MSc candidate, University of Technology Sydney
Improving human identification in forensics
This research tests the performance of newly-developed DNA markers that are of use in human and forensic identifications. Specifically, the study focuses on markers of mitochondrial DNA - that is the DNA passed down from mothers to children. By looking at this DNA, a snapshot of a person's ancestry and family history is captured. However, the recovery of DNA is difficult in harsh environments such as mass disasters and ancient remains. Therefore to improve DNA identification in forensics, this study looks at the performance of new markers to sequence artifically-degraded DNA samples.
Abstract: Mitochondrial DNA (mtDNA) genome analysis has been a potent tool in forensic practice as well as in the understanding of human phylogeny in the maternal lineage. The traditional mtDNA analysis is focused on the control region, but the introduction of massive parallel sequencing (MPS) has made the typing of the entire mtDNA genome (mtGenome) more accessible for routine analysis. The complete mtDNA information can provide large amounts of novel genetic data for diverse populations as well as improved discrimination power for identification. The genetic diversity of the mtDNA sequence in different ethnic populations has been revealed through MPS analysis, but the Korean population not only has limited MPS data for the entire mtGenome, the existing data is mainly focused on the control region. In this study, the complete mtGenome data for 186 Koreans, obtained using Ion Torrent Personal Genome Machine (PGM) technology and retrieved from rather common mtDNA haplogroups based on the control region sequence, are described. The results showed that 24 haplogroups, determined with hypervariable regions only, branched into 47 subhaplogroups, and point heteroplasmy was more frequent in the coding regions. In addition, sequence variations in the coding regions observed in this study were compared with those presented in other reports on different populations, and there were similar features observed in the sequence variants for the predominant haplogroups among East Asian populations, such as Haplogroup D and macrohaplogroups M9, G, and D. This study is expected to be the trigger for the development of Korean specific mtGenome data followed by numerous future studies.
Pub.: 01 Mar '17, Pinned: 27 Jul '17
Abstract: Massively Parallel (Next Generation) Sequencing (MPS) technologies have recently been proven useful and successful in typing various markers relevant in forensic genetics, such as STRs, SNPs and mitochondrial genomes. Early studies investigated self-developed DNA libraries, commercially supplied kits are currently being made available to allow a smoother and gradual implementation of such technologies in forensic laboratories. The ForenSeq™ DNA Signature Prep Kit (Illumina, CA) is the first commercially available STR kit that can be used on the MiSeq FGx™ (Illumina, CA) benchtop high-throughput sequencer. This kit allows the simultaneous typing of 59 STRs and up to 172 SNPs in a single reaction and presents a short library preparation protocol adapted to contemporary forensic requirements. In this study, we evaluated the beta version of the ForenSeq DNA Signature Prep Kit MiSeq FGx system by investigating reproducibility, sensitivity, mixtures, concordance, casework-type and aDNA samples and found it to perform successfully, proving to be a robust method for future forensic applications. MPS brings the possibility of complex multiplexing, high sensitivity and sequencing resolution to forensics; however, the need for consensual directions on databasing, data storage and nomenclature must be taken into consideration.
Pub.: 01 Mar '17, Pinned: 27 Jul '17
Abstract: Mitochondrial DNA (mtDNA) analysis has displayed an important role and been considered as a powerful tool in various fields of forensic science applications. Nowadays, single nucleotide polymorphisms (SNPs) on mtDNA have become additional DNA markers when conventional STR typing practically fails. mtDNA sequencing of polymerase chain reaction (PCR) products from the hypervariable region I (HVRI) and II (HVRII) is the standard method of mtDNA analysis. However, mtDNA sequencing is rather expensive, time consuming and technically complex. This study aims to develop the SNPs minisequencing for screening of Thai populations. For this purpose, sixteen SNPs that possess high discriminating power in hypervariable regions were selected. The DNA samples were obtained from 100 buccal swab samples of Thai healthy individuals. All DNA samples were extracted and were subsequently amplified by single duplex PCR technique. The duplex PCR products were genotyped by SNPs minisequencing. Based on 16 SNPs, a total of 63 haplotypes were observed of which 46 haplotypes were unique. The haplotype diversity, discriminating power and random match probability were calculated to be 0.9830, 0.9732 and 0.0268, respectively. The SNPs at 150, 199, 489, 16129, 16189, 16223, and 16304 were highly polymorphic in the studied population. Our results suggested that the SNPs minisequencing can be an alternative method of SNPs genotyping. This method can be used for an exclusion of a large number of mismatch samples and as a presumptive test prior to do confirmatory mtDNA sequencing.
Pub.: 12 Jul '17, Pinned: 27 Jul '17
Abstract: Accurate sequencing of the control region of the mitochondrial genome is notoriously difficult due to the presence of polycytosine bases, termed C-tracts. The precise number of bases that constitute a C-tract and the bases beyond the poly cytosines may not be accurately defined when analyzing Sanger sequencing data separated by capillary electrophoresis. Massively parallel sequencing has the potential to resolve such poor definition and provides the opportunity to discover variants due to length heteroplasmy. In this study, the control region of mitochondrial genomes from 20 samples was sequenced using both standard Sanger methods with separation by capillary electrophoresis and also using massively parallel DNA sequencing technology. After comparison of the two sets of generated sequence, with the exception of the C-tracts where length heteroplasmy was observed, all sequences were concordant. Sequences of three segments 16184-16193, 303-315 and 568-573 with C-tracts in HVI, II and III can be clearly defined from the massively parallel sequencing data using the program SEQ Mapper. Multiple sequence variants were observed in the length of C-tracts longer than 7 bases. Our report illustrates the accurate designation of all the length variants leading to heteroplasmy in the control region of the mitochondrial genome that can be determined by SEQ Mapper based on data generated by massively parallel DNA sequencing.
Pub.: 21 Jul '17, Pinned: 27 Jul '17