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.

中文翻译：

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从全基因组下一代测序数据中提取线粒体基因组并公开法医相关标记

摘要

法医学在遗传学水平上从STRs和SNP标记中受益匪浅，但是在基因组水平上对它们的分析，尤其是从整个基因组序列中分离线粒体基因组以及法医学标记的揭示仍然不清楚。在本研究中，使用Illumina HiSeq-4000平台进行了全基因组下一代测序，然后分离了mtDNA，并使用计算管线完成了SNP和STR的提取。从巴基斯坦Pothwari族个体的全基因组测序数据中成功提取了线粒体基因组序列。在基因MT-RNR1和ND6中鉴定出两个异质位点分别位于控制区和编码区。将靶标全基因组序列与参考基因组数据库进行比较，发现2 436 328个SNP，119 399个插入和119 290个缺失，观察到它们的转变/转化和杂合/纯合的可变比率。总共鉴定了63个与法医相关的SNP，包括21个祖先信息，40个身份信息和2个表型信息。除SNPs外，还获得了两种遗传标记，包括8个CODIS和39个Y-STR。CODIS STR比Y-STR表现出更多的变化，因为它们不交叉。因此，除了快速变异的YSTR（对区分近缘和远缘的雄性至关重要）以外，大多数世代都保持保守。