Identification and characterization of the highly polymorphic locus D14S739 in the Han Chinese population

A 16-plex Y-SNP typing system based on allele-specific PCR for the genotyping of Chinese Y-chromosomal haplogroups

Y-chromosomal SNP (Y-SNP), with its stable inheritance and low mutation, can provide Supplementary information in forensic investigation. While commonly used Y-chromosomal STR haplotypes show their limitations, typing of Y-SNP would become a powerful complement. In this study, a 16-plex Y-SNP typing system based on allele-specific PCR (AS-PCR) was developed to discriminate four dominant Y-chromosomal haplogroups (C-M130, D-CTS3946, N-M231, and O-M175) and 12 predominant sub-haplogroups of O-M175 (O1a-M119, O1a1a1a-CTS3265, O1b-M268, O1b1a2-Page59, O2-M122, O2a1-L127.1, O2a1b-F240, O2a1b1a1-CTS5820, O2a2-P201, O2a2b1a1-M177, O2a2b1a1a1a-Y17728, O2a2b1a2-F114). A series of experimental validation studies including sensitivity, species specificity, male-female mixture and inhibition were performed. The discrimination of the typing system was preliminarily proved with a haplogroup diversity of 0.9239. Altogether, the Y-SNP typing system based on AS-PCR should be capable of distinguishing China's dominant Y-chromosomal haplogroups in a rapid and reliable manner, thus can be employed as a useful complement in forensic casework.

Analysis of forensic genetic parameters of 22 autosomal STR markers (PowerPlex® Fusion System) in a population sample from Bosnia and Herzegovina

Background: Bosnia and Herzegovina is a multinational and multireligious country, located in the western part of the Balkan Peninsula. Migrations through history were a key factor in the genetic identity of the Bosnian-Herzegovinian population.Aim: To analyse genetic polymorphisms of 22 autosomal short tandem repeat (STR) loci in the population of Bosnia and Herzegovina and to compare STR allele frequencies for STR loci with the reference data for European populations.Subjects and methods: The study was conducted among 600 unrelated individuals from all regions of Bosnia and Herzegovina. Genotyping was performed using the PowerPlex^® Fusion amplification kit. Allele frequencies and statistical parameters were calculated, as well as the genetic distance among analysed populations through the construction of a neighbor-joining dendrogram.Results: STR loci included in the PowerPlex^® Fusion amplification kit showed high discriminatory power indicating their reliability for human identification and paternity testing. The neighbor-joining dendrogram based on the results of genetic distance analysis showed that the Bosnian and Herzegovinian population has the greatest genetic distance from Turkish and Hungarian populations and greatest similarity with Croatian, Slovenian, and Serbian populations.Conclusion: The results of this study strongly support the application of 22 autosomal genetic markers for paternity testing and personal identity testing and are in agreement with most previous human studies in the investigated human populations.

Characterization of the extra copy of TPOX locus with tri-allelic pattern

BACKGROUND

An STR locus with tri-allelic pattern is occasionally observed in routine forensic casework. The extra copy of TPOX locus with tri-allelic pattern in populations has been assumed to be inserted into an X chromosome, which took place forth before the Bantu expansion in Africa. Nonetheless, the exact location of the duplication and the form of rearrangement in the human genome has not been clarified yet.

RESULTS

In this study, we investigated the extra copy of type 2 tri-allelic pattern at TPOX in various populations. While allele 10 is the major third allele in Africa, allele 11 appears more frequent in America and overwhelming in Chinese and Korean populations, which might attribute to the population substructures. Results from the investigation of family cases showed that the transmission of the extra allele had a similar genetic pattern of autosomal genes. Furthermore, a whole-genome sequencing followed by bioinformatics analysis revealed that the intact form of chromosomal duplication and rearrangement occurred ~ 407 kb away from the authentic TPOX locus on chromosome 2 in two cases. The breakpoints of the insertion were further validated in most other tri-allelic subjects, which can imply the identical origin from the ancestral extra copy. Nevertheless, de novo chromosomal duplication and rearrangement at thyroid peroxidase gene occur in populations.

CONCLUSIONS

Instead of the extra allele 10 in African populations, the main third allele at TPOX with tri-allelic pattern is allele 11 in Chinese and Korean populations. The insertion of the extra copy into chromosome 2 occurs in most subjects with tri-allelic pattern at TPOX and demonstrates the transmission of the third allele from parents to offspring. The breakpoints of the ancestral extra copy are defined, which shows evidence of its inheritance from African populations. In addition, the simple validation method would help improve tri-allelic pattern calling, distinguish de novo chromosomal rearrangements, and also count the frequencies among different geographic regions. Therefore, the statistical interpretation of tri-allelic pattern at TPOX could be enhanced during forensic practice.