My-Forensic-Loci-Queries (MyFLq) Framework for Analysis of Forensic STR Data Generated by Massive Parallel Sequencing

• NCJ Number: 245525
• Journal: Forensic Science International: Genetics Volume: 9 Dated: March 2014 Pages: 1-8
• Author(s): Christophe Van Neste; Mado Vandewoestyne; Wim Van Criekinge; Dieter Deforce; Filip Van Nieuwerburgh
• Date Published: March 2014
• Length: 8 pages
• Sponsoring Agency: University of Ghent
• Publication Format: Article
• Publication Type: Research (Applied/Empirical); Report (Study/Research)
• Language: English
• Country: Ireland

Annotation

This project created a general bioinformatic framework, which the authors call My-Forensic-Loci-queries (MyFLq), for analyzing forensic data generated by massive parallel sequencing (MPS).

Abstract

The MyFLq framework was applied to an Illumina MiSeq dataset of a forensic Illumina amplicon library generated from a multilocus short tandem repeat (STR) polymerase chain reaction (PCR) on both single contribution samples and multiple person DNA mixtures. Although the multilocus PCR was not yet optimized for MPS in terms of amplicon length or locus selection, the results showed excellent results for most loci. They showed a high signal-to-noise ratio, correct allele calls, and a low limit of detection for minor DNA contributors in mixed DNA samples. Forensic DNA profiles of STR loci are currently obtained by using PCR followed by capillary electrophoresis (CE). CE separates fluorescently labeled PCR products based on their length. In order to produce unambiguous allele calls, the size ranges of STR loci with the same fluorescent tag must not overlap. This limits the number of loci that can be investigated in a single PCR and in a single capillary injection. MPS technologies do not rely on size separation, thus relieving the limitation on locus multiplexy. In addition, multiple samples can be multiplexed at the same time in a single run. MPS allows for analysis of millions of individual DNA strands in a DNA mixture, which, in theory, would allow for high resolution mixture analysis. Sequencing also enables the detection of single nucleotide polymorphism (SNPs) and STR sequence variants in addition to the gross STR repeat number. This enables analysts to determine the difference between equilength alleles in a DNA mixture. Certain mass spectrometry techniques also make it possible to differentiate equilength alleles, but complete characterization of polymorphism can only be accomplished by sequencing. 3 tables, 8 figures, and 12 references