Developmental Validation of a MPS Workflow with a PCR-Based Short Amplicon Whole Mitochondrial Genome Panel.

Genes
Jennifer Churchill CihlarBruce Budowle

Abstract

For the adoption of massively parallel sequencing (MPS) systems by forensic laboratories, validation studies on specific workflows are needed to support the feasibility of implementation and the reliability of the data they produce. As such, the whole mitochondrial genome sequencing methodology-Precision ID mtDNA Whole Genome Panel, Ion Chef, Ion S5, and Converge-has been subjected to a variety of developmental validation studies. These validation studies were completed in accordance with the Scientific Working Group on DNA Analysis Methods (SWGDAM) validation guidelines and assessed reproducibility, repeatability, accuracy, sensitivity, specificity to human DNA, and ability to analyze challenging (e.g., mixed, degraded, or low quantity) samples. Intra- and inter-run replicates produced an average maximum pairwise difference in variant frequency of 1.2%. Concordance with data generated with traditional Sanger sequencing and an orthogonal MPS platform methodology was used to assess accuracy, and generation of complete and concordant haplotypes at DNA input levels as low as 37.5 pg of nuclear DNA or 187.5 mitochondrial genome copies illustrated the sensitivity of the system. Overall, data presented herein demonstrate that highly ...Continue Reading

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Citations

Jan 31, 2021·Genes·Benjamin CrysupBruce Budowle
Mar 20, 2021·Forensic Science International. Genetics·Charla Marshall, Walther Parson
Mar 27, 2021·Forensic Science International. Genetics·Erin M GordenCharla Marshall
Aug 11, 2021·Emerging Topics in Life Sciences·Denise Syndercombe Court
Sep 8, 2021·International Journal of Legal Medicine·Christian FaccinettoGiovanni Vazza

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Methods Mentioned

BETA
electrophoresis
chip
PCR
chips
genotyping

Software Mentioned

MiSeq
RStudio
R
PhyloTree
HIDGenotyper
Converge
EMPOP
Torrent Suite
Quantifiler Trio
UCSC Genome Brower BLAT

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