DNAxs/DNAStatistX: Development and validation of a software suite for the data management and probabilistic interpretation of DNA profiles.

The data management, interpretation and comparison of sets of DNA profiles can be complex, time-consuming and error-prone when performed manually. This, combined with the growing numbers of genetic markers in forensic identification systems calls for expert systems that can automatically compare genotyping results within (large) sets of DNA profiles and assist in profile interpretation. To that aim, we developed a user-friendly software program or DNA eXpert System that is denoted DNAxs. This software includes features to view, infer and match autosomal short tandem repeat profiles with connectivity to up and downstream software programs. Furthermore, DNAxs has imbedded the 'DNAStatistX' module, a statistical library that contains a probabilistic algorithm to calculate likelihood ratios (LRs). This algorithm is largely based on the source code of the quantitative probabilistic genotyping system EuroForMix [1]. The statistical library, DNAStatistX, supports parallel computing which can be delegated to a computer cluster and enables automated queuing of requested LR calculations. DNAStatistX is written in Java and is accessible separately or via DNAxs. Using true and non-contributors to DNA profiles with up to four contributors, the DNAStatistX accuracy and precision were assessed by comparing the DNAStatistX results to those of EuroForMix. Results were the same up to rare differences that could be attributed to the different optimizers used in both software programs. Implementation of dye specific detection thresholds resulted in larger likelihood values and thus a better explanation of the data used in this study. Furthermore, processing time, robustness of DNAStatistX results and the circumstances under which model validations failed were examined. Finally, guidelines for application of the software are shared as an example. The DNAxs software is future-proof as it applies a modular approach by which novel functionalities can be incorporated.

A sensitive method to extract DNA from biological traces present on ammunition for the purpose of genetic profiling.

Exploring technological limits is a common practice in forensic DNA research. Reliable genetic profiling based on only a few cells isolated from trace material retrieved from a crime scene is nowadays more and more the rule rather than the exception. On many crime scenes, cartridges, bullets, and casings (jointly abbreviated as CBCs) are regularly found, and even after firing, these potentially carry trace amounts of biological material. Since 2003, the Forensic Laboratory for DNA Research is routinely involved in the forensic investigation of CBCs in the Netherlands. Reliable DNA profiles were frequently obtained from CBCs and used to match suspects, victims, or other crime scene-related DNA traces. In this paper, we describe the sensitive method developed by us to extract DNA from CBCs. Using PCR-based genotyping of autosomal short tandem repeats, we were able to obtain reliable and reproducible DNA profiles in 163 out of 616 criminal cases (26.5%) and in 283 out of 4,085 individual CBC items (6.9%) during the period January 2003-December 2009. We discuss practical aspects of the method and the sometimes unexpected effects of using cell lysis buffer on the subsequent investigation of striation patterns on CBCs.

Detection of three single nucleotide polymorphisms in the gene encoding mannose-binding lectin in a single pyrosequencing reaction.

Mannose-binding lectin (MBL) is a key molecule of innate immunity. Binding of MBL to carbohydrates present on pathogens activates the lectin pathway of complement activation, resulting into opsonization and anti-microbial protection. Three frequently occurring single nucleotide polymorphisms (SNPs) are described in the coding region of the MBL2 gene that are associated with abnormal polymerization of the MBL molecule, decreased serum concentrations of high molecular weight MBL, and strongly impaired function. Clinical studies have shown that these MBL SNPs are associated with increased susceptibility to infections, especially in immune-compromised persons, as well as with accelerated progression of chronic diseases. The present study describes a novel method to detect the three major MBL SNPs by pyrosequencing. The close proximity of these SNPs allows their detection in one single pyrosequencing reaction, resulting in clearly distinguishable patterns for each allele combination described until now. This method can be used for the easy and reliable detection of MBL SNPs to identify the basis of functional MBL deficiency in clinical diagnostics and research.