Implementing a biogeographic ancestry inference service for forensic casework.

The Centre of Forensic Sciences has validated the Precision ID Ancestry Panel on the Ion S5™ Massively Parallel Sequencing instrument for use in forensic casework. The focus of this paper is the development of reporting guidelines for implementation of the biogeographic ancestry inference service based on the Admixture Prediction results produced using the Torrent Suite™ Software (Thermo Fisher Scientific). The Admixture Prediction algorithm estimates the genetic ancestry of a sample using seven root populations (Europe, East Asia, Oceania, America, Africa, South Asia, and Southwest Asia). For individuals that declared a single ancestry, there was a high correlation between the declared ancestry and the ancestry predicted by the algorithm. However, some individuals with declared ancestries of Southern Europe, Southwest Asia, South Asia and Horn of Africa had Admixture Predictions that were composed of two or more root populations at 20% or greater. For individuals with known admixed ancestry, the major component of their declaration was included in their results in all but one case. Based on these results, reporting guidelines were developed and subsequently evaluated using the Admixture Predictions of additional samples. This paper discusses the development and evaluation of these reporting guidelines, along with an implementation plan for forensic casework.

Toward Analysis at the Point of Need: A Digital Microfluidic Approach to Processing Multi-Source Sexual Assault Samples.

Forensic case samples collected in sexual assaults typically contain DNA from multiple sources, which complicates short-tandem repeat (STR) profiling. These samples are typically sent to a laboratory to separate the DNA from sperm and non-sperm sources prior to analysis. Here, the automation and miniaturization of these steps using digital microfluidics (DMF) is reported, which may eventually enable processing sexual assault samples outside of the laboratory, at the point of need. When applied to vaginal swab samples collected up to 12 h post-coitus (PC), the new method identifies single-source (male) STR profiles. When applied to samples collected 24-72 h PC, the method identifies mixed STR profiles, suggesting room for improvement and/or potential for data deconvolution. In sum, an automated, miniaturized sample pre-processing method for separating the DNA contained in sexual assault samples is demonstrated. This type of automated processing using DMF, especially when combined with Rapid DNA Analysis, has the potential to be used for processing of sexual assault samples in hospitals, police offices, and other locations outside of the laboratory.

First all-in-one diagnostic tool for DNA intelligence: genome-wide inference of biogeographic ancestry, appearance, relatedness, and sex with the Identitas v1 Forensic Chip.

When a forensic DNA sample cannot be associated directly with a previously genotyped reference sample by standard short tandem repeat profiling, the investigation required for identifying perpetrators, victims, or missing persons can be both costly and time consuming. Here, we describe the outcome of a collaborative study using the Identitas Version 1 (v1) Forensic Chip, the first commercially available all-in-one tool dedicated to the concept of developing intelligence leads based on DNA. The chip allows parallel interrogation of 201,173 genome-wide autosomal, X-chromosomal, Y-chromosomal, and mitochondrial single nucleotide polymorphisms for inference of biogeographic ancestry, appearance, relatedness, and sex. The first assessment of the chip's performance was carried out on 3,196 blinded DNA samples of varying quantities and qualities, covering a wide range of biogeographic origin and eye/hair coloration as well as variation in relatedness and sex. Overall, 95 % of the samples (N = 3,034) passed quality checks with an overall genotype call rate >90 % on variable numbers of available recorded trait information. Predictions of sex, direct match, and first to third degree relatedness were highly accurate. Chip-based predictions of biparental continental ancestry were on average ~94 % correct (further support provided by separately inferred patrilineal and matrilineal ancestry). Predictions of eye color were 85 % correct for brown and 70 % correct for blue eyes, and predictions of hair color were 72 % for brown, 63 % for blond, 58 % for black, and 48 % for red hair. From the 5 % of samples (N = 162) with <90 % call rate, 56 % yielded correct continental ancestry predictions while 7 % yielded sufficient genotypes to allow hair and eye color prediction. Our results demonstrate that the Identitas v1 Forensic Chip holds great promise for a wide range of applications including criminal investigations, missing person investigations, and for national security purposes.

Addressing the alternate hypothesis: Transfer and persistence of saliva beneath fingernails.

This study investigated the transfer and persistence of salivary DNA under fingernails. This was performed to address a common alternate hypothesis presented to scientists in court, asserting that a relatively large quantity of DNA detected beneath the fingernails, typically from a victim of crime, originates from innocuous transfer of saliva in a casual setting. It was determined through these studies that contact with liquid saliva was an effective way to transfer foreign DNA beneath fingernails. However, when saliva was dried, DNA did not readily transfer through casual contact. When liquid saliva was placed directly beneath fingernails the amount of DNA detected from the saliva donor twenty-four hours later was several hundred-fold lower than the amount detected when sampling occurred immediately following deposition. Furthermore, when the recipients' hands were washed immediately following the deposition of liquid saliva beneath fingernails, the majority of foreign DNA was removed following one hand washing and all detectable foreign DNA was removed from most recipients' hands after three or six hand washings. This study demonstrates that casual contact with wet saliva can result in the transfer of substantial quantities of DNA beneath fingernails but that it does not typically persist for extended periods of time and is mostly removed if the hands are washed soon after deposition.

Differentiation of vaginal cells from epidermal cells using morphological and autofluorescence properties: Implications for sexual assault casework involving digital penetration.

Analysis of DNA mixtures from sexual assault evidence is an ongoing challenge for DNA casework laboratories. To assist the forensic scientist address source and activity level propositions there is a significant need for new techniques that can provide information as to the source of DNA, particularly for sexual assault samples that do not involve semen. The goal of this study was to develop a new biological signature system that provides additional probative value to samples comprised of mixtures of epidermal and vaginal cells, as may be observed in cases involving digital penetration. Signatures were based on morphological and autofluorescence properties of individual cells collected through Imaging Flow Cytometry (IFC). Comparisons to reference cell populations from vaginal tissue and epidermal cells collected from hands showed strong multivariate differences across > 80 cellular measurements. These differences were used to build a predictive framework for classifying unknown cell populations as originating from epithelial cells associated with digital penetration or epidermal tissue. As part of the classification scheme, posterior probabilities of specific tissue group membership were calculated for each cell, along with multivariate similarity to that tissue type. We tested this approach on cell populations from reference tissue as well as mock casework samples involving hand swabbings following digital vaginal penetration. Many more cells classifying as non-epidermal tissue were detected in digital penetration hand swab samples than control hand swabbings. Minimum interpretation thresholds were developed to minimize false positives; these thresholds were also effective when screening licked hands, indicating the potential utility of this method for a variety of biological mixture types and depositional events relevant to forensic casework. Results showed that samples collected subsequent to digital penetration possessed markedly higher numbers of cells classifying as vaginal tissue as well as higher posterior probabilities for vaginal tissue (≥ 0.90) compared to cell populations collected from hands without prior contact with vaginal tissue. Additionally, digital penetration cell populations may be resolved from saliva cell populations and other non-target tissue types.

Differentiation of vaginal cells from epidermal cells using morphological and autofluorescence properties: Implications for sexual assault casework involving digital penetration.

Analysis of DNA mixtures from sexual assault evidence is an ongoing challenge for DNA casework laboratories. There is a significant need for new techniques that can provide information as to the source of DNA, particularly for sexual assault samples that do not involve semen. The goal of this study was to develop a new biological signature system that provides additional probative value to samples comprised of mixtures of epidermal and vaginal cells, as may be observed in cases involving digital penetration. Signatures were based on morphological and autofluorescence properties of individual cells collected through Imaging Flow Cytometry (IFC). Comparisons to reference cell populations from vaginal tissue and epidermal cells collected from hands showed strong multivariate differences across >80 cellular measurements. These differences were used to build a predictive framework for classifying unknown cell populations as originating from epithelial cells associated with digital penetration or epidermal tissue. As part of the classification scheme, posterior probabilities of specific tissue group membership were calculated for each cell, along with multivariate similarity to that tissue type. We tested this approach on cell populations from reference tissue as well as mock casework samples involving digital penetration. Many more cells classifying as non-epidermal tissue were detected in digital penetration samples than control hand swabbings. Minimum interpretation thresholds were developed to minimize false positives; these thresholds were also effective when screening licked hands, indicating the potential utility of this method for a variety of biological mixture types and depositional events relevant to forensic casework. Results showed that samples collected subsequent to digital penetration possessed markedly higher numbers of cells classifying as vaginal tissue as well as higher posterior probabilities for vaginal tissue (≥ 0.90) compared to cell populations collected from hands without prior contact with vaginal tissue. Additionally, digital penetration cell populations may be resolved from saliva cell populations and other non-target tissue types.

Transfer and persistence of DNA on items routinely encountered in forensic casework following habitual and short-duration one-time use.

Empirical data obtained from controlled experiments is necessary to ensure that sound expert opinion evidence is provided regarding transfer and persistence of DNA in criminal proceedings. Knowledge in this area is also required at the outset of criminal investigations, to ensure that the proposed examinations can assist with answering questions that are relevant to forensic investigations. This study aimed to provide such data by examining the relative and absolute quantities of DNA deposited on items that are routinely submitted to the forensic laboratory by a habitual user, defined as someone who used it for ~1 week, and a subsequent one-time user. We found that the quantity of DNA deposited on routine household items spanned a broad range. The habitual user's DNA was detected on most items as the major donor, regardless of whether it was subsequently handled by another person for a short period of time. The one-time, short duration, user's DNA was detected on approximately two thirds of the items, albeit typically at quantities lower than the habitual user. Most of the household items we examined also had detectable DNA deposits from at least one other, unknown individual, typically in low quantities. Attempts to clean non-porous items with readily available household cleaners were partially effective but failed to completely eliminate detectable DNA from a habitual user in most cases.

Case study: Loss of Kastle-Meyer test specificity on jeans.

A pair of jeans produced false positive results upon testing for the presence of blood using the Kastle-Meyer (KM) test. Positive reactions were obtained from all unstained areas of the fabric tested. The peroxidase used in the manufacture of some jeans may be the causative agent for the observed false positive reactions; however, it was not possible to confirm this theory.

Inferring the presence of spermatozoa in forensic samples based on male DNA fractionation following differential extraction.

To address sexual assault kit backlogs some laboratories in North America have implemented 'Direct to DNA' (DTD) approaches for the examination of relevant vaginal, oral, rectal and external genitalia swabs from sexual assault examination kits. Using this approach no preliminary serological screening for semen or spermatozoa is performed. Instead, swabs are directly subjected to differential extraction and quantitation using a dual quantification system. Decisions regarding the next steps in processing each sample are typically based on the quantity of male DNA detected, the fraction in which it is detected, and its ratio to the total human DNA in the sample. In the absence of serological results it remains of value in many cases to determine whether spermatozoa are present in the sample and whether the male DNA profile may be attributed to this body fluid. In this study we examine the distribution of male DNA from various body fluids between epithelial and spermatozoa fractions following differential extraction. Based on these results we identified criteria under which a DNA profile can be reliably attributed to spermatozoa. A total of 18 blood samples, 129 saliva samples, and 78 semen samples were processed. The maximum amount of male DNA observed in the sperm fraction of a spermatozoa-free sample was 10.4 ng and the maximum portion of total male DNA observed in the sperm fraction was 7.7%. In contrast, when a sample contained spermatozoa the minimum portion of total male DNA observed in the sperm fraction was 52.6%. This research supports a 50% threshold of male DNA in the sperm fraction following differential extraction as a conservative criterion under which the scientist at the Centre of Forensic Sciences (CFS) may infer that spermatozoa is present in a sample in the absence of serological results. This general threshold is applicable to all sample types (underwear, clothing, swabs, condoms) tested. We further demonstrate that, if the same male DNA profile is represented more prominently in the sperm fraction versus the epithelial fraction, the analyst should not fall into the intuitive trap of inferring the presence of spermatozoa in the sample. Instead, enrichment calculations must be based on the measured quantity of male and total DNA in each fraction and not the male:female DNA ratios observed in the DNA profiles.

Kastle-Meyer blood test reagents are deleterious to DNA.

The Kastle-Meyer (KM) test is a quick and easy chemical test for blood used in forensic analyses. Two practical variations of this test are the KM-rub (indirect) test and the more sensitive KM-direct test, the latter of which is performed by applying reagents directly to a suspected blood stain. This study found that sodium hydroxide present in the KM reagents eliminated the potential to generate a DNA profile when applied directly to small quantities of blood. A modified approach to the KM-rub test that increases its sensitivity is presented as a method to replace destructive KM-direct testing.

Yeast functional genomics and cell biology: no longer in the dark.

A report on the Cold Spring Harbor Laboratory meeting 'Yeast Cell Biology', Cold Spring Harbor, USA, 12-17 August 2003.

CDK activity antagonizes Whi5, an inhibitor of G1/S transcription in yeast.

Cyclin-dependent kinase (CDK) activity initiates the eukaryotic cell division cycle by turning on a suite of gene expression in late G1 phase. In metazoans, CDK-dependent phosphorylation of the retinoblastoma tumor suppressor protein (Rb) alleviates repression of E2F and thereby activates G1/S transcription. However, in yeast, an analogous G1 phase target of CDK activity has remained elusive. Here we show that the cell size regulator Whi5 inhibits G1/S transcription and that this inhibition is relieved by CDK-mediated phosphorylation. Deletion of WHI5 bypasses the requirement for upstream activators of the G1/S transcription factors SBF/MBF and thereby accelerates the G1/S transition. Whi5 is recruited to G1/S promoter elements via its interaction with SBF/MBF in vivo and in vitro. In late G1 phase, CDK-dependent phosphorylation dissociates Whi5 from SBF and drives Whi5 out of the nucleus. Elimination of CDK activity at the end of mitosis allows Whi5 to reenter the nucleus to again repress G1/S transcription. These findings harmonize G1/S control in eukaryotes.