites, together with other factors like expression levels or evolutionary conservation, requires the joint study of multiple datasets. We have compiled information from multiple sources and compared it with predicted microRNA target sites to build a comprehensive database for the study of microRNA targets in human populations. PopTargs is a web-based tool that allows the easy extraction of multiple datasets and the joint analyses of them, including allele frequencies, ancestral status, population differentiation statistics and site conservation. The user can also compare the allele frequency spectrum between two groups of target sites and conveniently produce plots. The database can be easily expanded as new data becomes available and the raw database as well as code for creating new custom-made databases is available for downloading. We also describe a few illustrative examples.
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Affiliation(s)
- Andrea Hatlen
- School of Life Sciences, University of Essex, Wivenhoe Park, Colchester CO4 3SQ, UK
| | - Mohab Helmy
- School of Life Sciences, University of Essex, Wivenhoe Park, Colchester CO4 3SQ, UK
| | - Antonio Marco
- School of Life Sciences, University of Essex, Wivenhoe Park, Colchester CO4 3SQ, UK
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Tournebize R, Poncet V, Jakobsson M, Vigouroux Y, Manel S. McSwan: A joint site frequency spectrum method to detect and date selective sweeps across multiple population genomes. Mol Ecol Resour 2018; 19:283-295. [PMID: 30358170 DOI: 10.1111/1755-0998.12957] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2018] [Revised: 10/17/2018] [Accepted: 10/18/2018] [Indexed: 01/01/2023]
Abstract
Inferring the mode and tempo of natural selection helps further our understanding of adaptation to past environmental changes. Here, we introduce McSwan, a method to detect and date past and recent natural selection events in the case of a hard sweep. The method is based on the comparison of site frequency spectra obtained under various demographic models that include selection. McSwan demonstrated high power (high sensitivity and specificity) in capturing hard selective sweep events without requiring haplotype phasing. It performed slightly better than SweeD when the recent effective population size was low and the genomic region was small. We then applied our method to a European (CEU) and an African (LWK) human re-sequencing data set. Most hard sweeps were detected in the CEU population (96%). Moreover, hard sweeps in the African population were estimated to have occurred further back in time (mode: 43,625 years BP) compared to those of Europeans (mode: 24,850 years BP). Most of the estimated ages of hard sweeps in Europeans were associated with the Last Glacial Maximum and were enriched in immunity-associated genes.
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Affiliation(s)
- Rémi Tournebize
- IRD, University of Montpellier, UMR DIADE BP 64501, Montpellier Cedex 5, France
| | - Valérie Poncet
- IRD, University of Montpellier, UMR DIADE BP 64501, Montpellier Cedex 5, France
| | - Mattias Jakobsson
- Department of Organismal Biology and SciLifeLab, Uppsala University, Uppsala, Sweden.,Centre for Anthropological Research, Department of Anthropology and Development Studies, University of Johannesburg, Auckland Park, South Africa
| | - Yves Vigouroux
- IRD, University of Montpellier, UMR DIADE BP 64501, Montpellier Cedex 5, France
| | - Stéphanie Manel
- EPHE, PSL Research University, CNRS, University of Montpellier, Montpellier SupAgro, IRD, INRA, UMR:5175 CEFE, Montpellier, France
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Detection and Classification of Hard and Soft Sweeps from Unphased Genotypes by Multilocus Genotype Identity. Genetics 2018; 210:1429-1452. [PMID: 30315068 DOI: 10.1534/genetics.118.301502] [Citation(s) in RCA: 40] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2018] [Accepted: 10/08/2018] [Indexed: 11/18/2022] Open
Abstract
Positive natural selection can lead to a decrease in genomic diversity at the selected site and at linked sites, producing a characteristic signature of elevated expected haplotype homozygosity. These selective sweeps can be hard or soft. In the case of a hard selective sweep, a single adaptive haplotype rises to high population frequency, whereas multiple adaptive haplotypes sweep through the population simultaneously in a soft sweep, producing distinct patterns of genetic variation in the vicinity of the selected site. Measures of expected haplotype homozygosity have previously been used to detect sweeps in multiple study systems. However, these methods are formulated for phased haplotype data, typically unavailable for nonmodel organisms, and some may have reduced power to detect soft sweeps due to their increased genetic diversity relative to hard sweeps. To address these limitations, we applied the H12 and H2/H1 statistics proposed in 2015 by Garud et al., which have power to detect both hard and soft sweeps, to unphased multilocus genotypes, denoting them as G12 and G2/G1. G12 (and the more direct expected homozygosity analog to H12, denoted G123) has comparable power to H12 for detecting both hard and soft sweeps. G2/G1 can be used to classify hard and soft sweeps analogously to H2/H1, conditional on a genomic region having high G12 or G123 values. The reason for this power is that, under random mating, the most frequent haplotypes will yield the most frequent multilocus genotypes. Simulations based on parameters compatible with our recent understanding of human demographic history suggest that expected homozygosity methods are best suited for detecting recent sweeps, and increase in power under recent population expansions. Finally, we find candidates for selective sweeps within the 1000 Genomes CEU, YRI, GIH, and CHB populations, which corroborate and complement existing studies.
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