Study On Genetic Polymorphisms Of 19 X-STR Loci In Han And Zhuang Population And Anomalous X-STR Profiles

Background PCR-STR is a rapid,sensive and reliable method for DNA typing,which has been widely applied in forensic practice.Autosomal STR loci and the Y chromosome STR loci are common applied genetic marker.With unique genetic characteristics,X chromosome short tandem repeats are gradually followed with interest by forensic scientists.According to literatures,X-STR loci are of great value in some complex identification.The genetic polymorphism of X-STR loci varies among different ethnic groups.Although more than 50 X-STR loci have been reported resently,most of which lack data of population investigation.Therefore,to better implement the X-STR analysis in forensic practice,it is necessary to establish a reference database for a specific group.In our study,we used AGCU X19 kit to investigate the genetic polymorphism of Wuhan Han population(male)and Guangxi Zhuang population(male),to evaluate the value of the 19 X-STRs in forensic application.The inter-population comparisons were performed with the frequency distribution of 19 X-STR loci from different populations.We also deeply analyzed the abnormal patterns encountered during population investigation.Objective The aims of our study are investigating forensic parameters and genetic polymorphism of 19 X-STR loci in Wuhan Han population and Guangxi Zhuang population and evaluating their values of application in forensic science.The characteristics and genetic basis of male X-STR abnormal biallelic genotypes were also studied.⑴ Population investigation:(1)The smples of buccal swabs or dried blood spots were collected from 509 unrelated healthy males of Wuhan Hanpopulation and 266 unrelated healthy males of Guangxi Zhuang population.Extracted with the method of Chelex-100,genomic DNA was amplified by AGCU X19 kit,followed by capillary electrophoresis for DNA typing.(2)Tests of linkage disequilibrium were performed for all pairs of loci.(3)Genetic polymorphisms and forensic parameters of 19 X-STR loci in two populations were studied.(4)The allele frequency distribution were compared between different populations.⑵ Anomalous STR patterns:(1)We reanalyze the new samples and performed bidirectional Sanger sequencing for the singleplex polymerase chain reaction(PCR)products to verify abnormal patterns.(2)The genetic basis for their production was inferred based on the relative peak heights at the Amelogenin locus and the affected locus(DXS10159,DXS10134 and DXS10079)and the normalized peak-height ratios between the affected locus and adjacent loci relative to the control sample 9947 A.(3)Quantitative PCR was used to study reasons of abnormal patterns of samples of HS152 with biallelic pattern at DXS10159 locus.Results ⑴ In the Han and Zhuang populations,a total of alleles of all loci were 224 and 188,with the frequencies of 19 STR loci ranged from 0.0020 to 0.6095 and from 0.0038 to 0.6023,respectively.The combined powers of discrimination of Han and Zhuang population(males)are 0.99999999999965 and 0.999999999999555,respectively.DXS10135 was the most informative locus in the two population groups,whereas the least locus was DXS7423.After Bonferroni’s correction,the numbers of loci which have significant differences between the WuH ang Han and Zhuang,Yi,Guanzhong Han and Kazakh population(p < 0.005)were 3,3,0 and 6,respectively.Haplotype diversity obtained in our study was greater than 0.9 in all linkage Groups.⑶ The presence of these patterns was verified by reanalysis using new samples and bidirectional Sanger sequencing of the singleplex polymerase chain reaction(PCR)products.The inference results suggested that two cases of biallelic pattern at the DXS10159 locus would be caused by local duplications,while in the other two cases,both the biallelic patterns at loci DXS10134 and DXS10079 would be due to somaticmutations.The sample HS152 which genotyped as a biallelic pattern at the DXS10159 locus was further analysed.Quantitative PCR(qPCR)revealed a microduplication(< 0.2 Mb)spanning at least 13.4 kb in Xp11.21 encompassing the DXS10159 locus.Conclusion With highly polymorphism and informative linkage groups in above two populations,the 19 X-STR loci are valuable in forensic practice.The results of inter-comparison among different ethnic populations showed that there were significant differences in allele frequency distribution.Our study is a detailed report of X-STR biallelic patterns in human males,which serves as an effective complement to the database and provides an example for the analysis of anomalous STR patterns.