DNA Database Search Research Articles

Incorporating non-genetic evidence in large scale missing person searches: A general approach beyond filtering

The search for missing persons implies several steps, from the preliminary investigation that involves collecting background data related to the case to the genetic kinship testing. Despite its crucial importance in identifications, only some approaches mathematically formalize the possibility of using preliminary investigation data. In some cases, a filtering strategy is applied, which implies selecting a subset of possible victims where some non-genetic variables perfectly match those of the missing. Through a Bayesian approach, we propose a mathematical model for computing the prior odds based on non-genetic variables usually collected during the preliminary investigation, such as biological sex, hair colour, and age. We use computational simulations to show how to incorporate these prior odds in DNA-database searches. Importantly, our results suggest that applying the proposed model leads to better search performance in underpowered cases from the genetic point of view, where few or distant relatives of the missing person are available for genotyping. Furthermore, the results are also helpful when using non-genetic data for prior odds in well-powered cases, where genetic data are enough to reach a reliable conclusion. It performs better than other approaches, such as using non-genetic data for filtering. The software mispitools, freely available on CRAN, implements all described methods (https://CRAN.R-project.org/package=mispitools).

ProbRank: An efficient DNA database search method for complex mixtures per a quantitative likelihood ratio model

Searching a DNA Database with a DNA profile from an evidentiary trace can provide investigative leads in a forensic case. Various searching approaches exist such as conventional methods based on matching alleles or more advanced methods computing likelihood ratios (LR) while considering drop-in and drop-out. Here we examine the potential of using a quantitative LR model (EuroForMix model incorporated in ProbRank method) that takes peak heights into account in comparison to a qualitative LR model (LRmix model implemented in SmartRank method). Both methods present DNA database candidates in order of decreasing LR. Especially regarding minor contributors in complex mixtures, the method using the quantitative model outperforms the method using the qualitative model in terms of sensitivity and specificity as more true donors and less adventitious matches are retrieved. ProbRank is to be implemented in DNAStatistX and is sufficiently fast for daily use.

Evaluation of large-scale highly polymorphic microhaplotypes in complex DNA mixtures analysis using RMNE method

DNA mixture interpretation is one of the most challenging problems in forensics. Complex DNA mixtures are more difficult to analyze when there are more than two contributors or related contributors. Microhaplotypes (MHs) are polymorphic genetic markers recently discovered and employed in DNA mixture analysis. However, the evidentiary interpretation of the MH genotyping data needs more debate. The Random Man Not Excluded (RMNE) method analyzes DNA mixtures without using allelic peak height data or the number of contributors (NoC) assumptions. This study aimed to assess how well RMNE interpreted mixed MH genotyping data. We classified the MH loci from the 1000 Genomes Project database into groups based on their Ae values. Then we performed simulations of DNA mixtures with 2–10 unrelated contributors and DNA mixtures with a pair of sibling contributors. For each simulated DNA mixture, incorrectly included ratios were estimated for three types of non-contributors: random men, parents of contributors, and siblings of contributors. Meanwhile, RMNE probability was calculated for contributors and three types of non-contributors, allowing loci mismatch. The results showed that the MH number, the MH Ae values, and the NoC affected the RMNE probability of the mixture and the incorrectly included ratio of non-contributors. When there were more MHs, MHs with higher Ae values, and a mixture with less NoC, the RMNE probability, and the incorrectly included ratio decreased. The existence of kinship in mixtures complicated the mixture interpretation. Contributors’ relatives as non-contributors and related contributors in the mixture increased the demands on the genetic markers to identify the contributors correctly. When 500 highly polymorphic MHs with Ae values higher than 5 were used, the four individual types could be distinguished according to the RMNE probabilities. This study reveals the promising potential of MH as a genetic marker for mixed DNA interpretation and the broadening of RMNE as a parameter indicating the relationship of a specific individual with a DNA mixture in the DNA database search.

Interpretation of DNA data within the context of UK forensic science - evaluation.

Forensic DNA provides a striking contribution to the provision of justice worldwide. It has proven to be crucial in the investigative phase of an unsolved crime where a suspect needs to be identified, e.g. from a DNA database search both nationally and internationally. It is also a powerful tool in the assignment of evidential weight to the comparison of a profile of a person of interest and a crime scene profile. The focus of this document is the evaluation of autosomal profiles for criminal trials in the UK. A separate review covers investigation and evaluation of Y-STR profiles, investigation using autosomal profiles, kinship analysis, body identification and Forensic Genetic Genealogy investigations. In less than 40 years, forensic DNA profiling has developed from a specialist technique to everyday use. Borrowing on advances in genome typing technology, forensic DNA profiling has experienced a substantial increase in its sensitivity and informativeness. Alongside this development, novel interpretation methodologies have also been introduced. This document describes the state of the art and future advances in the interpretation of forensic DNA data.

Making decisions in missing person identification cases with low statistical power

The present work proposes a general strategy for dealing with missing person identification cases through DNA-database search. Our main example is the identification of abducted children in the last civic-dictatorship of Argentina, known as the “Missing Grandchildren of Argentina”. Particularly we focus on those pedigrees where few, or only distant relatives of the missing person are available, resulting in low statistical power. For such complex cases we provide a statistical method for selecting a likelihood ratio (LR) threshold for each pedigree based on error rates. Furthermore, we provide an open-source user friendly software for computing LR thresholds and error rates. The strategy described in the paper could be applied to other large-scale cases of DNA-based identification hampered by low statistical power.

New federal rules limit police searches of family tree DNA databases

New federal rules limit police searches of family tree DNA databases

How to avoid driving DNA caseworkers crazy: CaseSolver, an expert system to investigate complex crime scenes

DNA analyses can be used for both investigative (crime scene-focused), or evaluative (suspect-focused) reporting. Investigative, DNA-led exploration of serious crimes always involves the comparison of hundreds of biological samples submitted by the authorities for analysis. Crime stain comparisons include both evidence to evidence profiles and reference to evidence profiles. When many complex DNA results (mixtures, low template LT-DNA samples) are involved in the investigation of a crime, the manual comparison of DNA profiles is very time-consuming and prone to manual errors. In addition, if the person of interest is a minor contributor, the classical approach of performing searches of national DNA databases is problematic because it is realistically restricted to clear major contributors and the occurrence of masking and drop-out means that there will not be a definitive DNA profile to perform the search with.CaseSolver is an open source expert system that automates analysis of complex cases. It does this by three sequential steps: a) simple allele comparison b) likelihood ratio (LR) based on a qualitative model (forensim) c) LR based on a quantitative model (EuroForMix). The software generates a list of potential match candidates, ranked according to the LRs, which can be exported as a report. The software can also identify contributors from small or large databases (e.g., staff database or 1 mill. individuals). In addition, an informative graphical network plot is generated that easily identifies contributors in common to multiple stains. Here we describe recent improvements made to the software in version v1.5.0, made in response to user requirements during intensive casework usage.

Likelihood ratios for evaluating DNA matches obtained from a database search when there is substructure in the population.

DNA database searches are frequently conducted to identify the suspects of crimes. When a match is obtained from such a database search, the evidence must be evaluated. Existing methods for assessment of the DNA evidence in this scenario require assumption of stochastic independence between the profiles in the database. However, when there is substructure in the population, this assumption is violated. The problem of how to account for population substructure in the database search scenario is analyzed and a solution in the form of a bounded estimate for the likelihood ratio is presented. The implications of these methods are investigated in a realistic scenario using published forensic allele frequencies to simulate ten-locus DNA profiles. In the simulated example, it is observed that the strength of the evidence can be inflated by more than a factor of 10 in 11.6% of database search cases if mild population substructure is ignored. With these methods, the magnitude of the subpopulation effect in the database search scenario can be quantified and the weight of the evidence of a DNA match more accurately assessed.

Calculating the Posterior Odds from a Single-Match DNA Database Search under various Scenarios with Minimal Assumptions

Calculating the Posterior Odds from a Single-Match DNA Database Search under various Scenarios with Minimal Assumptions

Identification of the alternative oxidase gene and its expression in the copepod Tigriopus californicus.

In addition to the typical electron transport system (ETS) in animal mitochondria responsible for oxidative phosphorylation, in some species there exists an alternative oxidase (AOX) pathway capable of catalyzing the oxidation of ubiquinol and the reduction of oxygen to water. The discovery of AOX in animals is recent and further investigations into its expression, regulation, and physiological role have been hampered by the lack of a tractable experimental model organism. Our recent DNA database searches using bioinformatics revealed an AOX sequence in several marine copepods including Tigriopus californicus. This species lives in tidepools along the west coast of North America and is subject to a wide variety of daily environmental stresses. Here we verify the presence of the AOX gene in T. californicus and the expression of AOX mRNA and AOX protein in various life stages of the animal. We demonstrate that levels of the AOX protein increase in T. californicus in response to cold and heat stress compared to normal rearing temperature. We predict that a functional AOX pathway is present in T. californicus, propose that this species will be a useful model organism for the study of AOX in animals, and discuss future directions for animal AOX research.

Cloning and characterization of zebrafish K2P13.1 (THIK-1) two-pore-domain K+ channels

Two-pore-domain potassium (K2P) channels conduct background potassium currents in the heart and other tissues. K2P currents are involved in the repolarization of action potentials and stabilize the resting membrane potential. Human K2P13.1 (THIK-1) channels are expressed in the heart and have recently been implicated in atrial fibrillation. The in vivo significance of K2P13.1 currents in cardiac electrophysiology is not known. We hypothesized that Danio rerio (zebrafish) may serve as model to elucidate the functional role of cardiac K2P13.1 channels. This work was designed to characterize zebrafish orthologs of K2P13.1.Two zkcnk13 coding sequences were identified by DNA database searches and amplified from zebrafish cDNA. Human and zebrafish K2P13.1 proteins exhibit 70% (K2P13.1a) and 66% (K2P13.1b) identity. Kcnk13 expression in zebrafish was studied using polymerase chain reaction. Zebrafish kcnk13a and zkcnk13b mRNAs were detected in brain and heart. Human and zebrafish K2P13.1 currents were analyzed in the Xenopus oocyte expression system by voltage clamp electrophysiology. Zebrafish K2P13.1a polypeptides were non-functional, while zK2P13.1b channels exhibited K+ selective, outwardly rectifying currents. Zebrafish and human K2P13.1 currents were similarly activated by arachidonic acid and reduced by barium, mexiletine, lidocaine, and inhibition of phospholipase C.In conclusion, zebrafish K2P13.1b channels and their human orthologs exhibit structural and regulatory similarities. Zebrafish may be used as in vivo model for the assessment of physiology and therapeutic significance of K2P13.1.

Validation of SmartRank: A likelihood ratio software for searching national DNA databases with complex DNA profiles

Searching a national DNA database with complex and incomplete profiles usually yields very large numbers of possible matches that can present many candidate suspects to be further investigated by the forensic scientist and/or police. Current practice in most forensic laboratories consists of ordering these ‘hits’ based on the number of matching alleles with the searched profile. Thus, candidate profiles that share the same number of matching alleles are not differentiated and due to the lack of other ranking criteria for the candidate list it may be difficult to discern a true match from the false positives or notice that all candidates are in fact false positives. SmartRank was developed to put forward only relevant candidates and rank them accordingly. The SmartRank software computes a likelihood ratio (LR) for the searched profile and each profile in the DNA database and ranks database entries above a defined LR threshold according to the calculated LR. In this study, we examined for mixed DNA profiles of variable complexity whether the true donors are retrieved, what the number of false positives above an LR threshold is and the ranking position of the true donors. Using 343 mixed DNA profiles over 750 SmartRank searches were performed. In addition, the performance of SmartRank and CODIS were compared regarding DNA database searches and SmartRank was found complementary to CODIS. We also describe the applicable domain of SmartRank and provide guidelines. The SmartRank software is open-source and freely available. Using the best practice guidelines, SmartRank enables obtaining investigative leads in criminal cases lacking a suspect.

Exploration of SNP variants affecting hair colour prediction in Europeans.

DNA profiling is a key tool for forensic analysis; however, current methods identify a suspect either by direct comparison or from DNA database searches. In cases with unidentified suspects, prediction of visible physical traits e.g. pigmentation or hair distribution of the DNA donors can provide important probative information. This study aimed to explore single nucleotide polymorphism (SNP) variants for their effect on hair colour prediction. A discovery panel of 63 SNPs consisting of already established hair colour markers from the HIrisPlex hair colour phenotyping assay as well as additional markers for which associations to human pigmentation traits were previously identified was used to develop multiplex assays based on SNaPshot single-base extension technology. A genotyping study was performed on a range of European populations (n = 605). Hair colour phenotyping was accomplished by matching donor's hair to a graded colour category system of reference shades and photography. Since multiple SNPs in combination contribute in varying degrees to hair colour predictability in Europeans, we aimed to compile a compact marker set that could provide a reliable hair colour inference from the fewest SNPs. The predictive approach developed uses a naïve Bayes classifier to provide hair colour assignment probabilities for the SNP profiles of the key SNPs and was embedded into the Snipper online SNP classifier ( http://mathgene.usc.es/snipper/ ). Results indicate that red, blond, brown and black hair colours are predictable with informative probabilities in a high proportion of cases. Our study resulted in the identification of 12 most strongly associated SNPs to hair pigmentation variation in six genes.

Evaluation of the RapidHIT™ 200 System: A comparative study of its performance with Maxwell® DNA IQ™/Identifiler® Plus/ABI 3500xL workflow

RapidHIT™ System is a rapid DNA instrument that is capable of processing forensic samples from extraction through to capillary electrophoresis and profile generation within two hours. Evaluation of the RapidHIT™ 200 System was conducted to examine several key performance indicators of the instrument, including reproducibility, contamination, sensitivity, versatility and the possibility of sample re-extraction. Results indicated that the RapidHIT™ 200 System was capable of generating high quality DNA profiles which were comparable to those from the standard protocol comprising of Maxwell® 16 DNA IQ™ System, Identifiler® Plus and ABI 3500xL. No contamination was detected during the studies. Results also showed that the instrument was able to generate DNA profiles from samples containing lower amounts of DNA (0.5μl of blood) albeit with more allele and locus dropouts when compared to the standard protocol. The ability to process blood swabs, blood-stained FTA punches, semen swabs, buccal swabs, product of conception (POC), bone marrow, fingernail clippings and cigarette butts at a good success rate indicated the robustness and versatility of the RapidHIT™ 200 System. Furthermore, additional alleles could be recovered via re-analysis of the failed samples using the standard protocol. In summary, our results showed that the RapidHIT™ 200 System was able to process casework samples for the purpose of providing rapid intelligence through DNA database searches and reference matching. Confirmative DNA results can be obtained through either concurrent processing of duplicate samples via standard protocol or re-extraction of samples retrieved from the RapidHIT™ sample cartridge.

The effect of wild card designations and rare alleles in forensic DNA database searches

Forensic DNA databases are powerful tools used for the identification of persons of interest in criminal investigations. Typically, they consist of two parts: (1) a database containing DNA profiles of known individuals and (2) a database of DNA profiles associated with crime scenes. The risk of adventitious or chance matches between crimes and innocent people increases as the number of profiles within a database grows and more data is shared between various forensic DNA databases, e.g. from different jurisdictions.The DNA profiles obtained from crime scenes are often partial because crime samples may be compromised in quantity or quality. When an individual's profile cannot be resolved from a DNA mixture, ambiguity is introduced. A wild card, F, may be used in place of an allele that has dropped out or when an ambiguous profile is resolved from a DNA mixture.Variant alleles that do not correspond to any marker in the allelic ladder or appear above or below the extent of the allelic ladder range are assigned the allele designation R for rare allele. R alleles are position specific with respect to the observed/unambiguous allele. The F and R designations are made when the exact genotype has not been determined. The F and R designation are treated as wild cards for searching, which results in increased chance of adventitious matches. We investigated the probability of adventitious matches given these two types of wild cards.

Analysis of rare alleles of D13S325 falling in the range of adjacent locus

To analyze the rare alleles of D13S325 locus which fell in the size range of D12S391 locus with the STRtyper-10G kit. Genotyping results of cases with suspected rare alleles of D13S325 were verified with Sinofiler(TM) kit and a singleplex amplification system. The rare alleles were separated and sequenced. Five families were detected with rare alleles of the D13S325 locus, which were misread as allele 20 of D12S391 locus. The alleles were named as 5.1 based on DNA sequences and have a frequency of 0.156 × 10(-2). As the rare allele 5.1 of D13S325 locus with the STRtyper-10G kit is prone to be mistyped, attention should be paid in the paternity testing, personal identification and DNA database search.

Letting Innocence Suffer: The Need for Defense Access to the Law Enforcement DNA Database

Law enforcement has gradually amassed a sizable DNA database that holds considerable promise for solving cold cases and identifying suspects. The Supreme Court has blessed this effort, allowing investigators to include profiles of arrestees as well as convicted persons in the database. At present, though, law enforcement has a near monopoly on use of the DNA database, leaving defendants at the whim of the law enforcement officials who control access to this tool. Legal scholars have alternatively praised and decried the database, but none has examined its prospects for proving defendants’ innocence post-conviction. This Article fills that void by identifying a limited due process right to defense-initiated DNA database searches. The Article argues that the database is a powerful truth-promoting tool that should be available to law enforcement and defendants alike. Because legislators have failed to promote the search for actual offenders through statutory rights of access, this Article presents the constitutional authority for defense-initiated searches to vindicate the rights of innocent defendants.

The use of wildcards in forensic DNA database searches

Forensic genetic databases contain millions of DNA profiles worldwide. An allelic drop-out at a heterozygous locus (two different alleles) erroneously results in an observed homozygous profile. To guard against this, wildcards are induced for homozygous profiles. The wildcard represents any allele including the observed allele.In this paper, theoretical expressions for the number of matching loci are derived, results shown from a Danish dataset with more than 50,000 DNA profiles and simulations used to link homozygosity with the drop-out probability, which best mimics wildcard matching.

Regulating new forms of forensic DNA profiling under Australian legislation: familial matching and DNA phenotyping

Forensic DNA profiling uses ‘non-coding’ parts of the human genome to compare DNA profiles and establish links between individuals and crimes under investigation. In most situations, only a complete match between such profiles is significant. However, it is also possible to identify individuals through ‘familial matching’, for example, where a DNA database search yields a partial match with a suspect profile, suggesting that the suspect is a close relative of the person on the database. It has also become possible through ‘DNA phenotyping’ to analyse ‘coding’ parts of the human genome to produce a probabilistic assessment that the suspect is, for example, of a particular racial background, or has a particular hair or eye colour. Neither of these more novel techniques is mentioned in Australian forensic procedures legislation. This article argues that familial matching uses the traditional DNA profiling methodology and is no more invasive than established methods of investigation. However, DNA phenotyping employs a different methodology from traditional DNA profiling, and generates information beyond simply generating a means of identification. DNA phenotyping for externally visible traits should be permitted, but analysis for other traits, such as pathophysiology and psychopathology, should only be permitted if certain conditions are met.

DNA Based Familial Searching and Related Statistical Issues

Copyright: © 2012 Ge J. This is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited. DNA databases have become essential tools for forensic investigations. The typical DNA database search seeks direct matches between a forensic profile from crime scene evidence and an offender profile in the database. However, direct matches may not be obtained because the database does not contain all people in the population. As of January 2012, there are about 10.5 million offender profiles in the US National DNA Index (NDIS) [1], which only covers about 3% of the US population (i.e., there are more than 313 million people in the US [2]). To extend the investigative lead value of current databases, an additional approach, familial searching, has been used to determine the source of a forensic sample by searching the database for possible relatives (e.g., parents, children, full-sibs) of the true source of the sample. It also is an effective way to expand the utility of DNA databases with relatively low costs. This approach, when performed under stringent criteria, has been used to develop strong investigative leads and to successfully identify perpetrators of crimes [3-5].