DNA capture and next-generation sequencing can recover whole mitochondrial genomes from highly degraded samples for human identification

Abstract

BackgroundMitochondrial DNA (mtDNA) typing can be a useful aid for identifying people from compromised samples when nuclear DNA is too damaged, degraded or below detection thresholds for routine short tandem repeat (STR)-based analysis. Standard mtDNA typing, focused on PCR amplicon sequencing of the control region (HVS I and HVS II), is limited by the resolving power of this short sequence, which misses up to 70% of the variation present in the mtDNA genome.MethodsWe used in-solution hybridisation-based DNA capture (using DNA capture probes prepared from modern human mtDNA) to recover mtDNA from post-mortem human remains in which the majority of DNA is both highly fragmented (<100 base pairs in length) and chemically damaged. The method ‘immortalises’ the finite quantities of DNA in valuable extracts as DNA libraries, which is followed by the targeted enrichment of endogenous mtDNA sequences and characterisation by next-generation sequencing (NGS).ResultsWe sequenced whole mitochondrial genomes for human identification from samples where standard nuclear STR typing produced only partial profiles or demonstrably failed and/or where standard mtDNA hypervariable region sequences lacked resolving power. Multiple rounds of enrichment can substantially improve coverage and sequencing depth of mtDNA genomes from highly degraded samples. The application of this method has led to the reliable mitochondrial sequencing of human skeletal remains from unidentified World War Two (WWII) casualties approximately 70 years old and from archaeological remains (up to 2,500 years old).ConclusionsThis approach has potential applications in forensic science, historical human identification cases, archived medical samples, kinship analysis and population studies. In particular the methodology can be applied to any case, involving human or non-human species, where whole mitochondrial genome sequences are required to provide the highest level of maternal lineage discrimination. Multiple rounds of in-solution hybridisation-based DNA capture can retrieve whole mitochondrial genome sequences from even the most challenging samples.

Interordinal gene capture, the phylogenetic position of Steller’s sea cow based on molecular and morphological data, and the macroevolutionary history of Sirenia

“…Hybridization capture was performed a second time to further enrich the libraries (Templeton et al, 2013). After the second hybridization experiment, samples were only amplified for 10 cycles.…”

Massively parallel sequencing of complete mitochondrial genomes from hair shaft samples

“…These technologies largely remove the greatest existing technical and cost barriers to mtGenome sequencing of low DNA quality and quantity specimens. In fact, MPS has already been paired with assays developed by the ancient DNA community [21,22] to develop complete mtGenome haplotypes from some of the most compromised unidentified human remains [23,24].…”

Importância do DNA em Investigações Forenses: Análise de DNA Mitocondrial

“…Podemos perceber uma tendência nos últimos cinco anos no intuito de realizar a tipagem total do genoma mitocondrial 7,9,12,13 . Esta tendência é importante pois a tipagem do genoma mitocondrial total nos traz, além das informações já amplamente pesquisadas das regiões não codificantes, informações sobre as regiões codificantes que podem ser de interesse forense.…”

“…Em contrapartida, a abordagem de sequenciamento total do genoma mitocondrial é uma solução universal para a obtenção de dados de mtDNA de alta resolução, que podem discriminar entre linhagens maternas relacionadas. No entanto, embora a metodologia forneça um mecanismo para gerar sequências do genoma inteiro de mtDNA de amostras difíceis e degradadas, há uma clara necessidade para o desenvolvimento paralelo de bases de dados de alta qualidade do genoma mitocondrial 7 .Podemos perceber uma tendência nos últimos cinco anos no intuito de realizar a tipagem total do genoma mitocondrial 7,9,12,13 . Esta tendência é importante pois a tipagem do genoma mitocondrial total nos traz, além das informações já amplamente pesquisadas das regiões não codificantes, informações sobre as regiões codificantes que podem ser de interesse forense.…”