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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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2
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Kasu M, Cloete K, Pitere R, Tsiana K, D’Amato M. The Genetic Landscape of South African males: A Y-STR Perspective. Forensic Sci Int Genet 2022; 58:102677. [DOI: 10.1016/j.fsigen.2022.102677] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2021] [Revised: 01/21/2022] [Accepted: 02/04/2022] [Indexed: 11/04/2022]
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3
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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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Grochowalski Ł, Jarczak J, Urbanowicz M, Słomka M, Szargut M, Borówka P, Sobalska-Kwapis M, Marciniak B, Ossowski A, Lorkiewicz W, Strapagiel D. Y-Chromosome Genetic Analysis of Modern Polish Population. Front Genet 2020; 11:567309. [PMID: 33193657 PMCID: PMC7644898 DOI: 10.3389/fgene.2020.567309] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2020] [Accepted: 08/27/2020] [Indexed: 01/11/2023] Open
Abstract
The study presents a full analysis of the Y-chromosome variability of the modern male Polish population. It is the first study of the Polish population to be conducted with such a large set of data (2,705 individuals), which includes genetic information from inhabitants of all voivodeships, i.e., the first administrative level, in the country and the vast majority of its counties, i.e., the second level. In addition, the available data were divided into clusters corresponding to more natural geographic regions. Genetic analysis included the estimation of FST distances, the visualization with the use of multidimensional scaling plots and analysis of molecular variance. Y-chromosome binary haplogroups were classified and visualized with the use of interpolation maps. Results showed that the level of differentiation within Polish population is quite low, but some differences were indicated. It was confirmed that the Polish population is characterized by a high degree of homogeneity, with only slight genetic differences being observed at the regional level. The use of regional clustering as an alternative to counties and voivodeships provided a more detailed view of the genetic structure of the population. Those regional differences identified in the present study highlighted the need for additional division of the population by cultural and ethnic criteria in such studies rather than just by geographical or administrative regionalization.
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Affiliation(s)
- Łukasz Grochowalski
- Biobank Lab, Department of Molecular Biophysics, Faculty of Biology and Environmental Protection, University of Lodz, Łódź, Poland
| | - Justyna Jarczak
- Biobank Lab, Department of Molecular Biophysics, Faculty of Biology and Environmental Protection, University of Lodz, Łódź, Poland.,BBMRI.pl Consortium, Łódź, Poland
| | - Maria Urbanowicz
- Biobank Lab, Department of Molecular Biophysics, Faculty of Biology and Environmental Protection, University of Lodz, Łódź, Poland
| | - Marcin Słomka
- Biobank Lab, Department of Molecular Biophysics, Faculty of Biology and Environmental Protection, University of Lodz, Łódź, Poland.,BBMRI.pl Consortium, Łódź, Poland
| | - Maria Szargut
- Department of Forensic Genetics, Pomeranian Medical University in Szczecin, Szczecin, Poland.,The Polish Genetic Database of Totalitarianism Victims, Szczecin, Poland
| | - Paulina Borówka
- Department of Anthropology, Faculty of Biology and Environmental Protection, University of Lodz, Łódź, Poland
| | - Marta Sobalska-Kwapis
- Biobank Lab, Department of Molecular Biophysics, Faculty of Biology and Environmental Protection, University of Lodz, Łódź, Poland.,BBMRI.pl Consortium, Łódź, Poland
| | - Błażej Marciniak
- Biobank Lab, Department of Molecular Biophysics, Faculty of Biology and Environmental Protection, University of Lodz, Łódź, Poland.,BBMRI.pl Consortium, Łódź, Poland
| | - Andrzej Ossowski
- Department of Forensic Genetics, Pomeranian Medical University in Szczecin, Szczecin, Poland.,The Polish Genetic Database of Totalitarianism Victims, Szczecin, Poland
| | - Wiesław Lorkiewicz
- Department of Anthropology, Faculty of Biology and Environmental Protection, University of Lodz, Łódź, Poland
| | - Dominik Strapagiel
- Biobank Lab, Department of Molecular Biophysics, Faculty of Biology and Environmental Protection, University of Lodz, Łódź, Poland.,BBMRI.pl Consortium, Łódź, Poland
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5
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Delanghe JR, De Buyzere ML, De Bruyne S, Van Criekinge W, Speeckaert MM. The potential influence of human Y-chromosome haplogroup on COVID-19 prevalence and mortality. Ann Oncol 2020; 31:1582-1584. [PMID: 32835812 PMCID: PMC7442561 DOI: 10.1016/j.annonc.2020.08.2096] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2020] [Accepted: 08/11/2020] [Indexed: 11/26/2022] Open
Affiliation(s)
- J R Delanghe
- Department of Diagnostic Sciences, Ghent University, Belgium.
| | - M L De Buyzere
- Department of Internal Medicine, Ghent University, Belgium
| | - S De Bruyne
- Department of Diagnostic Sciences, Ghent University, Belgium
| | - W Van Criekinge
- Department of Data Analysis and Mathematical Modelling, Ghent University, Belgium
| | - M M Speeckaert
- Department of Internal Medicine, Ghent University, Belgium
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