Male individualization using 12 rapidly mutating Y-STRs in Araein ethnic group and shared paternal lineage of Pakistani population

Abstract

A multiplex assay has been developed with newly designed primer sets comprising high mutation rate 12 RM Y-STR markers (DYS570, DYF399S1, DYS547, DYS612, DYF387S1, DYS449, DYS576, DYS5626, DYF403S1 (a + b), DYS627, DYS526, and DYF404S1). Rapidly mutating Y-STRs were evaluated in 167 male individuals among 97 were unrelated from Araein ethnic group and 70 belonged to shared paternal lineage including 20 pairs of father-son and 15 pairs of brother-brother relationship collected from Punjabi population of Pakistan. Forensic competency parameters were implemented for each marker and exceptionally significant results found wherein polymorphism information content (PIC) was in range of 0.7494 (DYS576) to 0.8994 (DYS627). Samples were also analyzed with Y-filer kit for comparison and marked differentiations observed. Haplotype discrimination capacity was 100% as no haplotype shared among all the unrelated individuals of same ethnic group as compared to 17 Y-filer loci (78%). While in closely related males, discrimination capacity was 96.4% with haplotype diversity value of 0.98. Resulted high mutation rate 1 × 10 to 7.14 × 10 as compared to Y-filer (1 × 10 to 1 × 10) manifested the power of RM Y-STRs for considering absolute individualization of interrelated and unrelated male individuals. However, multiplex assay would be useful for male discrimination in mixed DNA specimen, azoospermic males, and multiple male DNA contributors in sexual assault cases and mass disasters victim's identification as well as anthropological studies.

Empirical Evidence on Enhanced Mutation Rates of 19 RM-YSTRs for Differentiating Paternal Lineages

“…However, no mutations were seen at DYS385 (ab) and DYS549, while the average mutation rate over all the loci was 2.92 × 10 −2 , as shown in Table 1 . The mutation rates observed in this study are higher than the mutation rates reported previously from Pakistan [ 8 , 9 ], as compared in Supplementary Table S4 .…”

“…Rakha et al [ 28 ] also found that RM Y STRs differentiated between paternal male relatives for 39% of cases, compared with only 9% and 7% for Yfiler and PowerPlex Y23, respectively. In a previous study [ 9 ], we observed 68 mutations in at least one of 12 RM Y STRs in 35 pairs of male relatives with a mutation rate of 7.14 × 10 −2 /locus/generation. According to Table 2 , the mutation rates in this study were all higher than previous studies [ 8 , 16 ], except for five meiosis.…”

“…Each male-rooted pedigree ( n = 97) was defined by at least one unique haplotype and therefore achieved 100% discrimination capacity (DC) with HD = 0.991512. The global HD of RM Y STRs has been previously reported by Ballantyne et al in 2014 as 0.9999985, while, from Pakistan, it has been reported to be 0.9921 in the Sindhi, Brahui and Punjabi regions [ 7 ] and 0.993 in the Arain ethnic group [ 9 ]. Elsewhere, HD has been found to be 1.00 for South Koreans and Portuguese, 0.9999 for Italians and 0.997 for the UAE [ 8 , 23 , 24 , 25 , 26 ].…”

“…PCR products were scanned with GeneScan™ 500 LIZ ® size standard (Applied Biosystems) and Hi-Di formamide and genotyped on a ABI 3130xl genetic analyzer (Applied Biosystems, Foster City, CA, USA) using the manufacturer’s recommended protocols. Genotyped data were analyzed using GeneMapper ID software, and allele numbers were designated following the guidelines of the International Society of Forensic Genetics (ISFG) [ 19 ] and size-based comparisons with control DNA 9948 [ 9 ].…”

“…These characteristics make RM Y STRs useful when autosomal STRs are uninformative, especially in crimes involving multiple male perpetrators or in mixed male/female DNA obtained from sexual assault cases [ 7 ]. Several studies have confirmed their high mutation rates in haplotype comparisons of populations, genealogies and father–son pairs from Pakistan [ 8 , 9 , 10 ], Italy [ 11 ], Serbia [ 12 ], China [ 13 ] and Turkey [ 14 ]. Using 13 well-established RM Y STRs, Adnan et al [ 8 ] were able to differentiate 27%, 46%, 54% and 62% s of males separated by one, two, three and four generations, respectively.…”