Characterization and haplotype analysis of 10 novel Y-STR loci in Chinese Han population

Harmonizing the forensic nomenclature for STR loci D6S474 and DYS612

The autosomal STR D6S474 and the Y-chromosomal STR DYS612 have been reported in multiple ways in the forensic literature, with differences in both the bracketed repeat structures and counting of numerical length-based capillary electrophoresis (CE) alleles. These issues often come to light when STR loci are introduced in commercial assays and results compared with historical publications of allele frequency data, or multiple assays are characterized with reference materials. We review the forensic literature and other relevant information, and provide suggestions for the future treatment of each STR.

Technical note: developmental validation of a novel 41-plex Y-STR system for the direct amplification of reference samples

The SureID^® PathFinder Plus is a new 6-dye, 41-plex Y-STR system that includes the 17 loci from the Yfiler^® kit (DYS19, DYS385a/b, DYS389I/II, DYS390, DYS391, DYS392, DYS393, DYS437, DYS438, DYS439, DYS448, DYS456, DYS458, DYS635, and Y-GATA-H4) plus 14 rapidly mutating Y-STR loci (DYS449, DYS481, DYS518, DYS527a/b, DYS533, DYS549, DYS570, DYS576, DYS627, DYF387S1a/b, and DYF404S1), and 10 low-medium mutation loci (DYS388, DYS444, DYS447, DYS460, DYS522, DYS557, DYS593, DYS596, DYS643, and DYS645). The inclusion of the 14 rapidly mutating Y-STR loci improves the discrimination of related individuals. Conversely, the 10 low-medium mutation loci are suitable not only for familial searching but also for providing a higher refinement in the construction of Y chromosome phylogenetic relationships among lineages. The 41-plex Y-STR system is designed for direct amplification of reference samples, such as blood samples on an FTA^® Card, gauze, tissue, or cotton substrates as well as hair root or buccal samples on swabs. We performed developmental validation work including accuracy, stability, stutter precision, species specificity, sensitivity, PCR inhibitors, reproducibility, parallel testing of the system, and suitability for use on DNA mixtures. In addition, mutations of the loci were analyzed by 754 DNA-confirmed father-son pairs. The results demonstrate that this kit, developed in-house, is time-efficient, accurate, reliable, and highly informative for forensic database, familial searching, and distinguishing related males.

Structure and polymorphism of 16 novel Y-STRs in Chinese Han population

Y-chromosome short tandem repeats (Y-STRs) are useful tools for identifying paternity origin and male-female mixed samples because of their male-specificity, haploid inheritance and relatively simplicity. We focused on novel Y-STRs deposited in the human Genome database from DYS708 to DYS726. We typed 16 male-specific Y-STRs from males of a Chinese Han population residing in Shanxi Province (north China), including DYS708-719, DYS721-723, and DYS726, but failed in typing DYS720, DYS724 and DYS725. The 16 Y-STRs, with mean gene diversity (GD) of 0.79, included three trinucleotide Y-STRs (711, 718, 719), nine tetranucleotide STRs (708, 709, 710, 712, 713, 715, 722, 723, 726) and four pentanucleotide repeat STRs (714, 716, 717, 721). DYS712, consisting of eight alleles, was the most informative STR in our population, with a GD of 0.843. The STRs were classified as simple STRs and complex STRs, according to their structures based on sequencing. Genetic indexes, including allele frequencies, haplotype distribution and male-specificity were determined. The Y-STRs, especially those male-specific, tetra- and penta-nucleotide, with only one copy on Y-chromosome, and relative simple structures, such as DYS709, DYS714, DYS715, DYS716, DYS718, DYS719, and DYS726, were suggested for the future forensic DNA analysis, while DYS724 and DYS725 were not recommended for their multi-copy distribution. The population data provided putative Y-STRs for future genetic and forensic applications.

Haplotype analysis of the polymorphic 17 YSTR markers in Kerala nontribal populations

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.

Y-short tandem repeat haplotype and paternal lineage of the Ezhava population of Kerala, south India

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.

Characterization of the highly discriminatory loci DYS449, DYS481, DYS518, DYS612, DYS626, DYS644 and DYS710

During the study of genetic diversity at non-core Y-STRs in South African population groups, we identified loci with high discrimination capacity. In this study we present a detailed account of the allele diversity, allele sequence data, gene diversity, allele frequency spectrum and informativeness for assignment in the European English, Asian Indian and Xhosa population groups at loci DYS449, DYS481, DYS518, DYS612, DYS626, DYS644 and DYS710. The suitability of these loci for forensic, genealogical and evolutionary studies is discussed, and nomenclature for loci DYS518, DYS612, DYS626 and DYS644 is suggested.

Haplotypes of 20 Y-chromosomal STRs in a population sample from southeast China (Chaoshan area)

In this study, 20 Y-specific short tandem repeat (STR) loci (DYS434, Y-GATA-A10, Y-GATA-H4, DYS438, DYS439, DYS443, DYS444, DYS446, DYS447, DYS448, DYS456, DYS458, DYS460, DYS520, DYS531, DYS557, DYS622, DYS630, DYS635(Y-GATA-C4), and DYS709) were analyzed in 158 unrelated healthy men from southeast China by three fluorescence-labeled multiplex polymerase chain reaction systems. The Y-STR multiplexes developed have followed the published nomenclature and International Society for Forensic Genetics (ISFG) guidelines for STR analysis. Gene diversity ranged from 0.2506 at DYS434 to 0.8034 at DYS447. A total of 157 different haplotypes were observed, and among these, 156 were unique, while 1 was found two times. The haplotype diversity value calculated from all 20 loci combined was 0.9997, which is informative. Furthermore, 80 father-son pairs, previously confirmed by autosomal STR analysis, were typed using the same 20 Y-STR loci, and four mutation events were identified at the Y-GATA-H4, DYS439, DYS456, and DYS458 loci, giving an average mutation rate of 0.25% per locus per generation (95% confidence interval 0.09-0.54). These results including the haplotype data at 20 Y-STR loci would enrich Chinese genetic informational resources and provide useful information in forensic practice.

Testing and evaluation of 43 "noncore" Y chromosome markers for forensic casework applications

A developmental validation study was performed on three Y-STR multiplex systems, Multiplex III (MPIII), Multiplex IV (MPIV), and Multiplex V (MPV), to ascertain their potential applicability to forensic casework. MPIII contains eight Y-STRs, including DYS426, DYS435, DYS436, DYS441, DYS442, DYS446, DYS462, and Y-GATA-A10, and one InDel, YAP (DYS287). MPIV contains 21 Y-STR loci, including DYS443, DYS444, DYS445, DYS447, DYS448, DYS449, DYS452, DYS453, DYS454, DYS455, DYS456, DYS458, DYS463, DYS464, DYS468, DYS484, DYS522, DYS527, DYS531 DYS557, and DYS588. MPV contains 13 Y-STR loci, including DYS459, DYS476, DYS488, DYS513, DYS549, DYS561, DYS570, DYS575, DYS576, DYS590, DYS594, DYS598, and DYS607. Full genetic profiles were consistently obtained for all three multiplexes with 25-50 pg of male DNA. No significant amplification was observed with 1 mug of female DNA. Each multiplex permitted the determination of the number of male donors in male:male DNA admixtures. Species specificity studies demonstrated some cross-reactivity with some primate samples. Environmentally compromised blood samples produced full or partial profiles after exposure to various conditions for up to 1 year. Full profiles were recovered from simulated casework specimens including cigarette butts and postcoital cervicovaginal swabs. Population data were collected to determine individual loci gene diversity and multiplex discriminatory capacity.

DNA Commission of the International Society of Forensic Genetics (ISFG): an update of the recommendations on the use of Y-STRs in forensic analysis

The DNA Commission of the International Society of Forensic Genetics (ISFG) regularly publishes guidelines and recommendations concerning the application of DNA polymorphisms to the problems of human identification. A previous recommendation published in 2001 has already addressed Y-chromosome polymorphisms, with particular emphasis on short tandem repeats (STRs). Since then, the use of Y-STRs has become very popular, and a numerous new loci have been introduced. The current recommendations address important aspects to clarify problems regarding the nomenclature, the definition of loci and alleles, population genetics and reporting methods.

Allele frequencies for 27 Y-STR loci with U.S. Caucasian, African American, and Hispanic samples

A total of 263 U.S. Caucasians, 260 African Americans and 140 U.S. Hispanics or a subset of 31 Caucasians, 32 African Americans, and 32 Hispanics were typed for 27 Y-chromosome short tandem repeat (Y-STR) markers: DYS444, DYS446, DYS449, DYS463, DYS485, DYS490, DYS495, DYS504, DYS505, DYS508, DYS520, DYS522, DYS525, DYS532, DYS533, DYS534, DYS540, DYS556, DYS557, DYS570, DYS575, DYS576, DYS594, DYS632, DYS635, DYS641, and DYS643. Allele frequencies for each locus are reported along with nomenclature based on sequence analysis.

DNA Commission of the International Society of Forensic Genetics (ISFG): an update of the recommendations on the use of Y-STRs in forensic analysis

The DNA Commission of the International Society of Forensic Genetics (ISFG) regularly publishes guidelines and recommendations concerning the application of DNA polymorphisms to the problems of human identification. A previous recommendation published in 2001 has already addressed Y-chromosome polymorphisms, with particular emphasis on short tandem repeats (STRs). Since then, the use of Y-STRs has become very popular, and numerous new loci have been introduced. The current recommendations address important aspects to clarify problems regarding the nomenclature, the definition of loci and alleles, population genetics and reporting methods

Identification, characterization and forensic application of novel Y-STRs

Y-chromosomal polymorphic STRs are a powerful tool for forensic and evolutionary studies. Within the last decade, a series of Y-STR systems have been developed and demonstrated to be suitable for a variety of forensic applications including sexual assault cases and paternity testing. This review describes our recent studies on novel male-specific Y-STRs, involving identification, development of a multiplex-PCR system, population study and forensic application.