Problems in Mitochondrial DNA forensics: while interpreting length heteroplasmy conundrum of various Sindhi and Baluchi ethnic groups of Pakistan

Abstract

The insight heterodox genetics of mtDNA infer new perspectives at the level of human mitochondrial control region heteroplasmy, which is substantial in evolutionary as well as forensic interpretation. The main goal of this study is to interrogate the recurrence and resolve the ambiguity of blurry spectrum of heteroplasmy in the human mtDNA control region of 50 Baluchi and 116 Sindhi unrelated individuals. Sanger sequencing was employed classically, that was further investigated by minisequencing. Only 20% Baluchi and 25.8% Sindhi were homoplasmic, whereas rest of 80% Baluchi and 74.1% Sindhi exhibited at least one heteroplasmy within the specimen. In total, 166 individuals have length heteroplasmy (LH) found at positions 16189, 303-315, 568-573, and 514-524, whilst point mutation heteroplasmy (PMH) was detected at positions 73, 16093, 16189, and 16234, respectively. Overall LH was observed albeit high frequency in Sindhi ethnic group (82%) rather than Baluchi's (37%), whereas PMH accumulation was relatively extensive (24%) in Baluchi's than Sindhi's (11.2%). The obtained results ascertained that growing knowledge of heteroplasmy assisted to develop consciences in the forensic community that heteroplasmy plays a pivotal role in the legal interpretation on a regular basis and knowledge of its biological underpinnings has a vital niche in the forensic science. Limited studies have focused on heteroplasmy, yet scientific attention should be given, in order to determine its magnitude in different ethnic boundaries.

Next generation database search algorithm for forensic mitogenome analyses

“…the SAM query of the CR mitotype 16519C 263 G 315.1C 523del 524del resulted in 23 matches in 26,127 EMPOP CR entries, while the same mitotype yielded 549 matches in SAM 2. It is yet unclear -and further studies are currently pending -whether the additional potential length variants (291, 524, 8289) are stable between tissues of an individual [46][47][48]. If they are not, then we suggest adding those to the list of ignored length hotspots in order to achieve conservative database query results.…”

“…The interpretation of AC indels in region 515-524 is still not clear, as not many data have been established to understand the somatic stability of this repeat in different (forensically relevant) tissues. Earlier work suggests that the interpretation of length heteroplasmy in the AC repeat varies with amplification and detection strategies [46][47][48]. However, further studies are required to clarify this issue, which is why the additional length variants at positions 291, 524 and 8289 will not be available in the online version of EMPOP until these issues are clarified.…”

Allele frequencies of mitochondrial DNA HVR III 514–524 (CA)n dinucleotide repeats in the Urali Kuruman tribal population of South India

“…The non-coding or control region, synonymously referred as the displacement loop (D-loop) segment of mitochondrial DNA (mtDNA) is most extensively studied in forensics, particularly the hypervariable regions (HVR I, II, and III) (Wilson et al 1995;Szibor et al 1997;Lutz et al 2000;Chung et al 2005;Lander et al 2008;Irwin et al 2009;Elmadawy et al 2013;Hayat et al 2015;Chaitanya et al 2016;Bhatti et al 2018). The hypervariable regions are mutation hotspots, which evolve~10 times rapidly than chromosomal DNA, with relatively higher mutation rate giving rise to more polymorphic sites (Stoneking 2000).…”

“…In addition to point mutations, repetition of nucleotides :single and dinucleotide repeatsoccurs in the D-loop segment known as length heteroplasmy (Li et al 2016). Commonly occurring length heteroplasmies are the Poly-C (Poly-cytosine) residues at np 16,189 in HVR I, np 303-315 in HVR II, and np 568-573 in HVR III and the five pairs of CA/AC residues at np 514-524 in the HVR III region (Bhatti et al 2018).…”

“…Nevertheless, the HVR III has proven to be useful as a supplementary polymorphic segment for the forensic application (Hoong and Lek 2005). Even though the majority of forensic cases utilize only the HVR I and HVR II sequences, it is noteworthy that HVR III (CA) n repeat segment has equal potential as an additional mtDNA marker in forensic investigations (Ivanov et al 1996;Lutz et al 2000;Chung et al 2005;Fridman and Gonzalez 2009;Bhatti et al 2018). No such study of (CA) n dinucleotide indels of mtDNA HVR III 514-524 region in Indian population has been reported so far; this study was aimed to evaluate the (CA) n dinucleotide repeats in the Urali Kuruman tribe of Kerala, South India.…”