Tags

Type your tag names separated by a space and hit enter

Utility of the Ion S5™ and MiSeq FGx™ sequencing platforms to characterize challenging human remains.
Leg Med (Tokyo). 2019 Nov; 41:101623.LM

Abstract

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.

Authors+Show Affiliations

Department of Forensic Science, Sam Houston State University, Huntsville, TX, USA. Electronic address: kee019@shsu.edu.Center for Human Identification, University of North Texas Health Science Center, Fort Worth, TX, USA.Center for Human Identification, University of North Texas Health Science Center, Fort Worth, TX, USA.Human Identification Division, Thermo Fisher Scientific, South San Francisco, CA, USA.Department of Forensic Science, Sam Houston State University, Huntsville, TX, USA; School of Biomedical Sciences, University of Queensland, Brisbane, QLD, Australia.Center for Human Identification, University of North Texas Health Science Center, Fort Worth, TX, USA.

Pub Type(s)

Journal Article

Language

eng

PubMed ID

31499459

Citation

Elwick, Kyleen, et al. "Utility of the Ion S5™ and MiSeq FGx™ Sequencing Platforms to Characterize Challenging Human Remains." Legal Medicine (Tokyo, Japan), vol. 41, 2019, p. 101623.
Elwick K, Bus MM, King JL, et al. Utility of the Ion S5™ and MiSeq FGx™ sequencing platforms to characterize challenging human remains. Leg Med (Tokyo). 2019;41:101623.
Elwick, K., Bus, M. M., King, J. L., Chang, J., Hughes-Stamm, S., & Budowle, B. (2019). Utility of the Ion S5™ and MiSeq FGx™ sequencing platforms to characterize challenging human remains. Legal Medicine (Tokyo, Japan), 41, 101623. https://doi.org/10.1016/j.legalmed.2019.08.001
Elwick K, et al. Utility of the Ion S5™ and MiSeq FGx™ Sequencing Platforms to Characterize Challenging Human Remains. Leg Med (Tokyo). 2019;41:101623. PubMed PMID: 31499459.
* Article titles in AMA citation format should be in sentence-case
TY - JOUR T1 - Utility of the Ion S5™ and MiSeq FGx™ sequencing platforms to characterize challenging human remains. AU - Elwick,Kyleen, AU - Bus,Magdalena M, AU - King,Jonathan L, AU - Chang,Joseph, AU - Hughes-Stamm,Sheree, AU - Budowle,Bruce, Y1 - 2019/08/14/ PY - 2019/03/22/received PY - 2019/07/10/revised PY - 2019/08/03/accepted PY - 2019/9/10/pubmed PY - 2020/4/23/medline PY - 2019/9/10/entrez KW - Challenged remains KW - Human remains KW - Ion S5™ KW - Massively parallel sequencing KW - MiSeq FGx™ KW - Missing persons SP - 101623 EP - 101623 JF - Legal medicine (Tokyo, Japan) JO - Leg Med (Tokyo) VL - 41 N2 - 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. SN - 1873-4162 UR - https://www.unboundmedicine.com/medline/citation/31499459/Utility_of_the_Ion_S5™_and_MiSeq_FGx™_sequencing_platforms_to_characterize_challenging_human_remains_ L2 - https://linkinghub.elsevier.com/retrieve/pii/S1344-6223(19)30284-6 DB - PRIME DP - Unbound Medicine ER -