Extraction of Mitochondrial Genome from Whole Genome Next Generation Sequencing Data and Unveiling of Forensically Relevant Markers

Abstract

Forensic science has benefitted a lot from STRs and SNP markers at genetic level but their analyses at genomic level especially isolation of mitochondrial genome from whole genome sequence and unveiling of forensic markers remained obscure. In the present study whole genome next generation sequencing using Illumina HiSeq-4000 platform was done followed by separation of mtDNA and extraction of SNPs and STRs was accomplished using computational pipelines. Mitochondrial genome sequence was successfully extracted from whole genome sequencing data of a Pothwari ethnic individual of Pakistan. Two heteroplasmic sites were identified in genes MT-RNR1 and ND6 which located in control and coding regions, respectively. Comparison of target whole genome sequence with reference genome database revealed 2 436 328 SNPs, 119 399 insertions and 119 290 deletions for which variable ratios of transitions/transversion and heterozygosity/homozygosity were observed. A total of 63 forensically relevant SNPs including 21 ancestry-informative, 40 identity-informative and 2 phenotypic-informative were identified. Besides SNPs, two types of genetic markers which include 8 CODIS and 39 Y-STRs were also obtained. CODIS STRs exhibited more variations than Y-STRs as these are not of crossing over; hence mostly remain conserved in generations with exception of rapidly mutating YSTRs which are crucial in differentiating closely and distantly related males. This study reports whole genome sequencing and development of pipelines for extraction of mitochondrial DNA as well as insight into detection of forensic markers i.e., SNPs and STRs which can be an initiative to develop local forensic databases and a record resource for ethnic crimination-detection in crimes and disasters.