Sensitivity of inferences in forensic genetics to assumptions about founding genes

Many forensic genetics problems can be handled using structured systems of discrete variables, for which Bayesian networks offer an appealing practical modeling framework, and allow inferences to be computed by probability propagation methods. However, when standard assumptions are violated--for example, when allele frequencies are unknown, there is identity by descent or the population is heterogeneous--dependence is generated among founding genes, that makes exact calculation of conditional probabilities by propagation methods less straightforward. Here we illustrate different methodologies for assessing sensitivity to assumptions about founders in forensic genetics problems. These include constrained steepest descent, linear fractional programming and representing dependence by structure. We illustrate these methods on several forensic genetics examples involving criminal identification, simple and complex disputed paternity and DNA mixtures.Comment: Published in at http://dx.doi.org/10.1214/09-AOAS235 the Annals of Applied Statistics (http://www.imstat.org/aoas/) by the Institute of Mathematical Statistics (http://www.imstat.org

Efficient Forward Simulation of Fisher-Wright Populations with Stochastic Population Size and Neutral Single Step Mutations in Haplotypes

In both population genetics and forensic genetics it is important to know how haplotypes are distributed in a population. Simulation of population dynamics helps facilitating research on the distribution of haplotypes. In forensic genetics, the haplotypes can for example consist of lineage markers such as short tandem repeat loci on the Y chromosome (Y-STR). A dominating model for describing population dynamics is the simple, yet powerful, Fisher-Wright model. We describe an efficient algorithm for exact forward simulation of exact Fisher-Wright populations (and not approximative such as the coalescent model). The efficiency comes from convenient data structures by changing the traditional view from individuals to haplotypes. The algorithm is implemented in the open-source R package 'fwsim' and is able to simulate very large populations. We focus on a haploid model and assume stochastic population size with flexible growth specification, no selection, a neutral single step mutation process, and self-reproducing individuals. These assumptions make the algorithm ideal for studying lineage markers such as Y-STR.Comment: 17 pages, 6 figure

DNA Typing Compatibility with a One Step Saliva Screening Test

Screening a substrate for bodily fluids is an extremely important step for locating areas that may contain DNA. Several different methods have been developed for saliva (1). The Phadebas® Forensic Press (PFP) test is a presumptive saliva test that utilizes a preloaded paper that will react with the enzyme amylase, a component of saliva (2-5). Because of its ability to screen for amylase while simultaneously locating stains, the PFP may prove to be an effective, rapid method for screening. However it is important to assess whether the PFP introduces any inhibitors (7) to downstream processing such as PCR amplification. Based on previous studies, we hypothesize that the PFP will provide a rapid and sensitive method for locating multiple saliva stains simultaneously, without introducing inhibitors to DNA profiling. To test the limitations of PFP as well as evaluated its effects on DNA profiling we first created a dilution series of saliva ranging from neat to 1:5000. After this we preformed sensitivity tests on an indirect method, UV degraded samples and washed samples as well as with bodily fluid mixtures. Once all sensitivity tests were done, cuttings were taken from the substrate and PFP paper and analyzed for DNA. Tests found that the sensitivity ranges of the PFP were between 1:10 and 1:1000, indirect tests were less sensitive than direct, all bodily fluid mixtures were detected, and UV degraded samples took more time to react. In addition our DNA results confirmed our hypothesis that PFP does not inhibit DNA and is a useful method for locating stains. This project was funded by NSFREU Grant DBI 1262832

Effect of multiple allelic drop-outs in forensic RMNE calculations

Technological advances such as massively parallel sequencing enable increasing amounts of genetic information to be obtained from increasingly challenging samples. Certainly on low template, degraded and multi-contributor samples, drop-outs will increase in number for many profiles simply by analyzing more loci, making it difficult to probabilistically assess how many drop-outs have occurred and at which loci they might have occurred. Previously we developed a Random Man Not Excluded (RMNE) method that can take into account allelic drop-out while avoiding detailed estimations of the probability that drop-outs have occurred, nor making assumptions about at which loci these drop-outs might have occurred. The number of alleles that have dropped out, does not need to be exactly known. Here we report a generic Python algorithm to calculate the RMNE probabilities for any given number of loci. The number of allowed drop-outs can be set between 0 and twice the number of analyzed loci. The source code has been made available on https://github.com/fvnieuwe/rmne. An online web-based RMNE calculation tool has been made available on http://forensic.ugent.be/rmne. The tool can calculate these RMNE probabilities from a custom list of probabilities of the observed and non-observed alleles from any given number of loci. Using this tool, we explored the effect of allowing allelic drop-outs on the evidential value of random forensic profiles with a varying number of loci. Our results give insight into how the number of allowed drop-outs affects the evidential value of a profile and how drop-out can be managed in the RMNE approach

Trumping communitarianism: crime control and forensic DNA typing and databasing in Singapore

Liberalism and communitarianism have figured prominently in discussions of how to govern forensic DNA practices (forensic DNA typing and databasing). Despite the prominence of these two political philosophies and their underlying values, no studies have looked at the governance of forensic DNA practices in a nondemocratic country governed by a communitarian logic. To fill this lacuna in the literature, this article considers Singapore as an authoritarian state governed by a communitarian philosophy. The article highlights basic innovations and technologies of forensic DNA practices and articulates a liberal democratic version of “biolegality” as described by Michael Lynch and Ruth McNally. It goes on to consider briefly various (political) philosophies (liberalism and communitarianism) and law enforcement models (due process and crime control models). The main part of the article records the trajectory, and hence biolegal progress, of forensic DNA practices in Singapore and compares it with trajectories in England and the United States. The article concludes that Singapore's forensic DNA practices are organized according to the crime control model and therefore safety and the war against crime and terrorism trump individual rights and legal principles such as privacy, bodily integrity, proportionality, presumption of innocence. and onus of proof

Optimizing Collection of Trace Biological Samples from Vehicle Headrests

Tape-lifting and swabbing are two methods commonly used for collecting biological samples in the United Kingdom and United States to investigate vehicle crimes. Determining the optimal collection method may lead to an increase in generating DNA profiles and crime-solving. The objective of this study is to evaluate the efficiency of adhesive tape and the double-swab collection methods for investigating vehicle crimes with possible touch DNA samples. Two experiments were conducted to evaluate the use of tape-lifts and swabs on spiked common vehicle fabric materials. The efficiency of recovery between the two collection methods was performed using qPCR. The results from the collection of fabric materials indicated tape-lifts outperformed swabbing on cloth and vinyl substrates, while swabbing resulted in comparable recovery on leather substrates. By optimizing sample collection techniques, we aim to aid not only investigations involving vehicles but also other crimes with touch DNA evidence present

DNA, Data and Ethics

The biophysical differences between different kinds of DNA data banks are described. The different ethical implications of DNA fingerprint data banks, data banks of known gene sequences, and data banks of total genomic sequences are considered. Ethical approaches using the concept of the common good and those based on human rights are evaluated in the context of DNA data. Additional theological considerations are discussed. In conclusion, a 'one size fits all' approach to bioethics in this area is rejected

Evaluation of Stem-Loop Reverse Transcription and Poly-A Tail Extension in MicroRNA Analysis of Body Fluids

MicroRNA has been demonstrated to be a viable tool for body fluid identification purposes in forensic casework. Stem-loop reverse transcription (slRT) is regularly used for cDNA synthesis from mature miRNA, along with poly-A tail extension. Both have been used in a forensic context, but no direct comparison has been carried out. It has also not been shown whether poly-A tail extension can be used upon DNA extracts, as previously shown with slRT. Blood and saliva samples were collected and underwent DNA extraction with or without on-column DNA digestion. All samples were then aliquoted and underwent slRT and poly-A tail extension separately. qPCR was then conducted targeting microRNA markers hsa-miR-451 and hsa-miR-205. It was shown that the DNA digestion step did not affect the ability to differentiate between blood and saliva. It was also shown that this differentiation was possible using poly-A tail extension, and that poly-A tail extension exhibited more amplification than slRT. So whilst the choice of slRT and poly-A tail extension for the purpose of forensic body fluid identification is not critical, it may be best to use poly-A tail extension, particularly where there are low traces of sample

Behavioral Genetics Research and Criminal DNA Databases

Kaye discusses DNA databanks and the potential use of such databanks for behavioral genetics research. He addresses the concern that DNA databanks serve as a limitless repository for future research and that the samples used in the databanks could be used for research into a crime gene