Analysis of mutation rates and haplotypes of 23 Y-chromosomal STRs in Korean father-son pairs

Y-chromosomal short tandem repeats (Y-STRs) have been widely used in forensic genetics, and accurate knowledge of mutation rates at Y-STR loci is essential in kinship analysis. The main aim of this study was to estimate Y-STR mutation rates in Korean males. To obtain locus-specific mutations and haplotypes at 23 Y-STRs, we analyzed samples from 620 Korean father-son pairs. In addition, we also analyzed 476 unrelated individuals using the PowerPlex® Y23 System, with the aim of augmenting the available data for the Korean population. The PowerPlex® Y23 system facilitates analysis of the 23 Y-STR loci (DYS576, DYS570, DYS458, DYS635, DYS389 II, DYS549, DYS385, DYS481, DYS439, DYS456, DYS389 I, DYS19, DYS393, DYS391, DYS533, DYS437, DYS390, Y GATA H4, DYS448, DYS438, DYS392, and DYS643). Locus-specific mutation rate estimates varied from 0.00 to 8.06 × 10^-3 per generation, with an average mutation rate of 2.17 × 10^-3 (95% CI, 1.5-3.1 × 10^-3). To obtain comprehensive genetic values for the Korean population, we combined data obtained in this study with previously reported values, thereby enabling us to estimate the locus-specific mutation rates regarding 22,711 allele transmissions. By combining these data, we obtained an overall average mutation rate of 2.91 × 10^-3 (95% CI, 2.3-3.7 × 10^-3). In addition, among the 476 unrelated Korean males, we detected 467 different haplotypes, with an overall haplotype diversity value of 0.9999. By extracting haplotypes of Y-STRs described in previous literature on 23 Y-STR reported in Korea, we obtained gene diversities for 1133 Korean individuals. We believe that the values and characteristics of the 23 Y-STRs analyzed in this study will contribute to establishing criteria for forensic genetic interpretation, including kinship analysis.

Technical note: multi-alleles at the DYS385ab locus with high frequency in a Han Chinese population from southwestern China

Y-chromosome short tandem repeat (Y-STR) markers have been widely used in forensic applications and usually show monoallelic or diallelic genotypic patterns at certain double-copied loci. In this study, we have found 13 samples among 703 males with multi-alleles at the DYS385ab locus, including one with five mutant alleles, nine with four, and three with three. The frequency of abnormal DYS385ab genotypes was 1.85% (13/703), which is very high in the Han Chinese population. The percentage of samples with diallelic patterns at DYS385ab was higher than that of monoallelic patterns (80.23% vs. 17.92%). Additionally, the percentage of samples with tetra-allelic patterns at DYS385ab was higher than that of tri-allelic patterns (1.28% vs. 0.43%), suggesting that there are possibly two copies with duplicated events happening frequently on the Y chromosome. Interestingly, the peak height of allele 13 was two to three-folds higher than that of other alleles. The allele 18 peak height was also two-fold higher than others, which could potentially be explained by a duplication event mechanism. We also found that tri-allelic genotypes for alleles 13, 17, and 20, tetra-allelic genotypes for alleles 13, 14, 19, and 20, and tetra-allelic genotypes for alleles 12, 13, 19 and 21 were more common than others. Furthermore, all 13 samples had multi-alleles containing allele 13, implying a founder effect in this particular Chinese-specific ethnic group. Taken together, this study provides new information for this population and will be useful for paternal lineage identification, kinship analysis, and family relationship reconstruction using Y-STR forensic DNA analysis methods.

Forensic features and genetic legacy of the Baloch population of Pakistan and the Hazara population across Durand line revealed by Y-chromosomal STRs

The Hazara population across Durand line has experienced extensive interaction with Central Asian and East Asian populations. Hazara individuals have typical Mongolian facial appearances and they called themselves descendants of Genghis Khan's army. The people who speak the Balochi language are called Baloch. Previously, a worldwide analysis of Y-chromosomal haplotype diversity for rapidly mutating (RM) Y-STRs and with PowerPlex Y23 System (Promega Corporation Madison, USA) kit was created with collaborative efforts, but Baloch and Hazara population from Pakistan and Hazara population from Afghanistan were missing. In the current study, Yfiler Plus PCR Amplification Kit loci were examined in 260 unrelated Hazara individuals from Afghanistan, 153 Hazara individuals, and 111 Balochi individuals from Baluchistan Pakistan. For the Hazara population from Afghanistan and Pakistan overall, 380 different haplotypes were observed on these 27 Y-STR loci, gene diversities ranged from 0.51288 (DYS389I) to 0.9257 (DYF387S1), and haplotype diversity was 0.9992. For the Baloch population, every individual was unique at 27 Y-STR loci; gene diversity ranged from 0.5718 (DYS460) to 0.9371(DYF387S1). Twelve haplotypes were shared between 178 individuals, while only two haplotypes among these twelve were shared between 87 individuals in Hazara populations. Rst and Fst pairwise genetic distance analyses, multidimensional scaling plot, neighbor-joining tree, linear discriminatory analysis, and median-joining network were performed, which shed light on the history of Hazara and Baloch populations. The results of our study showed that the Yfiler Plus PCR Amplification Kit marker set provided substantially stronger discriminatory power in the Baloch population of Pakistan and the Hazara population across the Durand line.

The Y-chromosomal haplotype and haplogroup distribution of modern Switzerland still reflects the alpine divide as a geographical barrier for human migration

A sample of 606 Swiss individuals has been characterized for 27 Y-STR and 34 Y-SNPs, defining major European haplogroups. For the first time, a subsample from the southernmost part of Switzerland, the Italian speaking canton Ticino, has been included. The data reveals significant intra-national differences in the distribution of haplogroups R1b-U106, R1b-U152, I1 and J2a north and south of the alpine divide, with R1b-U152 being the most frequent haplogroup among all Swiss subpopulations, reaching 26 % in average and 53 % in the Ticino sample. In addition, a high percentage of haplogroup E1b1b-M35 in Eastern Switzerland corresponds well with data reported from Western Austria. In general, we detected a low level of differentiation between the subgroups north of the alpine divide. The dataset also revealed a variety of microvariants. Some of them were previously known to be associated with particular haplogroups. However, we discovered one microvariant in DYS533 that seems to be closely associated with haplogroup I2-P215 (xM223). This association had not yet been reported to date. The concordance study with two STR-kits suggests that the DYS533 microvariant is due to an InDel in the flanking regions of the marker. One individual carried a large deletion, frequently detected in people of East Asian ancestry, encompassing the amelogenin locus. To our knowledge, this is the first time that such a deletion has been observed within European haplogroup R1b-U152. This is the first comprehensive Y chromosomal dataset for Switzerland, demonstrating significant population substructure due to an intra-national geographical barrier.

Analysis of 23 Y-STR loci in Chinese Jieyang Han population

Genetic polymorphisms of 23 Y-chromosomal short tandem repeats (Y-STR) were investigated by PowerPlex® Y23 System in 328 unrelated male participants from Jieyang, Guangdong Province of China. A total of 293 haplotypes were obtained, and the haplotype diversity (HD) and discrimination capacity (DC) were 0.9991 and 0.8933, respectively. By comparing Jieyang population with nine other populations, Jieyang Han showed close genetic relationships with southern China-related Han populations. In conclusion, our study increased the Y-chromosome haplotype reference database and could provide useful information for forensic investigation and population genetics.

Identification of extra alleles in DYS385a/b multi-allelic patterns

Y chromosome short tandem repeats (Y-STRs) are widely used in forensic DNA analysis. Y-STRs usually genotyped as a monoallelic pattern, or a diallelic pattern at some double-copy loci. Abnormal genotypes with three or four alleles have been reported at DYS385a/b, which is a double-copy locus. However, multi-allelic patterns with more than four alleles have not been reported at this locus. In this study, abnormal five-allelic patterns at DYS385a/b locus were observed in 2 out of 7760 unrelated males from Henan Province, detected by the HG19+14Y fluorescence detection kit; and abnormal six-allelic pattern was observed in 1 out of 4920 unrelated males from Guangdong Province, detected by the AGCU Data Y30 fluorescence kit. The genotypes of these abnormal samples were confirmed again by the Yfiler® Plus and PowerPlex® Y23 kits. In order to understand the genomic structure of the extra alleles at this locus, forward and reverse primers were designed to sequence the three samples. The results showed that the five-banded and six-banded pattern genotype did exist at DYS385a/b locus. These data enriched the knowledge about multi-allelic patterns at DYS385a/b locus, which allowed the use of DYS385a/b profile in forensic analysis, even with multi-allelic patterns.

Phylogenetic analysis and forensic evaluation among Rakhine, Marma, Hajong, and Manipuri tribes from four culturally defined regions of Bangladesh using 17 Y-chromosomal STRs

We have analyzed haplotypes for 17 Y chromosomal STR loci in Bangladeshi mainstream Bengali population and four largest ethnic groups inhabiting the North-Eastern and Southern region of Bangladesh using AmpFlSTR® Yfiler® PCR amplification systems. A total of 667 haplotypes from Bangladeshi Bangali, 157 from Rakhine, 144 from Marma, 112 from Hajong, and 136 from Manipuri individuals were observed with corresponding discrimination capacity (DC) of 0.973 for Bengali, 0.723 for Rakhine, 0.743 for Marma, 0.794 for Hajong, and 0.720 for Manipuri groups, respectively. In order to investigate genetic relationship and the pattern of paternal contributions of the studied population, a comparison of the studied data with the published data from Y-STR haplotype reference database (YHRD) was conducted based on analysis of molecular variance (AMOVA). Construction of neighbour-joining tree revealed that the Rakhine population lies closer to a clade consisting, Korean and Japanese population. The Hajong population showed close affinity with Riang (Tripura, India) tribe followed by Marma population. On the other hand, Manipuri group is closely related to Thai population followed by Tamil and mainstream Bengali population.

Investigation into the sequence structure of 23 Y chromosomal STR loci using massively parallel sequencing

Next-generation sequencing (NGS) can produce massively parallel sequencing (MPS) data for many targeted regions with a high depth of coverage, suggesting its successful application to the amplicons of forensic genetic markers. In the present study, we evaluated the practical utility of MPS in Y-chromosome short tandem repeat (Y-STR) analysis using a multiplex polymerase chain reaction (PCR) system. The multiplex PCR system simultaneously amplified 24 Y-chromosomal markers, including the PowerPlex^® Y23 loci (DYS19, DYS385ab, DYS389I, DYS389II, DYS390, DYS391, DYS392, DYS393, DYS437, DYS438, DYS439, DYS448, DYS456, DYS458, DYS481, DYS533, DYS549, DYS570, DYS576, DYS635, DYS643, and YGATAH4) and the M175 marker with the small-sized amplicons ranging from 85 to 253bp. The barcoded libraries for the amplicons of the 24 Y-chromosomal markers were produced using a simplified PCR-based library preparation method and successfully sequenced using MPS on a MiSeq^® System with samples from 250 unrelated Korean males. The genotyping concordance between MPS and the capillary electrophoresis (CE) method, as well as the sequence structure of the 23 Y-STRs, were investigated. Three samples exhibited discordance between the MPS and CE results at DYS385, DYS439, and DYS576. There were 12 Y-STR loci that showed sequence variations in the alleles by a fragment size determination, and the most varied alleles occurred in DYS389II with a different sequence structure in the repeat region. The largest increase in gene diversity between the CE and MPS results was in DYS437 at +34.41%. Single nucleotide polymorphisms (SNPs), insertions, and deletions (indels) were observed in the flanking regions of DYS481, DYS576, and DYS385, respectively. Stutter and noise ratios of the 23 Y-STRs using the developed MPS system were also investigated. Based on these results, the MPS analysis system used in this study could facilitate the investigation into the sequences of the 23 Y-STRs in forensic genetics laboratories.

Multiplex Y-STRs analysis using the ion torrent personal genome machine (PGM)

Massively parallel sequencing (MPS) technologies allow parallel sequencing analyses of many targeted regions of multiple samples at desirable depth of coverage. Routine use of MPS for forensic genetics is on the horizon. In this study, we explore the application of MPS technology in forensic Y-STR analysis. We designed a multiplex assay with 13 Y-STR loci (DYS19, DYS389 I, DYS389 II, DYS390, DYS391, DYS392, DYS437, DYS438, DYS439, DYS448, DYS456, DYS635, GATA-H4) for the purpose of MPS. The multiplex Y-STR assay was amplified in 42 unrelated male individuals and amplicons were sequenced simultaneously using the ion torrent personal genome machine (PGM) system. All loci were detected successfully, except for DYS389 II that exhibited a failure rate of 1.8% due to the relatively long amplicon sizes. We observed 7, 3, 2, 6 and 5 new alleles, respectively in DYS389 II, DYS390, DYS437, DYS448 and DYS635 due to the presence of sub-repeat composition differences, and a new allele in DYS438 because of nucleotide substitution. One allele of DYS390 was inconsistent with allele call from conventional capillary electrophoresis (CE) because of 4 bp deletions upstream of the core repeat unit. This study demonstrates that Y-STR typing by MPS can provide more genetic information, holding the promise for high discriminatory power.

Detection of the deletion on Yp11.2 in a Chinese population

Sex determination tests based on Amelogenin gene as part of commercial PCR multiplex reaction kits have been widely applied in forensic DNA analysis. Mutations that cause dropout of Y chromosomal Amelogenin gene (AMELY) could lead to errors in gender determination and mixture interpretation. To infer the mechanism and estimate the dropout frequency of AMELY and adjacent Y-STRs, we studied 3 samples with AMELY dropout combined with DYS458 and/or DYS456 and 37 samples with DYS456 dropout. DYS456, DYS458 and AMELY are located in the Yp11.2 region. The singleplex amplification system showed the null alleles could be caused by fragment deletion in Yp11.2 rather than a point mutation in the primer binding region. After detection of the 17 Y-STR and 77 STS markers, the deletion map showed different patterns. The DYS456-AMELY-DYS458 deletion pattern was the largest, breaking from 3.60 Mb to 8.29 Mb in the Y chromosome, and the overall frequency was 0.0077%. The AMELY-DYS458 deletion pattern was broke from 6.74 Mb to 9.17 Mb, with a 0.0155% frequency. The DYS456 negative pattern was concentrated in two main deletion regions, with a 0.8220% frequency. The frequency of all negative pattern was 0.0155%. All the AMELY-DYS458 and DYS456-AMELY-DYS458, and 92% of the DYS456 deletion patterns belonged to Hg O3, the rest belonged to Hg Q. The DYS456 deletion pattern was first reported in Chinese population. The current and previous findings suggest additional gender test for ambiguous sex determination may be required.

A Y-chromosomal haplotype with two short tandem repeat mutations

The male-specific Y-chromosomal short tandem repeat (STR) is a useful tool in forensic casework. The Y haplotype comprised of 16 loci, which is amplified simultaneously by AmpFlSTR(®) Yfiler(TM) PCR kit and provides strong exculpatory evidence in individual identification. We reported a rare Y-STR profile with a null allele at the DYS448 locus and an off-ladder allele at the DYS456 locus, when genotyping material from a vaginal swab in an alleged rape case. Sequence analysis revealed that the DYS448 null allele was a true type of null allele because of a total deletion of 11 upstream repeats and 9bp of the N(42) region, and there were numerous primer binding site mutations as well. The amplicon of the DYS456 locus was a small 92-bp fragment that was off-ladder, and sequencing analysis showed that there were only 10 repeats (AGAT)(10). This Y chromosome haplotype that was comprised of two variations provided helpful evidence for personal identification.