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

Kyleen Elwick, Magdalena M. Bus, Jonathan L. King, Joseph Chang, Sheree Hughes-Stamm, Bruce Budowle

Research output: Contribution to journalArticle

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.

Original languageEnglish
Article number101623
JournalLegal Medicine
Volume41
DOIs
StatePublished - Nov 2019

Fingerprint

Microsatellite Repeats
High-Throughput Nucleotide Sequencing
Capillary Electrophoresis
Ions
DNA
Embalming
Tooth
Cremation
Bone Nails
DNA Fingerprinting
Disasters
Hair
Single Nucleotide Polymorphism
Hot Temperature
Alleles
Technology
Bone and Bones
Polymerase Chain Reaction
Body Remains

Keywords

  • Challenged remains
  • Human remains
  • Ion S5™
  • Massively parallel sequencing
  • MiSeq FGx™
  • Missing persons

Cite this

Elwick, Kyleen ; Bus, Magdalena M. ; King, Jonathan L. ; Chang, Joseph ; Hughes-Stamm, Sheree ; Budowle, Bruce. / Utility of the Ion S5™ and MiSeq FGx™ sequencing platforms to characterize challenging human remains. In: Legal Medicine. 2019 ; Vol. 41.
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Utility of the Ion S5™ and MiSeq FGx™ sequencing platforms to characterize challenging human remains. / Elwick, Kyleen; Bus, Magdalena M.; King, Jonathan L.; Chang, Joseph; Hughes-Stamm, Sheree; Budowle, Bruce.

In: Legal Medicine, Vol. 41, 101623, 11.2019.

Research output: Contribution to journalArticle

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