In this paper, the authors report on their characterization of population variation with two InDel identification assays, with the goal of determining the utility of insertion-deletion length polymorphisms for forensic analysis.
Improving the amplification and analysis of highly degraded DNA extracts has been a longstanding area of research in forensic genetics. One of the most promising recent developments in analysis of degraded DNA is the availability of short, biallelic insertion–deletion length polymorphisms (InDels) in highly multiplexed assays. InDels share many of the favorable characteristics of single-nucleotide polymorphisms (SNPs) that make them ideal markers for analysis of degraded DNA, including: analysis in short amplicon size ranges, high multiplexing capability and low mutation rates. In addition, as length-based polymorphisms, InDels can be analyzed with the same simple dye-labelled PCR primer methods as standard forensic short tandem repeats. Separation and detection of fluorescently dye-labelled PCR products by capillary electrophoresis eliminate the multiple step protocols required by SNP typing with single-base extension assays and provide a closer relationship between the input DNA and the profile peak height ratios. Therefore InDel genotyping represents an effective new approach for human identification that adds informative new loci to the existing battery of forensic markers. To assess the utility of InDels for forensic analysis, the authors characterized population variation with two InDel identification assays: the 30-plex Qiagen DIPplex panel and a 38-plex panel developed by Pereira et al. in 2009 [1]. Allele frequencies were generated for the 68 markers in US African American, Caucasian, East Asian and Hispanic samples. They made a thorough assessment of the individual and combined performance of the InDel sets, as well as characterizing profile artifacts and other issues related to the routine use of these newly developed forensic assays based on artificially degraded DNA and mixed source samples. (Published Abstract Provided)