Sequence-based assessment of expediency of tri-, tetra-, and penta-nucleotides repeat autosomal STR markers in the central Indian population using Next Generation Sequencing (NGS)

Abstract Present-day forensic DNA analysis is witnessing a paradigm shift from size-based allele determination by capillary electrophoresis (CE) to sequence-based allele determination by Next Generation Sequencing (NGS). An attempt has been made to evaluate the sequence-based allelic data at two tri (D12ATA63, D22S1045), two tetra (D18S51, D1S1656), and two penta- (Penta D, Penta E) nucleotides repeat STR markers in the central Indian population. 183.33 times allele gain has been observed in D1S1656 after evaluating individual allelic sequences in comparison to the size-based alleles. Despite not witnessing any sequence-based allele gain, highest power of discrimination (0.978), Polymorphic Information Content (0.9), Power of Exclusion (0.807), typical paternity index (5.31), Expected heterozygosity (0.906), and lowest matching probability (0.022) was observed at Penta E marker suggesting its more usefulness among the considered markers for forensic and paternity applications. A giant leap in sequence-based allelic information showed a significant increase in forensic and paternity parameters (p = 0.646) in D1S1656. Substitution of TAGA with either TAGG or TAGC was found to be responsible for the generation of sequence variant alleles in D1S1656. Besides, the observation of rs4847015 SNP in 11.5% of sequences further increases the evidentiary value of D1S1656 in comparison to other STR markers analyzed in this study.