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Mutation analysis for newly suggested 30 Y-STR loci with high mutation rates in Chinese father-son pairs. Sci Rep 2022; 12:15680. [PMID: 36127390 PMCID: PMC9489694 DOI: 10.1038/s41598-022-20014-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2022] [Accepted: 09/07/2022] [Indexed: 11/08/2022] Open
Abstract
Rapidly mutating Y-STRs (RM Y-STRs) harbor great potential to distinguish male relatives and achieve male identification. However, forensic applications were greatly limited by the small number of the initially identified 14 RM Y-STRs. Recently, with the emergence of 12 novel RM Y-STRs, an integrated panel named RMplex was introduced, which contains all 26 RM Y-STRs and four fast mutating Y-STRs (FM Y-STRs). To obtain the first data on the mutation rates and father-son differentiation rates of the 30 newly proposed Y-STRs in Chinese populations, we performed an empirical mutation study on 307 DNA-confirmed Chinese paternal pairs. Previously reported mutation rates for 14 RM Y-STRs in Chinese and European populations were pooled and merged with our data. The highest meiosis number for the two groups reached 4771 and 2687, respectively. Five loci showed significant differences between the populations (DYS570, DYS399S1, DYS547, DYS612, and DYF403S1b). For the new panel covering 30 Y-STR loci, our results show extensive differences in the mutation rates between the two populations, as well. 10 RM Y-STR loci showed relatively low mutation rates (10-3-10-2 per meiosis) and 2 FM Y-STR loci had rapid mutation rates (> 10-2 per meiosis) in the Chinese population. Several-fold differences in mutation rates were found in nine Y-STR loci between the Chinese and reference populations, with two loci having significantly higher mutation rates and one locus with a significantly lower mutation rate in the Chinese population (P < 0.05). Eighteen RM Y-STRs (> 10-2 per meiosis), 8 FM Y-STR loci (5×10-3-10-2 per meiosis), 3 moderately mutating Y-STRs (MM Y-STRs, 10-3-5×10-3 per meiosis), and one locus with no observed mutation events were identified in the Chinese population. 40.06% of the Chinese paternity pairs were discriminated with RMplex while only 20.84% with the initial 14 RM Y-STRs, indicating that RMplex is beneficial for distinguishing paternally related males. Future studies on populations of different genetic backgrounds are necessary to obtain comprehensive estimates of mutation rates at these new loci.
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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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3
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Y-SNP Haplogroup Hierarchy Finder: a web tool for Y-SNP haplogroup assignment. J Hum Genet 2022; 67:487-493. [DOI: 10.1038/s10038-022-01033-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2021] [Revised: 03/03/2022] [Accepted: 03/09/2022] [Indexed: 11/08/2022]
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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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Improving the regional Y-STR haplotype resolution utilizing haplogroup-determining Y-SNPs and the application of machine learning in Y-SNP haplogroup prediction in a forensic Y-STR database: A pilot study on male Chinese Yunnan Zhaoyang Han population. Forensic Sci Int Genet 2021; 57:102659. [PMID: 35007855 DOI: 10.1016/j.fsigen.2021.102659] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2021] [Revised: 12/14/2021] [Accepted: 12/27/2021] [Indexed: 11/23/2022]
Abstract
Improving the resolution of the current widely used Y-chromosomal short tandem repeat (Y-STR) dataset is of great importance for forensic investigators, and the current approach is limited, except for the addition of more Y-STR loci. In this research, a regional Y-DNA database was investigated to improve the Y-STR haplotype resolution utilizing a Y-SNP Pedigree Tagging System that includes 24 Y-chromosomal single nucleotide polymorphism (Y-SNP) loci. This pilot study was conducted in the Chinese Yunnan Zhaoyang Han population, and 3473 unrelated male individuals were enrolled. Based on data on the male haplogroups under different panels, the matched or near-matching (NM) Y-STR haplotype pairs from different haplogroups indicated the critical roles of haplogroups in improving the regional Y-STR haplotype resolution. A classic median-joining network analysis was performed using Y-STR or Y-STR/Y-SNP data to reconstruct population substructures, which revealed the ability of Y-SNPs to correct misclassifications from Y-STRs. Additionally, population substructures were reconstructed using multiple unsupervised or supervised dimensionality reduction methods, which indicated the potential of Y-STR haplotypes in predicting Y-SNP haplogroups. Haplogroup prediction models were built based on nine publicly accessible machine-learning (ML) approaches. The results showed that the best prediction accuracy score could reach 99.71% for major haplogroups and 98.54% for detailed haplogroups. Potential influences on prediction accuracy were assessed by adjusting the Y-STR locus numbers, selecting Y-STR loci with various mutabilities, and performing data processing. ML-based predictors generally presented a better prediction accuracy than two available predictors (Nevgen and EA-YPredictor). Three tree models were developed based on the Yfiler Plus panel with unprocessed input data, which showed their strong generalization ability in classifying various Chinese Han subgroups (validation dataset). In conclusion, this study revealed the significance and application prospects of Y-SNP haplogroups in improving regional Y-STR databases. Y-SNP haplogroups can be used to discriminate NM Y-STR haplotype pairs, and it is important for forensic Y-STR databases to develop haplogroup prediction tools to improve the accuracy of biogeographic ancestry inferences.
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Lemos MP, Nandi V, Dragavon J, Fleming I, Krishnan K, Musuruana M, Kramer M, Glantz H, Andrasik M, Coombs RW, McElrath MJ, Tieu HV. HIV-1 Nucleic Acids Identify Rectal HIV Exposures in Self-Collected Rectal Swabs, Whereas Y-Chromosome Single Tandem Repeat Mixtures Are Not Reliable Biomarkers of Condomless Receptive Anal Intercourse. J Acquir Immune Defic Syndr 2021; 88:138-148. [PMID: 34506358 PMCID: PMC8439546 DOI: 10.1097/qai.0000000000002748] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2020] [Accepted: 05/10/2021] [Indexed: 11/26/2022]
Abstract
BACKGROUND To focus interventions, biomarkers of HIV-1 exposure could help in identifying subpopulations at highest risk of acquisition. We assessed whether Y-chromosome single tandem repeat (YSTR) mixtures obtained from rectal swabs could serve as a biomarker of condomless receptive anal intercourse (CRAI) among men who have sex with men and transgender women and evaluated the feasibility of detecting HIV-1 virions to assess exposures. METHODS Twenty-nine sexually active HIV-seronegative men who have sex with men and one transgender woman from New York City answered on-site and mobile app sexual behavior questionnaires. They were randomized to collecting self-administered rectal swabs every morning or after receptive anal intercourse (RAI). YSTR profiles were assessed from blood sample and swabs; HIV-1 exposure was measured by conducting quantitative polymerase chain reaction in swabs. RESULTS After 2 months, the daily mobile survey had 135%-201% more instances of anal sex acts and 170%-193% more RAI than on-site surveys. Daily mobile reporting had 11%-35% less CRAI events than those reported on-site (Pdaily = 0.001; Pper-sex = 0.047). The daily swabbing arm reported less RAI (P < 0.001) and CRAI (P < 0.038) and had 2.95 lower odds of detecting YSTR mixtures (P = 0.021) than the per-sex-event arm. Surprisingly, YSTR detection was not significantly modified by report of bowel movements and lubricant, enema, or condom use. No participant became HIV-1 infected, yet HIV-1 total nucleic acids were detected in 6 independent episodes of CRAI in 2 participants taking pre-exposure prophylaxis. CONCLUSIONS YSTR mixtures demonstrated 80% specificity but only 30% sensitivity as a biomarker of CRAI in self-collected rectal swabs. However, detection of HIV-1 exposures in self-collected swabs may help in identifying those needing further HIV risk reduction strategies.
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Affiliation(s)
- Maria P. Lemos
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - Vijay Nandi
- Laboratory of Data Analytics, Lindsley F. Kimball Research Institute, New York Blood Center, New York, NY
| | - Joan Dragavon
- Department of Laboratory Medicine, University of Washington, Seattle, WA, USA
| | - Ira Fleming
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - Keertana Krishnan
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - Martin Musuruana
- Laboratory of Data Analytics, Lindsley F. Kimball Research Institute, New York Blood Center, New York, NY
| | - Madeline Kramer
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - Hayley Glantz
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - Michele Andrasik
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
| | - Robert W. Coombs
- Department of Laboratory Medicine, University of Washington, Seattle, WA, USA
- Department of Pathology, University of Washington, Seattle, WA, USA
- Department of Medicine, University of Washington, Seattle, WA, USA
| | - M. Juliana McElrath
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, WA, USA
- Department of Global Health, University of Washington, Seattle, WA, USA
- Department of Medicine, University of Washington, Seattle, WA, USA
| | - Hong-Van Tieu
- Laboratory of Infectious Disease Prevention, Lindsley F. Kimball Research Institute, New York Blood Center, New York, NY
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Dudás E, Stier M, Czidor D. Forensic investigation of war graves from WWI and WWII in Hungary. Forensic Sci Int 2021; 320:110688. [PMID: 33486389 DOI: 10.1016/j.forsciint.2021.110688] [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: 09/24/2020] [Revised: 01/06/2021] [Accepted: 01/09/2021] [Indexed: 11/27/2022]
Abstract
The Hungarian war grave care professionals weren't in an easy situation when they started the work because, until 2012, the burial places of Hungarian soldiers had no legal protection. It was necessary to develop legal regulations and scientific methods. Since this is a multidisciplinary field, the work is quite compound as many professionals from different field of sciences work together. This work requires the harmonic work of military historians, archaeologists, anthropologists and geneticists. Thanks to the conscientious work of these professionals, nowadays, we can talk about a stable institutionalized, multidisciplinary war grave care in Hungary which encompasses the work of the above-mentioned professionals. Thanks to scientific development, new opportunities are available for the professionals to identify war heroic deads. In this article, the history and the formation of the Hungarian war grave care are introduced and the methodology of the Hungarian war grave care professionals work is shown. The paper also aims to illustrate the changes in laws and the standard practice currently followed by professionals during the exploration and the processing of the human remains.
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Affiliation(s)
- Eszter Dudás
- Hungarian Institute for Forensic Sciences, Institute of Forensic Genetics, Hungary.
| | - Márk Stier
- Institute and Museum of Military History, Hungary
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Mining the red deer genome (CerEla1.0) to develop X-and Y-chromosome-linked STR markers. PLoS One 2020; 15:e0242506. [PMID: 33226998 PMCID: PMC7986210 DOI: 10.1371/journal.pone.0242506] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2020] [Accepted: 11/03/2020] [Indexed: 12/13/2022] Open
Abstract
Microsatellites are widely applied in population and forensic genetics, wildlife studies and parentage testing in animal breeding, among others, and recently, high-throughput sequencing technologies have greatly facilitated the identification of microsatellite markers. In this study the genomic data of Cervus elaphus (CerEla1.0) was exploited, in order to identify microsatellite loci along the red deer genome and for designing the cognate primers. The bioinformatics pipeline identified 982,433 microsatellite motifs genome-wide, assorted along the chromosomes, from which 45,711 loci mapped to the X- and 1096 to the Y-chromosome. Primers were successfully designed for 170,873 loci, and validated with an independently developed autosomal tetranucleotide STR set. Ten X- and five Y-chromosome-linked microsatellites were selected and tested by two multiplex PCR setups on genomic DNA samples of 123 red deer stags. The average number of alleles per locus was 3.3, and the average gene diversity value of the markers was 0.270. The overall observed and expected heterozygosities were 0.755 and 0.832, respectively. Polymorphic Information Content (PIC) ranged between 0.469 and 0.909 per locus with a mean value of 0.813. Using the X- and Y-chromosome linked markers 19 different Y-chromosome and 72 X-chromosome lines were identified. Both the X- and the Y-haplotypes split to two distinct clades each. The Y-chromosome clades correlated strongly with the geographic origin of the haplotypes of the samples. Segregation and admixture of subpopulations were demonstrated by the use of the combination of nine autosomal and 16 sex chromosomal STRs concerning southwestern and northeastern Hungary. In conclusion, the approach demonstrated here is a very efficient method for developing microsatellite markers for species with available genomic sequence data, as well as for their use in individual identifications and in population genetics studies.
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27 Y-chromosomal STR haplotypic structure for the Chinese Han population from Changchun, Northeastern China. Leg Med (Tokyo) 2020; 48:101813. [PMID: 33264698 DOI: 10.1016/j.legalmed.2020.101813] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2020] [Revised: 10/11/2020] [Accepted: 11/12/2020] [Indexed: 11/23/2022]
Abstract
Y- Changchun is the capital and largest city of Jilin Province in the northeast China. In this study, we genotyped and investigated haplotypes of 27 Y-STR loci in 1037 Changchun Han male individuals using commercially available AmpFlSTR Yfiler® Plus kit. We calculated the Gene diversity (GD) values and haplotype diversity (HD) as important forensic parameters. Furthermore, we observed genetic affinities between Changchun Han with other Northern Han Chinese populations and also Korans in Yanbian in the Multidimensional scaling and phylogenetic tree analysis.
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10
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The Y Chromosome: A Complex Locus for Genetic Analyses of Complex Human Traits. Genes (Basel) 2020; 11:genes11111273. [PMID: 33137877 PMCID: PMC7693691 DOI: 10.3390/genes11111273] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2020] [Revised: 10/19/2020] [Accepted: 10/26/2020] [Indexed: 12/29/2022] Open
Abstract
The Human Y chromosome (ChrY) has been demonstrated to be a powerful tool for phylogenetics, population genetics, genetic genealogy and forensics. However, the importance of ChrY genetic variation in relation to human complex traits is less clear. In this review, we summarise existing evidence about the inherent complexities of ChrY variation and their use in association studies of human complex traits. We present and discuss the specific particularities of ChrY genetic variation, including Y chromosomal haplogroups, that need to be considered in the design and interpretation of genetic epidemiological studies involving ChrY.
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11
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Geographical structuring and low diversity of paternal lineages in Bahrain shown by analysis of 27 Y-STRs. Mol Genet Genomics 2020; 295:1315-1324. [PMID: 32588126 PMCID: PMC7524810 DOI: 10.1007/s00438-020-01696-4] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2020] [Accepted: 06/08/2020] [Indexed: 11/30/2022]
Abstract
We have determined the distribution of Y-chromosomal haplotypes and predicted haplogroups in the ethnically diverse Kingdom of Bahrain, a small archipelago in the Arabian Gulf. Paternal population structure within Bahrain was investigated using the 27 Y-STRs (short tandem repeats) in the Yfiler Plus kit to generate haplotypes from 562 unrelated Bahraini males, sub-divided into four geographical regions—Northern, Capital, Southern and Muharraq. Yfiler Plus provided a significant improvement over the 17-locus Yfiler kit in discrimination capacity (from 77% to 87.5% overall), but discrimination capacity differed widely between regions from 98.4% in Muharraq to 75.2% in the Northern region, an unusually low value possibly resulting from recent rapid population expansion. Clusters of closely related male lineages were seen, with only 79.4% of donors displaying unique haplotypes and 59% of instances of shared haplotypes occurring within, rather than between, regions. Haplogroup prediction indicated diverse origins of the population with a predominance of haplogroups J2 and J1, both typical of the Arabian Peninsula, but also haplogroups such as B2 and E1b1a likely originating in Africa, and H, L and R2 likely indicative of migration from South Asia. Haplogroup frequencies differed significantly between regions, with J2 significantly more common in the Northern region compared with the Southern, possibly due to differential settlement by Baharna and Arabs. Our study shows that paternal lineage population structure can exist even over small geographical scales, and that highly discriminating genetic tools are required where rapid expansions have occurred within tightly bounded populations.
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Oldoni F, Podini D. Forensic molecular biomarkers for mixture analysis. Forensic Sci Int Genet 2019; 41:107-119. [DOI: 10.1016/j.fsigen.2019.04.003] [Citation(s) in RCA: 37] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2018] [Revised: 03/06/2019] [Accepted: 04/17/2019] [Indexed: 01/10/2023]
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Haplotypes of 27 Y-STRs analyzed in Gelao and Miao ethnic minorities from Guizhou Province, Southwest China. Forensic Sci Int Genet 2019; 40:e264-e267. [DOI: 10.1016/j.fsigen.2019.03.002] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2018] [Revised: 02/18/2019] [Accepted: 03/02/2019] [Indexed: 11/17/2022]
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14
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Rapidly mutating Y-STRs in rapidly expanding populations: Discrimination power of the Yfiler Plus multiplex in northern Africa. Forensic Sci Int Genet 2019; 38:185-194. [DOI: 10.1016/j.fsigen.2018.11.002] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2018] [Revised: 10/02/2018] [Accepted: 11/02/2018] [Indexed: 11/18/2022]
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15
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Wang Q, Jin B, An G, Zhong Q, Chen M, Luo X, Li Z, Jiang Y, Liang W, Zhang L. Rapidly mutating Y-STRs study in Chinese Yi population. Int J Legal Med 2018; 133:45-50. [PMID: 30062654 DOI: 10.1007/s00414-018-1894-5] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2018] [Accepted: 07/17/2018] [Indexed: 12/01/2022]
Abstract
Y-chromosomal short tandem repeats (Y-STRs) have been widely used in forensic analysis and population genetics. With low to moderate mutation rates, conventional Y-STR panels, including commercially available Y-STR kits, enable the identification of male pedigrees but typically fail to differentiate related male individuals. The introduction of rapidly mutating Y-chromosomal short tandem repeats (RM Y-STRs) with higher mutation rates (μ > 10-2) has been demonstrated to increase the discrimination capacity of unrelated men and the differentiation rate of related men compared with standard Y-STRs. To date, several studies have been performed worldwide. Here, 260 father-son pairs from Chinese Yi population were investigated, and 18.8% of them were differentiated with the 13 RM Y-STR markers, which was close to the theoretical estimate of 19.5% based on the mutation rates of these markers. Among the 57 mutations observed, repeat gains were more common than repeat losses (1.48:1), and one-step mutations were more common than two-step mutations (27.5:1). Locus-specific mutation rates ranged from < 3.85 × 10-3 (95% CI 0.00-1.41 × 10-2) to 3.85 × 10-2 (95% CI 1.86 × 10-2-6.96 × 10-2), with an average mutation rate of 1.46 × 10-2 (95% CI 1.11 × 10-2-1.89 × 10-2). Furthermore, we combined the father-son pair data from the present study with the data from the previous studies, generating an overall mutation rate of 1.70 × 10-2. The high differentiation rate obtained in the present study indicates the suitability of RM Y-STRs to distinguish paternal lineages in Chinese Yi population.
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Affiliation(s)
- Qian Wang
- Department of Forensic Genetics, West China School of Basic Sciences and Forensic Medicine, Sichuan University, Chengdu, 610041, Sichuan, China
| | - Bo Jin
- Department of Forensic Genetics, West China School of Basic Sciences and Forensic Medicine, Sichuan University, Chengdu, 610041, Sichuan, China.,Department of Forensic Medicine, North Sichuan Medical College, Nanchong, 637000, Sichuan, China.,Forensic Science Service Center, North Sichuan Medical College, Nanchong, 637000, Sichuan, China
| | - Gang An
- Sichuan Forest Forensic Center, Chengdu, 610041, Sichuan, China
| | - Qian Zhong
- Sichuan Forest Forensic Center, Chengdu, 610041, Sichuan, China
| | - Meijun Chen
- Sichuan Forest Forensic Center, Chengdu, 610041, Sichuan, China
| | - Xiaoying Luo
- Sichuan Forest Forensic Center, Chengdu, 610041, Sichuan, China
| | - Zhilong Li
- Department of Forensic Genetics, West China School of Basic Sciences and Forensic Medicine, Sichuan University, Chengdu, 610041, Sichuan, China
| | - Youjing Jiang
- Department of Forensic Genetics, West China School of Basic Sciences and Forensic Medicine, Sichuan University, Chengdu, 610041, Sichuan, China
| | - Weibo Liang
- Department of Forensic Genetics, West China School of Basic Sciences and Forensic Medicine, Sichuan University, Chengdu, 610041, Sichuan, China.
| | - Lin Zhang
- Department of Forensic Genetics, West China School of Basic Sciences and Forensic Medicine, Sichuan University, Chengdu, 610041, Sichuan, China.
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16
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Wang J, Wen S, Shi M, Liu Y, Zhang J, Bai R, Li H. Haplotype structure of 27 Yfiler ®Plus loci in Chinese Dongxiang ethnic group and its genetic relationships with other populations. Forensic Sci Int Genet 2018; 33:e13-e16. [PMID: 29402655 DOI: 10.1016/j.fsigen.2017.12.014] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2017] [Revised: 12/26/2017] [Accepted: 12/30/2017] [Indexed: 11/25/2022]
Affiliation(s)
- Junfang Wang
- Collaborative Innovation Center of Judicial Civilization, Beijing 100088, P.R. China; Key Laboratory of Evidence Science (China University of Political Science and Law), Ministry of Education, Beijing 100088, P.R. China
| | - Shaoqing Wen
- State Key Laboratory of Genetic Engineering and Ministry of Education Key Laboratory of Contemporary Anthropology, Collaborative Innovation Center for Genetics and Development, School of Life Sciences, Fudan University, Shanghai, 200433, P.R. China
| | - Meisen Shi
- Collaborative Innovation Center of Judicial Civilization, Beijing 100088, P.R. China; Key Laboratory of Evidence Science (China University of Political Science and Law), Ministry of Education, Beijing 100088, P.R. China
| | - Yaju Liu
- Xuchang Institute of Forensic Sciences, Public Security Bureau of Henan Province, Xuchang 461000, P.R. China
| | - Jing Zhang
- Collaborative Innovation Center of Judicial Civilization, Beijing 100088, P.R. China; Key Laboratory of Evidence Science (China University of Political Science and Law), Ministry of Education, Beijing 100088, P.R.China
| | - Rufeng Bai
- Collaborative Innovation Center of Judicial Civilization, Beijing 100088, P.R. China; Key Laboratory of Evidence Science (China University of Political Science and Law), Ministry of Education, Beijing 100088, P.R. China.
| | - Hui Li
- State Key Laboratory of Genetic Engineering and Ministry of Education Key Laboratory of Contemporary Anthropology, Collaborative Innovation Center for Genetics and Development, School of Life Sciences, Fudan University, Shanghai 200433, P.R. China.
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Kremer K, Fritzsch S, Stahl F. DNA-Forensik. CHEM UNSERER ZEIT 2017. [DOI: 10.1002/ciuz.201700728] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Affiliation(s)
| | | | - Frank Stahl
- Institut für Technische Chemie; Callinstr. 5 30167 Hannover
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de la Puente M, Phillips C, Fondevila M, Gelabert-Besada M, Carracedo Á, Lareu MV. A forensic multiplex of nine novel pentameric-repeat STRs. Forensic Sci Int Genet 2017; 29:154-164. [PMID: 28445836 DOI: 10.1016/j.fsigen.2017.04.007] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2016] [Revised: 03/29/2017] [Accepted: 04/11/2017] [Indexed: 12/22/2022]
Abstract
Pentameric-repeat short tandem repeats (STRs), consisting of loci with repeat units of five base-pairs, have the advantage of reduced stutter products compared to their tetrameric-repeat STR counterparts. This characteristic potentially helps the interpretation of mixed DNA profiles when minor component alleles may coincide with stutter peaks from the major components. To develop a simple but informative forensic multiplex with the capability to aid mixture interpretation, we designed an 11-plex assay of nine pentameric STRs new to forensic analysis plus two male- specific markers: DYS391 and the Y-Indel rs2032678 used in GlobalFiler™ (Life Technologies). East Asian-specific variation in the recently adopted Y-Indel rs2032678 is reported in this study for the first time in its forensic use as a sex marker. We estimated the levels of variation observed in the nine pentameric STRs in three of the major population groups sampled in the HGDP-CEPH human genome diversity panel: African, European and East Asian (combining individual populations as their sample sizes were too small for STR allele frequency estimations); and we include genotype data from a population sample of Northwest Spain. From this data, forensic informativeness metrics were estimated when applying the nine novel STRs in identification or kinship analyses. The assay was assessed for forensic sensitivity and ability to successfully genotype highly degraded DNA. In the profiles from the 11-plex assay we observed an average 2.15% stutter ratio in all the pentameric loci compared to 7.32% across equivalently-sized tetrameric STRs in the Promega Powerplex® ESX-17 kit.
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Affiliation(s)
- M de la Puente
- Forensic Genetics Unit, Institute of Forensic Sciences, University of Santiago de Compostela, Spain
| | - C Phillips
- Forensic Genetics Unit, Institute of Forensic Sciences, University of Santiago de Compostela, Spain.
| | - M Fondevila
- Forensic Genetics Unit, Institute of Forensic Sciences, University of Santiago de Compostela, Spain
| | - M Gelabert-Besada
- Forensic Genetics Unit, Institute of Forensic Sciences, University of Santiago de Compostela, Spain
| | - Á Carracedo
- Forensic Genetics Unit, Institute of Forensic Sciences, University of Santiago de Compostela, Spain; Grupo de Medicina Xenómica (GMX), Faculty of Medicine, University of Santiago de Compostela, Spain; Center of Excellence in Genomic Medicine Research, King Abdulaziz University, Jeddah, Saudi Arabia
| | - M V Lareu
- Forensic Genetics Unit, Institute of Forensic Sciences, University of Santiago de Compostela, Spain
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Batini C, Jobling MA. Detecting past male-mediated expansions using the Y chromosome. Hum Genet 2017; 136:547-557. [PMID: 28349239 DOI: 10.1007/s00439-017-1781-z] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2017] [Accepted: 03/15/2017] [Indexed: 12/29/2022]
Abstract
Males and females display biological differences that lead to a higher variance of offspring number in males, and this is frequently exacerbated in human societies by mating practices, and possibly by past socio-cultural circumstances. This implies that the genetic record might contain the imprint of past male-mediated expansions, which can be investigated by analysing the male-specific region of the Y chromosome (MSY). Here, we review studies that have used MSY data to infer such expansions. Sets of short-tandem repeats define haplotypes of very low average frequencies, but in a few cases, high-frequency haplotypes are observed, forming the core of descent clusters. Estimates of the ages of such clusters, together with geographical information, have been used to propose powerful historical founders, including Genghis Khan, although without direct supporting evidence. Resequencing of multi-megabase segments of MSY has allowed the construction of detailed phylogenies in which branch lengths are proportional to time, leading to the identification of lineage expansions in the last few millennia as well as the more distant past. Comparisons with maternally-inherited mitochondrial DNA sequence data allow the male specificity of some of these expansions to be demonstrated. These include expansions in Europe in the last ~5000 years that may be associated with a cultural shift during the Bronze Age, as well as expansions elsewhere in the world for which explanations from archaeological evidence are not yet clear.
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Affiliation(s)
- Chiara Batini
- Department of Health Sciences, University of Leicester, University Road, Leicester, LE1 7RH, UK.
| | - Mark A Jobling
- Department of Genetics, University of Leicester, University Road, Leicester, LE1 7RH, UK.
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Kayser M. Forensic use of Y-chromosome DNA: a general overview. Hum Genet 2017; 136:621-635. [PMID: 28315050 PMCID: PMC5418305 DOI: 10.1007/s00439-017-1776-9] [Citation(s) in RCA: 199] [Impact Index Per Article: 28.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2017] [Accepted: 03/08/2017] [Indexed: 11/19/2022]
Abstract
The male-specific part of the human Y chromosome is widely used in forensic DNA analysis, particularly in cases where standard autosomal DNA profiling is not informative. A Y-chromosomal gene fragment is applied for inferring the biological sex of a crime scene trace donor. Haplotypes composed of Y-chromosomal short tandem repeat polymorphisms (Y-STRs) are used to characterise paternal lineages of unknown male trace donors, especially suitable when males and females have contributed to the same trace, such as in sexual assault cases. Y-STR haplotyping applied in crime scene investigation can (i) exclude male suspects from involvement in crime, (ii) identify the paternal lineage of male perpetrators, (iii) highlight multiple male contributors to a trace, and (iv) provide investigative leads for finding unknown male perpetrators. Y-STR haplotype analysis is employed in paternity disputes of male offspring and other types of paternal kinship testing, including historical cases, as well as in special cases of missing person and disaster victim identification involving men. Y-chromosome polymorphisms are applied for inferring the paternal bio-geographic ancestry of unknown trace donors or missing persons, in cases where autosomal DNA profiling is uninformative. In this overview, all different forensic applications of Y-chromosome DNA are described. To illustrate the necessity of forensic Y-chromosome analysis, the investigation of a prominent murder case is described, which initiated two changes in national forensic DNA legislation both covering Y-chromosome use, and was finally solved via an innovative Y-STR dragnet involving thousands of volunteers after 14 years. Finally, expectations for the future of forensic Y-chromosome DNA analysis are discussed.
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Affiliation(s)
- Manfred Kayser
- Department of Genetic Identification, Erasmus MC University Medical Center Rotterdam, PO Box 2040, 3000 CA, Rotterdam, The Netherlands.
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21
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Choi EJ, Park KW, Lee YH, Nam YH, Suren G, Ganbold U, Kim JA, Kim SY, Kim HM, Kim K, Kim W. Forensic and population genetic analyses of the GlobalFiler STR loci in the Mongolian population. Genes Genomics 2017. [DOI: 10.1007/s13258-016-0511-6] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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22
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Lee EY, Lee HY, Kwon SY, Oh YN, Yang WI, Shin KJ. A multiplex PCR system for 13 RM Y-STRs with separate amplification of two different repeat motif structures in DYF403S1a. Forensic Sci Int Genet 2017; 26:85-90. [DOI: 10.1016/j.fsigen.2016.10.019] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2016] [Revised: 09/28/2016] [Accepted: 10/26/2016] [Indexed: 12/09/2022]
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23
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Y-chromosomal haplogroup distribution in the Tuzla Canton of Bosnia and Herzegovina: A concordance study using four different in silico assignment algorithms based on Y-STR data. HOMO-JOURNAL OF COMPARATIVE HUMAN BIOLOGY 2016; 67:471-483. [DOI: 10.1016/j.jchb.2016.10.003] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/02/2016] [Accepted: 10/19/2016] [Indexed: 11/19/2022]
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24
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Multiplex assay development and mutation rate analysis for 13 RM Y-STRs in Chinese Han population. Int J Legal Med 2016; 131:345-350. [DOI: 10.1007/s00414-016-1489-y] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2016] [Accepted: 10/25/2016] [Indexed: 11/25/2022]
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25
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Niederstätter H, Berger B, Kayser M, Parson W. Differences in urbanization degree and consequences on the diversity of conventional vs. rapidly mutating Y-STRs in five municipalities from a small region of the Tyrolean Alps in Austria. Forensic Sci Int Genet 2016; 24:180-193. [DOI: 10.1016/j.fsigen.2016.07.009] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2016] [Revised: 06/23/2016] [Accepted: 07/17/2016] [Indexed: 12/09/2022]
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26
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Developmental Validation of a novel 5 dye Y-STR System comprising the 27 YfilerPlus loci. Sci Rep 2016; 6:29557. [PMID: 27406339 PMCID: PMC4942765 DOI: 10.1038/srep29557] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2016] [Accepted: 05/31/2016] [Indexed: 11/09/2022] Open
Abstract
In this study, a new STRtyper-27 system, including the same Yfiler Plus loci (DYS19, DYS389I, DYS389II, DYS390, DYS391, DYS392, DYS393, DYS385a/b, DYS437, DYS438, DYS439, DYS448, DYS456, DYS458, DYS635, Y-GATA H4, DYS449, DYS460, DYS481, DYS518, DYS533, DYS570, DYS576, DYS627 and DYF387S1a/b), was established using a set of 5 fluorescent dye labels. Primers, internal size standard, allelic ladders and matrix standard set were designed and created in-house for this multiplex system. This paper describes the validation studies conducted with the STRtyper-27Y system using a 3130XL genetic analyzer for fragment length detection that included the analysis of the following parameters and aspects: sensitivity, species specificity, inhibition, haplotype concordance, precision, stutter, DNA mixtures, and stability studies with crime scene samples. The studies demonstrated, that the STRtyper-27Y system provided equivalent overall performance comparable to the latest Yfiler Plus kit, but with enhanced compatibility in terms of instrument platforms and software allowing forensic laboratories to conduct its forensic application and evaluate its performance, all in their own 5 dye Y-STR chemistry system /environment without software or instrument upgrades.
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27
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Development of new PCR multiplex system by the simultaneous detection of 10 miniSTRs, SE33, Penta E, Penta D, and four Y-STRs. Int J Legal Med 2016; 130:1409-1419. [DOI: 10.1007/s00414-016-1372-x] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2015] [Accepted: 04/29/2016] [Indexed: 11/26/2022]
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Bai R, Liu Y, Zhang J, Shi M, Dong H, Ma S, Bai RF, Shi MS. Analysis of 27 Y-chromosomal STR haplotypes in a Han population of Henan province, Central China. Int J Legal Med 2016; 130:1191-4. [DOI: 10.1007/s00414-016-1326-3] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2015] [Accepted: 02/02/2016] [Indexed: 10/22/2022]
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29
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Toscanini U, Vullo C, Berardi G, Llull C, Borosky A, Gómez A, Pardo-Seco J, Salas A. A comprehensive Y-STR portrait of Argentinean populations. Forensic Sci Int Genet 2016; 20:1-5. [DOI: 10.1016/j.fsigen.2015.09.002] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2015] [Revised: 08/09/2015] [Accepted: 09/02/2015] [Indexed: 01/10/2023]
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Shang J, Hu SP. Haplotype data of 23 Y-chromosome markers in Minnan Han Chinese and comparison with those of 12 Y-chromosome markers. JOURNAL OF HUAZHONG UNIVERSITY OF SCIENCE AND TECHNOLOGY. MEDICAL SCIENCES = HUA ZHONG KE JI DA XUE XUE BAO. YI XUE YING DE WEN BAN = HUAZHONG KEJI DAXUE XUEBAO. YIXUE YINGDEWEN BAN 2015; 35:456-463. [PMID: 26072089 DOI: 10.1007/s11596-015-1453-y] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/23/2014] [Revised: 12/10/2014] [Indexed: 02/05/2023]
Abstract
We genotyped 23 Y-STR loci (DYS576, DYS389I, DYS448, DYS389II, DYS19, DYS391, DYS481, DYS549, DYS533, DYS438, DYS437, DYS570, DYS635, DYS390, DYS439, DYS392, DYS643, DYS393, DYS458, DYS385a/b, DYS456, and GATA-H4) in a sample of 109 unrelated male Chinese people residing in Minnan area and compared the results with those from our previous study on 12 Y-STR. The haplotype diversity and the discrimination capacity of the 23 Y-STR reached 0.9903 and 0.9725, respectively, and the genetic diversity for each locus ranged from 0.321 (DYS391) to 0.955 (DYS385). Besides, we observed a strong correlation between the number of Y-STR markers and the substantial improvement of forensic parameters used to discriminate between individuals. The results indicated that these highly polymorphic Y-STR markers were useful for human identification in forensic cases and paternity tests within the Minnan Han Chinese population.
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Affiliation(s)
- Jie Shang
- Molecular Biology and Forensic Genetics Laboratory, Shantou University Medical College, Shantou, 515031, China
| | - Sheng-Ping Hu
- Molecular Biology and Forensic Genetics Laboratory, Shantou University Medical College, Shantou, 515031, China.
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31
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Nayak BP, Khajuria H, Gupta S. Y-STR haplotype diversity among the Khandayat population of Odisha, India. EGYPTIAN JOURNAL OF FORENSIC SCIENCES 2015. [DOI: 10.1016/j.ejfs.2014.07.003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022] Open
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32
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Westen AA, Kraaijenbrink T, Clarisse L, Grol LJ, Willemse P, Zuniga SB, Robles de Medina EA, Schouten R, van der Gaag KJ, Weiler NE, Kal AJ, Kayser M, Sijen T, de Knijff P. Analysis of 36 Y-STR marker units including a concordance study among 2085 Dutch males. Forensic Sci Int Genet 2015; 14:174-81. [DOI: 10.1016/j.fsigen.2014.10.012] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2014] [Revised: 10/13/2014] [Accepted: 10/14/2014] [Indexed: 12/09/2022]
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33
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Zhang S, Tian H, Wang Z, Zhao S, Hu Z, Li C, Ji C. Development of a new 26plex Y-STRs typing system for forensic application. Forensic Sci Int Genet 2014; 13:112-20. [DOI: 10.1016/j.fsigen.2014.06.015] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2014] [Revised: 06/08/2014] [Accepted: 06/23/2014] [Indexed: 11/26/2022]
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Lee EY, Shin KJ, Rakha A, Sim JE, Park MJ, Kim NY, Yang WI, Lee HY. Analysis of 22 Y chromosomal STR haplotypes and Y haplogroup distribution in Pathans of Pakistan. Forensic Sci Int Genet 2014; 11:111-6. [DOI: 10.1016/j.fsigen.2014.03.004] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2013] [Revised: 03/03/2014] [Accepted: 03/04/2014] [Indexed: 10/25/2022]
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35
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Genetic population study of 11 Y chromosome STR loci in Greece. Forensic Sci Int Genet 2013; 7:e56-8. [DOI: 10.1016/j.fsigen.2013.02.001] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2012] [Revised: 11/27/2012] [Accepted: 02/06/2013] [Indexed: 11/21/2022]
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Paleo-Balkan and Slavic contributions to the genetic pool of Moldavians: insights from the Y chromosome. PLoS One 2013; 8:e53731. [PMID: 23341985 PMCID: PMC3547065 DOI: 10.1371/journal.pone.0053731] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2012] [Accepted: 12/04/2012] [Indexed: 11/25/2022] Open
Abstract
Moldova has a rich historical and cultural heritage, which may be reflected in the current genetic makeup of its population. To date, no comprehensive studies exist about the population genetic structure of modern Moldavians. To bridge this gap with respect to paternal lineages, we analyzed 37 binary and 17 multiallelic (STRs) polymorphisms on the non-recombining portion of the Y chromosome in 125 Moldavian males. In addition, 53 Ukrainians from eastern Moldova and 54 Romanians from the neighboring eastern Romania were typed using the same set of markers. In Moldavians, 19 Y chromosome haplogroups were identified, the most common being I-M423 (20.8%), R-M17* (17.6%), R-M458 (12.8%), E-v13 (8.8%), R-M269* and R-M412* (both 7.2%). In Romanians, 14 haplogroups were found including I-M423 (40.7%), R-M17* (16.7%), R-M405 (7.4%), E-v13 and R-M412* (both 5.6%). In Ukrainians, 13 haplogroups were identified including R-M17 (34.0%), I-M423 (20.8%), R-M269* (9.4%), N-M178, R-M458 and R-M73 (each 5.7%). Our results show that a significant majority of the Moldavian paternal gene pool belongs to eastern/central European and Balkan/eastern Mediterranean Y lineages. Phylogenetic and AMOVA analyses based on Y-STR loci also revealed that Moldavians are close to both eastern/central European and Balkan-Carpathian populations. The data correlate well with historical accounts and geographical location of the region and thus allow to hypothesize that extant Moldavian paternal genetic lineages arose from extensive recent admixture between genetically autochthonous populations of the Balkan-Carpathian zone and neighboring Slavic groups.
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BAI RF, YANG LH, YUAN L, LIANG QZ, LU D, YANG X, SHI MS. Polymorphism of 17 Y-STR loci in She ethnic population in Fujian and genetic relationship with 11 populations. YI CHUAN = HEREDITAS 2012; 34:1020-30. [DOI: 10.3724/sp.j.1005.2012.01020] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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Distinguishing the co-ancestries of haplogroup G Y-chromosomes in the populations of Europe and the Caucasus. Eur J Hum Genet 2012; 20:1275-82. [PMID: 22588667 DOI: 10.1038/ejhg.2012.86] [Citation(s) in RCA: 56] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022] Open
Abstract
Haplogroup G, together with J2 clades, has been associated with the spread of agriculture, especially in the European context. However, interpretations based on simple haplogroup frequency clines do not recognize underlying patterns of genetic diversification. Although progress has been recently made in resolving the haplogroup G phylogeny, a comprehensive survey of the geographic distribution patterns of the significant sub-clades of this haplogroup has not been conducted yet. Here we present the haplogroup frequency distribution and STR variation of 16 informative G sub-clades by evaluating 1472 haplogroup G chromosomes belonging to 98 populations ranging from Europe to Pakistan. Although no basal G-M201* chromosomes were detected in our data set, the homeland of this haplogroup has been estimated to be somewhere nearby eastern Anatolia, Armenia or western Iran, the only areas characterized by the co-presence of deep basal branches as well as the occurrence of high sub-haplogroup diversity. The P303 SNP defines the most frequent and widespread G sub-haplogroup. However, its sub-clades have more localized distribution with the U1-defined branch largely restricted to Near/Middle Eastern and the Caucasus, whereas L497 lineages essentially occur in Europe where they likely originated. In contrast, the only U1 representative in Europe is the G-M527 lineage whose distribution pattern is consistent with regions of Greek colonization. No clinal patterns were detected suggesting that the distributions are rather indicative of isolation by distance and demographic complexities.
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Parvathy SN, Geetha A, Jagannath C. Haplotype analysis of the polymorphic 17 YSTR markers in Kerala nontribal populations. Mol Biol Rep 2012; 39:7049-59. [PMID: 22311032 DOI: 10.1007/s11033-012-1536-9] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2011] [Accepted: 01/24/2012] [Indexed: 11/28/2022]
Abstract
The origin of the Kerala non tribal population has been a matter of contention for centuries. While some claim that Negritos were the first inhabitants, some historians suggest a Dravidian origin for all Keralites. The aim of our study has been to provide sufficient scientific evidence based on Y chromosome short tandem repeat (Y STR) analysis for tracing the paternal lineage and also to create a database of the Y STR haplotype of the male population for future forensic analysis. Whole blood samples (n = 168) were collected from unrelated healthy men of the Kerala non-tribal population over a period of 2 years from October 2009. Genomic DNA was extracted by salting out method. All samples were genotyped for the 17 Y STR loci by the AmpFLSTR Y-filer PCR Amplification Kit. The haplotype and allele frequencies were determined by direct counting and analyzed using Arlequin 3.1 software, and molecular variance was calculated with the Y chromosome haplotype reference database online analysis tool, www.yhrd.org . Haplotype diversity was calculated using HaPYDive ( http://portugene.com/hapydive.html ). The majority of haplotypes were unique (149/168). The variant allele 17.1 was observed in DYS 385 loci in three samples. Fifteen samples (8.93%) showed the presence of alleles that are not within the established marker range denoted as outside marker range (OMR). The allele frequency of Kerala non tribal population ranged from 0.00003 to 0.5809. The most polymorphic single locus marker was DYS 458. The haplotype diversity value for Kerala non tribal population was 0.9978. The pairwise difference value ranged from 0.0531 to 0.0854 on comparison of the haplotypes of the Kerala non tribals with other Indian populations. The multi dimensional scaling plot depicted the proximity of Kerala non tribal population with Vasterbotten population (Swedish) and Paiwan, Patyal population of Taiwan, Thailand, and Zhuang population of China. The results of the study indicate towards a European paternal lineage in the non tribal Kerala population.
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Affiliation(s)
- Seema Nair Parvathy
- Department of Biotechnology and Biochemical Engineering, Sree Buddha College of Engineering, Kerala, India.
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Nair SP, Geetha A, Jagannath C. Y-short tandem repeat haplotype and paternal lineage of the Ezhava population of Kerala, south India. Croat Med J 2012; 52:344-50. [PMID: 21674830 PMCID: PMC3118723 DOI: 10.3325/cmj.2011.52.344] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022] Open
Abstract
AIM To analyze the haplotype of the Ezhava population of Kerala, south India, using 8 short tandem repeat (STR) loci on the Y chromosome and trace the paternal genetic lineage of the population. METHODS Whole blood samples (n=104) were collected from unrelated healthy men of the Ezhava population over a period of one year from October 2009. Genomic DNA was extracted by salting out method. All samples were genotyped for the 8 Y-STR loci by the AmpFiSTR Y-filer PCR Amplification Kit. The haplotype and allele frequencies were determined by direct counting and analyzed using Arlequin 3.1 software, and molecular variance was calculated with the Y-chromosome haplotype reference database online analysis tool, www.yhrd.org. RESULTS Among the 104 examined haplotypes, we found 98 unique ones. The average gene diversity was 0.669, with the highest diversity of 0.9462 observed for the biallelic Y-STR marker DYS 385. The allele frequency among DYS loci varied between 0.0096 and 0.75. Out of the 104 haplotypes, 10 were identical to the Jat Sikh population of Punjab, which is the greatest number among the Indian populations, and 4 to the Turkish population, which is the greatest number among the European populations. According to the allele frequency of Y-STR, the Ezhavas were genetically more similar to the Europeans (60%) than to the East Asians (40%). CONCLUSION The vast majority of haplotypes were observed only once, reflecting the enormous genetic heterogeneity of the Ezhavas. Based on the genotype, the Ezhavas showed more resemblance to Jat Sikh population of Punjab and the Turkish populations than to the East Asians, hence indicating a paternal lineage of European origin.
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Affiliation(s)
- Seema P Nair
- Center for Biotechnology and Nanotechnology, Department of Biotechnology and Biochemical Engineering, Sree Buddha College of Engineering, Kerala, India.
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Shi MS, Bai RF, Fu B. [Polymorphism of 17 Y-STR loci in Shanxi Han population and genetic relationship with 13 populations]. YI CHUAN = HEREDITAS 2011; 33:228-38. [PMID: 21402530 DOI: 10.3724/sp.j.1005.2011.00228] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
To investigate the genetic polymorphisms of 17 Y-chromosomal short tandem repeats (Y-STR) loci in Shanxi Han population and to explore their forensic application values and genetic relationship with neighboring populations, 17 Y-STR in 222 unrelated healthy Shanxi Han individuals were amplified with Y-filerTM System, and the PCR products were detected with 3130 Genetic Aanalyzer. The allele frequencies and haplotype diversity were calculated. Y-STR data of another 13 populations were collected from publications. Cluster analysis and phylogenic trees were applied to show the genetic distance among the populations. As a result, a total of 219 haplotypes were identified, and the observed haplotypes diversity value was 0.9999. The gene diversity values (GD) for each locus ranged from 0.3894 (DYS391) to 0.9755 (DYS385a/b). Comparing with 13 populations, the genetic distance between Shanxi and Jihei Han populations was the smallest (0.0001), while the genetic distance between Shanxi and Taiwan population was the largest (0.0152). The phylogenetic tree was similar to the results of clustering analysis. Multiplex detection of the 17 Y-STR loci revealed a highly polymorphic genetic distribution, which would be very powerful for establishing a Y-STR database, for population genetics and forensic practice.
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Affiliation(s)
- Mei-Sen Shi
- Key Laboratory of Evidence Science, Ministry of Education, China University of Political Science and Law, Beijing 100088, China.
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Siddiqi S, Mansoor A, Usman S, Nasir M, Khan KM, Qamar R. Characterization of Y-chromosomal short tandem repeat markers in Pakistani populations. Genet Test Mol Biomarkers 2011; 15:165-72. [PMID: 21198376 DOI: 10.1089/gtmb.2010.0147] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
The Y chromosome microsatellite markers have been extensively used for population genetic studies and in individual identification and paternity testing in forensic medicine. In the present study, we report the data of five male-specific, polymorphic microsatellites in 740 unrelated male individuals from 12 different ethnic groups of Pakistan. The overall diversities of these individual loci in Pakistan ranged from 0.236 to 0.799. The total haplotypes identified were 152, and of these, 70 different haplotypes were present in only single individuals. Two haplotypes were found more frequently, 9_8_17_11_24 (13.5%) and 9_8_17_11_25 (8.6%), showing population-specific clustering in the Mohanna and the Brahui, respectively. An overall haplotype diversity of 0.965 in Pakistan suggested a high power of discrimination for these loci. Few populations, particularly the Mohanna and the Balti, showed lower haplotype diversity values for these loci (0.662 and 0.758, respectively). This set of microsatellite loci reported in the study can be used for population genetics and forensic medicine analysis. This study also demonstrates the importance of studying haplotype distribution pattern in population genetics.
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Affiliation(s)
- Saima Siddiqi
- Institute of Biomedical and Genetic Engineering, Islamabad, Pakistan.
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Decorte R. Genetic identification in the 21st century—Current status and future developments. Forensic Sci Int 2010; 201:160-4. [DOI: 10.1016/j.forsciint.2010.02.029] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2010] [Accepted: 02/23/2010] [Indexed: 11/25/2022]
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Kim SH, Chun BW, Jung J, Kemp BM, Kwak KD, Cho NS, Kim JJ, Han MS, Kim W. A preliminary study on the origin of Koreans based on Y-STR variation. Genes Genomics 2010. [DOI: 10.1007/s13258-010-0030-9] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
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Xu Z, Sun H, Yu Y, Jin Y, Meng X, Sun D, Bai J, Chen F, Fu S. Diversity of five novel Y-STR loci and their application in studies of north Chinese populations. J Genet 2010; 89:29-36. [PMID: 20505244 DOI: 10.1007/s12041-010-0008-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
Abstract
Y-chromosomal short tandem repeats (Y-STRs) show sufficient variability among individuals in a population and high degree of geographical differentiation, so their polymorphic character makes them especially suited for population genetic studies. In this study, five novel Y-STR loci were analysed in 174 samples from five minority populations residing in north China (Daur, Kazak, Xibe, Uighur and Kirgiz) to determine the diversity of these loci in north China and to evaluate their usefulness in population study. Ninety-seven haplotypes were constructed, with 30 in Daur, 24 in Kazak, 28 in Uighur, 27 in Xibe and 16 in Kirgiz. Sixty-six (68.04%) of them were unique. The R(ST) showed that there was no significant difference in Daur and Xibe (R(ST) = 0.02231, P > 0.05), while among the Kazak, Uighur and Kirgiz, who reside in northwest China, there were significant differences. These results showed that these five Y-STR loci were polymorphic in the five populations. The results of AMOVA showed that majority of the differences were found within populations. By RST, the relationships of the five populations were accordance with the historical records: Xibe migrated to Xinjiang during the Qing dynasty, and Kazak, Uighur and Kirgiz have different ancestors.
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Affiliation(s)
- Zhaoyang Xu
- Laboratory of Medical Genetics, Harbin Medical University, Harbin 150081, People's Republic of China
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Park SW, Hwang CH, Cho EM, Park JH, Choi BO, Chung KW. Development of a Y-STR 12-plex PCR system and haplotype analysis in a Korean population. J Genet 2010; 88:353-8. [PMID: 20086305 DOI: 10.1007/s12041-009-0053-7] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Affiliation(s)
- Sun Wha Park
- Department of Biological Science, Kongju National University, 182 Gongju, Chungnam 314-701, Korea
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Hwa HL, Tseng LH, Ko TM, Chang YY, Yin HY, Su YN, Lee JCI. Seventeen Y-chromosomal short tandem repeat haplotypes in seven groups of population living in Taiwan. Int J Legal Med 2010; 124:295-300. [DOI: 10.1007/s00414-010-0425-9] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2009] [Accepted: 01/21/2010] [Indexed: 10/19/2022]
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48
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Bailliet G, Ramallo V, Muzzio M, García A, Santos MR, Alfaro EL, Dipierri JE, Salceda S, Carnese FR, Bravi CM, Bianchi NO, Demarchi DA. Brief communication: Restricted geographic distribution for Y-Q* paragroup in South America. AMERICAN JOURNAL OF PHYSICAL ANTHROPOLOGY 2010; 140:578-82. [PMID: 19591214 DOI: 10.1002/ajpa.21133] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
We analyzed 21 paragroup Q* Y chromosomes from South American aboriginal and urban populations. Our aims were to evaluate the phylogenetic status, geographic distribution, and genetic diversity in these groups of chromosomes and compare the degree of genetic variation in relation to Q1a3a haplotypes. All Q* chromosomes from our series and five samples from North American Q* presented the derivate state for M346, that is present upstream to M3, and determined Q1a3* paragroup. We found a restrictive geographic distribution and low frequency of Q1a3* in South America. We assumed that this low frequency could be reflecting extreme drift effects. However, several estimates of gene diversity do not support the existence of a severe bottleneck. The mean haplotype diversity expected was similar to that for South American Q1a3* and Q1a3a (0.478 and 0.501, respectively). The analysis of previous reports from other research groups and this study shows the highest frequencies of Q* for the West Corner and the Grand Chaco regions of South America. At present, there is no information on whether the phylogenetic status of Q* paragoup described in previous reports is similar to that of Q1a3* paragroup though our results support this possibility.
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Affiliation(s)
- Graciela Bailliet
- Laboratorio de Genética Molecular Poblacional, Instituto Multidisciplinario de Biología Celular (IMBICE), CCT- CONICET-La Plata 1900, Argentina.
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Muzzio M, Ramallo V, Motti JMB, Santos MR, López Camelo JS, Bailliet G. Software for Y-haplogroup predictions: a word of caution. Int J Legal Med 2010; 125:143-7. [DOI: 10.1007/s00414-009-0404-1] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2009] [Accepted: 12/10/2009] [Indexed: 10/20/2022]
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50
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Salazar-Flores J, Dondiego-Aldape R, Rubi-Castellanos R, Anaya-Palafox M, Nuño-Arana I, Canseco-Ávila L, Flores-Flores G, Morales-Vallejo M, Barojas-Pérez N, Muñoz-Valle J, Campos-Gutiérrez R, Rangel-Villalobos H. Population structure and paternal admixture landscape on present-day Mexican-Mestizos revealed by Y-STR haplotypes. Am J Hum Biol 2009; 22:401-9. [DOI: 10.1002/ajhb.21013] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022] Open
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