1
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Hong JS, Tindall JM, Tindall SR, Sorscher EJ. Mutation accumulation in H. sapiens F508del CFTR countermands dN/dS type genomic analysis. PLoS One 2024; 19:e0305832. [PMID: 39024311 PMCID: PMC11257350 DOI: 10.1371/journal.pone.0305832] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2024] [Accepted: 06/05/2024] [Indexed: 07/20/2024] Open
Abstract
Understanding the mechanisms that underlie de novo mutations (DNMs) can be essential for interpreting human evolution, including aspects such as rapidly diverging genes, conservation of non-coding regulatory elements, and somatic DNA adaptation, among others. DNM accumulation in Homo sapiens is often limited to evaluation of human trios or quads across a single generation. Moreover, human SNPs in exons, pseudogenes, or other non-coding elements can be ancient and difficult to date, including polymorphisms attributable to founder effects and identity by descent. In this report, we describe multigenerational evolution of a human coding locus devoid of natural selection, and delineate patterns and principles by which DNMs have accumulated over the past few thousand years. We apply a data set comprising cystic fibrosis transmembrane conductance regulator (CFTR) alleles from 2,393 individuals homozygous for the F508del defect. Additional polymorphism on the F508del background diversified subsequent to a single mutational event during recent human history. Because F508del CFTR is without function, SNPs observed on this haplotype are effectively attributable to factors that govern accumulating de novo mutations. We show profound enhancement of transition, synonymous, and positionally repetitive polymorphisms, indicating appearance of DNMs in a manner evolutionarily designed to protect protein coding DNA against mutational attrition while promoting diversity.
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Affiliation(s)
- Jeong S. Hong
- Emory University School of Medicine, Atlanta, Georgia, United States of America
| | - Janice M. Tindall
- Emory University School of Medicine, Atlanta, Georgia, United States of America
| | - Samuel R. Tindall
- Emory University School of Medicine, Atlanta, Georgia, United States of America
| | - Eric J. Sorscher
- Emory University School of Medicine, Atlanta, Georgia, United States of America
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2
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Dirican CD, Nelson PS. Y Chromosome Loss and Implications for Oncology. Mol Cancer Res 2024; 22:603-612. [PMID: 38647375 PMCID: PMC11217729 DOI: 10.1158/1541-7786.mcr-24-0105] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2024] [Revised: 03/28/2024] [Accepted: 04/02/2024] [Indexed: 04/25/2024]
Abstract
The Y chromosome has recognized functions in promoting male sex determination and regulating aspects of fertility. However, recent work has demonstrated important roles for the Y chromosome and Y-encoded genes in multiple domains of male health, including cancer. It is well established that males experience shorter lifespans than females, and this sex bias on overall mortality is accentuated in populations with longer life expectancy, in part related to elevated rates of cancer. The majority of human malignancies exhibit a sex bias with elevated frequencies in males. For many of these cancer types, the disparity has not been explained by environmental risk factors such as tobacco use. Notably, loss of the Y chromosome (LOY) detected in blood cells, termed mosaic LOY, is a common event that is related to advancing age and is associated with a shortened lifespan. Mosaic LOY is linked to increased incidence and mortality across a range of malignancies. Furthermore, tumors arising in different anatomic sites exhibit different frequencies of partial or complete Y chromosome loss. Causal oncogenic or tumor-suppressive roles have been documented for several Y-encoded genes, such as lysine-specific demethylase 5 D, that exert pleiotropic effects on cellular functions by virtue of genome-wide regulation of gene activity. In this review, we discuss aspects of the Y chromosome relevant to oncology. The recent completion of the entire human Y-chromosome sequence provides a reference map of Y-encoded genes and regulatory elements to enable causal molecular studies that may explain and exploit the marked disparity in male cancer risk and mortality.
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Affiliation(s)
- Canan D. Dirican
- Divisions of Human Biology and Clinical Research, Fred Hutchinson Cancer Center, Seattle, Washington.
| | - Peter S. Nelson
- Divisions of Human Biology and Clinical Research, Fred Hutchinson Cancer Center, Seattle, Washington.
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3
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Primorac D, Šarac J, Havaš Auguštin D, Novokmet N, Bego T, Pinhasi R, Šlaus M, Novak M, Marjanović D. Y Chromosome Story-Ancient Genetic Data as a Supplementary Tool for the Analysis of Modern Croatian Genetic Pool. Genes (Basel) 2024; 15:748. [PMID: 38927684 PMCID: PMC11202852 DOI: 10.3390/genes15060748] [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: 05/04/2024] [Revised: 05/25/2024] [Accepted: 06/04/2024] [Indexed: 06/28/2024] Open
Abstract
Due to its turbulent demographic history, marked by extensive settlement and gene flow from diverse regions of Eurasia, Southeastern Europe (SEE) has consistently served as a genetic crossroads between East and West and a junction for the migrations that reshaped Europe's population. SEE, including modern Croatian territory, was a crucial passage from the Near East and even more distant regions and human populations in this region, as almost any other European population represents a remarkable genetic mixture. Modern humans have continuously occupied this region since the Upper Paleolithic era, and different (pre)historical events have left a distinctive genetic signature on the historical narrative of this region. Our views of its history have been mostly renewed in the last few decades by extraordinary data obtained from Y-chromosome studies. In recent times, the international research community, bringing together geneticists and archaeologists, has steadily released a growing number of ancient genomes from this region, shedding more light on its complex past population dynamics and shaping the genetic pool in Croatia and this part of Europe.
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Affiliation(s)
- Dragan Primorac
- St. Catherine Specialty Hospital, 10000 Zagreb, Croatia
- Faculty of Dental Medicine and Health, Josip Juraj Strossmayer University of Osijek, 31000 Osijek, Croatia
- School of Medicine, Josip Juraj Strossmayer University of Osijek, 31000 Osijek, Croatia
- Medical School, University of Split, 21000 Split, Croatia
- Department of Biochemistry & Molecular Biology, The Pennsylvania State University, State College, PA 16802, USA
- The Henry C. Lee College of Criminal Justice and Forensic Sciences, University of New Haven, West Haven, CT 06516, USA
- Regiomed Kliniken, 96450 Coburg, Germany
- Medical School, University of Rijeka, 51000 Rijeka, Croatia
- National Forensic Sciences University, Gandhinagar 382007, India
| | - Jelena Šarac
- Centre for Applied Bioanthropology, Institute for Anthropological Research, Gajeva 32, 10000 Zagreb, Croatia
| | - Dubravka Havaš Auguštin
- Centre for Applied Bioanthropology, Institute for Anthropological Research, Gajeva 32, 10000 Zagreb, Croatia
| | - Natalija Novokmet
- Centre for Applied Bioanthropology, Institute for Anthropological Research, Gajeva 32, 10000 Zagreb, Croatia
| | - Tamer Bego
- Faculty of Pharmacy, University of Sarajevo, 71000 Sarajevo, Bosnia and Herzegovina
| | - Ron Pinhasi
- Department of Evolutionary Anthropology, University of Vienna, 1030 Vienna, Austria
- Human Evolution and Archaeological Sciences (HEAS), University of Vienna, 1030 Vienna, Austria
| | - Mario Šlaus
- Anthropological Center, Croatian Academy of Sciences and Arts, 10000 Zagreb, Croatia
| | - Mario Novak
- Centre for Applied Bioanthropology, Institute for Anthropological Research, Gajeva 32, 10000 Zagreb, Croatia
- Department of Archaeology and Heritage, Faculty of Humanities, University of Primorska, 6000 Koper, Slovenia
| | - Damir Marjanović
- Centre for Applied Bioanthropology, Institute for Anthropological Research, Gajeva 32, 10000 Zagreb, Croatia
- International Burch University, 71000 Sarajevo, Bosnia and Herzegovina
- Faculty of Biotechnology and Drug Development, University of Rijeka, 51000 Rijeka, Croatia
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4
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Borbély N, Dudás D, Tapasztó A, Dudás-Boda E, Csáky V, Szeifert B, Mende BG, Egyed B, Szécsényi-Nagy A, Pamjav H. Phylogenetic insights into the genetic legacies of Hungarian-speaking communities in the Carpathian Basin. Sci Rep 2024; 14:11480. [PMID: 38769390 PMCID: PMC11106325 DOI: 10.1038/s41598-024-61978-4] [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: 01/31/2024] [Accepted: 05/13/2024] [Indexed: 05/22/2024] Open
Abstract
This study focuses on exploring the uniparental genetic lineages of Hungarian-speaking minorities residing in rural villages of Baranja (Croatia) and the Zobor region (Slovakia). We aimed to identify ancestral lineages by examining genetic markers distributed across the entire mitogenome and on the Y-chromosome. This allowed us to discern disparities in regional genetic structures within these communities. By integrating our newly acquired genetic data from a total of 168 participants with pre-existing Eurasian and ancient DNA datasets, our goal was to enrich the understanding of the genetic history trajectories of Carpathian Basin populations. Our findings suggest that while population-based analyses may not be sufficiently robust to detect fine-scale uniparental genetic patterns with the sample sizes at hand, phylogenetic analysis of well-characterized Y-chromosomal Short Tandem Repeat (STR) data and entire mitogenome sequences did uncover multiple lineage ties to far-flung regions and eras. While the predominant portions of both paternal and maternal DNA align with the East-Central European spectrum, rarer subhaplogroups and lineages have unveiled ancient ties to both prehistoric and historic populations spanning Europe and Eastern Eurasia. This research augments the expansive field of phylogenetics, offering critical perspectives on the genetic constitution and heritage of the communities in East-Central Europe.
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Affiliation(s)
- Noémi Borbély
- Institute of Archaeogenomics, HUN-REN Research Centre for the Humanities, Tóth Kálmán utca 4, Budapest, 1097, Hungary
- Doctoral School of Biology, Institute of Biology, ELTE Eötvös Loránd University, Pázmány Péter sétány 1/C, Budapest, 1117, Hungary
| | - Dániel Dudás
- Department of Reference Sample Analysis, Institute of Forensic Genetics, Hungarian Institute for Forensic Sciences, Gyorskocsi u. 25, Budapest, 1027, Hungary
| | - Attila Tapasztó
- Department of Reference Sample Analysis, Institute of Forensic Genetics, Hungarian Institute for Forensic Sciences, Gyorskocsi u. 25, Budapest, 1027, Hungary
| | - Eszter Dudás-Boda
- Department of Reference Sample Analysis, Institute of Forensic Genetics, Hungarian Institute for Forensic Sciences, Gyorskocsi u. 25, Budapest, 1027, Hungary
| | - Veronika Csáky
- Institute of Archaeogenomics, HUN-REN Research Centre for the Humanities, Tóth Kálmán utca 4, Budapest, 1097, Hungary
| | - Bea Szeifert
- Institute of Archaeogenomics, HUN-REN Research Centre for the Humanities, Tóth Kálmán utca 4, Budapest, 1097, Hungary
| | - Balázs Gusztáv Mende
- Institute of Archaeogenomics, HUN-REN Research Centre for the Humanities, Tóth Kálmán utca 4, Budapest, 1097, Hungary
| | - Balázs Egyed
- Department of Genetics, ELTE Eötvös Loránd University, Pázmány Péter sétány 1/C, Budapest, 1117, Hungary
| | - Anna Szécsényi-Nagy
- Institute of Archaeogenomics, HUN-REN Research Centre for the Humanities, Tóth Kálmán utca 4, Budapest, 1097, Hungary.
| | - Horolma Pamjav
- Department of Reference Sample Analysis, Institute of Forensic Genetics, Hungarian Institute for Forensic Sciences, Gyorskocsi u. 25, Budapest, 1027, Hungary.
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5
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Plyler ZE, McAtee CW, Hill AE, Crowley MR, Tindall JM, Tindall SR, Joshi D, Sorscher EJ. Relationships between genomic dissipation and de novo SNP evolution. PLoS One 2024; 19:e0303257. [PMID: 38753830 PMCID: PMC11098520 DOI: 10.1371/journal.pone.0303257] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2024] [Accepted: 04/23/2024] [Indexed: 05/18/2024] Open
Abstract
Patterns of single nucleotide polymorphisms (SNPs) in eukaryotic DNA are traditionally attributed to selective pressure, drift, identity descent, or related factors-without accounting for ways in which bias during de novo SNP formation, itself, might contribute. A functional and phenotypic analysis based on evolutionary resilience of DNA points to decreased numbers of non-synonymous SNPs in human and other genomes, with a predominant component of SNP depletion in the human gene pool caused by robust preferences during de novo SNP formation (rather than selective constraint). Ramifications of these findings are broad, belie a number of concepts regarding human evolution, and point to a novel interpretation of evolving DNA across diverse species.
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Affiliation(s)
- Zackery E. Plyler
- Department of Biology, University of Alabama at Birmingham, Birmingham, Alabama, United States of America
- Gregory Fleming James Cystic Fibrosis Research Center, University of Alabama at Birmingham, Birmingham, Alabama, United States of America
| | - Christopher W. McAtee
- Department of Biology, University of Alabama at Birmingham, Birmingham, Alabama, United States of America
- Gregory Fleming James Cystic Fibrosis Research Center, University of Alabama at Birmingham, Birmingham, Alabama, United States of America
| | - Aubrey E. Hill
- Gregory Fleming James Cystic Fibrosis Research Center, University of Alabama at Birmingham, Birmingham, Alabama, United States of America
- Department of Computer and Information Sciences, University of Alabama at Birmingham, Birmingham, Alabama, United States of America
| | - Michael R. Crowley
- Department of Genetics, University of Alabama at Birmingham, Birmingham, Alabama, United States of America
| | | | | | - Disha Joshi
- Emory University, Atlanta, Georgia, United States of America
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6
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Jia L, Wang M, Duan S, Chen J, Zhao M, Ji S, Lv B, Jiang X, He G, Yang J. Genetic history of esophageal cancer group in southwestern China revealed by Y-chromosome STRs and genomic evolutionary connection analysis. Heliyon 2024; 10:e29867. [PMID: 38720733 PMCID: PMC11076658 DOI: 10.1016/j.heliyon.2024.e29867] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2023] [Revised: 04/09/2024] [Accepted: 04/16/2024] [Indexed: 05/12/2024] Open
Abstract
Genetic and environmental factors play crucial roles in the development of esophageal cancer (EC) and contribute uniquely or cooperatively to human cancer susceptibility. Sichuan is located in the interior of southwestern China, and the northern part of Sichuan is one of the regions with a high occurrence of EC. However, the factors influencing the high incidence rate of EC in the Sichuan Han Chinese population and its corresponding genetic background and origins are still poorly understood. Here, we utilized genome-wide single nucleotide polymorphisms (SNPs) and Y-chromosome short tandem repeats (Y-STRs) to characterize the genetic structure, connection, and origin of cancer groups and general populations. We generated Y-STR-based haplotype data from 214 Sichuan individuals, including the Han Chinese EC population and a control group of Han Chinese individuals. Our results, obtained from Y-STR-based population statistical methods (analysis of molecular variance (AMOVA), principal component analysis (PCA), and phylogenetic analysis), demonstrated that there was a genetic substructure difference between the EC population in the high-incidence area of northern Sichuan Province and the control population. Additionally, there was a strong genetic relationship between the EC population in the northern Sichuan high-incidence area and those at high risk in both the Fujian and Chaoshan areas. In addition, we obtained high-density SNP data from saliva samples of 60 healthy Han Chinese individuals from three high-prevalence areas of EC in China: Sichuan Nanchong, Fujian Quanzhou, and Henan Xinxiang. As inferred from the allele frequency of SNPs and sharing patterns of haplotype segments, the evolutionary history and admixture events suggested that the Han population from Nanchong in northern Sichuan Province shared a close genetic relationship with the Han populations from Xinxiang in Henan Province and Quanzhou in Fujian Province, both of which are regions with a high prevalence of EC. Our study illuminated the genetic profile and connection of the Northern Sichuan Han population and enriched the genomic resources and features of the Han Chinese populations in China, especially for the Y-STR genetic data of the Han Chinese EC population. Populations living in different regions with high incidences of EC may share similar genetic backgrounds, which offers new insights for further exploring the genetic mechanisms underlying EC.
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Affiliation(s)
- Lihua Jia
- Institute of Basic Medicine and Forensic Medicine, North Sichuan Medical College and Center for Genetics and Prenatal diagnosis, Affiliated Hospital of Northern Sichuan Medical College, Nanchong, Sichuan, 637007, China
| | - Mengge Wang
- Center for Archaeological Science, Sichuan University, Chengdu, 610000, China
- Institute of Rare Diseases, West China Hospital of Sichuan University, Sichuan University, Chengdu, 610000, China
| | - Shuhan Duan
- Institute of Basic Medicine and Forensic Medicine, North Sichuan Medical College and Center for Genetics and Prenatal diagnosis, Affiliated Hospital of Northern Sichuan Medical College, Nanchong, Sichuan, 637007, China
- Institute of Rare Diseases, West China Hospital of Sichuan University, Sichuan University, Chengdu, 610000, China
| | - Jianghua Chen
- Institute of Basic Medicine and Forensic Medicine, North Sichuan Medical College and Center for Genetics and Prenatal diagnosis, Affiliated Hospital of Northern Sichuan Medical College, Nanchong, Sichuan, 637007, China
| | - Mei Zhao
- Institute of Basic Medicine and Forensic Medicine, North Sichuan Medical College and Center for Genetics and Prenatal diagnosis, Affiliated Hospital of Northern Sichuan Medical College, Nanchong, Sichuan, 637007, China
| | - Simeng Ji
- School of Laboratory Medicine, North Sichuan Medical College, Nanchong, Sichuan, 637000, China
| | - Bingbing Lv
- School of Laboratory Medicine, North Sichuan Medical College, Nanchong, Sichuan, 637000, China
| | - Xiucheng Jiang
- Institute of Basic Medicine and Forensic Medicine, North Sichuan Medical College and Center for Genetics and Prenatal diagnosis, Affiliated Hospital of Northern Sichuan Medical College, Nanchong, Sichuan, 637007, China
- Institute of Rare Diseases, West China Hospital of Sichuan University, Sichuan University, Chengdu, 610000, China
| | - Guanglin He
- Center for Archaeological Science, Sichuan University, Chengdu, 610000, China
- Institute of Rare Diseases, West China Hospital of Sichuan University, Sichuan University, Chengdu, 610000, China
| | - Junbao Yang
- Institute of Basic Medicine and Forensic Medicine, North Sichuan Medical College and Center for Genetics and Prenatal diagnosis, Affiliated Hospital of Northern Sichuan Medical College, Nanchong, Sichuan, 637007, China
- School of Laboratory Medicine, North Sichuan Medical College, Nanchong, Sichuan, 637000, China
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7
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González-Fernández M, Vázquez-Coto D, Albaiceta GM, Amado-Rodríguez L, Clemente MG, Velázquez-Cuervo L, García-Lago C, Gómez J, Coto E. Chromosome-Y haplogroups in Asturias (Northern Spain) and their association with severe COVID-19. Mol Genet Genomics 2024; 299:49. [PMID: 38704518 PMCID: PMC11069473 DOI: 10.1007/s00438-024-02143-4] [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: 10/31/2023] [Accepted: 04/17/2024] [Indexed: 05/06/2024]
Abstract
The main objective of this study was to determine whether the common Y-haplogroups were be associated with the risk of developing severe COVID-19 in Spanish male. We studied 479 patients who required hospitalization due to COVID-19 and 285 population controls from the region of Asturias (northern Spain), They were genotyped for several polymorphisms that define the common European Y-haplogroups. We compared the frequencies between patients and controls aged ≤ 65 and >65 years. There were no different haplogroup frequencies between the two age groups of controls. Haplogroup R1b was less common in patients aged ≤65 years. Haplogroup I was more common in the two patient´s groups compared to controls (p = 0.02). Haplogroup R1b was significantly more frequent among hypertensive patients, without difference between the hypertensive and normotensive controls. This suggested that R1b could increase the risk for severe COVID-19 among male with pre-existing hypertension. In conclusion, we described the Y-haplogroup structure among Asturians. We found an increased risk of severe COVID-19 among haplogroup I carriers, and a significantly higher frequency of R1b among hypertensive patients. These results indicate that Y-chromosome variants could serve as markers to define the risk of developing a severe form of COVID-19.
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Affiliation(s)
| | - Daniel Vázquez-Coto
- Instituto de Investigación Sanitaria del Principado de Asturias, ISPA, Oviedo, Spain
| | - Guillermo M Albaiceta
- Instituto de Investigación Sanitaria del Principado de Asturias, ISPA, Oviedo, Spain
- Unidad de Cuidados Intensivos Cardiológicos, Hospital Universitario Central Asturias, Oviedo, Spain
- Universidad de Oviedo, Oviedo, Spain
- CIBER-Enfermedades Respiratorias, Instituto de Salud Carlos III, Madrid, Spain
- Instituto Universitario de Oncología del Principado de Asturias, Oviedo, Spain
| | - Laura Amado-Rodríguez
- Instituto de Investigación Sanitaria del Principado de Asturias, ISPA, Oviedo, Spain
- Unidad de Cuidados Intensivos Cardiológicos, Hospital Universitario Central Asturias, Oviedo, Spain
- Universidad de Oviedo, Oviedo, Spain
- CIBER-Enfermedades Respiratorias, Instituto de Salud Carlos III, Madrid, Spain
- Instituto Universitario de Oncología del Principado de Asturias, Oviedo, Spain
| | - Marta G Clemente
- Instituto de Investigación Sanitaria del Principado de Asturias, ISPA, Oviedo, Spain
- Neumología, Hospital Universitario Central Asturias, Oviedo, Spain
| | | | - Claudia García-Lago
- Instituto de Investigación Sanitaria del Principado de Asturias, ISPA, Oviedo, Spain
| | - Juan Gómez
- Genética Molecular, Hospital Universitario Central Asturias, Oviedo, Spain
- Instituto de Investigación Sanitaria del Principado de Asturias, ISPA, Oviedo, Spain
- CIBER-Enfermedades Respiratorias, Instituto de Salud Carlos III, Madrid, Spain
| | - Eliecer Coto
- Genética Molecular, Hospital Universitario Central Asturias, Oviedo, Spain.
- Instituto de Investigación Sanitaria del Principado de Asturias, ISPA, Oviedo, Spain.
- Universidad de Oviedo, Oviedo, Spain.
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8
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Hodișan R, Zaha DC, Jurca CM, Petchesi CD, Bembea M. Genetic Diversity Based on Human Y Chromosome Analysis: A Bibliometric Review Between 2014 and 2023. Cureus 2024; 16:e58542. [PMID: 38887511 PMCID: PMC11182565 DOI: 10.7759/cureus.58542] [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] [Accepted: 04/18/2024] [Indexed: 06/20/2024] Open
Abstract
The Y chromosome has gained significant importance in the examination of genetic studies of populations because of its non-recombinant character and its form of uniparental inheritance. This work seeks to offer a comprehensive review of the specialty literature in the field of population genetics, focusing specifically on the analysis of the human Y chromosome using a bibliometric approach and knowledge mapping. This involves establishing worldwide structural networks by identifying the primary research themes, authors, and papers that have had a significant impact on the academic community. The objective is to examine global publications by analyzing citations at both the document and country level. This will involve conducting co-citation analysis for references with a high number of citations, examining bibliographic coupling through journal analysis, analyzing the co-occurrence of keywords, and investigating collaboration between authors from a country perspective. The research papers have been extracted from the Web of Science database. The bibliometric analysis was performed using the Bibliometrix and VOSviewer software tools. The purpose of this article is to serve as a starting point for future research dedicated to the analysis of the diversity of human Y chromosome haplotypes. The objectives of the study were to identify and present the most cited publications and references with the highest number of citations, and to highlight current publications at the national level.
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Affiliation(s)
- Ramona Hodișan
- Doctoral School of Biomedical Sciences, University of Oradea, Oradea, ROU
- Department of Preclinical Disciplines, University of Oradea, Faculty of Medicine and Pharmacy, Oradea, ROU
| | - Dana C Zaha
- Department of Preclinical Disciplines, University of Oradea, Faculty of Medicine and Pharmacy, Oradea, ROU
| | - Claudia M Jurca
- Department of Preclinical Disciplines, University of Oradea, Faculty of Medicine and Pharmacy, Oradea, ROU
| | - Codruta D Petchesi
- Department of Preclinical Disciplines, University of Oradea, Faculty of Medicine and Pharmacy, Oradea, ROU
| | - Marius Bembea
- Doctoral School of Biomedical Sciences, University of Oradea, Oradea, ROU
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Xie S, Ma Y, Liu Y, Tao D, Wang Z, Yang Y. Primary azoospermia factor C duplication associated with spermatogenic impariment: a case-control study based on Y-chromosome haplogrouping in a Han Chinese population. Andrology 2024; 12:561-569. [PMID: 37594248 DOI: 10.1111/andr.13510] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2023] [Revised: 06/22/2023] [Accepted: 08/06/2023] [Indexed: 08/19/2023]
Abstract
BACKGROUND Azoospermia factor C (AZFc) in the male-specific region of Y-chromosome (MSY) presents wide structure variation mainly due to frequent non-allele homologous recombination, leading to significant copy number variation of the AZFc-linked coding sequences involving in spermatogenesis. A large number of studies had been conducted to investigate the association between AZFc deletions and male infertility in certain Y chromosome genetic backgrounds, however, the influence of primary AZFc duplication on spermatogenesis remained controversial and the cause of the discrepant outcomes is unknown. METHODS In the present study, a total of 1,102 unrelated Han Chinese males without any detectable AZF deletions were recruited from 2014 to 2019, including 411 controls with normozoospermia and 691 patients with idiopathic spermatogenic failure. Using multiple paralog ratio tests (PRTs), the structure duplications were classified by the copy number of the AZFc-linked amplicons and genes. The Y-chromosome haplogroup (Y-hg) was categorized by genetyping of MSY-linked polymorphism loci. The association of primary AZFc duplication with spermatogenic phenotype was investigated in males with the same Y-hg. RESULTS Within Y-hg O3* group, the frequency of the gr/gr duplication in patients is significantly higher than that of controls (P = 1.29×10-3 , odds ratio (OR) 7.64, 95% confidence interval (CI) 1.79-32.57). Moreover, Y-hg O3* males with the gr/gr duplication presented a significantly lower sperm production compared with non-AZFc duplicated ones (sperm concentration: P = 1.46×10-3 ; total sperm count: P = 1.82 ×10-3 ). The b2/b3 duplication were identified clustered in Y-hg Cα2*, and the significant difference in the distribution was not observed between patients with spermatogenic failure and controls. CONCLUSION The results suggest that, in the Han Chinese population, the gr/gr duplication is a predisposing genetic factor for spermatogenic impairment in males harboring Y-hg O3* . Meanwhile, the b2/b3 duplication may be fixed on a yet-unidentified subbranch of Y-hg Cα2* without significantly deleterious effect on spermatogenesis. Our findings provide evidence that the difference in the Y-hg composition may cause the discrepancy on the association of AZFc duplication with spermatogenic failure among the studied populations.
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Affiliation(s)
- Shengyu Xie
- Department of Medical Genetics, State Key Laboratory of Biotherapy, West China Hospital, West China School of medicine, Sichuan University, Chengdu, China
| | - Yongyi Ma
- Department of Medical Genetics, State Key Laboratory of Biotherapy, West China Hospital, West China School of medicine, Sichuan University, Chengdu, China
- Precision Medicine Center, Precision Medicine Key Laboratory of Sichuan Province, West China Hospital, Sichuan University, Chengdu, China
| | - Yunqiang Liu
- Department of Medical Genetics, State Key Laboratory of Biotherapy, West China Hospital, West China School of medicine, Sichuan University, Chengdu, China
| | - Dachang Tao
- Department of Medical Genetics, State Key Laboratory of Biotherapy, West China Hospital, West China School of medicine, Sichuan University, Chengdu, China
| | - Zhaokun Wang
- Department of Medical Genetics, State Key Laboratory of Biotherapy, West China Hospital, West China School of medicine, Sichuan University, Chengdu, China
| | - Yuan Yang
- Department of Medical Genetics, State Key Laboratory of Biotherapy, West China Hospital, West China School of medicine, Sichuan University, Chengdu, China
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Alinaghi S, Mohseni M, Fattahi Z, Beheshtian M, Ghodratpour F, Zare Ashrafi F, Arzhangi S, Jalalvand K, Najafipour R, Khorram Khorshid HR, Kahrizi K, Najmabadi H. Genetic Analysis of 27 Y-STR Haplotypes in 11 Iranian Ethnic Groups. ARCHIVES OF IRANIAN MEDICINE 2024; 27:79-88. [PMID: 38619031 PMCID: PMC11017261 DOI: 10.34172/aim.2024.13] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/21/2023] [Accepted: 01/23/2024] [Indexed: 04/16/2024]
Abstract
BACKGROUND The study of Y-chromosomal variations provides valuable insights into male susceptibility in certain diseases like cardiovascular disease (CVD). In this study, we analyzed paternal lineage in different Iranian ethnic groups, not only to identify developing medical etiology, but also to pave the way for gender-specific targeted strategies and personalized medicine in medical genetic research studies. METHODS The diversity of eleven Iranian ethnic groups was studied using 27 Y-chromosomal short tandem repeat (Y-STR) haplotypes from Y-filer® Plus kit. Analysis of molecular variance (AMOVA) based on pair-wise RST along with multidimensional scaling (MDS) calculation and Network phylogenic analysis was employed to quantify the differences between 503 unrelated individuals from each ethnicity. RESULTS Results from AMOVA calculation confirmed that Gilaks and Azeris showed the largest genetic distance (RST=0.35434); however, Sistanis and Lurs had the smallest considerable genetic distance (RST=0.00483) compared to other ethnicities. Although Azeris had a considerable distance from other ethnicities, they were still close to Turkmens. MDS analysis of ethnic groups gave the indication of lack of similarity between different ethnicities. Besides, network phylogenic analysis demonstrated insignificant clustering between samples. CONCLUSION The AMOVA analysis results explain that the close distance of Azeris and Turkmens may be the effect of male-dominant expansions across Central Asia that contributed to historical and demographics of populations in the region. Insignificant differences in network analysis could be the consequence of high mutation events that happened in the Y-STR regions over the years. Considering the ethnic group affiliations in medical research, our results provided an understanding and characterization of Iranian male population for future medical and population genetics studies.
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Affiliation(s)
- Somayeh Alinaghi
- Genetics Research Center, University of Social Welfare and Rehabilitation Sciences, Tehran, Iran
| | - Marzieh Mohseni
- Genetics Research Center, University of Social Welfare and Rehabilitation Sciences, Tehran, Iran
| | - Zohreh Fattahi
- Genetics Research Center, University of Social Welfare and Rehabilitation Sciences, Tehran, Iran
| | - Maryam Beheshtian
- Genetics Research Center, University of Social Welfare and Rehabilitation Sciences, Tehran, Iran
| | - Fatemeh Ghodratpour
- Genetics Research Center, University of Social Welfare and Rehabilitation Sciences, Tehran, Iran
| | - Farzane Zare Ashrafi
- Genetics Research Center, University of Social Welfare and Rehabilitation Sciences, Tehran, Iran
| | - Sanaz Arzhangi
- Genetics Research Center, University of Social Welfare and Rehabilitation Sciences, Tehran, Iran
| | - Khadijeh Jalalvand
- Genetics Research Center, University of Social Welfare and Rehabilitation Sciences, Tehran, Iran
| | - Reza Najafipour
- Genetics Research Center, University of Social Welfare and Rehabilitation Sciences, Tehran, Iran
| | | | - Kimia Kahrizi
- Genetics Research Center, University of Social Welfare and Rehabilitation Sciences, Tehran, Iran
| | - Hossein Najmabadi
- Genetics Research Center, University of Social Welfare and Rehabilitation Sciences, Tehran, Iran
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11
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Mut P, Bertoni B, Sapiro R, Hidalgo PC, Torres A, Azambuja C, Sans M. Insights into the Y chromosome human diversity in Uruguay. Am J Hum Biol 2023; 35:e23963. [PMID: 37493343 DOI: 10.1002/ajhb.23963] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2022] [Revised: 04/26/2023] [Accepted: 07/04/2023] [Indexed: 07/27/2023] Open
Abstract
BACKGROUND With regard to the origin of its population and microevolutionary processes, Uruguay exhibits distinctive features that distinguish it from other countries in Latin America, while at the same time sharing several similarities. In this article, we will focus on the variability of paternal genetic lineages in two geographical regions with different histories that can be considered as examples of distinct populations for the continent. In general terms, the genetic diversity is a result of different demographic processes related to the American conquest and colonisation. These resulted in distinct ancestral components which vary geographical and depend on the distribution by sex within these components. In Uruguay, native maternal haplogroups are significantly more frequent in the North. Although there are several studies about the geneticvariability of Uruguay, little is known about male genetic lineages. AIMS The aim of this work is to present an updated study of the male genetic variability of the Uruguayan population. METHODS We analyzed 13 biallelic markers and 27 STRs located in the male-specific region of the Y chromosome for 157 males: 98 from the capital, Montevideo, and 59 from Tacuarembó. RESULTS Almost all haplogroups found in both locations are European (99% and 93.2% respectively). One Sub-Saharan African haplogroup was found in Montevideo (1%) and 2 in Tacuarembó (3%), while Native haplogroups were found only in Tacuarembó, evidencing a strong sex-biased admixture. By crossing genetic and genealogical information we could relate European haplogroups with different waves and times of migrations. DISCUSSION Network analysis indicated a very diverse male population, suggesting that European migrants came from heterogeneous geographic locations and in different waves. Tacuarembó has closer population affinities with Iberian populations while Montevideo is more diverse. Male population expansion expansion, can be explained by the large number of migrants that arrived during the XIX century and the first half of the XX century. CONCLUSIONS The Uruguayan male gene pool is the result of several migration waves with diverse origins, with strong sex-biased admixture that can be explained by the European migration, the violence against the indigenous males, and the segregation of the Africansadmixture that can be explained due to European migration, violence against Natives, and segregation against African males.admixture that can be explained due to European migration, violence against Natives, and segregation against African males.admixture that can be explained due to European migration, violence against Natives, and segregation against African males.admixture that can be explained due to European migration, violence against Natives, and segregation of hte Africans.
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Affiliation(s)
- Patricia Mut
- Departamento de Antropología Biológica, Facultad de Humanidades y Ciencias de la Educación, UdelaR, Montevideo, Uruguay
| | - Bernardo Bertoni
- Departamento de Genética, Facultad de Medicina, UdelaR, Montevideo, Uruguay
| | - Rossana Sapiro
- Departamento de Histología y Embriología, Facultad de Medicina, UdelaR, Montevideo, Uruguay
| | - Pedro C Hidalgo
- Polo de Desarrollo Universitario Diversidad Genética Humana, Centro Universitario Noreste, Tacuarembó, Uruguay
| | | | | | - Mónica Sans
- Departamento de Antropología Biológica, Facultad de Humanidades y Ciencias de la Educación, UdelaR, Montevideo, Uruguay
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Wen Y, Liu J, Su Y, Chen X, Hou Y, Liao L, Wang Z. Forensic biogeographical ancestry inference: recent insights and current trends. Genes Genomics 2023; 45:1229-1238. [PMID: 37081293 DOI: 10.1007/s13258-023-01387-5] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2023] [Accepted: 04/01/2023] [Indexed: 04/22/2023]
Abstract
BACKGROUND As a powerful complement to the paradigmatic DNA profiling strategy, biogeographical ancestry inference (BGAI) plays a significant part in human forensic investigation especially when a database hit or eyewitness testimony are not available. It indicates one's biogeographical profile based on known population-specific genetic variations, and thus is crucial for guiding authority investigations to find unknown individuals. Forensic biogeographical ancestry testing exploits much of the recent advances in the understanding of human genomic variation and improving of molecular biology. OBJECTIVE In this review, recent development of prospective ancestry informative markers (AIMs) and the statistical approaches of inferring biogeographic ancestry from AIMs are elucidated and discussed. METHODS We highlight the research progress of three potential AIMs (i.e., single nucleotide polymorphisms, microhaplotypes, and Y or mtDNA uniparental markers) and discuss the prospects and challenges of two methods that are commonly used in BGAI. CONCLUSION While BGAI for forensic purposes has been thriving in recent years, important challenges, such as ethics and responsibilities, data completeness, and ununified standards for evaluation, remain for the use of biogeographical ancestry information in human forensic investigations. To address these issues and fully realize the value of BGAI in forensic investigation, efforts should be made not only by labs/institutions around the world independently, but also by inter-lab/institution collaborations.
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Affiliation(s)
- Yufeng Wen
- Key Laboratory of Evidence Science (China University of Political Science and Law), Ministry of Education, Beijing, 100088, China
- Institute of Forensic Medicine, West China School of Basic Medical Sciences & Forensic Medicine, Sichuan University, Chengdu, 610041, China
- School of Life Sciences, Jilin University, Changchun, 130012, China
| | - Jing Liu
- Institute of Forensic Medicine, West China School of Basic Medical Sciences & Forensic Medicine, Sichuan University, Chengdu, 610041, China
| | - Yonglin Su
- Department of Rehabilitation Medicine, West China Hospital Sichuan University, Chengdu, 610041, China
| | - Xiacan Chen
- Institute of Forensic Medicine, West China School of Basic Medical Sciences & Forensic Medicine, Sichuan University, Chengdu, 610041, China
| | - Yiping Hou
- Institute of Forensic Medicine, West China School of Basic Medical Sciences & Forensic Medicine, Sichuan University, Chengdu, 610041, China
| | - Linchuan Liao
- Institute of Forensic Medicine, West China School of Basic Medical Sciences & Forensic Medicine, Sichuan University, Chengdu, 610041, China.
| | - Zheng Wang
- Key Laboratory of Evidence Science (China University of Political Science and Law), Ministry of Education, Beijing, 100088, China.
- Institute of Forensic Medicine, West China School of Basic Medical Sciences & Forensic Medicine, Sichuan University, Chengdu, 610041, China.
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Zhang H, Huang X, Jin X, Ren Z, Wang Q, Yang M, Xu R, Yuan X, Yang D, Liu H, Shen W, Zhang H, Que Y, Huang J. Comprehensive analyses of genetic diversities and population structure of the Guizhou Dong group based on 44 Y-markers. PeerJ 2023; 11:e16183. [PMID: 37780380 PMCID: PMC10538297 DOI: 10.7717/peerj.16183] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2023] [Accepted: 09/05/2023] [Indexed: 10/03/2023] Open
Abstract
Background The non-recombining region of the human Y chromosome (NRY) is a strictly paternally inherited genetic marker and the best material to trace the paternal lineages of populations. Y chromosomal short tandem repeat (Y-STR) is characterized by high polymorphism and paternal inheritance pattern, so it has been widely used in forensic medicine and population genetic research. This study aims to understand the genetic distribution of Y-STRs in the Guizhou Dong population, provide reference data for forensic application, and explore the phylogenetic relationships between the Guizhou Dong population and other comparison populations. Methods Based on the allele profile of 44 Y-markers in the Guizhou Dong group, we estimate their allele frequencies and haplotype frequencies. In addition, we also compare the forensic application efficiency of different Y-STR sets in the Guizhou Dong group. Finally, genetic relationships among Guizhou Dong and other reference populations are dissected by the multi-dimensional scaling and the phylogenetic tree. Results A total of 393 alleles are observed in 312 Guizhou Dong individuals for these Y-markers, with allele frequencies ranging from 0.0032 to 0.9679. The haplotype diversity and discriminatory capacity for these Y-markers in the Guizhou Dong population are 0.99984 and 0.97440, respectively. The population genetic analyses of the Guizhou Dong group and other reference populations show that the Guizhou Dong group has the closest genetic relationship with the Hunan Dong population, and followed by the Guizhou Tujia population. Conclusions In conclusion, these 44 Y-markers can be used as an effective tool for male differentiation in the Guizhou Dong group. The haplotype data in this study not only enrich the Y-STR data of different ethnic groups in China, but also have important significance for population genetics and forensic research.
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Affiliation(s)
- Hongling Zhang
- Department of Forensic Medicine, Guizhou Medical University, Guiyang, Guizhou, China
| | - Xiaolan Huang
- Department of Forensic Medicine, Guizhou Medical University, Guiyang, Guizhou, China
| | - Xiaoye Jin
- Department of Forensic Medicine, Guizhou Medical University, Guiyang, Guizhou, China
| | - Zheng Ren
- Department of Forensic Medicine, Guizhou Medical University, Guiyang, Guizhou, China
| | - Qiyan Wang
- Department of Forensic Medicine, Guizhou Medical University, Guiyang, Guizhou, China
| | - Meiqing Yang
- Department of Forensic Medicine, Guizhou Medical University, Guiyang, Guizhou, China
| | - Ronglan Xu
- Department of Forensic Medicine, Guizhou Medical University, Guiyang, Guizhou, China
| | - Xiang Yuan
- Department of Forensic Medicine, Guizhou Medical University, Guiyang, Guizhou, China
| | - Daiquan Yang
- Department of Forensic Medicine, Guizhou Medical University, Guiyang, Guizhou, China
| | - Hongyan Liu
- Department of Forensic Medicine, Guizhou Medical University, Guiyang, Guizhou, China
| | - Wanyi Shen
- Department of Forensic Medicine, Guizhou Medical University, Guiyang, Guizhou, China
| | - Huiying Zhang
- Department of Forensic Medicine, Guizhou Medical University, Guiyang, Guizhou, China
| | - Yangjie Que
- Department of Forensic Medicine, Guizhou Medical University, Guiyang, Guizhou, China
| | - Jiang Huang
- Department of Forensic Medicine, Guizhou Medical University, Guiyang, Guizhou, China
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Kuznetsova IL, Uralsky LI, Tyazhelova TV, Andreeva TV, Rogaev EI. Mosaic loss of the Y chromosome in human neurodegenerative and oncological diseases. Vavilovskii Zhurnal Genet Selektsii 2023; 27:502-511. [PMID: 37808213 PMCID: PMC10551935 DOI: 10.18699/vjgb-23-61] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2022] [Revised: 02/14/2023] [Accepted: 02/14/2023] [Indexed: 10/10/2023] Open
Abstract
The development of new biomarkers for prediction and early detection of human diseases, as well as for monitoring the response to therapy is one of the most relevant areas of modern human genetics and genomics. Until recently, it was believed that the function of human Y chromosome genes was limited to determining sex and controlling spermatogenesis. Thanks to occurance of large databases of the genome-wide association study (GWAS), there has been a transition to the use of large samples for analyzing genetic changes in both normal and pathological conditions. This has made it possible to assess the association of mosaic aneuploidy of the Y chromosome in somatic cells with a shorter lifespan in men compared to women. Based on data from the UK Biobank, an association was found between mosaic loss of the Y chromosome (mLOY) in peripheral blood leukocytes and the age of men over 70, as well as a number of oncological, cardiac, metabolic, neurodegenerative, and psychiatric diseases. As a result, mLOY in peripheral blood cells has been considered a potential marker of biological age in men and as a marker of certain age-related diseases. Currently, numerous associations have been identified between mLOY and genes based on GWAS and transcriptomes in affected tissues. However, the exact cause of mLOY and the impact and consequences of this phenomenon at the whole organism level have not been established. In particular, it is unclear whether aneuploidy of the Y chromosome in blood cells may affect the development of pathologies that manifest in other organs, such as the brain in Alzheimer's disease, or whether it is a neutral biomarker of general genomic instability. This review examines the main pathologies and genetic factors associated with mLOY, as well as the hypotheses regarding their interplay. Special attention is given to recent studies on mLOY in brain cells in Alzheimer's disease.
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Affiliation(s)
- I L Kuznetsova
- Vavilov Institute of General Genetics, Russian Academy of Sciences, Department of Genomics and Human Genetics, Moscow, Russia Sirius University of Science and Technology, Scientific Center for Genetics and Life Sciences, Sochi, Russia
| | - L I Uralsky
- Vavilov Institute of General Genetics, Russian Academy of Sciences, Department of Genomics and Human Genetics, Moscow, Russia Sirius University of Science and Technology, Scientific Center for Genetics and Life Sciences, Sochi, Russia
| | - T V Tyazhelova
- Vavilov Institute of General Genetics, Russian Academy of Sciences, Department of Genomics and Human Genetics, Moscow, Russia
| | - T V Andreeva
- Vavilov Institute of General Genetics, Russian Academy of Sciences, Department of Genomics and Human Genetics, Moscow, Russia Sirius University of Science and Technology, Scientific Center for Genetics and Life Sciences, Sochi, Russia Lomonosov Moscow State University, Center for Genetics and Genetic Technologies, Faculty of Biology, Moscow, Russia
| | - E I Rogaev
- Vavilov Institute of General Genetics, Russian Academy of Sciences, Department of Genomics and Human Genetics, Moscow, Russia Sirius University of Science and Technology, Scientific Center for Genetics and Life Sciences, Sochi, Russia Lomonosov Moscow State University, Center for Genetics and Genetic Technologies, Faculty of Biology, Moscow, Russia
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15
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Li J, Song F, Lang M, Xie M. Comprehensive insights into the genetic background of Chinese populations using Y chromosome markers. ROYAL SOCIETY OPEN SCIENCE 2023; 10:230814. [PMID: 37736526 PMCID: PMC10509572 DOI: 10.1098/rsos.230814] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/26/2023] [Accepted: 09/01/2023] [Indexed: 09/23/2023]
Abstract
China is located in East Asia. With a high genetic and cultural diversity, human migration in China has always been a hot topic of genetics research. To explore the origins and migration routes of Chinese males, 3333 Chinese individuals (Han, Hui, Mongolia, Yi and Kyrgyz) with 27 Y-STRs and 143 Y-SNPs from published literature were analysed. Our data showed that there are five dominant haplogroups (O2-M122, O1-F265, C-M130, N-M231, R-M207) in China. Combining analysis of haplogroup frequencies, geographical positions and time with the most recent common ancestor (TMRCA), we found that haplogroups C-M130, N-M231 and R1-M173 and O1a-M175 probably migrated into China via the northern route. Interestingly, we found that haplogroup C*-M130 in China may originate in South Asia, whereas the major subbranches C2a-L1373 and C2b-F1067 migrated from northern China. The results of BATWING showed that the common ancestry of Y haplogroup in China can be traced back to 17 000 years ago, which was concurrent with global temperature increases after the Last Glacial Maximum.
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Affiliation(s)
- Jienan Li
- Department of Forensic Science, School of Basic Medical Sciences, Central South University, Changsha, Hunan Province, People's Republic of China
| | - Feng Song
- Institute of Forensic Medicine, West China School of Basic Medical Sciences & Forensic Medicine, Sichuan University, Chengdu, People's Republic of China
| | - Min Lang
- Sichuan University Law School, Sichuan University, Chengdu, People's Republic of China
| | - Mingkun Xie
- Department of Obstetrics, Xiangya Hospital, Central South University, 87 Xiangya Road, Changsha, Hunan 410008, People's Republic of China
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16
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Mutti G, Oteo-Garcia G, Caldon M, da Silva MJF, Minhós T, Cowlishaw G, Gottelli D, Huchard E, Carter A, Martinez FI, Raveane A, Capelli C. Assessing the recovery of Y chromosome microsatellites with population genomic data using Papio and Theropithecus genomes. Sci Rep 2023; 13:13839. [PMID: 37620368 PMCID: PMC10449864 DOI: 10.1038/s41598-023-40931-x] [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: 04/03/2023] [Accepted: 08/18/2023] [Indexed: 08/26/2023] Open
Abstract
Y chromosome markers can shed light on male-specific population dynamics but for many species no such markers have been discovered and are available yet, despite the potential for recovering Y-linked loci from available genome sequences. Here, we investigated how effective available bioinformatic tools are in recovering informative Y chromosome microsatellites from whole genome sequence data. In order to do so, we initially explored a large dataset of whole genome sequences comprising individuals at various coverages belonging to different species of baboons (genus: Papio) using Y chromosome references belonging to the same genus and more distantly related species (Macaca mulatta). We then further tested this approach by recovering Y-STRs from available Theropithecus gelada genomes using Papio and Macaca Y chromosome as reference sequences. Identified loci were validated in silico by a) comparing within-species relationships of Y chromosome lineages and b) genotyping male individuals in available pedigrees. Each STR was selected not to extend in its variable region beyond 100 base pairs, so that loci can be developed for PCR-based genotyping of non-invasive DNA samples. In addition to assembling a first set of Papio and Theropithecus Y-specific microsatellite markers, we released TYpeSTeR, an easy-to-use script to identify and genotype Y chromosome STRs using population genomic data which can be modulated according to available male reference genomes and genomic data, making it widely applicable across taxa.
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Affiliation(s)
- Giacomo Mutti
- Department of Chemistry, Life Sciences and Environmental Sustainability, University of Parma, Parco Area Delle Scienze, 11/a, 43124, Parma, Italy
- Barcelona Supercomputing Centre (BSC-CNS), Plaça Eusebi Güell, 1-3, 08034, Barcelona, Spain
- Institute for Research in Biomedicine (IRB Barcelona), The Barcelona Institute of Science and Technology, Baldiri Reixac, 10, 08028, Barcelona, Spain
| | - Gonzalo Oteo-Garcia
- Department of Chemistry, Life Sciences and Environmental Sustainability, University of Parma, Parco Area Delle Scienze, 11/a, 43124, Parma, Italy
| | - Matteo Caldon
- Department of Chemistry, Life Sciences and Environmental Sustainability, University of Parma, Parco Area Delle Scienze, 11/a, 43124, Parma, Italy
| | - Maria Joana Ferreira da Silva
- BIOPOLIS Program in Genomics, Biodiversity and Land Planning, CIBIO, Campus de Vairão, Vairão, Portugal
- Centro de Investigação Em Biodiversidade E Recursos Genéticos, CIBIOInBIO Laboratório AssociadoUniversidade Do Porto, Campus de Vairão, Vairão, Portugal
- ONE ‑ Organisms and Environment Group, School of Biosciences, Cardiff University, Sir Martin Evans Building, Cardiff, UK
| | - Tânia Minhós
- Centre for Research in Anthropology (CRIA-NOVA FCSH), Av. Forças Armadas, Edifício ISCTE, Sala 2w2, 1649-026, Lisboa, Portugal
- Anthropology Department, School of Social Sciences and Humanities, Universidade Nova de Lisboa (NOVA FCSH), Av. de Berna, 26-C, 1069-061, Lisboa, Portugal
| | - Guy Cowlishaw
- Institute of Zoology, Zoological Society of London, Regent's Park, London, NW1 4RY, UK
| | - Dada Gottelli
- Institute of Zoology, Zoological Society of London, Regent's Park, London, NW1 4RY, UK
| | - Elise Huchard
- Institut Des Sciences de L'Evolution, CNRS, Universite de Montpellier, CC 065, 34095, Montpellier 05, France
| | - Alecia Carter
- Department of Anthropology, University College London, 14 Taviton Street, London, WC1H 0BW, UK
| | - Felipe I Martinez
- Escuela de Antropología, Facultad de Ciencias Sociales, Pontificia Universidad Católica de Chile, Santiago, Chile
| | | | - Cristian Capelli
- Department of Chemistry, Life Sciences and Environmental Sustainability, University of Parma, Parco Area Delle Scienze, 11/a, 43124, Parma, Italy.
- Department of Biology, University of Oxford, 11a Mansfield Road, Oxford, OX1 3SZ, UK.
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Lorca R, Aparicio A, Salgado M, Álvarez-Velasco R, Pascual I, Gomez J, Vazquez-Coto D, Garcia-Lago C, Velázquez-Cuervo L, Cuesta-Llavona E, Avanzas P, Coto E. Chromosome Y Haplogroup R Was Associated with the Risk of Premature Myocardial Infarction with ST-Elevation: Data from the CholeSTEMI Registry. J Clin Med 2023; 12:4812. [PMID: 37510926 PMCID: PMC10381015 DOI: 10.3390/jcm12144812] [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: 06/21/2023] [Revised: 07/11/2023] [Accepted: 07/18/2023] [Indexed: 07/30/2023] Open
Abstract
Cardiovascular disease (CVD) is the leading cause of death worldwide, with coronary artery disease (CAD) being one of its main manifestations. Both environmental and genetic factors are widely known to be related to CAD, such as smoking, diabetes mellitus, dyslipidemia, and a family history of CAD. However, there is still a lack of information about other risk factors, especially those related to genetic mutations. Sex represents a classic CAD risk factor, as men are more likely to suffer CAD, but there is lack of evidence with regard to sex-specific genetic factors. We evaluated the Y chromosome haplogroups in a cohort of young Spanish male patients who suffered from STEMI. In this cohort, haplogroup R was significantly more frequent in STEMI patients.
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Affiliation(s)
- Rebeca Lorca
- Área del Corazón, Hospital Universitario Central Asturias (HUCA), 33011 Oviedo, Spain
- Unidad de Cardiopatías Familiares, Área del Corazón y Departamento de Genética Molecular, Hospital Universitario Central Asturias, 33011 Oviedo, Spain
- Área de Fisiología, Departamento de Biología Funcional, Universidad de Oviedo, 33003 Oviedo, Spain
- Instituto de Investigación Sanitaria del Principado de Asturias (ISPA), 33011 Oviedo, Spain
- Redes de Investigación Cooperativa Orientadas a Resultados en Salud (RICORs), 28029 Madrid, Spain
| | - Andrea Aparicio
- Área del Corazón, Hospital Universitario Central Asturias (HUCA), 33011 Oviedo, Spain
| | - María Salgado
- Área del Corazón, Hospital Universitario Central Asturias (HUCA), 33011 Oviedo, Spain
| | - Rut Álvarez-Velasco
- Área del Corazón, Hospital Universitario Central Asturias (HUCA), 33011 Oviedo, Spain
| | - Isaac Pascual
- Área del Corazón, Hospital Universitario Central Asturias (HUCA), 33011 Oviedo, Spain
- Departamento de Medicina, Universidad de Oviedo, 33003 Oviedo, Spain
| | - Juan Gomez
- Unidad de Cardiopatías Familiares, Área del Corazón y Departamento de Genética Molecular, Hospital Universitario Central Asturias, 33011 Oviedo, Spain
- Instituto de Investigación Sanitaria del Principado de Asturias (ISPA), 33011 Oviedo, Spain
- CIBER-Enfermedades Respiratorias, 28029 Madrid, Spain
- Genética Molecular, Hospital Universitario Central Asturias (HUCA), 33011 Oviedo, Spain
| | - Daniel Vazquez-Coto
- Genética Molecular, Hospital Universitario Central Asturias (HUCA), 33011 Oviedo, Spain
| | - Claudia Garcia-Lago
- Genética Molecular, Hospital Universitario Central Asturias (HUCA), 33011 Oviedo, Spain
| | | | - Elías Cuesta-Llavona
- Genética Molecular, Hospital Universitario Central Asturias (HUCA), 33011 Oviedo, Spain
| | - Pablo Avanzas
- Área del Corazón, Hospital Universitario Central Asturias (HUCA), 33011 Oviedo, Spain
- Instituto de Investigación Sanitaria del Principado de Asturias (ISPA), 33011 Oviedo, Spain
- Departamento de Medicina, Universidad de Oviedo, 33003 Oviedo, Spain
- Centro de Investigación Biomédica en Red de Enfermedades Cardiovasculares (CIBERCV), 28029 Madrid, Spain
| | - Eliecer Coto
- Unidad de Cardiopatías Familiares, Área del Corazón y Departamento de Genética Molecular, Hospital Universitario Central Asturias, 33011 Oviedo, Spain
- Instituto de Investigación Sanitaria del Principado de Asturias (ISPA), 33011 Oviedo, Spain
- Redes de Investigación Cooperativa Orientadas a Resultados en Salud (RICORs), 28029 Madrid, Spain
- Departamento de Medicina, Universidad de Oviedo, 33003 Oviedo, Spain
- CIBER-Enfermedades Respiratorias, 28029 Madrid, Spain
- Genética Molecular, Hospital Universitario Central Asturias (HUCA), 33011 Oviedo, Spain
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Tancredi D, Cardinali I. Being a Dog: A Review of the Domestication Process. Genes (Basel) 2023; 14:genes14050992. [PMID: 37239352 DOI: 10.3390/genes14050992] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2023] [Revised: 04/19/2023] [Accepted: 04/26/2023] [Indexed: 05/28/2023] Open
Abstract
The process of canine domestication represents certainly one of the most interesting questions that evolutionary biology aims to address. A "multiphase" view of this process is now accepted, with a first phase during which different groups of wolves were attracted by the anthropogenic niche and a second phase characterized by the gradual establishment of mutual relationships between wolves and humans. Here, we provide a review of dog (Canis familiaris) domestication, highlighting the ecological differences between dogs and wolves, analyzing the molecular mechanisms which seem to have influenced the affiliative behaviors first observed in Belyaev's foxes, and describing the genetics of ancient European dogs. Then, we focus on three Mediterranean peninsulas (Balkan, Iberian and Italian), which together represent the main geographic area for studying canine domestication dynamics, as it has shaped the current genetic variability of dog populations, and where a well-defined European genetic structure was pinpointed through the analysis of uniparental genetic markers and their phylogeny.
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Affiliation(s)
- Domenico Tancredi
- Department of Chemistry, Biology and Biotechnology, Università degli Studi di Perugia, 06123 Perugia, Italy
| | - Irene Cardinali
- Department of Chemistry, Biology and Biotechnology, Università degli Studi di Perugia, 06123 Perugia, Italy
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He G, Wang M, Miao L, Chen J, Zhao J, Sun Q, Duan S, Wang Z, Xu X, Sun Y, Liu Y, Liu J, Wang Z, Wei L, Liu C, Ye J, Wang L. Multiple founding paternal lineages inferred from the newly-developed 639-plex Y-SNP panel suggested the complex admixture and migration history of Chinese people. Hum Genomics 2023; 17:29. [PMID: 36973821 PMCID: PMC10045532 DOI: 10.1186/s40246-023-00476-6] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2023] [Accepted: 03/15/2023] [Indexed: 03/29/2023] Open
Abstract
BACKGROUND Non-recombining regions of the Y-chromosome recorded the evolutionary traces of male human populations and are inherited haplotype-dependently and male-specifically. Recent whole Y-chromosome sequencing studies have identified previously unrecognized population divergence, expansion and admixture processes, which promotes a better understanding and application of the observed patterns of Y-chromosome genetic diversity. RESULTS Here, we developed one highest-resolution Y-chromosome single nucleotide polymorphism (Y-SNP) panel targeted for uniparental genealogy reconstruction and paternal biogeographical ancestry inference, which included 639 phylogenetically informative SNPs. We genotyped these loci in 1033 Chinese male individuals from 33 ethnolinguistically diverse populations and identified 256 terminal Y-chromosomal lineages with frequency ranging from 0.0010 (singleton) to 0.0687. We identified six dominant common founding lineages associated with different ethnolinguistic backgrounds, which included O2a2b1a1a1a1a1a1a1-M6539, O2a1b1a1a1a1a1a1-F17, O2a2b1a1a1a1a1b1a1b-MF15397, O2a2b2a1b1-A16609, O1b1a1a1a1b2a1a1-F2517, and O2a2b1a1a1a1a1a1-F155. The AMOVA and nucleotide diversity estimates revealed considerable differences and high genetic diversity among ethnolinguistically different populations. We constructed one representative phylogenetic tree among 33 studied populations based on the haplogroup frequency spectrum and sequence variations. Clustering patterns in principal component analysis and multidimensional scaling results showed a genetic differentiation between Tai-Kadai-speaking Li, Mongolic-speaking Mongolian, and other Sinitic-speaking Han Chinese populations. Phylogenetic topology inferred from the BEAST and Network relationships reconstructed from the popART further showed the founding lineages from culturally/linguistically diverse populations, such as C2a/C2b was dominant in Mongolian people and O1a/O1b was dominant in island Li people. We also identified many lineages shared by more than two ethnolinguistically different populations with a high proportion, suggesting their extensive admixture and migration history. CONCLUSIONS Our findings indicated that our developed high-resolution Y-SNP panel included major dominant Y-lineages of Chinese populations from different ethnic groups and geographical regions, which can be used as the primary and powerful tool for forensic practice. We should emphasize the necessity and importance of whole sequencing of more ethnolinguistically different populations, which can help identify more unrecognized population-specific variations for the promotion of Y-chromosome-based forensic applications.
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Affiliation(s)
- Guanglin He
- Institute of Rare Diseases, West China Hospital of Sichuan University, Sichuan University, Chengdu, 610041, China.
| | - Mengge Wang
- Faculty of Forensic Medicine, Zhongshan School of Medicine, Sun Yat-Sen University, Guangzhou, 510275, China
| | - Lei Miao
- National Engineering Laboratory for Forensic Science, Key Laboratory of Forensic Genetics of Ministry of Public Security, Institute of Forensic Science, Ministry of Public Security, Beijing, 100038, China
| | - Jing Chen
- School of Forensic Medicine, Shanxi Medical University, Jinzhong, 030001, China
| | - Jie Zhao
- National Engineering Laboratory for Forensic Science, Key Laboratory of Forensic Genetics of Ministry of Public Security, Institute of Forensic Science, Ministry of Public Security, Beijing, 100038, China
| | - Qiuxia Sun
- Institute of Rare Diseases, West China Hospital of Sichuan University, Sichuan University, Chengdu, 610041, China
- Department of Forensic Medicine, College of Basic Medicine, Chongqing Medical University, Chongqing, 400331, China
| | - Shuhan Duan
- Institute of Rare Diseases, West China Hospital of Sichuan University, Sichuan University, Chengdu, 610041, China
- School of Basic Medical Sciences, North Sichuan Medical College, Nanchong, 637000, China
| | - Zhiyong Wang
- Institute of Rare Diseases, West China Hospital of Sichuan University, Sichuan University, Chengdu, 610041, China
- School of Forensic Medicine, Kunming Medical University, Kunming, 650500, China
| | - Xiaofei Xu
- Institute of Rare Diseases, West China Hospital of Sichuan University, Sichuan University, Chengdu, 610041, China
| | - Yuntao Sun
- Institute of Rare Diseases, West China Hospital of Sichuan University, Sichuan University, Chengdu, 610041, China
- Institute of Forensic Medicine, West China School of Basic Science and Forensic Medicine, Sichuan University, Chengdu, 610041, China
| | - Yan Liu
- Institute of Rare Diseases, West China Hospital of Sichuan University, Sichuan University, Chengdu, 610041, China
- School of Basic Medical Sciences, North Sichuan Medical College, Nanchong, 637000, China
| | - Jing Liu
- Institute of Forensic Medicine, West China School of Basic Science and Forensic Medicine, Sichuan University, Chengdu, 610041, China
| | - Zheng Wang
- Institute of Forensic Medicine, West China School of Basic Science and Forensic Medicine, Sichuan University, Chengdu, 610041, China
| | - Lanhai Wei
- School of Ethnology and Anthropology, Inner Mongolia Normal University, Hohhot, 010028, Inner Mongolia, China
| | - Chao Liu
- Faculty of Forensic Medicine, Zhongshan School of Medicine, Sun Yat-Sen University, Guangzhou, 510275, China
- Guangzhou Key Laboratory of Forensic Multi-Omics for Precision Identification, School of Forensic Medicine, Southern Medical University, Guangzhou, 510515, China
| | - Jian Ye
- National Engineering Laboratory for Forensic Science, Key Laboratory of Forensic Genetics of Ministry of Public Security, Institute of Forensic Science, Ministry of Public Security, Beijing, 100038, China.
| | - Le Wang
- National Engineering Laboratory for Forensic Science, Key Laboratory of Forensic Genetics of Ministry of Public Security, Institute of Forensic Science, Ministry of Public Security, Beijing, 100038, China.
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20
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Budowle B, Sajantila A. Revisiting informed consent in forensic genomics in light of current technologies and the times. Int J Legal Med 2023; 137:551-565. [PMID: 36642749 PMCID: PMC9902322 DOI: 10.1007/s00414-023-02947-w] [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: 08/10/2022] [Accepted: 12/14/2022] [Indexed: 01/17/2023]
Abstract
Informed consent is based on basic ethical principles that should be considered when conducting biomedical and behavioral research involving human subjects. These principles-respect, beneficence, and justice-form the foundations of informed consent which in itself is grounded on three fundamental elements: information, comprehension, and voluntary participation. While informed consent has focused on human subjects and research, the practice has been adopted willingly in the forensic science arena primarily to acquire reference samples from family members to assist in identifying missing persons. With advances in molecular biology technologies, data mining, and access to metadata, it is important to assess whether the past informed consent process and in particular associated risks are concomitant with these increased capabilities. Given the state-of-the-art, areas in which informed consent may need to be modified and augmented are as follows: reference samples from family members in missing persons or unidentified human remains cases; targeted analysis of an individual(s) during forensic genetic genealogy cases to reduce an investigative burden; donors who provide their samples for validation studies (to include population studies and entry into databases that would be applied to forensic statistical calculations) to support implementation of procedures and operations of the forensic laboratory; family members that may contribute samples or obtain genetic information from a molecular autopsy; and use of medical and other acquired samples that could be informative for identification purposes. The informed consent process should cover (1) purpose for collection of samples; (2) process to analyze the samples (to include type of data); (3) benefits (to donor, target, family, community, etc. as applicable); (4) risks (to donor, target, family, community, etc. as applicable); (5) access to data/reports by the donor; (6) sample disposition; (7) removal of data process (i.e., expungement); (8) process to ask questions/assessment of comprehension; (9) follow-up processes; and (10) voluntary, signed, and dated consent. Issues surrounding these topics are discussed with an emphasis on addressing risk factors. Addressing informed consent will allow human subjects to make decisions voluntarily and with autonomy as well as secure the use of samples for intended use.
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Affiliation(s)
- Bruce Budowle
- Department of Forensic Medicine, University of Helsinki, Helsinki, Finland.
| | - Antti Sajantila
- Department of Forensic Medicine, University of Helsinki, Helsinki, Finland
- Forensic Medicine Unit, Finnish Institute for Health and Welfare, Helsinki, Finland
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21
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Ashirbekov Y, Nogay A, Abaildayev A, Zhunussova A, Sabitov Z, Zhabagin M. Genetic polymorphism of 27 Y-STR loci in Kazakh populations from Eastern Kazakhstan. Ann Hum Biol 2023; 50:48-51. [PMID: 36650935 DOI: 10.1080/03014460.2023.2170465] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Abstract
BACKGROUND The establishment of a national haplotype database is important for forensic and genetic applications and requires studying genetic polymorphisms at Y-STR sites. However, the genetic structure of the Eastern Kazakhstan population is poorly characterised. AIM To investigate the genetic polymorphisms of 27 Y-STR loci in the Kazakh population from Eastern Kazakhstan and analyse the population genetic relationships of the Eastern Kazakhs with other populations. SUBJECTS AND METHODS The Yfiler Plus kit was utilised to genotype 246 healthy, unrelated males from Eastern Kazakhstan. Based on the raw data, haplotype and allele frequencies along with forensic parameters were calculated, and an MDS plot was constructed. RESULTS A total of 207 haplotypes were detected, of which 186 were unique. The haplotype diversity and discrimination capacity were 0.997 and 0.841, respectively. Population comparisons showed that Eastern Kazakhs have close genetic relationships with Kazakhs from Xinjiang, China. At the same time, a difference was found between the studied population and the previous one in the same part of Kazakhstan. CONCLUSIONS The obtained haplotypes will help to expand the Kazakhstan Y-chromosome reference database and will be useful for future genetic research and forensic applications.
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Affiliation(s)
- Yeldar Ashirbekov
- M. Aitkhozhin Institute of Molecular Biology and Biochemistry, Almaty, Republic of Kazakhstan
| | - Anastassiya Nogay
- National Center for Biotechnology, Astana, Republic of Kazakhstan.,School of Sciences and Humanities, Nazarbayev University, Astana, Kazakhstan
| | - Arman Abaildayev
- M. Aitkhozhin Institute of Molecular Biology and Biochemistry, Almaty, Republic of Kazakhstan
| | - Aigul Zhunussova
- National Center for Biotechnology, Astana, Republic of Kazakhstan
| | - Zhaxylyk Sabitov
- National Center for Biotechnology, Astana, Republic of Kazakhstan.,L.N. Gumilyov Eurasian National University, Astana, Republic of Kazakhstan.,Research Institute for Jochi Ulus Studies, Astana, Republic of Kazakhstan
| | - Maxat Zhabagin
- National Center for Biotechnology, Astana, Republic of Kazakhstan
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22
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Vilà-Valls L, Aizpurua-Iraola J, Casinge S, Bojs K, Flores-Bello A, Font-Porterias N, Comas D. Genomic Insights into the Population History of the Resande or Swedish Travelers. Genome Biol Evol 2023; 15:6991919. [PMID: 36655389 PMCID: PMC9907538 DOI: 10.1093/gbe/evad006] [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: 09/23/2022] [Revised: 12/29/2022] [Accepted: 01/09/2023] [Indexed: 01/20/2023] Open
Abstract
The Resande are a minority ethnic group in Sweden, who were characterized by an itinerant way of life, and they have been suggested to originate from the mixture between Swedish and Romani populations. Because the population history of the Resande has been scarcely studied, we analyzed genome-wide genotype array data from unrelated Resande individuals in order to shed light on their origins and demographic history for the first time from a genetic perspective. Our results confirm the Romani-related ancestry of this population and suggest an admixture event between a Romani-like population and a general Swedish-like population that occurred approximately between the mid-18th and mid-19th centuries, two centuries after the arrival of the first historically reported Romani families in Sweden. This inferred date suggests that the Romani group involved in the admixture is related to the pre-18th-century arrivals of Romani in Scandinavia. In addition, a reduction in the population size is detected previous to the admixture event, suggesting a subtle signal of isolation. The present work constitutes a step forward toward a better representation of ethnic minorities and underrepresented groups in population genetic analyses. In order to know in more detail the complete history of human populations, it is time to focus on studying populations that have not been previously considered for a general scenario and that can provide valuable information to fill in the gaps that still remain uncovered.
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Affiliation(s)
- Laura Vilà-Valls
- Institute of Evolutionary Biology (UPF-CSIC), Department of Medicine and Life Sciences, Universitat Pompeu Fabra, Barcelona, Spain
| | - Julen Aizpurua-Iraola
- Institute of Evolutionary Biology (UPF-CSIC), Department of Medicine and Life Sciences, Universitat Pompeu Fabra, Barcelona, Spain
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23
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Zhou Z, Li Z, Yao Y, Qian J, Ji Q, Shao C, Xie J. Validation of phylogenetic informative Y-InDels in Y-chromosomal haplogroup O-M175. Front Genet 2023; 14:1182028. [PMID: 37205119 PMCID: PMC10185902 DOI: 10.3389/fgene.2023.1182028] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2023] [Accepted: 04/17/2023] [Indexed: 05/21/2023] Open
Abstract
The Y-chromosomal haplogroup tree, which consists of a group of Y-chromosomal loci with phylogenetic information, has been widely applied in anthropology, archaeology and population genetics. With the continuous updating of the phylogenetic structure, Y-chromosomal haplogroup tree provides more information for recalling the biogeographical origin of Y chromosomes. Generally, Y-chromosomal insertion-deletion polymorphisms (Y-InDels) are genetically stable as Y-chromosomal single nucleotide polymorphisms (Y-SNPs), and therefore carry mutations that can accumulate over generations. In this study, potential phylogenetic informative Y-InDels were filtered out in haplogroup O-M175, which is dominant in East Asia, based on population data retrieved from the 1000 Genomes Project. A group of 22 phylogenetic informative Y-InDels were identified and then assigned to their corresponding subclades of haplogroup O-M175, which provided a supplement for the update and application of Y-chromosomal markers. Especially, four Y-InDels were introduced to define subclades determined using a single Y-SNP.
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24
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Kim HJ, Jin HJ. Lack of association between the Y chromosome haplogroups and attention deficit hyperactivity disorder (ADHD) in Korean boys. Gene 2023; 850:146954. [DOI: 10.1016/j.gene.2022.146954] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2022] [Revised: 09/26/2022] [Accepted: 10/03/2022] [Indexed: 02/13/2023]
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25
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Timmers PRHJ, Wilson JF. Limited Effect of Y Chromosome Variation on Coronary Artery Disease and Mortality in UK Biobank-Brief Report. Arterioscler Thromb Vasc Biol 2022; 42:1198-1206. [PMID: 35861954 PMCID: PMC9394501 DOI: 10.1161/atvbaha.122.317664] [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] [Indexed: 11/16/2022]
Abstract
BACKGROUND The effect of genetic variation in the male-specific region of the Y chromosome (MSY) on coronary artery disease and cardiovascular risk factors has been disputed. In this study, we systematically assessed the association of MSY genetic variation on these traits using a kin-cohort analysis of family disease history in the largest sample to date. METHODS We tested 90 MSY haplogroups against coronary artery disease, hypertension, blood pressure, classical lipid levels, and all-cause mortality in up to 152 186 unrelated, genomically British individuals from UK Biobank. Unlike previous studies, we did not adjust for heritable lifestyle factors (to avoid collider bias) and instead adjusted for geographic variables and socioeconomic deprivation, given the link between MSY haplogroups and geography. For family history traits, subject MSY haplogroups were tested against father and mother disease as validation and negative control, respectively. RESULTS Our models find little evidence for an effect of any MSY haplogroup on cardiovascular risk in participants. Parental models confirm these findings. CONCLUSIONS Kin-cohort analysis of the Y chromosome uniquely allows for discoveries in subjects to be validated using family history data. Despite our large sample size, improved models, and parental validation, there is little evidence to suggest cardiovascular risk in UK Biobank is influenced by genetic variation in MSY.
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Affiliation(s)
- Paul R H J Timmers
- MRC Human Genetics Unit, MRC Institute of Genetics and Cancer (P.R.H.J.T., J.F.W.), University of Edinburgh, United Kingdom.,Centre for Global Health Research, Usher Institute (P.R.H.J.T., J.F.W.), University of Edinburgh, United Kingdom
| | - James F Wilson
- MRC Human Genetics Unit, MRC Institute of Genetics and Cancer (P.R.H.J.T., J.F.W.), University of Edinburgh, United Kingdom.,Centre for Global Health Research, Usher Institute (P.R.H.J.T., J.F.W.), University of Edinburgh, United Kingdom
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26
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de Knijff P. On the Forensic Use of Y-Chromosome Polymorphisms. Genes (Basel) 2022; 13:genes13050898. [PMID: 35627283 PMCID: PMC9141910 DOI: 10.3390/genes13050898] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2022] [Revised: 05/09/2022] [Accepted: 05/13/2022] [Indexed: 12/26/2022] Open
Abstract
Nowadays, the use of Y-chromosome polymorphisms forms an essential part of many forensic DNA investigations. However, this was not always the case. Only since 1992 have we seen that some forensic scientists started to have an interest in this chromosome. In this review, I will sketch a brief history focusing on the forensic use of Y-chromosome polymorphisms. Before describing the various applications of short-tandem repeats (STRs) and single nucleotide polymorphisms (SNPs) on the Y-chromosome, I will discuss a few often ignored aspects influencing proper use and interpretation of Y-chromosome information: (i) genotyping Y-SNPs and Y-STRs, (ii) Y-STR haplotypes shared identical by state (IBS) or identical by descent (IBD), and (iii) Y-haplotype database frequencies.
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Affiliation(s)
- Peter de Knijff
- Department of Human Genetics, Leiden University Medical Center, P.O. Box 9600, 2300 RC Leiden, The Netherlands
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27
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Huszar TI, Bodmer WF, Hutnik K, Wetton JH, Jobling MA. Sequencing of autosomal, mitochondrial and Y-chromosomal forensic markers in the People of the British Isles cohort detects population structure dominated by patrilineages. Forensic Sci Int Genet 2022; 59:102725. [DOI: 10.1016/j.fsigen.2022.102725] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2022] [Revised: 05/08/2022] [Accepted: 05/13/2022] [Indexed: 11/27/2022]
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Examination of d-loop region and DBY gene as tools for identifying hybridisation in alpacas (Vicugna pacos) based on Polish populations. Small Rumin Res 2022. [DOI: 10.1016/j.smallrumres.2022.106690] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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29
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Reyes-Madrid M, Flores-Alvarado S, Pezo-Valderrama P, Orellana-Soto M, Apata M, Moraga M, de Saint Pierre M. An approach on the migratory processes in the north of Chile based on Y chromosome analysis. Am J Hum Biol 2022; 34:e23736. [PMID: 35263492 DOI: 10.1002/ajhb.23736] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2020] [Revised: 12/23/2021] [Accepted: 02/12/2022] [Indexed: 11/09/2022] Open
Abstract
OBJECTIVES Northern Chile is an area characterized by a complex cultural and demographic trajectory. During the last few centuries, this complex trajectory has become the destination of intra- and intercontinental migratory waves. In this study, we analyzed the Y chromosome to evaluate how migratory and admixture patterns have affected the genetic composition of the populations in northern Chile compared with other populations of the country. METHODS A total of 311 people from urban (Antofagasta and Calama), rural (Azapa and Camarones), and Native (Aymara and Atacameño) populations from northern Chile were characterized by 26 SNPs and the STR DYS393 of the Y chromosome, along with 69 individuals from Native populations (Mapuche, Pehuenche, and Huilliche) from southern Chile. In addition to characterizing the paternal lineages, multivariate analyses were performed to compare with published data from other Chilean populations. RESULTS Both the Antofagasta and Calama populations show differences compared with the rest of the Chilean population. On one side, Antofagasta shows a high diversity of non-Amerindian lineages, including the highest value for haplogroup I (12%) for all Chileans populations. Otherwise, Calama has the highest value of any Chilean urban population (31.9%) for Amerindian lineages, including the only Q-M3 sub-lineage detected in the entire sample. Regarding the Native population, Aymara presents the highest percentage of Q-M3 (94.4%). CONCLUSIONS The Y chromosome haplogroup distribution allowed us to identify recent migratory processes typical of the northern populations studied. These have shaped the demographic and cultural dynamics of local and migrant groups in the territory.
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Affiliation(s)
- Margarita Reyes-Madrid
- Departamento de Antropología, Facultad de Ciencias Sociales, Universidad de Chile, Santiago, Chile
| | - Sandra Flores-Alvarado
- Programa de Bioestadística, Instituto de Salud Pública, Facultad de Medicina, Universidad de Chile, Santiago, Chile
| | | | - Michael Orellana-Soto
- Instituto de Ciencias Biomédicas, Facultad de Medicina, Universidad de Chile, Santiago, Chile
| | - Mario Apata
- Instituto de Ciencias Biomédicas, Facultad de Medicina, Universidad de Chile, Santiago, Chile
| | - Mauricio Moraga
- Departamento de Antropología, Facultad de Ciencias Sociales, Universidad de Chile, Santiago, Chile.,Instituto de Ciencias Biomédicas, Facultad de Medicina, Universidad de Chile, Santiago, Chile
| | - Michelle de Saint Pierre
- Departamento de Antropología, Facultad de Ciencias Sociales, Universidad de Chile, Santiago, Chile
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30
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Zho Z, Zhou Y, Li Z, Yao Y, Yang Q, Qian J, Shao C, Qian X, Sun K, Tang Q, Xie J. Identification and assessment of a subset of Y-SNPs with recurrent mutation for forensic purpose. Forensic Sci Int 2022; 334:111270. [DOI: 10.1016/j.forsciint.2022.111270] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2021] [Revised: 01/18/2022] [Accepted: 03/09/2022] [Indexed: 11/26/2022]
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A multi-dimensional evaluation of the 'NIST 1032' sample set across four forensic Y-STR multiplexes. Forensic Sci Int Genet 2022; 57:102655. [PMID: 35007854 PMCID: PMC9901497 DOI: 10.1016/j.fsigen.2021.102655] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2021] [Revised: 12/09/2021] [Accepted: 12/12/2021] [Indexed: 02/08/2023]
Abstract
This manuscript reports Y-chromosomal short tandem repeat (Y-STR) haplotypes for 1032 male U.S. population samples across 30 Y-STR loci characterized by three capillary electrophoresis (CE) length-based kits (PowerPlex Y23 System, Yfiler Plus PCR Amplification Kit, and Investigator Argus Y-28 QS Kit) and one sequence-based kit (ForenSeq DNA Signature Prep Kit): DYF387S1, DYS19, DYS385 a/b, DYS389I, DYS389II, DYS390, DYS391, DYS392, DYS393, DYS437, DYS438, DYS439, DYS448, DYS449, DYS456, DYS458, DYS460, DYS481, DYS505, DYS518, DYS522, DYS533, DYS549, DYS570, DYS576, DYS612, DYS627, DYS635, DYS643, and Y-GATA-H4. The length-based Y-STR haplotypes include six loci that are not reported in the sequence-based kit (DYS393, DYS449, DYS456, DYS458, DYS518, and DYS627), whereas three loci included in the sequence-based kit are not present in length-based kits (DYS505, DYS522, and DYS612). For the latter, a custom multiplex was used to generate CE length-based data, allowing 1032 samples to be evaluated for concordance across the 30 Y-STR loci included in these four commercial Y-STR typing kits. Discordances between typing methods were analyzed further to assess underlying causes such as primer binding site mutations and flanking region insertions/deletions. Allele-level frequency and statistical information is provided for sequenced loci, excluding the multi-copy loci DYF387S1 and DYS385 a/b, for which locus-specific haplotype-level frequencies are provided instead. The resulting data reveals the degree of information gained through sequencing: 88% of sequenced Y-STR loci contain additional sequence-based alleles compared to length-based data, with the DYS389II locus containing the most additional alleles (51) observed by sequencing. Despite these allelic increases, only minimal improvement was observed in haplotype resolution by sequence, with all four commercial kits providing a similar ability to differentiate length-based haplotypes in this sample set. Finally, a subset of 369 male samples were compared to their corresponding additionally sequenced father samples, revealing the sequence basis for the 50 length-based changes observed, and no additional sequence-based mutations. GenBank accession numbers are reported for each unique sequence, and associated records are available in the STRSeq Y-Chromosomal STR Loci National Center for Biotechnology Information (NCBI) BioProject, accession PRJNA380347. Haplotype data is updated in the Y-STR Haplotype Reference Database (YHRD) for the 'NIST 1032' data set to now achieve the level of maximal haplotype of YHRD. All supplementary files including revisions to previously published Y-STR data are available in the NIST Public Data Repository: U.S. population data for human identification markers, DOI 10.18434/t4/1500024.
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Moon MH, Hong SR, Shin KJ. Sequence Variations of 31 Υ-Chromosomal Short Tandem Repeats Analyzed by Massively Parallel Sequencing in Three U.S. Population Groups and Korean Population. J Korean Med Sci 2022; 37:e40. [PMID: 35166077 PMCID: PMC8845103 DOI: 10.3346/jkms.2022.37.e40] [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] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/26/2021] [Accepted: 12/19/2021] [Indexed: 12/02/2022] Open
Abstract
BACKGROUND Rapidly mutating (RM) Y-chromosomal short tandem repeats (Y-STRs) have been demonstrated to increase the possibility of distinguishing between male relatives due to a higher mutation rate than conventional Y-STRs. Massively parallel sequencing (MPS) can be useful for forensic DNA typing as it allows the detection of sequence variants of many forensic markers. Here, we present sequence variations of 31 Y-STRs including nine RM Y-STRs (DYF387S1, DYF399S1, DYF404S1, DYS449, DYS518, DYS570, DYS576, DYS612, and DYS627), their frequencies, distribution, and the gain in the number of alleles using MPS. METHODS We constructed a multiplex MPS assay capable of simultaneously amplifying 32 Y-chromosomal markers, producing amplicons ranging from 85-274 bp. Barcoded libraries from 220 unrelated males from four populations-African Americans, Caucasians, Hispanics, and Koreans-were generated via two-step polymerase chain reaction and sequenced on a MiSeq system. Genotype concordance between the capillary electrophoresis (CE) and MPS method and sequence variation of Y-STRs were investigated. RESULTS In total, 195 alleles were increased by MPS compared to CE-based alleles (261 to 456). The DYS518 marker showed the largest increase due to repeat region variation (a 3.69-fold increase). The highest increase in the number of alleles due to single nucleotide polymorphisms in the flanking region was found in DYF399S1. RM Y-STRs had more diverse sequences than conventional Y-STRs. Furthermore, null alleles were observed in DYS576 due to primer-binding site mutation, and allele drop-outs in DYS449 resulted from low marker coverage of less than the threshold. CONCLUSION The results suggest that the expanded and discriminative MPS assay could provide more genetic information for Y-STRs, especially for RM Y-STRs, and could advance male individualization. Compiling sequence-based Y-STR data for worldwide populations would facilitate the application of MPS in the field of forensic genetics and could be applicable in solving male-related forensic cases.
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Affiliation(s)
- Mi Hyeon Moon
- Department of Forensic Medicine, Yonsei University College of Medicine, Seoul, Korea
- Graduate School of Medical Science and Brain Korea 21 Project, Yonsei University, Seoul, Korea
| | - Sae Rom Hong
- Department of Forensic Medicine, Yonsei University College of Medicine, Seoul, Korea
| | - Kyoung-Jin Shin
- Department of Forensic Medicine, Yonsei University College of Medicine, Seoul, Korea
- Graduate School of Medical Science and Brain Korea 21 Project, Yonsei University, Seoul, Korea.
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33
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Takagi T, Tsuda Y, Torii H, Tamate HB, Kaneko S, Nagata J. Development of paternally‐inherited Y chromosome simple sequence repeats of sika deer and their application in genetic structure, artificial introduction, and interspecific hybridization analyses. POPUL ECOL 2022. [DOI: 10.1002/1438-390x.12109] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Affiliation(s)
- Toshihito Takagi
- Graduate School of Symbiotic Systems Science and Technology Fukushima University Kanayagawa Fukushima Japan
| | - Yoshiaki Tsuda
- Sugadaira Research Station, Mountain Science Center (MSC) University of Tsukuba Ueda Nagano Japan
| | - Harumi Torii
- Center for Natural Environment Education Nara University of Education Takahata‐cho Nara Japan
| | | | - Shingo Kaneko
- Faculty of Symbiotic Systems Science Fukushima University Kanayagawa Fukushima Japan
| | - Junco Nagata
- Forestry and Forest Products Research Institute (FFPRI) Tsukuba Ibaraki Japan
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Flores-Bello A, Font-Porterias N, Aizpurua-Iraola J, Duarri-Redondo S, Comas D. The genetic scenario of Mercheros: an under-represented group within the Iberian Peninsula. BMC Genomics 2021; 22:897. [PMID: 34911433 PMCID: PMC8672588 DOI: 10.1186/s12864-021-08203-y] [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: 07/19/2021] [Accepted: 11/18/2021] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND The general picture of human genetic variation has been vastly depicted in the last years, yet many populations remain broadly understudied. In this work, we analyze for the first time the Merchero population, a Spanish minority ethnic group that has been scarcely studied and historically persecuted. Mercheros have been roughly characterised by an itinerant history, common traditional occupations, and the usage of their own language. RESULTS Here, we examine the demographic history and genetic scenario of Mercheros, by using genome-wide array data, whole mitochondrial sequences, and Y chromosome STR markers from 25 individuals. These samples have been complemented with a wide-range of present-day populations from Western Eurasia and North Africa. Our results show that the genetic diversity of Mercheros is explained within the context of the Iberian Peninsula, evidencing a modest signal of Roma admixture. In addition, Mercheros present low genetic isolation and intrapopulation heterogeneity. CONCLUSIONS This study represents the first genetic characterisation of the Merchero population, depicting their fine-scale ancestry components and genetic scenario within the Iberian Peninsula. Since ethnicity is not only influenced by genetic ancestry but also cultural factors, other studies from multiple disciplines are needed to further explore the Merchero population. As with Mercheros, there is a considerable gap of underrepresented populations and ethnic groups in publicly available genetic data. Thus, we encourage the consideration of more ethnically diverse population panels in human genetic studies, as an attempt to improve the representation of human populations and better reconstruct their fine-scale history.
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Affiliation(s)
- André Flores-Bello
- Departament de Ciències de la Salut i de la Vida, Institut de Biologia Evolutiva (CSIC-UPF), Universitat Pompeu Fabra, 08003, Barcelona, Spain
| | - Neus Font-Porterias
- Departament de Ciències de la Salut i de la Vida, Institut de Biologia Evolutiva (CSIC-UPF), Universitat Pompeu Fabra, 08003, Barcelona, Spain
| | - Julen Aizpurua-Iraola
- Departament de Ciències de la Salut i de la Vida, Institut de Biologia Evolutiva (CSIC-UPF), Universitat Pompeu Fabra, 08003, Barcelona, Spain
| | - Sara Duarri-Redondo
- Departament de Ciències de la Salut i de la Vida, Institut de Biologia Evolutiva (CSIC-UPF), Universitat Pompeu Fabra, 08003, Barcelona, Spain
| | - David Comas
- Departament de Ciències de la Salut i de la Vida, Institut de Biologia Evolutiva (CSIC-UPF), Universitat Pompeu Fabra, 08003, Barcelona, Spain.
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35
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Ghaiyed AP, Sutherland H, Lea RA, Gardam T, Chaseling J, James K, Bernie A, Haupt LM, Christie J, Griffiths LR, Wright KM. Evaluation of an ancestry prediction strategy for historical military remains using a World War II-era sample and pedigrees with family-level admixture. AUST J FORENSIC SCI 2021. [DOI: 10.1080/00450618.2021.2005144] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
Affiliation(s)
- A. P. Ghaiyed
- Genomics Research Centre, Centre for Genomics and Personalised Health, Queensland University of Technology, Kelvin Grove, Australia
| | - H. Sutherland
- Genomics Research Centre, Centre for Genomics and Personalised Health, Queensland University of Technology, Kelvin Grove, Australia
| | - R. A. Lea
- Genomics Research Centre, Centre for Genomics and Personalised Health, Queensland University of Technology, Kelvin Grove, Australia
| | - T. Gardam
- Genomics Research Centre, Centre for Genomics and Personalised Health, Queensland University of Technology, Kelvin Grove, Australia
| | - J. Chaseling
- School of Environment and Science, Griffith University, Nathan, Australia
| | - K. James
- Genomics Research Centre, Centre for Genomics and Personalised Health, Queensland University of Technology, Kelvin Grove, Australia
| | - A. Bernie
- Unrecovered War Casualties-Army, Australian Defence Force, Russell Offices, Canberra, Australia
| | - L. M. Haupt
- Genomics Research Centre, Centre for Genomics and Personalised Health, Queensland University of Technology, Kelvin Grove, Australia
| | - J. Christie
- School of Environment and Science, Griffith University, Nathan, Australia
| | - L. R. Griffiths
- Genomics Research Centre, Centre for Genomics and Personalised Health, Queensland University of Technology, Kelvin Grove, Australia
| | - K. M. Wright
- Genomics Research Centre, Centre for Genomics and Personalised Health, Queensland University of Technology, Kelvin Grove, Australia
- Unrecovered War Casualties-Army, Australian Defence Force, Russell Offices, Canberra, Australia
- Royal Australian Air Force (RAAF), Williamtown, Australia
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36
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Genealogy: The Tree Where History Meets Genetics. GENEALOGY 2021. [DOI: 10.3390/genealogy5040098] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
Although biological relationships are a universal reality for all human beings, the concepts of “family” and “family bond” depend on both the geographic region and the historical moment to which they refer. However, the concept of “family” can be determinant in a large variety of societies, since it can influence the lines of succession, inheritances and social relationships, as well as where and with whom an individual is buried. The relation between a deceased person and other members of a community, other individuals of the same necropolis, or even with those who are buried in the same tomb can be analysed from the genetic point of view, considering different perspectives: archaeological, historical, and forensic. In the present work, the concepts of “family” and “kinship” are discussed, explaining the relevance of genetic analysis, such as nuclear and lineage markers, and their contribution to genealogical research, for example in the heritage of surnames and Y-chromosome, as well as those cases where some discrepancies with historical record are detected, such as cases of adoption. Finally, we explain how genetic genealogical analyses can help to solve some cold cases, through the analysis of biologically related relatives.
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Bini C, Cilli E, Sarno S, Traversari M, Fontani F, Boattini A, Pelotti S, Luiselli D. Twenty-Seven Y-Chromosome Short Tandem Repeats Analysis of Italian Mummies of the 16th and 18th Centuries: An Interdisciplinary Research. Front Genet 2021; 12:720640. [PMID: 34659342 PMCID: PMC8514714 DOI: 10.3389/fgene.2021.720640] [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: 06/04/2021] [Accepted: 08/12/2021] [Indexed: 11/13/2022] Open
Abstract
Roccapelago (MO) is a small village located in the Northern Central Apennines, with a population of 31 inhabitants (2014). In 2010, more than 400 individuals dated between the end of the 16th and the 18th century, many of which partially mummified, were discovered in the crypt of the church. This small village, because of its geographical location and surrounding environment, seems to possess the characteristics of a genetic isolate, useful for population genetics and genealogical analyses. Thus, a diachronic study of DNA aimed at investigating the structure and dynamics of the population of Roccapelago over the about 4 centuries, was conducted by analyzing ancient and modern inhabitants of the village. The 14 modern samples were selected by considering both the founder surnames of the village, identified thanks to the study of parish registers, and the grandparent's criterion. From 25 ancient mummies, morphologically assigned to male individuals, the petrous bone, that harbors high DNA amounts, was selected for the DNA extraction. The quantification and qualitative assessment of total human male DNA were evaluated by a real-time PCR assay using the Quantifiler Trio DNA Quantification Kit and multiplex PCR of 27 Y-chromosome short tandem repeat (Y-STR) markers included in the Yfiler Plus PCR Amplification Kit, with seven rapidly mutating Y-STR loci for improving discrimination of male lineages, was performed to genotype the samples. Y-STRs were analyzed according to the criteria of ancient DNA (aDNA) analysis to ensure that authentic DNA typing results were obtained from these ancient samples. The molecular analysis showed the usefulness of the Y chromosome to identify historically relevant remains and discover patterns of relatedness in communities moving from anthropology to genetic genealogy and forensics.
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Affiliation(s)
- Carla Bini
- Laboratory of Forensic Genetics, Department of Medical and Surgical Sciences, University of Bologna, Bologna, Italy
| | - Elisabetta Cilli
- Laboratory of Ancient DNA (aDNALab), Department of Cultural Heritage, University of Bologna, Ravenna, Italy
| | - Stefania Sarno
- Laboratory of Molecular Anthropology and Centre for Genome Biology, Department of Biological, Geological and Environmental Sciences, University of Bologna, Bologna, Italy
| | - Mirko Traversari
- Laboratory of Ancient DNA (aDNALab), Department of Cultural Heritage, University of Bologna, Ravenna, Italy
| | - Francesco Fontani
- Laboratory of Ancient DNA (aDNALab), Department of Cultural Heritage, University of Bologna, Ravenna, Italy
| | - Alessio Boattini
- Laboratory of Molecular Anthropology and Centre for Genome Biology, Department of Biological, Geological and Environmental Sciences, University of Bologna, Bologna, Italy
| | - Susi Pelotti
- Laboratory of Forensic Genetics, Department of Medical and Surgical Sciences, University of Bologna, Bologna, Italy
| | - Donata Luiselli
- Laboratory of Ancient DNA (aDNALab), Department of Cultural Heritage, University of Bologna, Ravenna, Italy
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38
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Razali RM, Rodriguez-Flores J, Ghorbani M, Naeem H, Aamer W, Aliyev E, Jubran A, Clark AG, Fakhro KA, Mokrab Y. Thousands of Qatari genomes inform human migration history and improve imputation of Arab haplotypes. Nat Commun 2021; 12:5929. [PMID: 34642339 PMCID: PMC8511259 DOI: 10.1038/s41467-021-25287-y] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2020] [Accepted: 08/02/2021] [Indexed: 12/15/2022] Open
Abstract
Arab populations are largely understudied, notably their genetic structure and history. Here we present an in-depth analysis of 6,218 whole genomes from Qatar, revealing extensive diversity as well as genetic ancestries representing the main founding Arab genealogical lineages of Qahtanite (Peninsular Arabs) and Adnanite (General Arabs and West Eurasian Arabs). We find that Peninsular Arabs are the closest relatives of ancient hunter-gatherers and Neolithic farmers from the Levant, and that founder Arab populations experienced multiple splitting events 12–20 kya, consistent with the aridification of Arabia and farming in the Levant, giving rise to settler and nomadic communities. In terms of recent genetic flow, we show that these ancestries contributed significantly to European, South Asian as well as South American populations, likely as a result of Islamic expansion over the past 1400 years. Notably, we characterize a large cohort of men with the ChrY J1a2b haplogroup (n = 1,491), identifying 29 unique sub-haplogroups. Finally, we leverage genotype novelty to build a reference panel of 12,432 haplotypes, demonstrating improved genotype imputation for both rare and common alleles in Arabs and the wider Middle East. Arab populations are relatively understudied, especially their genetic architecture and historical relationship with early founders of the ancient Near East. Here, the authors examine 6,218 Qatari whole genomes, revealing insights on migration, population history and genetic structure of populations across the Middle Eastern region.
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Affiliation(s)
| | | | | | - Haroon Naeem
- Department of Human Genetics, Sidra Medicine, Doha, Qatar
| | - Waleed Aamer
- Department of Human Genetics, Sidra Medicine, Doha, Qatar
| | - Elbay Aliyev
- Department of Human Genetics, Sidra Medicine, Doha, Qatar
| | - Ali Jubran
- Department of Human Genetics, Sidra Medicine, Doha, Qatar
| | | | - Andrew G Clark
- Department of Molecular Biology and Genetics, Cornell University, New York, NY, USA
| | - Khalid A Fakhro
- Department of Human Genetics, Sidra Medicine, Doha, Qatar. .,Weill Cornell Medicine-Qatar, Doha, Qatar. .,College of Health and Life Sciences, Hamad Bin Khalifa University, Doha, Qatar.
| | - Younes Mokrab
- Department of Human Genetics, Sidra Medicine, Doha, Qatar. .,Weill Cornell Medicine-Qatar, Doha, Qatar. .,College of Health and Life Sciences, Hamad Bin Khalifa University, Doha, Qatar.
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39
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Pamjav H, Krizsán K. Biologia futura: confessions in genes. Biol Futur 2021; 71:435-441. [PMID: 34554462 DOI: 10.1007/s42977-020-00049-x] [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: 06/08/2020] [Accepted: 10/07/2020] [Indexed: 10/23/2022]
Abstract
Y-DNA and mtDNA have been a widely used tool not only in forensic genetic applications but in human evolutionary and population genetic studies. Its paternal or maternal inheritance and lack of recombination have offered the opportunity to explore genealogical relationships among individuals and to study the frequency differences of paternal and maternal clades among human populations at continental and regional levels. It is unbelievable, but true, that the disadvantages of paternal and maternal lineages in forensic genetic studies, i.e., everyone within a family have the same paternal or maternal haplotype and haplogroup, become advantages in human evolutionary studies, i.e., reveal the genetic history of successful mothers and successful fathers. Thanks to these amazing properties of haploid markers, they provide tools for mapping the migration routes of human populations during prehistoric and historical periods, separately as maternal and paternal lineages, and together as the genetic history of a population.
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Affiliation(s)
- Horolma Pamjav
- Institute of Forensic Genetics, Hungarian Institute for Forensic Sciences, PO: 314/4, Budapest, 1903, Hungary.
| | - Krisztina Krizsán
- Institute of Forensic Genetics, Hungarian Institute for Forensic Sciences, PO: 314/4, Budapest, 1903, Hungary
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40
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Kharkov VN. Y-Chromosome Markers in Population Genetics: Fundamental and Applied Results of Ethnogenomic Research. RUSS J GENET+ 2021. [DOI: 10.1134/s1022795421090040] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
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41
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Claerhout S, Verstraete P, Warnez L, Vanpaemel S, Larmuseau M, Decorte R. CSYseq: The first Y-chromosome sequencing tool typing a large number of Y-SNPs and Y-STRs to unravel worldwide human population genetics. PLoS Genet 2021; 17:e1009758. [PMID: 34491993 PMCID: PMC8423258 DOI: 10.1371/journal.pgen.1009758] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2020] [Accepted: 08/05/2021] [Indexed: 11/26/2022] Open
Abstract
Male-specific Y-chromosome (chrY) polymorphisms are interesting components of the DNA for population genetics. While single nucleotide polymorphisms (Y-SNPs) indicate distant evolutionary ancestry, short tandem repeats (Y-STRs) are able to identify close familial kinships. Detailed chrY analysis provides thus both biogeographical background information as paternal lineage identification. The rapid advancement of high-throughput massive parallel sequencing (MPS) technology in the past decade has revolutionized genetic research. Using MPS, single-base information of both Y-SNPs as Y-STRs can be analyzed in a single assay typing multiple samples at once. In this study, we present the first extensive chrY-specific targeted resequencing panel, the 'CSYseq', which simultaneously identifies slow mutating Y-SNPs as evolution markers and rapid mutating Y-STRs as patrilineage markers. The panel was validated by paired-end sequencing of 130 males, distributed over 65 deep-rooted pedigrees covering 1,279 generations. The CSYseq successfully targets 15,611 Y-SNPs including 9,014 phylogenetic informative Y-SNPs to identify 1,443 human evolutionary Y-subhaplogroup lineages worldwide. In addition, the CSYseq properly targets 202 Y-STRs, including 81 slow, 68 moderate, 27 fast and 26 rapid mutating Y-STRs to individualize close paternal relatives. The targeted chrY markers cover a high average number of reads (Y-SNP = 717, Y-STR = 150), easy interpretation, powerful discrimination capacity and chrY specificity. The CSYseq is interesting for research on different time scales: to identify evolutionary ancestry, to find distant family and to discriminate closely related males. Therefore, this panel serves as a unique tool valuable for a wide range of genetic-genealogical applications in interdisciplinary research within evolutionary, population, molecular, medical and forensic genetics.
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Affiliation(s)
- Sofie Claerhout
- Forensic Biomedical Sciences, Department of Imaging & Pathology, KU Leuven, Leuven, Belgium
| | - Paulien Verstraete
- Forensic Biomedical Sciences, Department of Imaging & Pathology, KU Leuven, Leuven, Belgium
| | - Liesbeth Warnez
- Forensic Biomedical Sciences, Department of Imaging & Pathology, KU Leuven, Leuven, Belgium
| | - Simon Vanpaemel
- KU Leuven, Department of Mechanical Engineering, Noise and Vibration Engineering, Leuven, Belgium
- DMMS Lab, Flanders Make, Heverlee, Belgium
| | - Maarten Larmuseau
- Histories vzw, Mechelen, Belgium
- Department of Human Genetics, KU Leuven, Leuven, Belgium
| | - Ronny Decorte
- Forensic Biomedical Sciences, Department of Imaging & Pathology, KU Leuven, Leuven, Belgium
- Laboratory of Forensic genetics and Molecular Archaeology, UZ Leuven, Leuven, Belgium
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42
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Rohrlach AB, Papac L, Childebayeva A, Rivollat M, Villalba-Mouco V, Neumann GU, Penske S, Skourtanioti E, van de Loosdrecht M, Akar M, Boyadzhiev K, Boyadzhiev Y, Deguilloux MF, Dobeš M, Erdal YS, Ernée M, Frangipane M, Furmanek M, Friederich S, Ghesquière E, Hałuszko A, Hansen S, Küßner M, Mannino M, Özbal R, Reinhold S, Rottier S, Salazar-García DC, Diaz JS, Stockhammer PW, de Togores Muñoz CR, Yener KA, Posth C, Krause J, Herbig A, Haak W. Using Y-chromosome capture enrichment to resolve haplogroup H2 shows new evidence for a two-path Neolithic expansion to Western Europe. Sci Rep 2021; 11:15005. [PMID: 34294811 PMCID: PMC8298398 DOI: 10.1038/s41598-021-94491-z] [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: 02/26/2021] [Accepted: 07/09/2021] [Indexed: 01/08/2023] Open
Abstract
Uniparentally-inherited markers on mitochondrial DNA (mtDNA) and the non-recombining regions of the Y chromosome (NRY), have been used for the past 30 years to investigate the history of humans from a maternal and paternal perspective. Researchers have preferred mtDNA due to its abundance in the cells, and comparatively high substitution rate. Conversely, the NRY is less susceptible to back mutations and saturation, and is potentially more informative than mtDNA owing to its longer sequence length. However, due to comparatively poor NRY coverage via shotgun sequencing, and the relatively low and biased representation of Y-chromosome variants on capture assays such as the 1240 k, ancient DNA studies often fail to utilize the unique perspective that the NRY can yield. Here we introduce a new DNA enrichment assay, coined YMCA (Y-mappable capture assay), that targets the "mappable" regions of the NRY. We show that compared to low-coverage shotgun sequencing and 1240 k capture, YMCA significantly improves the mean coverage and number of sites covered on the NRY, increasing the number of Y-haplogroup informative SNPs, and allowing for the identification of previously undiscovered variants. To illustrate the power of YMCA, we show that the analysis of ancient Y-chromosome lineages can help to resolve Y-chromosomal haplogroups. As a case study, we focus on H2, a haplogroup associated with a critical event in European human history: the Neolithic transition. By disentangling the evolutionary history of this haplogroup, we further elucidate the two separate paths by which early farmers expanded from Anatolia and the Near East to western Europe.
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Affiliation(s)
- Adam B Rohrlach
- Department of Archaeogenetics, Max Planck Institute for the Science of Human History, 07745, Jena, Germany. .,ARC Centre of Excellence for Mathematical and Statistical Frontiers, School of Mathematical Sciences, The University of Adelaide, Adelaide, SA, 5005, Australia.
| | - Luka Papac
- Department of Archaeogenetics, Max Planck Institute for the Science of Human History, 07745, Jena, Germany
| | - Ainash Childebayeva
- Department of Archaeogenetics, Max Planck Institute for the Science of Human History, 07745, Jena, Germany
| | - Maïté Rivollat
- Department of Archaeogenetics, Max Planck Institute for the Science of Human History, 07745, Jena, Germany.,Université de Bordeaux, CNRS, PACEA-UMR 5199, 33615, Pessac, France
| | - Vanessa Villalba-Mouco
- Department of Archaeogenetics, Max Planck Institute for the Science of Human History, 07745, Jena, Germany.,Institute of Evolutionary Biology, CSIC-Universitat Pompeu Fabra, Barcelona, Spain
| | - Gunnar U Neumann
- Department of Archaeogenetics, Max Planck Institute for the Science of Human History, 07745, Jena, Germany
| | - Sandra Penske
- Department of Archaeogenetics, Max Planck Institute for the Science of Human History, 07745, Jena, Germany
| | - Eirini Skourtanioti
- Department of Archaeogenetics, Max Planck Institute for the Science of Human History, 07745, Jena, Germany
| | - Marieke van de Loosdrecht
- Department of Archaeogenetics, Max Planck Institute for the Science of Human History, 07745, Jena, Germany
| | - Murat Akar
- Department of Archaeology, Mustafa Kemal University, 31060, Alahan-Antakya, Hatay, Turkey
| | - Kamen Boyadzhiev
- National Institute of Archaeology with Museum, Bulgarian Academy of Sciences, 1000, Sofia, Bulgaria
| | - Yavor Boyadzhiev
- National Institute of Archaeology with Museum, Bulgarian Academy of Sciences, 1000, Sofia, Bulgaria
| | | | - Miroslav Dobeš
- Department of Prehistory, Institute of Archaeology CAS, Prague, Czech Republic
| | - Yilmaz S Erdal
- Department of Anthropology, Hacettepe University, 06800, Ankara, Turkey
| | - Michal Ernée
- Department of Prehistory, Institute of Archaeology CAS, Prague, Czech Republic
| | | | | | - Susanne Friederich
- State Office for Heritage Management and Archaeology Saxony-Anhalt and State Museum of Prehistory, Halle, Germany
| | - Emmanuel Ghesquière
- Inrap Grand Ouest, Bourguébus, France.,Université de Rennes 1, CNRS, CReAAH-UMR, 6566, Rennes, France
| | - Agata Hałuszko
- Institute of Archaeology, University of Wrocław, Wrocław, Poland.,Archeolodzy.org Foundation, Wrocław, Poland
| | - Svend Hansen
- Eurasia Department, German Archaeological Institute, Berlin, Germany
| | - Mario Küßner
- Thuringian State Office for Heritage Management and Archeology, Weimar, Germany
| | - Marcello Mannino
- Department of Archaeology, School of Culture and Society, Aarhus University, 8270, Højbjerg, Denmark
| | - Rana Özbal
- Department of Archaeology and History of Art, Koç University, 34450, Istanbul, Turkey
| | - Sabine Reinhold
- Eurasia Department, German Archaeological Institute, Berlin, Germany
| | - Stéphane Rottier
- Université de Bordeaux, CNRS, PACEA-UMR 5199, 33615, Pessac, France
| | - Domingo Carlos Salazar-García
- Grupo de Investigación en Prehistoria IT-1223-19 (UPV-EHU)/IKERBASQUE-Basque Foundation for Science, Vitoria, Spain.,Departament de Prehistòria, Arqueologia i Història Antiga, Universitat de València, Valencia, Spain.,Department of Geological Sciences, University of Cape Town, Cape Town, South Africa
| | | | - Philipp W Stockhammer
- Department of Archaeogenetics, Max Planck Institute for the Science of Human History, 07745, Jena, Germany.,Ludwig Maximilian University Munich, 80799, Munich, Germany
| | | | - K Aslihan Yener
- Institute for the Study of the Ancient World (ISAW), New York University, New York, NY, 10028, USA
| | - Cosimo Posth
- Department of Archaeogenetics, Max Planck Institute for the Science of Human History, 07745, Jena, Germany.,Archaeo- and Palaeogenetics Group, Institute for Archaeological Sciences Eberhard Karls University Tübingen, 72070, Tübingen, Germany
| | - Johannes Krause
- Department of Archaeogenetics, Max Planck Institute for the Science of Human History, 07745, Jena, Germany
| | - Alexander Herbig
- Department of Archaeogenetics, Max Planck Institute for the Science of Human History, 07745, Jena, Germany
| | - Wolfgang Haak
- Department of Archaeogenetics, Max Planck Institute for the Science of Human History, 07745, Jena, Germany. .,School of Biological Sciences, The University of Adelaide, Adelaide, SA, 5005, Australia.
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43
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Azulay RSDS, Porto LC, Silva DA, Tavares MDG, Reis RMDF, Nascimento GC, Damianse SDSP, Rocha VCDC, Magalhães M, Rodrigues V, Carvalho PRVB, Faria MDS, Gomes MB. Genetic ancestry inferred from autosomal and Y chromosome markers and HLA genotypes in Type 1 Diabetes from an admixed Brazilian population. Sci Rep 2021; 11:14157. [PMID: 34239025 PMCID: PMC8266844 DOI: 10.1038/s41598-021-93691-x] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2021] [Accepted: 06/29/2021] [Indexed: 12/19/2022] Open
Abstract
This study aimed to investigate the relationship between genetic ancestry inferred from autosomal and Y chromosome markers and HLA genotypes in patients with Type 1 Diabetes from an admixed Brazilian population. Inference of autosomal ancestry; HLA-DRB1, -DQA1 and -DQB1 typifications; and Y chromosome analysis were performed. European autosomal ancestry was about 50%, followed by approximately 25% of African and Native American. The European Y chromosome was predominant. The HLA-DRB1*03 and DRB1*04 alleles presented risk association with T1D. When the Y chromosome was European, DRB1*03 and DRB1*04 homozygote and DRB1*03/DRB1*04 heterozygote genotypes were the most frequent. The results suggest that individuals from Maranhão have a European origin as their major component; and are patrilineal with greater frequency from the R1b haplogroup. The predominance of the HLA-DRB1*03 and DRB1*04 alleles conferring greater risk in our population and being more frequently related to the ancestry of the European Y chromosome suggests that in our population, the risk of T1D can be transmitted by European ancestors of our process miscegenation. However, the Y sample sizes of Africans and Native Americans were small, and further research should be conducted with large mixed sample sizes to clarify this possible association.
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Affiliation(s)
- Rossana Santiago de Sousa Azulay
- Service of Endocrinology, University Hospital of the Federal University of Maranhão (HUUFMA/EBSERH), Rua Barão de Itapary, 227, Centro, São Luís, Maranhão, 65020-070, Brazil.
- Research Group in Clinical and Molecular Endocrinology and Metabology (ENDOCLIM), São Luís, Brazil.
| | - Luís Cristóvão Porto
- Histocompatibility and Cryopreservation Laboratory (HLA), Rio de Janeiro State University (UERJ), Rio de Janeiro, Rio de Janeiro, Brazil
| | - Dayse Aparecida Silva
- DNA Diagnostic Laboratory (LDD), Rio de Janeiro State University (UERJ), Rio de Janeiro, Rio de Janeiro, Brazil
| | - Maria da Glória Tavares
- Service of Endocrinology, University Hospital of the Federal University of Maranhão (HUUFMA/EBSERH), Rua Barão de Itapary, 227, Centro, São Luís, Maranhão, 65020-070, Brazil
- Research Group in Clinical and Molecular Endocrinology and Metabology (ENDOCLIM), São Luís, Brazil
| | | | - Gilvan Cortês Nascimento
- Service of Endocrinology, University Hospital of the Federal University of Maranhão (HUUFMA/EBSERH), Rua Barão de Itapary, 227, Centro, São Luís, Maranhão, 65020-070, Brazil
- Research Group in Clinical and Molecular Endocrinology and Metabology (ENDOCLIM), São Luís, Brazil
| | - Sabrina da Silva Pereira Damianse
- Service of Endocrinology, University Hospital of the Federal University of Maranhão (HUUFMA/EBSERH), Rua Barão de Itapary, 227, Centro, São Luís, Maranhão, 65020-070, Brazil
- Research Group in Clinical and Molecular Endocrinology and Metabology (ENDOCLIM), São Luís, Brazil
| | - Viviane Chaves de Carvalho Rocha
- Service of Endocrinology, University Hospital of the Federal University of Maranhão (HUUFMA/EBSERH), Rua Barão de Itapary, 227, Centro, São Luís, Maranhão, 65020-070, Brazil
- Research Group in Clinical and Molecular Endocrinology and Metabology (ENDOCLIM), São Luís, Brazil
| | - Marcelo Magalhães
- Research Group in Clinical and Molecular Endocrinology and Metabology (ENDOCLIM), São Luís, Brazil
- Clinical Research Center of the University Hospital of the Federal University of Maranhão (CEPEC - HUUFMA), São Luís, Brazil
| | - Vandilson Rodrigues
- Research Group in Clinical and Molecular Endocrinology and Metabology (ENDOCLIM), São Luís, Brazil
| | - Paulo Ricardo Vilas Boas Carvalho
- Histocompatibility and Cryopreservation Laboratory (HLA), Rio de Janeiro State University (UERJ), Rio de Janeiro, Rio de Janeiro, Brazil
| | - Manuel Dos Santos Faria
- Service of Endocrinology, University Hospital of the Federal University of Maranhão (HUUFMA/EBSERH), Rua Barão de Itapary, 227, Centro, São Luís, Maranhão, 65020-070, Brazil
- Research Group in Clinical and Molecular Endocrinology and Metabology (ENDOCLIM), São Luís, Brazil
- Clinical Research Center of the University Hospital of the Federal University of Maranhão (CEPEC - HUUFMA), São Luís, Brazil
| | - Marília Brito Gomes
- Diabetes Unit, State University of Rio de Janeiro (UERJ), Rio de Janeiro, Brazil
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44
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Idiopathic Infertility as a Feature of Genome Instability. Life (Basel) 2021; 11:life11070628. [PMID: 34209597 PMCID: PMC8307193 DOI: 10.3390/life11070628] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2021] [Revised: 06/23/2021] [Accepted: 06/24/2021] [Indexed: 12/18/2022] Open
Abstract
Genome instability may play a role in severe cases of male infertility, with disrupted spermatogenesis being just one manifestation of decreased general health and increased morbidity. Here, we review the data on the association of male infertility with genetic, epigenetic, and environmental alterations, the causes and consequences, and the methods for assessment of genome instability. Male infertility research has provided evidence that spermatogenic defects are often not limited to testicular dysfunction. An increased incidence of urogenital disorders and several types of cancer, as well as overall reduced health (manifested by decreased life expectancy and increased morbidity) have been reported in infertile men. The pathophysiological link between decreased life expectancy and male infertility supports the notion of male infertility being a systemic rather than an isolated condition. It is driven by the accumulation of DNA strand breaks and premature cellular senescence. We have presented extensive data supporting the notion that genome instability can lead to severe male infertility termed “idiopathic oligo-astheno-teratozoospermia.” We have detailed that genome instability in men with oligo-astheno-teratozoospermia (OAT) might depend on several genetic and epigenetic factors such as chromosomal heterogeneity, aneuploidy, micronucleation, dynamic mutations, RT, PIWI/piRNA regulatory pathway, pathogenic allelic variants in repair system genes, DNA methylation, environmental aspects, and lifestyle factors.
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45
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Babić Jordamović N, Kojović T, Dogan S, Bešić L, Salihefendić L, Konjhodžić R, Škaro V, Projić P, Hadžiavdić V, Ašić A, Marjanović D. Haplogroup Prediction Using Y-Chromosomal Short Tandem Repeats in the General Population of Bosnia and Herzegovina. Front Genet 2021; 12:671467. [PMID: 34178033 PMCID: PMC8226213 DOI: 10.3389/fgene.2021.671467] [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: 02/23/2021] [Accepted: 04/28/2021] [Indexed: 11/20/2022] Open
Abstract
Human Y-chromosomal haplogroups are an important tool used in population genetics and forensic genetics. A conventional method used for Y haplogroup assignment is based on a set of Y-single nucleotide polymorphism (SNP) markers deployed, which exploits the low mutation rate nature of these markers. Y chromosome haplogroups can be successfully predicted from Y-short tandem repeat (STR) markers using different software packages, and this method gained much attention recently due to its labor-, time-, and cost-effectiveness. The present study was based on the analysis of a total of 480 adult male buccal swab samples collected from different regions of Bosnia and Herzegovina. Y haplogroup prediction was performed using Whit Athey’s Haplogroup Predictor, based on haplotype data on 23 Y-STR markers contained within the PowerPlex® Y23 kit. The results revealed the existence of 14 different haplogroups, with I2a, R1a, and E1b1b being the most prevalent with frequencies of 43.13, 14.79, and 14.58%, respectively. Compared to the previously published studies on Bosnian-Herzegovinian population based on Y-SNP and Y-STR data, this study represents an upgrade of molecular genetic data with a significantly larger number of samples, thus offering more accurate results and higher probability of detecting rare haplogroups.
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Affiliation(s)
- Naida Babić Jordamović
- Department of Genetics and Bioengineering, International Burch University, Sarajevo, Bosnia and Herzegovina
| | - Tamara Kojović
- Department of Genetics and Bioengineering, International Burch University, Sarajevo, Bosnia and Herzegovina
| | - Serkan Dogan
- Department of Genetics and Bioengineering, International Burch University, Sarajevo, Bosnia and Herzegovina
| | - Larisa Bešić
- Department of Genetics and Bioengineering, International Burch University, Sarajevo, Bosnia and Herzegovina
| | - Lana Salihefendić
- Department of Genetics and Bioengineering, International Burch University, Sarajevo, Bosnia and Herzegovina.,ALEA Genetic Center, Sarajevo, Bosnia and Herzegovina
| | | | - Vedrana Škaro
- Molecular Anthropology Laboratory, Center for Applied Bioanthropology, Institute for Anthropological Research, Zagreb, Croatia.,DNA Laboratory, Genos Ltd., Zagreb, Croatia
| | - Petar Projić
- Molecular Anthropology Laboratory, Center for Applied Bioanthropology, Institute for Anthropological Research, Zagreb, Croatia.,DNA Laboratory, Genos Ltd., Zagreb, Croatia
| | - Vesna Hadžiavdić
- Department of Biology, University of Tuzla, Tuzla, Bosnia and Herzegovina
| | - Adna Ašić
- Department of Genetics and Bioengineering, International Burch University, Sarajevo, Bosnia and Herzegovina
| | - Damir Marjanović
- Department of Genetics and Bioengineering, International Burch University, Sarajevo, Bosnia and Herzegovina.,Molecular Anthropology Laboratory, Center for Applied Bioanthropology, Institute for Anthropological Research, Zagreb, Croatia
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46
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Sakurai-Yageta M, Kumada K, Gocho C, Makino S, Uruno A, Tadaka S, Motoike IN, Kimura M, Ito S, Otsuki A, Narita A, Kudo H, Aoki Y, Danjoh I, Yasuda J, Kawame H, Minegishi N, Koshiba S, Fuse N, Tamiya G, Yamamoto M, Kinoshita K. Japonica Array NEO with increased genome-wide coverage and abundant disease risk SNPs. J Biochem 2021; 170:399-410. [PMID: 34131746 PMCID: PMC8510329 DOI: 10.1093/jb/mvab060] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2021] [Accepted: 04/27/2021] [Indexed: 01/12/2023] Open
Abstract
Ethnic-specific SNP arrays are becoming more important to increase the power of genome-wide association studies in diverse population. In the Tohoku Medical Megabank Project, we have been developing a series of Japonica Arrays (JPA) for genotyping participants based on reference panels constructed from whole-genome sequence data of the Japanese population. Here, we designed a novel version of the SNP array for the Japanese population, called Japonica Array NEO (JPA NEO), comprising a total of 666,883 markers. Among them, 654,246 tag SNPs of autosomes and X chromosome were selected from an expanded reference panel of 3,552 Japanese, 3.5KJPNv2, using pairwise r2 of linkage disequilibrium measures. Additionally, 28,298 markers were included for the evaluation of previously identified disease risk markers from the literature and databases, and those present in the Japanese population were extracted using the reference panel. Through genotyping 286 Japanese samples, we found that the imputation quality r2 and INFO score in the minor allele frequency bin >2.5–5% were >0.9 and >0.8, respectively, and >12 million markers were imputed with an INFO score >0.8. From these results, JPA NEO is a promising tool for genotyping the Japanese population with genome-wide coverage, contributing to the development of genetic risk scores.
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Affiliation(s)
- Mika Sakurai-Yageta
- Tohoku Medical Megabank Organization, Tohoku University, 2-1 Seiryo-machi, Aoba-ku, Sendai, Miyagi 980-8573, Japan.,Advanced Research Center for Innovations in Next-Generation Medicine, Tohoku University, 2-1 Seiryo-machi, Aoba-ku, Sendai, Miyagi 980-8573, Japan
| | - Kazuki Kumada
- Tohoku Medical Megabank Organization, Tohoku University, 2-1 Seiryo-machi, Aoba-ku, Sendai, Miyagi 980-8573, Japan.,Advanced Research Center for Innovations in Next-Generation Medicine, Tohoku University, 2-1 Seiryo-machi, Aoba-ku, Sendai, Miyagi 980-8573, Japan
| | - Chinatsu Gocho
- Tohoku Medical Megabank Organization, Tohoku University, 2-1 Seiryo-machi, Aoba-ku, Sendai, Miyagi 980-8573, Japan
| | - Satoshi Makino
- Tohoku Medical Megabank Organization, Tohoku University, 2-1 Seiryo-machi, Aoba-ku, Sendai, Miyagi 980-8573, Japan
| | - Akira Uruno
- Tohoku Medical Megabank Organization, Tohoku University, 2-1 Seiryo-machi, Aoba-ku, Sendai, Miyagi 980-8573, Japan.,Graduate School of Medicine, Tohoku University, 2-1 Seiryo-machi, Aoba-ku, Sendai, Miyagi 980-8575, Japan
| | - Shu Tadaka
- Tohoku Medical Megabank Organization, Tohoku University, 2-1 Seiryo-machi, Aoba-ku, Sendai, Miyagi 980-8573, Japan
| | - Ikuko N Motoike
- Tohoku Medical Megabank Organization, Tohoku University, 2-1 Seiryo-machi, Aoba-ku, Sendai, Miyagi 980-8573, Japan.,Graduate School of Information Sciences, Tohoku University, 6-3-09 Aramaki-Aza-Aoba, Aoba-ku, Sendai, Miyagi 980-8579, Japan
| | - Masae Kimura
- Tohoku Medical Megabank Organization, Tohoku University, 2-1 Seiryo-machi, Aoba-ku, Sendai, Miyagi 980-8573, Japan
| | - Shin Ito
- Tohoku Medical Megabank Organization, Tohoku University, 2-1 Seiryo-machi, Aoba-ku, Sendai, Miyagi 980-8573, Japan
| | - Akihito Otsuki
- Tohoku Medical Megabank Organization, Tohoku University, 2-1 Seiryo-machi, Aoba-ku, Sendai, Miyagi 980-8573, Japan.,Graduate School of Medicine, Tohoku University, 2-1 Seiryo-machi, Aoba-ku, Sendai, Miyagi 980-8575, Japan
| | - Akira Narita
- Tohoku Medical Megabank Organization, Tohoku University, 2-1 Seiryo-machi, Aoba-ku, Sendai, Miyagi 980-8573, Japan
| | - Hisaaki Kudo
- Tohoku Medical Megabank Organization, Tohoku University, 2-1 Seiryo-machi, Aoba-ku, Sendai, Miyagi 980-8573, Japan
| | - Yuichi Aoki
- Tohoku Medical Megabank Organization, Tohoku University, 2-1 Seiryo-machi, Aoba-ku, Sendai, Miyagi 980-8573, Japan.,Graduate School of Information Sciences, Tohoku University, 6-3-09 Aramaki-Aza-Aoba, Aoba-ku, Sendai, Miyagi 980-8579, Japan
| | - Inaho Danjoh
- Tohoku Medical Megabank Organization, Tohoku University, 2-1 Seiryo-machi, Aoba-ku, Sendai, Miyagi 980-8573, Japan
| | - Jun Yasuda
- Tohoku Medical Megabank Organization, Tohoku University, 2-1 Seiryo-machi, Aoba-ku, Sendai, Miyagi 980-8573, Japan
| | - Hiroshi Kawame
- Tohoku Medical Megabank Organization, Tohoku University, 2-1 Seiryo-machi, Aoba-ku, Sendai, Miyagi 980-8573, Japan
| | - Naoko Minegishi
- Tohoku Medical Megabank Organization, Tohoku University, 2-1 Seiryo-machi, Aoba-ku, Sendai, Miyagi 980-8573, Japan.,Advanced Research Center for Innovations in Next-Generation Medicine, Tohoku University, 2-1 Seiryo-machi, Aoba-ku, Sendai, Miyagi 980-8573, Japan
| | - Seizo Koshiba
- Tohoku Medical Megabank Organization, Tohoku University, 2-1 Seiryo-machi, Aoba-ku, Sendai, Miyagi 980-8573, Japan.,Advanced Research Center for Innovations in Next-Generation Medicine, Tohoku University, 2-1 Seiryo-machi, Aoba-ku, Sendai, Miyagi 980-8573, Japan
| | - Nobuo Fuse
- Tohoku Medical Megabank Organization, Tohoku University, 2-1 Seiryo-machi, Aoba-ku, Sendai, Miyagi 980-8573, Japan.,Advanced Research Center for Innovations in Next-Generation Medicine, Tohoku University, 2-1 Seiryo-machi, Aoba-ku, Sendai, Miyagi 980-8573, Japan.,Graduate School of Medicine, Tohoku University, 2-1 Seiryo-machi, Aoba-ku, Sendai, Miyagi 980-8575, Japan
| | - Gen Tamiya
- Tohoku Medical Megabank Organization, Tohoku University, 2-1 Seiryo-machi, Aoba-ku, Sendai, Miyagi 980-8573, Japan.,Advanced Research Center for Innovations in Next-Generation Medicine, Tohoku University, 2-1 Seiryo-machi, Aoba-ku, Sendai, Miyagi 980-8573, Japan.,Graduate School of Medicine, Tohoku University, 2-1 Seiryo-machi, Aoba-ku, Sendai, Miyagi 980-8575, Japan
| | - Masayuki Yamamoto
- Tohoku Medical Megabank Organization, Tohoku University, 2-1 Seiryo-machi, Aoba-ku, Sendai, Miyagi 980-8573, Japan.,Advanced Research Center for Innovations in Next-Generation Medicine, Tohoku University, 2-1 Seiryo-machi, Aoba-ku, Sendai, Miyagi 980-8573, Japan.,Graduate School of Medicine, Tohoku University, 2-1 Seiryo-machi, Aoba-ku, Sendai, Miyagi 980-8575, Japan
| | - Kengo Kinoshita
- Tohoku Medical Megabank Organization, Tohoku University, 2-1 Seiryo-machi, Aoba-ku, Sendai, Miyagi 980-8573, Japan.,Advanced Research Center for Innovations in Next-Generation Medicine, Tohoku University, 2-1 Seiryo-machi, Aoba-ku, Sendai, Miyagi 980-8573, Japan.,Graduate School of Information Sciences, Tohoku University, 6-3-09 Aramaki-Aza-Aoba, Aoba-ku, Sendai, Miyagi 980-8579, Japan
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47
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Flores-Alvarado S, Orellana-Soto M, Moraga M. Ancestry and admixture of a southernmost Chilean population: The reflection of a migratory history. Am J Hum Biol 2021; 34:e23598. [PMID: 33763944 DOI: 10.1002/ajhb.23598] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2020] [Revised: 02/08/2021] [Accepted: 02/25/2021] [Indexed: 11/07/2022] Open
Abstract
OBJECTIVES Punta Arenas is a Chilean city situated on ancestral Aönikenk territory. The city was founded by 19th- and 20th-century colonists from Chile (Chiloé) and Europe (Croatia). This work uses uniparental and ancestry-informative markers (AIMs) to explore the effects of historic migratory and admixture patterns on the current genetic composition of Punta Arenas. METHODS We analyzed mitochondrial DNA (mtDNA), Y-chromosome single-nucleotide polymorphisms (SNPs), and 141 AIMs obtained from 129 DNA samples from male residents with regional ancestry. After characterizing uniparental lineages and ancestry proportions, multivariate analysis was used to explore relationships among the various types of data. RESULTS Punta Arenas has an admixed population with three main genetic components: European (56.5%), northern Native (11.3%), and south-central Native (28.6%). The Native component is preponderant in the mtDNA (83.76%), while the foreign component predominates in the Y-chromosome (92.25%). Non-Native mtDNA lineages are associated with European genetic ancestry, and Native mtDNA lineages originated mainly in the southern and southernmost regions of Chile. Most non-Native Y-chromosome SNPs originated in Spain, and secondly, in Croatia. CONCLUSIONS The population of Punta Arenas is mainly of Chilote origin with south-central Native and Spanish ancestral components, as well as some Croatian components. The persistence of local Native lineages is notable, suggesting continuity with the ancestral populations of the region such as the Kawésqar, Aönikenk, Yámana, or Selknam peoples. This study contributes to our knowledge of local history and its links to national and global developments in genetic ancestry.
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Affiliation(s)
- Sandra Flores-Alvarado
- Programa de Bioestadística, Instituto de Salud Poblacional, Facultad de Medicina, Universidad de Chile, Santiago, Chile
- Programa de Genética Humana, ICBM, Facultad de Medicina, Universidad de Chile, Santiago, Chile
- Departamento de Antropología, Facultad de Ciencias Sociales, Universidad de Chile, Santiago, Chile
| | - Michael Orellana-Soto
- Programa de Genética Humana, ICBM, Facultad de Medicina, Universidad de Chile, Santiago, Chile
| | - Mauricio Moraga
- Programa de Genética Humana, ICBM, Facultad de Medicina, Universidad de Chile, Santiago, Chile
- Departamento de Antropología, Facultad de Ciencias Sociales, Universidad de Chile, Santiago, Chile
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48
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Abstract
A common assumption in dating patrilineal events using Y-chromosome sequencing data is that the Y-chromosome mutation rate is invariant across haplogroups. Previous studies revealed interhaplogroup heterogeneity in phylogenetic branch length. Whether this heterogeneity is caused by interhaplogroup mutation rate variation or nongenetic confounders remains unknown. Here, we analyzed whole-genome sequences from cultured cells derived from >1,700 males. We confirmed the presence of branch length heterogeneity. We demonstrate that sex-chromosome mutations that appear within cell lines, which likely occurred somatically or in vitro (and are thus not influenced by nongenetic confounders) are informative for germline mutational processes. Using within-cell-line mutations, we computed a relative Y-chromosome somatic mutation rate, and uncovered substantial variation (up to 83.3%) in this proxy for germline mutation rate among haplogroups. This rate positively correlates with phylogenetic branch length, indicating that interhaplogroup mutation rate variation is a likely cause of branch length heterogeneity.
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Affiliation(s)
- Qiliang Ding
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY
| | - Ya Hu
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY
- New York Genome Center, New York, NY
| | - Amnon Koren
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY
| | - Andrew G Clark
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, NY
- Department of Computational Biology, Cornell University, Ithaca, NY
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49
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Feron R, Pan Q, Wen M, Imarazene B, Jouanno E, Anderson J, Herpin A, Journot L, Parrinello H, Klopp C, Kottler VA, Roco AS, Du K, Kneitz S, Adolfi M, Wilson CA, McCluskey B, Amores A, Desvignes T, Goetz FW, Takanashi A, Kawaguchi M, Detrich HW, Oliveira MA, Nóbrega RH, Sakamoto T, Nakamoto M, Wargelius A, Karlsen Ø, Wang Z, Stöck M, Waterhouse RM, Braasch I, Postlethwait JH, Schartl M, Guiguen Y. RADSex: A computational workflow to study sex determination using restriction site-associated DNA sequencing data. Mol Ecol Resour 2021; 21:1715-1731. [PMID: 33590960 DOI: 10.1111/1755-0998.13360] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2020] [Revised: 02/09/2021] [Accepted: 02/11/2021] [Indexed: 12/13/2022]
Abstract
The study of sex determination and sex chromosome organization in nonmodel species has long been technically challenging, but new sequencing methodologies now enable precise and high-throughput identification of sex-specific genomic sequences. In particular, restriction site-associated DNA sequencing (RAD-Seq) is being extensively applied to explore sex determination systems in many plant and animal species. However, software specifically designed to search for and visualize sex-biased markers using RAD-Seq data is lacking. Here, we present RADSex, a computational analysis workflow designed to study the genetic basis of sex determination using RAD-Seq data. RADSex is simple to use, requires few computational resources, makes no prior assumptions about the type of sex-determination system or structure of the sex locus, and offers convenient visualization through a dedicated R package. To demonstrate the functionality of RADSex, we re-analysed a published data set of Japanese medaka, Oryzias latipes, where we uncovered a previously unknown Y chromosome polymorphism. We then used RADSex to analyse new RAD-Seq data sets from 15 fish species spanning multiple taxonomic orders. We identified the sex determination system and sex-specific markers in six of these species, five of which had no known sex-markers prior to this study. We show that RADSex greatly facilitates the study of sex determination systems in nonmodel species thanks to its speed of analyses, low resource usage, ease of application and visualization options. Furthermore, our analysis of new data sets from 15 species provides new insights on sex determination in fish.
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Affiliation(s)
- Romain Feron
- INRAE, LPGP, Rennes, France.,Department of Ecology and Evolution, University of Lausanne, Lausanne, Switzerland.,Swiss Institute of Bioinformatics, Lausanne, Switzerland
| | - Qiaowei Pan
- INRAE, LPGP, Rennes, France.,Department of Ecology and Evolution, University of Lausanne, Lausanne, Switzerland
| | - Ming Wen
- INRAE, LPGP, Rennes, France.,State Key Laboratory of Developmental Biology of Freshwater Fish, College of Life Science, Hunan Normal University, Changsha, China
| | | | | | - Jennifer Anderson
- INRAE, LPGP, Rennes, France.,Department of Organismal Biology, Systematic Biology, Uppsala University, Uppsala, Sweden
| | | | - Laurent Journot
- Institut de Génomique Fonctionnelle, IGF, CNRS, INSERM, Univ. Montpellier, Montpellier, France
| | - Hugues Parrinello
- Institut de Génomique Fonctionnelle, IGF, CNRS, INSERM, Univ. Montpellier, Montpellier, France
| | - Christophe Klopp
- SIGENAE, Mathématiques et Informatique Appliquées de Toulouse, INRAE, Castanet Tolosan, France
| | - Verena A Kottler
- Physiological Chemistry, Biocenter, University of Wuerzburg, Wuerzburg, Germany
| | - Alvaro S Roco
- Physiological Chemistry, Biocenter, University of Wuerzburg, Wuerzburg, Germany
| | - Kang Du
- Department of Chemistry and Biochemistry, The Xiphophorus Genetic Stock Center, Texas State University, San Marcos, TX, USA.,Developmental Biochemistry, Biocenter, University of Wuerzburg, Wuerzburg, Germany
| | - Susanne Kneitz
- Physiological Chemistry, Biocenter, University of Wuerzburg, Wuerzburg, Germany
| | - Mateus Adolfi
- Developmental Biochemistry, Biocenter, University of Wuerzburg, Wuerzburg, Germany
| | | | | | - Angel Amores
- Institute of Neuroscience, University of Oregon, Eugene, OR, USA
| | - Thomas Desvignes
- Institute of Neuroscience, University of Oregon, Eugene, OR, USA
| | - Frederick W Goetz
- Environmental and Fisheries Sciences Division, Northwest Fisheries Science Center, National Marine Fisheries Service, National Oceanic and Atmospheric Administration, Seattle, WA, USA
| | - Ato Takanashi
- Department of Materials and Life Sciences, Faculty of Science and Technology, Sophia University, Tokyo, Japan
| | - Mari Kawaguchi
- Department of Materials and Life Sciences, Faculty of Science and Technology, Sophia University, Tokyo, Japan
| | - Harry William Detrich
- Department of Marine and Environmental Sciences, Marine Science Center, Northeastern University, Nahant, MA, USA
| | - Marcos A Oliveira
- Reproductive and Molecular Biology Group, Department of Structural and Functional Biology, Institute of Biosciences, São Paulo State University, Botucatu, Brazil
| | - Rafael H Nóbrega
- Reproductive and Molecular Biology Group, Department of Structural and Functional Biology, Institute of Biosciences, São Paulo State University, Botucatu, Brazil
| | - Takashi Sakamoto
- Department of Aquatic Marine Biosciences, Tokyo University of Marine Science and Technology, Tokyo, Japan
| | - Masatoshi Nakamoto
- Department of Aquatic Marine Biosciences, Tokyo University of Marine Science and Technology, Tokyo, Japan
| | | | | | - Zhongwei Wang
- Physiological Chemistry, Biocenter, University of Wuerzburg, Wuerzburg, Germany.,Institute of Hydrobiology, Chinese Academy of Sciences, Beijing, China
| | - Matthias Stöck
- Leibniz-Institute of Freshwater Ecology and Inland Fisheries, IGB, Berlin, Germany
| | - Robert M Waterhouse
- Department of Ecology and Evolution, University of Lausanne, Lausanne, Switzerland.,Swiss Institute of Bioinformatics, Lausanne, Switzerland
| | - Ingo Braasch
- Department of Integrative Biology, Ecology, Evolution, and Behavior Program, Michigan State University, East Lansing, MI, USA
| | | | - Manfred Schartl
- Department of Chemistry and Biochemistry, The Xiphophorus Genetic Stock Center, Texas State University, San Marcos, TX, USA.,Developmental Biochemistry, Biocenter, University of Wuerzburg, Wuerzburg, Germany
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Pelzman DL, Hwang K. Genetic testing for men with infertility: techniques and indications. Transl Androl Urol 2021; 10:1354-1364. [PMID: 33850771 PMCID: PMC8039607 DOI: 10.21037/tau-19-725] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022] Open
Abstract
Genetic testing is an integral component in the workup of male infertility as genetic conditions may be responsible for up to 15% of all cases. Currently, three genetic tests are commonly performed and recommended by major urologic associations: karyotype analysis (KA), Y-chromosome microdeletion testing, and CFTR mutation testing. Despite widespread adoption of these tests, an etiology for infertility remains elusive in up to 80% of cases. Recent work has identified intriguing new targets for genetic testing which may soon see clinical relevance. This review will discuss the indications and techniques for currently offered genetic tests and briefly explore ongoing research directions within this field.
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Affiliation(s)
- Daniel L Pelzman
- Department of Urology, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
| | - Kathleen Hwang
- Department of Urology, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
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