Development of a 16 X-STR multiplex PCR system for kinship analysis and its applicability for the Sinhalese population in Sri Lanka

Recent advances in forensic biology and forensic DNA typing: INTERPOL review 2019-2022

This review paper covers the forensic-relevant literature in biological sciences from 2019 to 2022 as a part of the 20th INTERPOL International Forensic Science Managers Symposium. Topics reviewed include rapid DNA testing, using law enforcement DNA databases plus investigative genetic genealogy DNA databases along with privacy/ethical issues, forensic biology and body fluid identification, DNA extraction and typing methods, mixture interpretation involving probabilistic genotyping software (PGS), DNA transfer and activity-level evaluations, next-generation sequencing (NGS), DNA phenotyping, lineage markers (Y-chromosome, mitochondrial DNA, X-chromosome), new markers and approaches (microhaplotypes, proteomics, and microbial DNA), kinship analysis and human identification with disaster victim identification (DVI), and non-human DNA testing including wildlife forensics. Available books and review articles are summarized as well as 70 guidance documents to assist in quality control that were published in the past three years by various groups within the United States and around the world.

Linkage, recombination and mutation rate analyses of 16 X-chromosomal STR loci in Sri Lankan Sinhalese pedigrees

This study investigated genetic linkage, recombination fractions and mutation rates of 16 X chromosomal short tandem repeat (X-STR) markers using a recently developed multiplex PCR assay for Sinhalese population of Sri Lanka, by analyzing 81 three-generation families including 81 grandfathers with daughters and 162 grandsons. In addition, 31 two generation families involving mother father daughter trios were included for mutation analysis. The analysis of recombination fractions between marker pairs identified two linkage blocks (maximum LOD scores > 3.0) each spanning a physical distance of 44.35 Mb and 6.04 Mb respectively. Though recombination events are usually rare among closely linked markers, crossovers were observed for markers located < 1.0 Mb apart. The recombination fractions observed are not fully concordant with those reported earlier, including the second-generation Rutgers combined linkage-physical map. This suggests that linkage is not uniform among different populations. However, the overall and marker-specific mutation rates of the present study did not differ from previous reports, though it needs confirmation with a much larger sample set. The findings presented here will provide the baseline information required for biostatistical calculations conducted using X-STR markers, in complex kinship analysis of Sinhalese population.

X-chromosomal STRs for genetic composition analysis of Guizhou Dong group and its phylogenetic relationships with other reference populations

BACKGROUND

X-chromosomes show a specific genetic mode, which makes genetic markers on the X chromosome play crucial roles in forensic research and human evolution. Dong group, one of 55 minority groups in China, live in Guizhou, Guangxi and Hunan provinces. Even though some genetic data of Y chromosomal short tandem repeats (STRs) and autosomal insertion/deletion polymorphism (InDels) in Dong groups have been reported, there is little research about X-STRs in the Dong group.

AIM

Purposes of this study are to investigate allelic distributions and forensic statistical parameters of 19 X-STRs in the Guizhou Dong group, and explore the genetic composition of the Guizhou Dong group and its phylogenetic relationships with other reference populations.

SUBJECTS AND METHODS

507 Dongs (272 males and 235 females) living in Guizhou province were typed using the AGCU X19 STR kit. Allelic frequencies and forensic parameters of 19 X-STRs in the Guizhou Dong group were calculated. Population genetic analyses of Guizhou Dong and other 17 reference populations were conducted using D_A genetic distances, phylogenetic tree, principal component analysis and multidimensional scaling.

RESULTS

A total of 230 alleles of 19 X-STRs were identified in all Dongs. The frequencies of 19 loci ranged from 0.0013 to 0.6838. Cumulative power of discrimination in males (PDM), Cumulative power of discrimination in females (PDF), four different kinds of mean exclusion chance (MEC_Kruger, MEC_Kishida, MEC_Desmarais and MEC_Desmarais_du) values of 19 X-STRs in all individuals were 0.999999999999761, 0.9999999999999999999993951, 0.999999964841617, 0.999999999997261, 0.999999999997297 and 0.999999993623172, respectively. Besides, genetic polymorphisms of seven linkage clusters ranged from 0.9381 to 0.9963. In addition, these seven groups showed high polymorphism information content (PIC), PDM, PDF, MEC_Kruger, MEC_Kishida, MEC_Desmarais and MEC_Desmarais_duo values. Population genetic analyses of Guizhou Dong and other 17 reference populations showed that the Guizhou Dong group had close genetic relationships with surrounding Tai-Kadai-speaking, Hmong-Mien-speaking and Han groups.

CONCLUSION

Nineteen X-STRs displayed high genetic diversities and could be employed for forensic personal identification and paternity analysis in the Guizhou Dong group. Close genetic affinities between Guizhou Dong and surrounding populations were observed based on the 19 X-STRs in 17 reference populations.

Polymorphism and haplotype analysis of three novel short tandem repeat loci in the p11.4 region of human X chromosome

X-chromosomal short tandem repeats (X-STRs) are useful for the identification of absent single parents and complex blood relations. In the present study, we aimed to identify novel STR loci for use as DNA markers by conducting polymorphism and haplotype analyses. We detected three novel STR loci (LC552061, LC552062, and LC552063, with repetitive structures of (GGAA)_n(GGGA)_m, (CCTT)_n(CCCT)_m, and (ATTT)_n, respectively) in the p11.4 region of the X chromosome. For these X-STRs, the polymorphism information content values ranged from 0.5766 to 0.6377 and the power of discrimination in males and females ranged from 0.6269 to 0.6844 and from 0.8105 to 0.8537, respectively. The linkage disequilibrium analysis revealed p values of < 0.0001, < 0.0001, and 0.00909 between LC552061 and LC552062, LC552061 and LC552063, and LC552062 and LC552063, respectively. Additional linkage disequilibrium analysis including seven previously analyzed loci (LC149476, LC149479, LC149480, LC149484, LC317283, LC317284, and LC317285) revealed a p value of < 0.001 among each of the five loci (LC149476, LC149479, LC149480, LC149484, and LC317283) and between LC317284 and LC317285, indicating that they were a linked group. These results indicate that, in addition to the seven previously detected loci, the three novel X-STR loci identified in the present study might be useful DNA markers for complex kinship analysis and might support the Investigator® Argus X-12 kit.

X-chromosomal STR based genetic polymorphisms and demographic history of Sri Lankan ethnicities and their relationship with global populations

A new 16 X-short tandem repeat (STR) multiplex PCR system has recently been developed for Sr Lankans, though its applicability in evolutionary genetics and forensic investigations has not been thoroughly assessed. In this study, 838 unrelated individuals covering all four major ethnic groups (Sinhalese, Sri Lankan Tamils, Indian Tamils and Moors) in Sri Lanka were successfully genotyped using this new multiplex system. The results indicated a high forensic efficiency for the tested loci in all four ethnicities confirming its suitability for forensic applications of Sri Lankans. Allele frequency distribution of Indian Tamils showed subtle but statistically significant differences from those of Sinhalese and Moors, in contrast to frequency distributions previously reported for autosomal STR alleles. This suggest a sex biased demographic history among Sri Lankans requiring a separate X-STR allele frequency database for Indian Tamils. Substantial differences observed in the patterns of LD among the four groups demand the use of a separate haplotype frequency databases for each individual ethnicity. When analysed together with other 14 world populations, all Sri Lankan ethnicities except Indian Tamils clustered closely with populations from Indian Bhil tribe, Bangladesh and Europe reflecting their shared Indo-Aryan ancestry.