Y chromosome specific polymorphisms in forensic analysis

Haplotype Frequencies of Eight Y-Chromosome Short Tandem Repeats Loci in Four Amerindian Populations (State of Hidalgo, Mexico)

POPULATION

Amerindian populations: Huastecos (n=97), Otomies de la Sierra (n=41), Otomies del Valle (n=40), and Tepehuas (n=13).

Introduction of an single nucleodite polymorphism-based "Major Y-chromosome haplogroup typing kit" suitable for predicting the geographical origin of male lineages

The European Consortium "High-throughput analysis of single nucleotide polymorphisms for the forensic identification of persons--SNPforID", has performed a selection of candidate Y-chromosome single nucleotide polymorphisms (SNPs) for making inferences on the geographic origin of an unknown sample. From more than 200 SNPs compiled in the phylogenetic tree published by the Y-Chromosome Consortium, and looking at the population studies previously published, a package of 29 SNPs has been selected for the identification of major population haplogroups. A "Major Y-chromosome haplogroup typing kit" has been developed, which allows the multiplex amplification of all 29 SNPs in a single reaction. Allele genotyping was performed with a single base extension reaction (minisequencing) detected by CE. The validation of the multiplex was performed in a total of 1126 unrelated males distributed among 12 worldwide populations. The approach takes advantage of the specific geographic distribution of the Y-chromosome haplogroups and demonstrates the utility of binary polymorphisms to infer the origin of a male lineage.

Population study of Y-chromosome STR haplotypes in Japanese from the Tokushima

The Y-chromosome short tandem repeat (STR) systems including DYS19, DYS389I/II, DYS390, DYS391, DYS392, DYS393, DYS385 and YCAII were investigated in 121 Japanese males (Tokushima area). Analysis of the nine loci permitted classification of the samples into 107 haplotypes, and the haplotype diversity was estimated to be 0.989. DYS385 showed the highest gene diversity (GD) value (GD=0.946), while DYS391 showed the lowest GD value (GD=0.27). Furthermore, in DYS392, we found a new mutant allele that added a T within the repeat region (a mutation in the repetitive region), and the allele was designated 13.1 according to the sequence structure. We also detected allele 20 in DYS392 as a new allele. In DYS385, a new allele 26 that has not been previously reported was observed.

Sequence structure of 12 novel Y chromosome microsatellites and PCR amplification strategies

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.

Personal identification using Y-chromosomal short tandem repeats from bodily fluids mixed with semen

The male-specific, human Y-chromosomal short tandem repeats (Y-STRs) are very useful in forensic analysis. The authors report a sexual crime case in which the direct Y-STR haplotype analysis of several mixtures of various bodily fluids including semen was very effective for identifying the perpetrator of the crime. The typing of three Y-STRs (DYS19, DYS389II, and DYS390) could be detected from the mixed DNA of sperm and female cells in the victim's vagina, vaginal orifice, and anus. These haplotypes originated from one man and matched those of the suspect. Accordingly, the combination of direct extraction of DNA and Y-STR haplotype analysis is considered to be very useful for mixtures of bodily fluids, including semen or other male cells.

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

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.

Distribution of Y-chromosome STR defined haplotypes in Iberia

Seven Y-specific STR loci (DYS19, DYS389I, DY5389II, DYS390, DYS391, DYS392 and DYS393) were studied in five populations from the Iberian Peninsula: Andalusia, Valencia, Basque Country, Galicia and Northern Portugal. Haplotype and allele frequencies of these seven Y-chromosome STRs were estimated. Observed haplotype diversities are in a range between 0.96 (Basque Country) and 0.99 (Valencia and Andalusia). Significant population differentiation was registered between Basques and all the other Iberian populations and also between Valencia and Northern Portugal.