Optimizing DNA recovery and forensic typing of degraded blood and dental remains using a specialized extraction method, comprehensive qPCR sample characterization, and massively parallel sequencing

Patricio Carrasco, Carolina Inostroza Silva, Meghan Didier, Marianela Godoy, Cydne L. Holt, Jonathan Tabak, Andrew Loftus

Research output: Contribution to journalArticlepeer-review

6 Scopus citations

Abstract

Human dental remains encountered in criminal casework evidence, missing person cases, or mass disaster tragedies provide a valuable sample source for DNA typing when suitable soft tissue is unavailable. Using traditional methods, teeth samples can be challenging to process, resulting in low-quantity and/or quality nuclear DNA and insufficient profiles for comparisons. This study examines the performance of a three-part nuclear DNA analysis workflow for teeth samples based on (1) improved dental tissue recovery using the Dental Forensic Kit (DFKMR) (Universidad de los Andes) and DNA extraction with QuickExtract™ FFPE DNA Extraction Kit (Lucigen®), (2) quantification with InnoQuant® HY (InnoGenomics Technologies) for sensitive assessment of total human and male DNA quantity/quality, and (3) massively parallel sequencing for simultaneous genotyping of 231 short tandem repeat (STR) and single-nucleotide polymorphism (SNP) markers with the ForenSeq® DNA Signature Prep Kit (Verogen, Inc.). Initial evaluation of artificially degraded blood samples (n = 10) achieved highly sensitive and informative quantification results with InnoQuant® HY, enabling successful first pass genotyping with the MiSeq FGx® System. Twenty-three STR alleles (out of 85) and 70 identity informative SNP loci (out of 94) were recovered from two pg total long target DNA input (0.86 ng total short target input) and an InnoQuant degradation index (DI) of 460 (severely degraded). The three-part workflow was subsequently applied to teeth samples (dental pulp, root cement tissues; n = 13) with postmortem intervals (PMI) of the teeth ranging from 8 days to approximately 6 months. Informative SNP and STR DNA profiles were obtained, to include 78 STR alleles and 85 identity informative SNP loci typed (of 94 total SNP targets) in a 1 month, four-day PMI root cement sample with one pg total long target DNA input and a DI of 76. These data indicate successful performance of the proposed workflow from degraded DNA from teeth samples.

Original languageEnglish
Pages (from-to)79-91
Number of pages13
JournalInternational Journal of Legal Medicine
Volume134
Issue number1
DOIs
StatePublished - 1 Jan 2020

Bibliographical note

Funding Information:
The authors would like to acknowledge Joe Varlaro for his work in planning and organizing this collaborative study, Sudhir K. Sinha for the dedication of laboratory resources and helpful feedback and Martin Fabani for thoughtful manuscript review. Additional thanks to the Dental School and the Innovation Direction of Universidad de los Andes for the support, medical technologist Maria Jos? Lagos for laboratory support and Cedin Dental for teeth sample collection.

Publisher Copyright:
© 2019, The Author(s).

Keywords

  • Degraded DNA
  • Dental Forensic Kit (DFK)
  • ForenSeq
  • InnoQuant HY
  • Massively Parallel Sequencing (MPS)
  • Single-Nucleotide Polymorphism (SNP)

Fingerprint Dive into the research topics of 'Optimizing DNA recovery and forensic typing of degraded blood and dental remains using a specialized extraction method, comprehensive qPCR sample characterization, and massively parallel sequencing'. Together they form a unique fingerprint.

Cite this