Utility of the Ion S5™ and MiSeq FGx™ sequencing platforms to characterize challenging human remains

• Published in: Legal medicine (Tokyo, Japan) Vol. 41; p. 101623
• Main Authors: Elwick, Kyleen, Bus, Magdalena M., King, Jonathan L., Chang, Joseph, Hughes-Stamm, Sheree, Budowle, Bruce
• Format: Journal Article
• Language: English
• Published: Ireland Elsevier B.V 01.11.2019
• Subjects: Body Remains; Bone and Bones - chemistry; Challenged remains; Cremation; DNA - genetics; DNA - isolation & purification; DNA Fingerprinting - methods; Electrophoresis, Capillary; Embalming; Female; Fires; Forensic Genetics; High-Throughput Nucleotide Sequencing - instrumentation; Human remains; Humans; Ion S5; Male; Massively parallel sequencing; Microsatellite Repeats; MiSeq FGx; Missing persons; Polymerase Chain Reaction; Polymorphism, Single Nucleotide; Postmortem Changes; Tooth - chemistry; Massively parallel sequencing; Challenged remains; Ion S5; MiSeq FGx; Missing persons; Human remains
• ISSN: 1344-6223; 1873-4162
• DOI: 10.1016/j.legalmed.2019.08.001

•Two MPS chemistries and platforms were compared to traditional CE-based genotyping for use with challenged human remains.•MPS generated more genetic data in 22 samples compared to CE.•Using only the 20 CODIS loci, CE produced more alleles than MPS for some more difficult samples.•MPS may recover more probative information because of the greater number of markers available.•CE methods were more robust for identifying challenging human remains. Often in missing persons’ and mass disaster cases, the samples remaining for analysis are hard tissues such as bones, teeth, nails, and hair. These remains may have been exposed to harsh environmental conditions, which pose challenges for downstream genotyping. Short tandem repeat analysis (STR) via capillary electrophoresis (CE) is still the gold standard for DNA typing; however, a newer technology known as massively parallel sequencing (MPS) could improve upon our current techniques by typing different and more markers in a single analysis, and consequently improving the power of discrimination. In this study, bone and tooth samples exposed to a variety of DNA insults (cremation, embalming, decomposition, thermal degradation, and fire) were assessed and sequenced using the Precision ID chemistry and a custom AmpliSeq™ STR and iiSNP panel on the Ion S5™ System, and the ForenSeq DNA Signature Prep Kit on the MiSeq FGx™ system, as well as the GlobalFiler™ PCR Amplification Kit on the 3500™ Genetic Analyzer. The results demonstrated that using traditional CE-based genotyping performed as expected, producing a partial or full DNA profile for all samples, and that both sequencing chemistries and platforms were able to recover sufficient STR and SNP information from a majority of the same challenging samples. Run metrics including profile completeness and mean read depth produced good results with each system, considering the degree of damage of some samples. Most sample insults (except decomposed) produced similar numbers of alleles for both MPS systems. Comparable markers produced full concordance between the two platforms.