Blind study evaluation illustrates utility of the Ion PGM™ system for use in human identity DNA typing

Jennifer D. Churchill, Joseph Chang, Jianye Ge, Narasimhan Rajagopalan, Sharon C. Wootton, Chien Wei Chang, Robert Lagacé, Wenchi Liao, Jonathan L. King, Bruce Budowle

Research output: Contribution to journalArticle

30 Scopus citations

Abstract

Aim To perform a blind study to assess the capability of the Ion Personal Genome Machine® (PGM™) system to sequence forensically relevant genetic marker panels and to characterize unknown individuals for ancestry and possible relatedness. Methods Twelve genomic samples were provided by a third party for blinded genetic analysis. For these 12 samples, the mitochondrial genome and three PGM™ panels containing human identity single nucleotide polymorphisms (SNPs), ancestry informative SNPs, and short tandem repeats (STRs) were sequenced on the PGM™ system and analyzed. Results All four genetic systems were run and analyzed on the PGM™ system in a reasonably quick time frame. Completeness of genetic profiles, depth of coverage, strand balance, and allele balance were informative metrics that illustrated the quality and reliability of the data produced. SNP genotypes allowed for identification of sex, paternal lineage, and population ancestry. STR genotypes were shown to be in complete concordance with genotypes generated by standard capillary electrophoresis-based technologies. Variants in the mitochondrial genome data provided information on population background and maternal relationships. Conclusion All results from analysis of the 12 genomic samples were consistent with sample information provided by the sample providers at the end of the blinded study. The relatively easy identification of intra-STR allele SNPs offered the potential for increased discrimination power. The promising nature of these results warrants full validation studies of this massively parallel sequencing technology and its further development for forensic data analysis.

Original languageEnglish
Pages (from-to)218-229
Number of pages12
JournalCroatian Medical Journal
Volume56
Issue number3
DOIs
StatePublished - 2015

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