Genetic portrait and phylogenetic analysis of an Aksu Uyghur population based on the 19 X-STR system.

The X chromosome has a special mode of inheritance, and is thus a rich resource for population studies. In this study, the allele frequencies and forensic statistics of the 19 X chromosomal short tandem repeat loci were evaluated in 500 Uyghur individuals from Aksu Prefecture in northwest China. We further aimed to study whether the Uyghur populations located in various regions of Xinjiang share similar allele and haplotype frequency distributions, as they have experienced genetic exchanges. Population comparisons, PCA and MDS were performed for the Uyghurs and 27 populations and the results indicate that the Uyghur minority in Aksu has a relatively close phylogenetic relationship with East Asians, especially the Kazakh minority.

Genetic diversity and phylogenetic study of the Chinese Gelao ethnic minority via 23 Y-STR loci.

Haplotype diversity for 23 Y chromosomal short tandem repeat (Y-STR) loci included in the PowerPlex® Y23 System was analyzed in the Chinese Gelao minority group of 234 unrelated males living in Daozhen Gelao-Miao Autonomous County in Guizhou Province, southwest China. A total of 216 different haplotypes were detected, of which 199 haplotypes were unique. The overall haplotype diversity (HD) and discrimination capacity (DC) were 0.9996 and 0.9231, respectively. The gene diversity (GD) ranged from 0.4159 (DYS438) to 0.9650 (DYS385a/b). The haplotype frequencies varied from 0.0043 to 0.0128. The population data presented here showed high genetic polymorphism and extraordinary discriminatory power in the studied population. Population difference was observed between the Chinese Gelao ethnicity and 42 populations out of overall 59 neighboring populations in Asia region. Both multidimensional scaling (MDS) and the phylogenetic tree demonstrated that the genetic structure affinity and differentiation with Chinese Gelao ethnicity were identified in those populations geographically adjacent (Hunan Han) and distant (Chinese Tibetan), respectively. In conclusion, our study enriched the Chinese ethnic genetic information and could be used as a powerful tool in forensic genetics for male testing, paternal lineage analysis, and Gelao ethnic population evolutionary studies.

Forensic characteristics and phylogenetic analyses of the Chinese Yi population via 19 X-chromosomal STR loci.

The demographic characteristics and genetic polymorphism data of 56 Chinese nationalities or 31 administrative divisions in Chinese mainland have repeatedly been the genetic research hotspots. While most genetic studies focused on some particular Chinese populations based on autosomal or Y-chromosomal genetic markers, the forensic characteristics and phylogenetic analyses of the seventh largest Chinese population (Yi ethnicity) on the X-chromosomal genetic markers are scarce. Here, allele frequencies and forensic statistical parameters for 19 X-chromosomal short tandem repeat loci (DXS7424-DXS101, DXS6789-DXS6809, DXS7423-DXS10134, DXS10103-HPRTB-DXS10101, DXS10159-DXS10162-DXS10164, DXS10148-DXS10135-DXS8378, and DXS7132-DXS10079-DXS10074-DXS10075) of 331 Chinese Yi individuals were obtained. All 19 X-chromosomal short tandem repeat (STR) loci in females were consistent with the Hardy-Weinberg equilibrium test. A total of 214 alleles were identified with the corresponding allele frequencies spanned from 0.0019 to 0.6106. The combined PE, PDF, and PDM were 0.9999999214, 0.9999999999999999999993, and 0.9999999999998, respectively. The high combined MECKrüger, MECKishida, MECDesmarais, and MECDesmarais Duo were achieved as 0.9999999617638, 0.9999999999971, 0.9999999999971, and 0.9999999931538, respectively. The findings suggested that the panel of 19 X-STR loci is highly polymorphic and informative in the Yi ethnic population and can be considered to be a powerful tool in forensic complex kinship identification. Population differentiation analyses among 12 populations indicated that significant differences in genetic structure were observed in between the Yi ethnicity and the Chinese Uyghur as well as Kazakh, and genetic homogeneity existed in similar ethno-origin or geographic origin populations.

Population genetics of 23 Y-STR loci in the Mongolian minority population in Inner Mongolia of China.

In this study, 23 Y chromosomal STRs (DYS19, DYS389I, DYS389II, DYS390, DYS391, DYS392, DYS393, DYS385a, DYS385b, DYS438, DYS439, DYS437, DYS448, DYS456, DYS458, DYS635, YGATAH4, DYS576, DYS481, DYS549, DYS533, DYS570, and DYS643) were investigated in 258 unrelated individuals of Mongolian descent living in the Inner Mongolia Autonomous Region. A total of 233 different haplotypes were found, and 209 of them were unique. Haplotype diversity was 0.9992 and gene diversity ranged from 0.4840 (DYS391) to 0.9679 (DYS385ab). Both R st pairwise analysis and multidimensional scaling plot showed that the genetic structure of the Mongolian population was significantly different from some Chinese ethnic groups and neighboring populations. It is notable that there were null features existing at DYS448 as observed by the PowerPlex® Y23 System, which could be also obtained by sequencing in the Tibetan population.

Evaluation of 12 Multi-InDel markers for forensic ancestry prediction in Asian populations.

Various types of genetic markers have been applied to forensic ancestry inference. Biallelic markers, such as SNPs and InDels, have proven to be optimal choices except for the low information content provided by a single locus. Multi-InDel marker is defined as a specific DNA fragment with several InDel markers located tightly in the physical position. Previous research indicates that multi-InDel markers perform well in population analysis and ancestry inference because of higher degree of polymorphism and remarkable population differences. In this study, a panel consisting of 12 multi-InDel markers was employed to evaluate the general performance in forensic practice and the discrimination power for population analysis. Sample types encountered in routine forensic practice were genotyped to validate the feasibility of regular use. A population study was performed on a total of five Asian populations to verify the discrimination power. Moreover, a double-blind test for ancestry prediction was conducted to assess the predictive capability. In conclusion, these results revealed the significance of multi-InDel markers for population structure stratification. The present panel showed the potential as a valid complementary tool in forensic applications.

Validation of the Microreader™ 23sp ID system: A new STR 23-plex system for forensic application.

Microreader™ 23sp ID system is a new 23-plex STR genotyping system that amplified 21 non-CODIS STR loci (D6S477, D18S535, D19S253, D15S659, D11S2368, D20S470, D1S1656, D22-GATA198B05, D7S3048, D8S1132, D4S2366, D21S1270, D13S325, D9S925, D3S3045, D14S608, D10S1435, D12S391, D2S1338, D17S1290 and D5S2500), one CODIS STR locus (D16S539) and the amelogenin locus in one reaction. Microreader™ 23sp ID system was validated according to the guidelines of "Validation Guidelines for DNA Analysis Methods (2012)" described by the Scientific Working Group on DNA Analysis Methods (SWGDAM), including PCR-based studies, sensitivity study, precision and accuracy evaluation, stutter percentage and peak height ratio, inhibitors, species specificity and DNA mixture studies. Our results suggested that Microreader™ 23sp ID system is a useful tool for identification and parentage testing.

Next Generation Sequencing Plus (NGS+) with Y-chromosomal Markers for Forensic Pedigree Searches.

There is high demand for forensic pedigree searches with Y-chromosome short tandem repeat (Y-STR) profiling in large-scale crime investigations. However, when two Y-STR haplotypes have a few mismatched loci, it is difficult to determine if they are from the same male lineage because of the high mutation rate of Y-STRs. Here we design a new strategy to handle cases in which none of pedigree samples shares identical Y-STR haplotype. We combine next generation sequencing (NGS), capillary electrophoresis and pyrosequencing under the term 'NGS+' for typing Y-STRs and Y-chromosomal single nucleotide polymorphisms (Y-SNPs). The high-resolution Y-SNP haplogroup and Y-STR haplotype can be obtained with NGS+. We further developed a new data-driven decision rule, FSindex, for estimating the likelihood for each retrieved pedigree. Our approach enables positive identification of pedigree from mismatched Y-STR haplotypes. It is envisaged that NGS+ will revolutionize forensic pedigree searches, especially when the person of interest was not recorded in forensic DNA database.

Phylogenetic analysis and forensic characteristics of 12 populations using 23 Y-STR loci.

Genetic analysis of Y-STRs has the potential to be used to explore the complexity in population substructures and to perform forensic ancestry inference. In this study, 334 individuals from 12 populations were typed using the PowerPlex(®) Y23 System (Promega, USA) to investigate their relationship. Population comparisons with other East Asian populations collated from YHRD (Y-STR Haplotype Reference Database) were also performed. Variant alleles, including seven intermediate alleles in 15 samples were observed, while the novel allele 11.3 at the DYS549 locus was confirmed by sequencing. Our results showed that the fraction of unique haplotypes differed among the 12 populations studied here. A close relationship was found between Chinese and other East Asian populations. The present study contributed to the enrichment of the forensic Y-chromosome databases with a high resolution 23 Y-STR marker set, which is informative in forensic casework, such as familial searching and estimating the geographical origin of the offender.