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de la Fuente C, Galimany J, Kemp BM, Judd K, Reyes O, Moraga M. Ancient marine hunter-gatherers from Patagonia and Tierra Del Fuego: Diversity and differentiation using uniparentally inherited genetic markers. AMERICAN JOURNAL OF PHYSICAL ANTHROPOLOGY 2015. [DOI: 10.1002/ajpa.22815] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Affiliation(s)
- Constanza de la Fuente
- Human Genetic Program; ICBM; Faculty of Medicine; University of Chile; Santiago 8380453 Chile
| | - Jacqueline Galimany
- Human Genetic Program; ICBM; Faculty of Medicine; University of Chile; Santiago 8380453 Chile
| | - Brian M. Kemp
- Human Genetic Program; ICBM; Faculty of Medicine; University of Chile; Santiago 8380453 Chile
| | - Kathleen Judd
- Human Genetic Program; ICBM; Faculty of Medicine; University of Chile; Santiago 8380453 Chile
| | - Omar Reyes
- Human Genetic Program; ICBM; Faculty of Medicine; University of Chile; Santiago 8380453 Chile
| | - Mauricio Moraga
- Human Genetic Program; ICBM; Faculty of Medicine; University of Chile; Santiago 8380453 Chile
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A comparative analysis of two different sets of Y-chromosome short tandem repeats (Y-STRs) on a common population panel. Forensic Sci Int Genet 2009; 4:11-20. [PMID: 19948329 DOI: 10.1016/j.fsigen.2009.03.004] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2008] [Revised: 03/15/2009] [Accepted: 03/29/2009] [Indexed: 11/23/2022]
Abstract
A comparative analysis of two Y-STR loci sets was conducted on a population sample of 224 individuals, 114 Caucasians and 110 African Americans. One set of loci, designated the OSU 10-locus set, comprises variable, single copy, male-specific loci that are dispersed across the Y-chromosome. Parallel evaluations were performed using the 10 Y-chromosome loci most frequently used for forensic analysis, the loci chosen as the SWGDAM Y-STR loci. The OSU 10-locus set had a greater average number of alleles per locus and higher average gene diversity than the SWGDAM loci. The OSU 10-locus set found 220 unique haplotypes in 224 individuals. In approximately 6000 pairwise haplotype comparisons for each population with each set of loci, the OSU 10-locus set also yielded a greater average number of allelic differences per pair than the SWGDAM loci. Finally, the overall linkage disequilibrium levels were lower for the OSU 10-locus set in the Caucasian population. In general, the OSU 10-locus set revealed a higher power of discrimination than the SWGDAM set.
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Lopes AM, Calafell F, Amorim A. Microsatellite variation and evolutionary history of PCDHX/Y gene pair within the Xq21.3/Yp11.2 hominid-specific homology block. Mol Biol Evol 2004; 21:2092-101. [PMID: 15297598 DOI: 10.1093/molbev/msh218] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
To better understand the evolutionary dynamics of repetitive sequences in human sex chromosomes, we have analyzed seven new X/Y homologous microsatellites located within PCDHX/Y, one of the two recently described gene pairs in the Xq21.3/Yp11.2 hominid-specific homology block, in samples from Portugal and Mozambique. Sharp differences were observed on X/Y allele distributions, concerning both the presence of private alleles and a different modal repeat length for X-linked and Y-linked markers, and this difference was statistically significant. Higher diversity was found in X-linked microsatellites than in their Y chromosome counterparts; when comparing populations, Mozambicans showed more allele diversity for the X chromosome, but the contrary was true for the Y chromosome microsatellites. Evolutionary patterns, relying on intragenic PCDHX/Y SNPs, also revealed distinct scenarios for X and Y chromosomes. Greater microsatellite diversity was displayed by African X chromosomes within the most common haplotypes shared by both populations, whereas higher microsatellite diversity was found in Portugal for the ancestral Y chromosome haplotype. The most frequent PCDHY haplotype in Portuguese was the derived one, and it was not found in Mozambicans. TMRCA estimated by the rho parameter resulted in 13,700 years (7,500-20,000 years), which is consistent with a recent, post-Out-of-Africa origin for this haplotype. In conclusion, the newly described microsatellite loci generally displayed greater X-linked to Y-linked diversity and this pattern was also detected with slower evolving markers, with a remarkable differentiation between populations observed for Y chromosome haplotypes and, thus, greater divergence among Y chromosomes in human populations.
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Affiliation(s)
- Alexandra M Lopes
- IPATIMUP, Instituto de Patologia e Imunologia Molecular da Universidade do Porto, Portugal.
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Butler JM, Schoske R, Vallone PM, Kline MC, Redd AJ, Hammer MF. A novel multiplex for simultaneous amplification of 20 Y chromosome STR markers. Forensic Sci Int 2002; 129:10-24. [PMID: 12230993 DOI: 10.1016/s0379-0738(02)00195-0] [Citation(s) in RCA: 114] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
Abstract
A multiplex polymerase chain reaction (PCR) assay capable of simultaneously amplifying 20 Y chromosome short tandem repeat (STR) markers has been developed to aid human identity testing and male population studies. These markers include all of the Y STRs that make up the "extended haplotype" used in Europe (DYS19, DYS385, DYS389I/II, DYS390, DYS391, DYS392, DYS393, and YCAII) plus additional polymorphic Y STRs (DYS437, DYS438, DYS439, DYS447, DYS448, DYS388, DYS426, GATA A7.1, and GATA H4). Primers for the markers DYS385, DYS389, and YCAII target duplicated regions of the Y chromosome and thus can provide two polymorphic peaks for each respective primer set. This Y STR 20plex, which utilizes 34 different PCR primers, is the first to include a simultaneous amplification of all the markers within the European "minimal" and "extended" haplotypes. Relative primer positions are compared between the newly developed primers described here and previously published ones. Efforts were made to avoid X chromosome homology in the primer design as well as close packing of PCR product size ranges in order to keep all alleles less than 350 bp through careful examination of known allele ranges. Haplotype comparisons between the 20plex and a commercially available kit found excellent agreement across the 76 samples in the Y chromosome consortium panel.
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Affiliation(s)
- John M Butler
- Biotechnology Division, National Institute of Standards and Technology, 100 Bureau Drive, Mail Stop 8311, Gaithersburg, MD 20899, USA.
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Gill P, Brenner C, Brinkmann B, Budowle B, Carracedo A, Jobling MA, de Knijff P, Kayser M, Krawczak M, Mayr WR, Morling N, Olaisen B, Pascali V, Prinz M, Roewer L, Schneider PM, Sajantila A, Tyler-Smith C. DNA Commission of the International Society of Forensic Genetics: recommendations on forensic analysis using Y-chromosome STRs. Forensic Sci Int 2001; 124:5-10. [PMID: 11741752 DOI: 10.1016/s0379-0738(01)00498-4] [Citation(s) in RCA: 122] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
During the past few years, the DNA Commission of the International Society of Forensic Genetics has published a series of documents providing guidelines and recommendations concerning the application of DNA polymorphisms to the problems of human identification. This latest report addresses a relatively new area - namely, Y-chromosome polymorphisms, with particular emphasis on short tandem repeats (STRs). This report addresses nomenclature, use of allelic ladders, population genetics and reporting methods.
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Affiliation(s)
- P Gill
- Forensic Science Service, Trident Court, 2960 Solihull Parkway, Birmingham, UK
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DNA Commission of the International Society of Forensic Genetics: recommendations on forensic analysis using Y-chromosome short tandem repeats. Leg Med (Tokyo) 2001. [DOI: 10.1016/s1344-6223(01)00029-3] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
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González-Neira A, Elmoznino M, Lareu MV, Sánchez-Diz P, Gusmão L, Prinz M, Carracedo A. Sequence structure of 12 novel Y chromosome microsatellites and PCR amplification strategies. Forensic Sci Int 2001; 122:19-26. [PMID: 11587861 DOI: 10.1016/s0379-0738(01)00405-4] [Citation(s) in RCA: 21] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Abstract
In this work, we present sequencing data for 12 recently reported Y STR loci (DYS434, DYS435, DYS436, DYS437, DYS438, DYS439, GATA A10, GATA 7.1, GATA 7.2, GATA C4, GATA H4, GATA A4), as well as the PCR multiplex strategies we implemented for their detection. Sequenced allelic ladders were constructed and a nomenclature for these new systems is proposed based on the sequence structure and following ISFG recommendations.GATA A4 and DYS439 are likely the same STR. They have the same STR structure and the alleles are always the same in the same individuals.Sequence polymorphisms were observed in the GATA C4 and DYS437 STRs. The variation in DYS437 was associated with a specific population group and is very interesting not only for forensic genetics but also for anthropological studies.
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Affiliation(s)
- A González-Neira
- Institute of Legal Medicine, University of Santiago de Compostela, E-15705 Santiago de Compostela, Galicia, Spain
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Carracedo A, Beckmann A, Bengs A, Brinkmann B, Caglia A, Capelli C, Gill P, Gusmão L, Hagelberg C, Hohoff C, Hoste B, Kihlgren A, Kloosterman A, Myhre Dupuy B, Morling N, O'Donnell G, Parson W, Phillips C, Pouwels M, Scheithauer R, Schmitter H, Schneider PM, Schumm J, Skitsa I, Stradmann-Bellinghausen B, Stuart M, Syndercombe Court D, Vide C. Results of a collaborative study of the EDNAP group regarding the reproducibility and robustness of the Y-chromosome STRs DYS19, DYS389 I and II, DYS390 and DYS393 in a PCR pentaplex format. Forensic Sci Int 2001; 119:28-41. [PMID: 11348791 DOI: 10.1016/s0379-0738(00)00395-9] [Citation(s) in RCA: 21] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
Abstract
A collaborative exercise was carried out by the European DNA Profiling Group (EDNAP) in the frame work of the STADNAP program, i.e. standardization of DNA profiling in Europe, in order to evaluate the performance of a Y-chromosome STR pentaplex, which includes the loci DYS19, DYS389 I and II, DYS390 and DYS393 and to determine whether uniformity of results could be achieved among different European laboratories. Laboratories were asked to analyze the five Y-STRs using singleplex and multiplex conditions in three bloodstains and one mixed stain (95% female and 5% male). All the laboratories reported the same results even for the mixed stain included in the exercise. This demonstrates the reproducibility and robustness of Y-chromosome STR typing even with multiplex formats and proves the usefulness of Y-STR systems for analyzing mixed stains with a male component.A total of 930 male samples from 10 different populations from Europe were also analysed for all the loci included in the pentaplex. Eight of these ten populations also included haplotype data. As for single gene analysis, haplotype diversity was higher in Germany and Italy and lower in Western European countries and Finland. Pairwise haplotype analysis shows the Finnish departure from the rest of the populations and a relatively homogeneity in the other European populations with F(ST) estimates lower than 0.05.UPGMA analysis shows an association of Western European population (Ireland, UK, Portugal and Galicia) on the one hand and central European populations on the other.
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Affiliation(s)
- A Carracedo
- Institute of Legal Medicine, Faculty of Medicine 15705 Santiago de Compostela, Galicia, Spain.
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Affiliation(s)
- T A Brettell
- Forensic Science Bureau, New Jersey State Police, West Trenton 08628, USA
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Gusmão L, González-Neira A, Sánchez-Diz P, Lareu MV, Amorim A, Carracedo A. Alternative primers for DYS391 typing: advantages of their application to forensic genetics. Forensic Sci Int 2000; 112:49-57. [PMID: 10882830 DOI: 10.1016/s0379-0738(00)00171-7] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
Abstract
The amplification of the STR DYS391, using the primers described in the Genome Data Base (GDB: G00-365-251), shows not only an additional band to the Y-specific one in males with a size range of 26 bp less than those of DYS391 locus alleles, but also a polymorphic pattern in females in the same size range as the additional band observed in males. The DYS391 pattern in families reflects a Y-specific linked locus and also a polymorphic X locus with an X-linked pattern of inheritance. A first screening in the X homologous locus allowed the identification of five different alleles. Allele frequencies were explored in different population groups for both the Y locus and the homologous locus in the X chromosome showing a similar allele distribution pattern in the X and Y homologous loci. An alternative reverse primer was designed to amplify the Y-chromosome specific STR in order to improve the specificity and applicability of this system to forensic genetics. Comparative results of the amplification with the new and the previously described primers proved that with this new primer there is a substantial increase in the specificity of the amplification. Moreover, a smaller fragment is amplified with a size out of the range of the alleles of the other Y-STRs usually used in forensic applications, therefore simplifying its inclusion in multiplex systems.
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Affiliation(s)
- L Gusmão
- Institute of Legal Medicine, University of Santiago de Compostela, E-15705, Galicia, Santiago de Compostela, Spain
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