Single Source Samples Research Articles

How degraded is our DNA? A review of single source live case work samples with optimal DNA inputs processed with the PowerPlex® ESI17 Fast kit

LGC validated the PowerPlex® ESI17 Fast system (ESI17F), (Promega) in July 2014. As part of the validation a characterisation study was performed to assess kit performance at different DNA inputs.Following implementation of the ESI17F system, reports of lower than expected peak heights and heterozygous imbalance being present in optimal input (500pg) samples were made. A review of profile quality for single source samples with optimal DNA input was carried out. A number of variables were assessed to see if there was a connection with the observed reduced peak height and heterozygous events. Sample degradation was observed to be the major cause of reduced peak heights and heterozygous imbalance in samples with optimal DNA input.Evidence of DNA degradation was observed in ∼50% of samples reviewed. Although the ESI17F system provides smaller amplicons for the loci that are required to load to the UK National DNA database; the larger number of loci present within the kit results in a larger number of large amplicons that are more likely to be affected by DNA degradation.

An evaluation of the PowerSeq™ Auto System: A multiplex short tandem repeat marker kit compatible with massively parallel sequencing

Capillary electrophoresis (CE) and multiplex amplification with fluorescent tagging have been routinely used for STR typing in forensic genetics. However, CE-based methods restrict the number of markers that can be multiplexed simultaneously and cannot detect any intra-repeat variations within STRs. Several studies already have indicated that massively parallel sequencing (MPS) may be another potential technology for STR typing. In this study, the prototype PowerSeq™ Auto System (Promega) containing the 23 STR loci and amelogenin was evaluated using Illumina MiSeq. Results showed that single source complete profiles could be obtained using as little as 62pg of input DNA. The reproducibility study showed that the profiles generated were consistent among multiple typing experiments for a given individual. The mixture study indicated that partial STR profiles of the minor contributor could be detected up to 19:1 mixture. The mock forensic casework study showed that full or partial profiles could be obtained from different types of single source and mixture samples. These studies indicate that the PowerSeq Auto System and the Illumina MiSeq can generate concordant results with current CE-based methods. In addition, MPS-based systems can facilitate mixture deconvolution with the detection of intra-repeat variations within length-based STR alleles.

PE-Swab Direct STR Amplification of Forensic Touch DNA Samples.

The PE-Swab direct STR amplification workflow was developed to process low-level "touch DNA" samples. In this workflow, a forensic sample is first collected on a 4-mm PE-Swab (a novel sample collection device); two 2-mm punches containing collected samples are then generated from the PE-Swab and directly amplified for STR typing. Compared to the conventional STR workflow, which involves DNA extraction, purification, and elution volume reduction, the PE-Swab direct STR amplification workflow does not require sample preparation and takes <60 sec before a touch sample is ready for STR amplification. Because there is no DNA loss due to sample preparation, the PE-Swab workflow is more sensitive than the conventional STR workflow. The average peak height per sample obtained by the PE-swab workflow is 3 times higher than that from the conventional workflow with both low-level single source and two-contributor mixture samples tested in this study.

Evaluation of the RapidHIT™ 200, an automated human identification system for STR analysis of single source samples.

The RapidHIT™ 200 Human Identification System was evaluated to determine its suitability for STR analysis of single source buccal swabs. Overall, the RapidHIT™ 200 performed as well as our traditional capillary electrophoresis based method in producing useable profile information on a first-pass basis. General observations included 100% concordance with known profile information, consistent instrument performance after two weeks of buccal swab storage, and an absence of contamination in negative controls. When data analysis was performed by the instrument software, 95.3% of the 85 samples in the reproducibility study gave full profiles. Including the 81 full profiles, a total of 2682 alleles were correctly called by the instrument software, or 98.6% of 2720 possible alleles tested. Profile information was generated from as little as 10,000 nucleated cells, with swab collection technique being a major contributing factor to profile quality. The average peak-height-ratio for heterozygote profiles (81%) was comparable to conventional STR analysis, and while a high analytical threshold was required when offline profile analysis was performed (800 RFU), it was proportionally consistent with traditional methods. Stochastic sampling effects were evaluated, and a manageable approach to address limits of detection for homozygote profiles is provided. These results support consideration of the RapidHIT™ 200 as an acceptable alternative to conventional, laboratory based STR analysis for the testing of single source buccal samples, with review of profile information as a requirement until an expert software system is incorporated, and when proper developmental and internal validation studies have been completed.

Facile semi-automated forensic body fluid identification by multiplex solution hybridization of NanoString® barcode probes to specific mRNA targets.

A DNA profile from the perpetrator does not reveal, per se, the circumstances by which it was transferred. Body fluid identification by mRNA profiling may allow extraction of contextual 'activity level' information from forensic samples. Here we describe the development of a prototype multiplex digital gene expression (DGE) method for forensic body fluid/tissue identification based upon solution hybridization of color-coded NanoString(®) probes to 23 mRNA targets. The method identifies peripheral blood, semen, saliva, vaginal secretions, menstrual blood and skin. We showed that a simple 5 min room temperature cellular lysis protocol gave equivalent results to standard RNA isolation from the same source material, greatly enhancing the ease-of-use of this method in forensic sample processing. We first describe a model for gene expression in a sample from a single body fluid and then extend that model to mixtures of body fluids. We then describe calculation of maximum likelihood estimates (MLEs) of body fluid quantities in a sample, and we describe the use of likelihood ratios to test for the presence of each body fluid in a sample. Known single source samples of blood, semen, vaginal secretions, menstrual blood and skin all demonstrated the expected tissue-specific gene expression for at least two of the chosen biomarkers. Saliva samples were more problematic, with their previously identified characteristic genes exhibiting poor specificity. Nonetheless the most specific saliva biomarker, HTN3, was expressed at a higher level in saliva than in any of the other tissues. Crucially, our algorithm produced zero false positives across this study's 89 unique samples. As a preliminary indication of the ability of the method to discern admixtures of body fluids, five mixtures were prepared. The identities of the component fluids were evident from the gene expression profiles of four of the five mixtures. Further optimization of the biomarker 'CodeSet' will be required before it can be used in casework, particularly with respect to increasing the signal-to-noise ratio of the saliva biomarkers. With suitable modifications, this simplified protocol with minimal hands on requirement should facilitate routine use of mRNA profiling in casework laboratories.

Rapid PCR protocols for forensic DNA typing on six thermal cycling platforms.

Rapid PCR protocols for the amplification of typing STR multiplexes were evaluated on six different thermal cyclers. Through the use of a faster DNA polymerase coupled with the use of rapid thermal cyclers the amplification cycling times were reduced down to as little as 14 min using PCR primers from the commercially available multiplex STR typing kit Identifiler. Previously described two-step and three-step thermal cycling protocols were evaluated for the six thermal cyclers on 95 unique single-source DNA extracts. CE characterization of the PCR products indicates good peak balance between loci (median values greater than 0.84), and N minus four stutter ratios on averages were 30 to 40% higher than for standard Identifiler PCR conditions. Nonspecific amplification artifacts were observed, but were not observed to migrate within the allele calling bins. With the exception of one locus (D18S51) in a single sample, genotyping results were concordant with manufacturer's recommended amplification conditions utilizing standard thermal cycling procedures. Assay conditions were robust enough to routinely amplify 250 to 500 pg of template DNA. This work describes the protocols for the rapid PCR amplification of STR multiplexes on various PCR thermal cyclers with the future intent to support validation for typing single-source samples in a database laboratory.

Analysis of allelic drop-out using the Identifiler(®) and PowerPlex(®) 16 forensic STR typing systems.

Low-template (LT) DNA profiles continue to present interpretational challenges to the forensic community. Whether the LT contribution comprises the main profile, or whether it is present as the minor component of a mixture, ambiguity arises from the possibility that alleles present in the biological sample may not be detected in the resulting DNA profile. This phenomenon is known as allelic drop-out. This ambiguity complicates both the assessment of the potential number of contributors and estimation of the weight of the DNA evidence for or against specific propositions. One solution to estimating the weight of the evidence is to use a likelihood ratio (LR) that incorporates the probability of allelic drop-out P(DO) estimated for the specific evidence sample under consideration. However, although a vast repository of data exists, few empirical studies to determine allelic drop-out probabilities have been performed to date. Here we characterized patterns of allelic drop-out in single-source samples using both universal and run-specific analytical thresholds. Not surprisingly, we found fewer instances of apparent drop-out when using a lower (run-specific) detection threshold. Also, unsurprisingly, a positive correlation exists between allele drop-out and allele length, even in good quality samples. We used logistic regression to model the fraction of alleles that dropped out of a profile as a function of the average height of the detected peaks. The equation derived from the logistic regression model allowed us to estimate the expected drop-out probability for an evidentiary sample based on the average peak height of the profile. We show that the LRs calculated using the estimated drop-out probabilities were similar to those calculated using the benchmark drop-out probabilities, suggesting that the estimates of the drop-out probability are accurate and useful. This trend holds even when using the data from the PowerPlex(®) 16 typing system to estimate the drop-out probability for an Identifiler(®) profile, and vice versa. Thus we demonstrate that use of a LR that incorporates empirically estimated allelic drop-out probabilities provides a reliable means for extracting additional information from LT forensic DNA profiles.

Lab Automation Insights in Sample Preparation for LC/MS Analysis

Copyright: © 2014 Rogatsky E. 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. This week in San Diego, USA the Society for Lab Automation and Screening (SLAS) annual meeting and expo is taking place. This conference features 132 word class podium presentations and 400 poster presentations attracting experts from industry and academia, students, engineers and business leaders from around the World. This is only the third annual meeting, representing a relatively young and rapidly growing and developing field of automation for different laboratory workflows and processes, which is steadily replacing semi-automatic or manual methods. Initially, the complete automation of manufacturing processes was achieved in industry for various production lines. Next, automation has brought benefits to sterile environments, e.g. vaccine production and blood banks in order to minimize employee exposure to biological hazards, minimizing human error, and ensuring product purity and integrity. The next breakthrough of automation was in routine laboratory operations, such as immunoassays, crystallography, DNA screening/sequencing, cell culture and stem cells assays. Automation of immunoassays has allowed multiplexing (multiple parallel assays) using single source serum samples significantly speeding up analysis while enhancing sample integrity by eliminating multiple freeze thaw cycles, and/or reducing sample requirements by reformatting from a single source sample. ELISA and other plate based immunoassay are the most frequently used assays in clinical diagnostics. They allow fast, relatively specific and sensitive assays of many analytes or metabolites. A workflow bottleneck for immunoassays is a typical incubation time of several hours, that makes the processing throughput of manual processing relatively slow only a few plates per day per lab technician. Automation of plate based assays, which has matured over the past few years has increased the productivity of clinical laboratories, decreased operational costs, minimized (human) errors, while enhancing workplace safety for laboratory personnel.

Developmental validation of the PowerPlex® 21 System

The PowerPlex(®) 21 System is a STR multiplex that has been optimized for casework samples while still being capable of database workflows including direct amplification. The loci included in the multiplex offer increasing overlap with core loci used in different countries and regions throughout the world. The PowerPlex(®) 21 System contains D1S1656, D2S1338, D3S1358, D5S818, D6S1043, D7S820, D8S1179, D12S391, D13S317, D16S539, D18S51, D19S433, D21S11, Amelogenin, CSF1PO, FGA, Penta D, Penta E, TH01, TPOX, and vWA. These loci represent all 13 core CODIS loci in addition to loci commonly used in Asia and Europe. A developmental validation study was completed to document performance capabilities and limitations of the PowerPlex(®) 21 System. Data from this validation work served as the basis for the following conclusions: genotyping of single-source samples was reliable across a range of template DNA concentrations with >95% alleles called at 50 pg. Direct amplification of samples from FTA(®) storage cards was successfully performed using the reagents provided with the system and modified cycling protocols provided in the technical manual. Mixture analysis showed that over 95% of minor alleles were detected at 1:9 ratios. Reaction conditions including volume and annealing temperature as well as the concentrations of primers, DNA polymerase, magnesium, and Master Mix were shown to be optimal and able to withstand moderate variations without affecting system performance. Reproducible results were generated by different users at different sites. Finally, concordance studies showed consistent results when comparing the PowerPlex(®) 21 System with other commercially available STR-genotyping systems.

Modeling one complete versus triplicate analyses in low template DNA typing

There are generally two strategies for low template DNA typing: the complete strategy, which uses all available DNA in a single PCR and subsequent typing, and the consensus strategy, in which the biological sample is divided into two or more aliquots and the genotype profile is determined by consensus from these "replicates." In this study, the consensus and complete strategies are compared by a statistical approach in terms of the accuracy of obtaining the correct genotype at a single locus for single source samples. Logistic models were employed to describe the allele drop-out and drop-in events. The parameters of the models were estimated with empirical or hypothetical data. The probabilities of obtaining the true genotype and the chances to observe drop-out and drop-in alleles were estimated and compared for both strategies. Consistent with a previous experimental study, this study found that, with relatively high input DNA (e.g., ≥ 100 pg), the complete strategy performs better than the consensus strategy to obtain the true genotype and the complete strategy will display less dropped out alleles. The consensus strategy had less drop-in alleles for ≤ 100 pg DNA samples. Moreover, the limitations of the logistic models were discussed. Ideal models with better fit of empirical data approximating casework conditions were proposed for future studies.

Antecedents of dynamic cross-cultural competence in adult third culture kids (ATCKs)

Purpose – The “adult third culture kid” (ATCK) is an individual who has spent significant periods of childhood living outside his or her parents’ culture(s). Research is needed to identify specific experiential variables responsible for the development of components of cross-cultural competencies (CC) in ATCKs. The goal of this study is to gain insight into these relationships and provide a foundation for continuing investigation by examining how early international experience and personality variables impact CC in ATCKs. Specifically, the study examines how four components of early international experience and two characteristics of stable CC impact three dynamic characteristics of CC. Design/methodology/approach – Study participants (159) had spent their childhood years living in one or more foreign countries. In all, 54 percent of the sample was women, and the average age was 22 (SD=1.52). None of the subjects had any international work experience, allowing us to look at the impact of non-work experience without the confounding effect found in other research of this type. Data were collected at the beginning and end of a three-week period. Findings – There are five important predictors of CC in ATCKs: variety of early international experience (number of different countries lived in), language diversity (the number of languages they speak), family diversity (the number of different ethnicities in their family's background), and the personality trait of openness to experience. Research limitations/implications – The generalizability of study findings is limited by the nature and size of the sample. In addition, the single source sample of this study is also a limitation, as single source samples are subject to common method bias. We reduced this potential bias by using a time lag (Podsakoff et al., 2003) to create a temporal separation between the measurement of the predictors and the dependent variables, a procedural remedy suggested by Podsakoff et al. (2003). Practical implications – The practical uses for the findings of this study by human resource management (HRM) professionals are in the areas of hiring and assignment of expatriate managers. Study findings provide HRM professionals with an initial set of criteria to assist in the process of identification and training of expatriate managers. Global organizations have traditionally used training to increase the pool of effective global managers. This study provides initial evidence that identification of individuals with early international experiences should prove a useful addition to the process of selecting candidates for foreign assignment. Social implications – The practical uses for the findings of this study by HRM professionals are in the areas of hiring and assignment of expatriate managers. Study findings provide HRM professionals with an initial set of criteria to assist in the process of identification and training of expatriate managers. Global organizations have traditionally used training to increase the pool of effective global managers. This study provides initial evidence that identification of individuals with early international experiences should prove a useful addition to the process of selecting candidates for foreign assignment. Originality/value – To the best of our knowledge this is one of the first studies to empirically examine ATCKs and provides a starting point for future researchers in this area. Obtaining a sample of ATCKs is extremely challenging.

Performance evaluation of canine-associated Bacteroidales assays in a multi-laboratory comparison study

The contribution of fecal pollution from dogs in urbanized areas can be significant and is an often underestimated problem. Microbial source tracking methods (MST) utilizing quantitative PCR of dog-associated gene sequences encoding 16S rRNA of Bacteroidales are a useful tool to estimate these contributions. However, data about the performance of available assays are scarce. The results of a multi-laboratory study testing two assays for the determination of dog-associated Bacteroidales (DogBact and BacCan-UCD) on 64 single and mixed fecal source samples created from pooled fecal samples collected in California are presented here. Standardization of qPCR data treatment lowered inter-laboratory variability of sensitivity and specificity results. Both assays exhibited 100% sensitivity. Normalization methods are presented that eliminated random and confirmed non-target responses. The combination of standardized qPCR data treatment, use of normalization via a non-target specific Bacteroidales assay (GenBac3), and application of threshold criteria improved the calculated specificity significantly for both assays. Such measures would reasonably improve MST data interpretation not only for canine-associated assays, but for all qPCR assays used in identifying and monitoring fecal pollution in the environment.

Improved analysis of long STR amplicons from degraded single source and mixed DNA

DNA profiles from degraded samples often suffer from information loss at the longer short tandem repeat (STR) loci. Sensitising the reactions, either by performing additional PCR cycles or increasing the capillary electrophoresis injection settings, carries the risk of over-amplifying or overloading the shorter fragments. We explored whether profiling of degraded DNA can be improved by preferential capturing of the longer amplified fragments. To this aim, a post-PCR purification protocol was developed that is based on AMPure XP beads that have size-selective properties. A comparison was made with an unselective post-PCR purification system (DTR gel filtration) and no purification of the PCR products. Besides a set of differently and serially degraded single source samples, unequal mixtures of degraded DNAs were analysed, in order to extract more genotyping information for the minor contributor without overloading the major component at the shorter amplicons. Purification by the AMPure protocol resulted in higher peak heights especially for the longer amplicons, while DTR gel filtration gave higher peaks for all amplicon sizes. Both purification methods presented more detected alleles, with the AMPure protocol performing slightly better, on average. In conclusion, the in-house developed AMPure protocol can be employed to improve STR profile analysis of degraded single source and (unequally) mixed DNA samples.

Enhancing the sexual assault workflow: Testing of next generation DNA assessment and Y-STR systems

Sexual assault samples are among the most difficult sample types encountered by forensic laboratories. Typically, a sexual assault sample has multiple challenges including small quantity of male DNA, relatively high quantity of female DNA, and presence of PCR inhibitors. These factors make it difficult to obtain an interpretable male profile. Therefore, there is a need for a more robust, highly sensitive, and faster method for the assessment (i.e. quality and quantity) of DNA extracts to determine optimal downstream processing methods, as well as an improve Y-STR amplification system for profiling these difficult samples.We tested newly developed tools, including a DNA quantification kit (Quantifiler® Trio) that exhibits high sensitivity higher inhibitor tolerance and includes additional useful tools for the determination of DNA quality to inform downstream processing methodology. We also tested a new Y-STR kit (Yfiler® Plus) with enhanced capabilities. This 27-marker kit permits rapid amplification of single source and complex casework samples. These two next generation systems can generate an improved workflow for obtaining interpretable profiles from sexual assault samples. We have successfully used the Quantifiler® Trio and Yfiler® Plus systems to obtain informative Y-STR profiles from challenging sexual assault sample types, including low quantity male DNA, extended interval post coital samples and samples containing high amounts of female DNA. We evaluated more routinely encountered post-coital samples collected 1–3 days after intercourse. Based on the Quantifiler® Trio results, observed outcomes were as expected after subsequent Yfiler® Plus and GlobalFilerTM analysis.

Validation of a DNA mixture statistics tool incorporating allelic drop-out and drop-in

DNA mixture analysis is a current topic of discussion in the forensics literature. Of particular interest is how to approach mixtures where allelic drop-out and/or drop-in may have occurred. The Office of Chief Medical Examiner (OCME) of The City of New York has developed and validated the Forensic Statistical Tool (FST), a software tool for likelihood ratio analysis of forensic DNA samples, allowing for allelic drop-out and drop-in. FST can be used for single source samples and for mixtures of DNA from two or three contributors, with or without known contributors. Drop-out and drop-in probabilities were estimated empirically through analysis of over 2000 amplifications of more than 700 mixtures and single source samples. Drop-out rates used by FST are a function of the Identifiler(®) locus, the quantity of template DNA amplified, the number of amplification cycles, the number of contributors to the sample, and the approximate mixture ratio (either unequal or approximately equal). Drop-out rates were estimated separately for heterozygous and homozygous genotypes. Drop-in rates used by FST are a function of number of amplification cycles only. FST was validated using 454 mock evidence samples generated from DNA mixtures and from items handled by one to four persons. For each sample, likelihood ratios (LRs) were computed for each true contributor and for each profile in a database of over 1200 non-contributors. A wide range of LRs for true contributors was obtained, as true contributors' alleles may be labeled at some or all of the tested loci. However, the LRs were consistent with OCME's qualitative assessments of the results. The second set of data was used to evaluate FST LR results when the test sample in the prosecution hypothesis of the LR is not a contributor to the mixture. With this validation, we demonstrate that LRs generated using FST are consistent with, but more informative than, OCME's qualitative sample assessments and that LRs for non-contributors are appropriately assigned.

Validation of the PLEX-IDTM mass spectrometry mitochondrial DNA assay

For very challenged biological samples, mitochondrial DNA (mtDNA) analysis can often provide results when the more traditional nuclear DNA markers fail. While reliable, the current method of mtDNA analysis by Sanger sequencing is expensive, labor-intensive, and time-consuming and is limited by its inability to quantify mixed samples. The Abbott PLEX-ID™ instrument, which enables analysis of mtDNA amplicons via electrospray ionization mass spectrometry (ESI-MS), produces comparable accuracy and sensitivity while offering a faster and less expensive alternative to Sanger sequencing. Unlike Sanger sequencing, this system is capable of quantifying DNA species and thus may be exploited for evaluating heteroplasmy and, possibly, mixture deconvolution. Validation studies of the PLEX-ID™ mtDNA assay confirmed that the instrument is highly sensitive and capable of yielding reproducible results. Samples commonly encountered in a forensic setting, as well as population samples, were typed correctly. The PLEX-ID™ mtDNA assay yields reliable results for single-source samples, which are the same sample types currently examined in forensic laboratories via Sanger sequencing, at a level that meets or exceeds that of the current method. While the instrument has the demonstrated capability to quantify mixed samples, the specific assay design for mtDNA analysis can be used only in a limited fashion to analyze mixtures due to the formation of chimeric mtDNA products.

THE BROWN DWARF KINEMATICS PROJECT (BDKP). III. PARALLAXES FOR 70 ULTRACOOL DWARFS

We report parallax measurements for 70 ultracool dwarfs (UCDs). Using both literature values and our sample, we report new polynomial relations between spectral type and M$_{JHK}$. Including resolved L/T transition binaries in the relations, we find no reason to differentiate between a "bright" (unresolved binary) and "faint" (single source) sample across the L/T boundary. Isolating early T dwarfs, we find that the brightening of T0-T4 sources is prominent in M$_{J}$ where there is a [1.2 - 1.4] magnitude difference. A similar yet dampened brightening of [0.3 - 0.5] magnitude happens at M$_{H}$ and a plateau or dimming of [-0.2 - -0.3] magnitude is seen in M$_{K}$. Comparing with evolutionary models that vary gravity, metallicity, and cloud thickness we find that a near constant temperature of 1200 $\pm$100 K along a narrow spectral subtype of T0-T4 is required to account for the brightening and color magnitude diagram of the L-dwarf/T-dwarf transition. Furthermore, there is a significant population of both L and T dwarfs which are red or potentially "ultra-cloudy" compared to the models, many of which are known to be young indicating a correlation between enhanced photospheric dust and youth. For the low surface-gravity or young companion L dwarfs we find that 8 out of 10 are at least [0.2-1.0] magnitude underluminous in M$_{JH}$ and/or M$_{K}$ compared to equivalent spectral type objects. We speculate that this is a consequence of increased dust opacity and conclude that low-surface gravity L dwarfs require a completely new spectral-type/absolute magnitude polynomial for analysis.

A forensic DNA profiling system for Northern European brown bears (Ursus arctos)

A set of 13 dinucleotide STR loci (G1A, G10B, G1D, G10L, MU05, MU09, MU10, MU15, MU23, MU26, MU50, MU51, MU59) were selected as candidate markers for a DNA forensic profiling system for Northern European brown bear (Ursus arctos). We present results from validation of the markers with respect to their sensitivity, species specificity and performance (precision, heterozygote balance and stutter ratios). All STRs were amplified with 0.6ng template input, and there were no false bear genotypes in the cross-species amplification tests. The validation experiments showed that stutter ratios and heterozygote balance was more pronounced than in the tetranucleotide loci used in human forensics. The elevated ratios of stutter and heterozygote balance at the loci validated indicate that these dinucleotide STRs are not well suited for interpretation of individual genotypes in mixtures. Based on the results from the experimental validations we discuss the challenges related to genotyping dinucleotide STRs in single source samples. Sequence studies of common alleles showed that, in general, the size variation of alleles corresponded with the variation in number of repeats. The samples characterized by sequence analysis may serve as standard DNA samples for inter laboratory calibration. A total of 479 individuals from eight Northern European brown bear populations were analyzed in the 13 candidate STRs. Locus MU26 was excluded as a putative forensic marker after revealing large deviations from expected heterozygosity likely to be caused by null-alleles at this locus. The remaining STRs did not reveal significant deviations from Hardy–Weinberg equilibrium expectations except for loci G10B and MU10 that showed significant deviations in one population each, respectively. There were 9 pairwise locus comparisons that showed significant deviation from linkage equilibrium in one or two out of the eight populations. Substantial genetic differentiation was detected in some of the pairwise population comparisons and the average estimate of population substructure (FST) was 0.09. The average estimate of inbreeding (FIS) was 0.005. Accounting for population substructure and inbreeding the total average probability of identity in each of the eight populations was lower than 1.1×10−9 and the total average probability of sibling identity was lower than 1.3×10−4. The magnitude of these measurements indicates that if applying these twelve STRs in a DNA profiling system this would provide individual specific evidence.

Single-Sample Robust Joint Source–Channel Coding: Achieving Asymptotically Optimum Scaling of SDR Versus SNR

In this paper, we consider the problem of zero-delay (encoding a single-source sample) robust joint source-channel coding over an additive white Gaussian noise channel. We propose a new scheme that, unlike previously known coding schemes, achieves the optimal scaling of the source signal-to-distortion ratio (SDR) versus channel signal-to-noise ratio (SNR). Also, we propose a family of robust codes, which together maintain a bounded gap with the optimum SDR curve (in terms of decibel). To show the importance of this result, we derive some theoretical bounds on the asymptotic performance of a widely used class of delay-limited hybrid digital-analog (HDA) coding schemes based on superposition of analog and digital components. We show that, unlike the delay-unlimited case, for this class of delay-limited HDA codes, the asymptotic performance loss is unbounded (in terms of decibels). Although the main focus of this paper is on uniform sources, it is also shown that the results are also valid for a more general class of well-behaved distributions.

Likelihood ratio statistics for DNA mixtures allowing for drop-out and drop-in

The likelihood ratio (LR) is the recommended approach for forensic DNA mixture analysis by the DNA commission of the ISFG, as it makes maximum use of available data and parameters for allelic drop-out and drop-in can be incorporated. We have developed and validated a LR method and software for analysis of mixed evidence samples in which drop-out of true contributors′ alleles and drop-in of extraneous alleles may have occurred. This method, the forensic statistical tool (FST), employs empirically determined drop-out and drop-in probabilities for single source samples and mixtures. The LR is computed for pairs of prosecution and defense hypotheses based on sample characteristics specified by the user. Data from up to three evidence amplifications may be considered simultaneously. The performance of the program was evaluated with hundreds of profiles generated from blood and buccal samples, purposefully degraded samples, and touched items with one, two, three, and four known contributors. The validation demonstrated that FST assigns an appropriate weight to all types of comparisons. FST is now being used in casework and results continue to be consistent with qualitative assessments.