Forensic performance of two insertion–deletion marker assays

Abstract

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 favourable 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 analysed 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, we characterised 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. Allele frequencies were generated for the 68 markers in US African American, Caucasian, East Asian and Hispanic samples. We made a thorough assessment of the individual and combined performance of the InDel sets, as well as characterising 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.

Revisión sobre los marcadores del origen biogeográfico y su aplicación en la investigación forense

“…Por último, proporcionan una capacidad superior para detectar mezclas de adn de individuos distintos, dado que en los electroferogramas producen patrones de picos mucho más equilibrados que los snp. Y son más exitosos en el análisis de adn degradado, debido al menor tamaño del producto de pcr [17].…”

“…Igualmente, ha sido demostrada su capacidad de distinguir grupos de Oceanía, aunque con menor precisión [17]. Sin embargo, la población de Oriente Medio no es correctamente identificada, siendo descritos como "europeos" con componentes africanos minoritarios [18].…”

“…Sin embargo, debido a la falta de recombinación, presentan una limitación: este marcador no permite asignar un perfil a un individuo sino a un linaje extenso; es decir, tiene un bajo poder de discriminación. De esta forma, no se puede hablar del origen biogeográfico de un individuo sino de un linaje [17].…”

INNULs: A Novel Design Amplification Strategy for Retrotransposable Elements for Studying Population Variation

“…They are appealing in that they have similar properties as INNULs, and there have been some studies describing multiplexes that could be suited for human identity testing [25,[36][37][38][39][40][41][42] . Indeed, there is one commercially available kit, the Investigator DIPplex Kit (Qiagen), which enables multiplex typing of 30 INDELs [25,36,42] . Another promising INDEL multiplex (with 38 markers) was described by Pereira and colleagues [36,41] .…”

“…Indeed, there is one commercially available kit, the Investigator DIPplex Kit (Qiagen), which enables multiplex typing of 30 INDELs [25,36,42] . Another promising INDEL multiplex (with 38 markers) was described by Pereira and colleagues [36,41] . These INDEL multiplexes show great promise and particularly so because the alleles at a locus can be contained within short amplicons and are different but close in size.…”