Males commit 79% of violent crimes and 98% of all sexual assaults. In some cases a failure to obtain the male donor profile by standard DNA techniques is due to the presence of large quantities of female derived DNA. In such cases probative investigative information may still be obtainable by the judicious use of Y chromosome markers.  Such markers are essentially blind to the contaminating female derived DNA in male/female DNA admixtures.  We continue to develop and refine a number of Y chromosome analysis techniques for forensic casework use.

Due to the availability of commercial kits and a broader understanding of the usefulness of Y chromosome markers in certain cases, an increasing number of laboratories in the US have the capability of performing Y-STR analysis in casework.  Although commercial Y-STR kits perform well in casework, the match probability of a Y-STR match is modest due to the limited number of loci used.  We have developed and validated 10 multiplex analytical systems containing > 100 novel Y-STR loci.  The most forensically useful loci have been combined into an Ultra High Discrimination system that we believe has the highest discriminatory power of any multiplex.

For a variety of reasons, some victims of sexual assault provide vaginal samples more than 24-36 hours after the incident.  The ability to obtain an autosomal STR profile of the semen donor from the living victim diminishes rapidly as the post coital interval is extended.  We have used a number of carefully selected Y-STR loci in a variety of multiplex formats to extend the post coital interval (up to 5 days) from which a genetic profile of the semen donor can be obtained.  We attribute our success to a number of factors that significantly improve the sensitivity and specificity of the analysis.  This work is likely to have a significant impact on the investigation of rape cases.

This project is concerned with the investigation of potential strategies for analyzing samples containing low copy number (LCN) DNA templates.  Biological evidence is often encountered with an extremely low number of starting templates (1-15 cells) and requires the development of novel strategies for its collection, analysis and interpretation.  We are investigating different strategies by which samples containing low copy numbers of starting DNA template could be DNA profiled, including whole genome amplification and single cell methods.  For single cells we capture cells using a laser capture microscope in order to perform what we term ‘smart single cell DNA profiling’

Conventional methods of body fluid identification use labor-intensive, technologically diverse techniques that are costly in terms of time and sample.  For some frequently encountered body fluids (e.g. saliva, vaginal secretions and menstrual blood) no definitive identification technique exists.  A pattern of gene expression is produced in body fluid secretions and tissues that uniquely defines each cell type present. This is evidenced by the presence and relative abundance of specific mRNA species. We have developed a number of highly specific mRNA profiling assays for body fluid and tissue identification and transferred them to a variety of commonly used analytical platforms.   

The use of mRNA technology in forensic genetics offers the ability to obtain probative information not readily achievable using other methods.  Many of the stains recovered from crime scenes are contaminated with non-human DNA from a variety of organisms including microbial species.  The RNA assays developed require the input of a certain quantity of human RNA.  In this project we are developing an assay for the accurate and reliable quantitation of human specific RNA in the presence of RNA from other organisms.

One of the limiting factors with DNA typing technology is that sometimes DNA isolated from physiological stains recovered from the crime scene is so damaged as to be intractable to analysis.  However, current knowledge of the biochemical nature and extent of the DNA damage in biological stains of forensic importance is rudimentary.  We are characterizing the molecular lesions that prevent the ability to obtain a standard DNA profile in damaged DNA recovered from crime scene physiological stains with a view to   determining possible DNA repair strategies. 

The objective of this study is to investigate the basic chemistry of the dried state, specifically that of the most common expected type of chemical reactions, namely hydrolysis and oxidation.  Specifically we are performing kinetic analysis of dry state DNA degradation by determine the rates of such reactions under different environmental conditions.  We have concentrated our early efforts on hydrolytic damage to the relatively labile glycosidic bond and deamination of the nitrogenous bases. The general approach is to allow reactions to occur over a period of time at predetermined set temperatures and perform quantitative measurements to determine rate constants and activation energies. 

Double strand breaks, which arise as a result of microbial action or terrestrial UV irradiation, are the cause of most DNA degradation in forensic samples.  We are developing methods for the in vitro repair of double strand DNA breaks using a variety of different approaches, which include one or more of the following: recombination substrate-mediated gap repair, homologous recombination and non-homologous end-joining. The goal is human identification from degraded DNA, indicated by the recovery of a genetic profile from otherwise non-typeable samples.  DNA repair success is initially evaluated using SNPs with the ultimate goal the recovery of STR profiles.

The donor of a body fluid recovered from the crime scene is identified by comparing the crime scene DNA profile to profiles obtained from reference samples obtained from known individuals.  However, in the absence of appropriate comparison reference samples, the DNA profile per se presently provides no meaningful information to investigators, with the notable exception of gender determination.  A number of other physically recognizable characteristics of an individual may be amenable to molecular genetic analysis and these include skin-, hair- and eye- color, stature (height and weight), age and facial morphology. 

  

We are investigating whether determination of ethnogeographic origin is feasible by the analysis of Y-SNP markers in body fluid stains.  As a result of mutation and geographic-specific genetic bottlenecks throughout human history, modern Y chromosome lineages, called haplogroups, exhibit the genetic signatures of their bio-geographical past.  We are discovering novel Y-SNP markers that better resolve some of the common haplogroups and to develop hierarchical typing assays for biogeographic ancestry prediction. Maternal lineage and pigmentation markers are being incorporated into the analysis to help resolve haplogroups with a high proportion of ethnically admixed individuals.

Forensic anthropologists can sometimes predict the ethnic identity of a bone using bone morphology.  It becomes increasingly difficult or impossible with bone fragments.  We are investigating the possibility of obtaining the ethnogeographic ancestry of male bone by Y-SNP typing using both modern and ancient bones.  This work could have significant implications for both forensic and archaeological studies. 

As humans proceed through developmental from birth to adulthood, sub-sets of the estimated 20-25 thousand human genes will be differentially expressed. Theoretically, a comparison of the gene expression profile from individuals of different ages should reveal constellations of genes whose expression is correlated with a specific age. We discovered novel newborn-specific isoforms of HBG mRNA from which we developed assays that determine whether a bloodstain originated from a newborn baby. We are in the process of identifying other age predictor genes that are expressed at other ages.

The ability to determine the time since deposition (TSD) of a biological stain found at a crime scene could prove invaluable to investigators, defining the time frame in which the individual depositing the evidence was present.  No reliable TSD methods are available at present.  The fundamental assumption of this project is that biochemical reactions still occur in the dried state and as dried stains age, damage and degradation to macromolecules such as DNA, RNA and protein occur. We are investigating whether macromolecular degradation intermediates and/or specific nucleic acid base damage can serve as molecular clocks for time since deposition (TSD) estimation.

The field of microbial forensics is conventionally confined to the analysis and characterization of evidence from a bio terrorism act. However we are investigating whether certain microbes are sufficiently restricted in their growth potential within different body fluids, or within different individuals, to be of broader use in forensic science. We are characterizing the bacteria that normally grow in human body fluids (e.g. saliva and vaginal secretions) by means of species/strain determination and determining their persistence and stability. Our initial observations indicate that some microbes are likely to be the source of useful biomarkers for certain body fluids.

Casework forensic biologists often need to access information from previously published material such as journal articles, monographs, books and the internet.  A useful tool would be a convenient web-accessible Forensic DNA Sourcebook that provides, in a ‘one-stop shopping’ mode, a comprehensive compilation of all relevant resources, and a survey of the published literature. A prototype master DNA Sourcebook document has been created.  Each reference in the master document has a link to its abstract/publisher site/full article, depending on the source and availability of the reference. More than 11,000 references have been collected, categorized and hyper-linked to their abstracts.

The National Institute of Justice funds a wide variety of R&D projects whose express aim is the development of novel DNA technologies to make DNA analysis quicker, better or cheaper. NCFS is assisting NIJ in transferring selected novel technologies to the crime lab community by providing assistance to principal investigators (PI), particularly those who are not forensic scientists. Such assistance includes, in consultation with the PI, optimization of the technology for the analysis of forensic specimens of limited quantity and quality, testing of the methodology and, if warranted, a full-scale developmental validation of the refined technology.

The use of mitochondrial DNA in forensic analysis has traditionally relied on genetic variation within the two hyper variable (HV) regions of the non-coding Control region to differentiate individuals.  However common HV haplotypes exist that may comprise a up to 7% of the Caucasian population.  We have investigated the mitochondrial coding region for single nucleotide (SNP) polymorphisms that could differentiate between samples with identical control region haplotypes.  The result was the development of a set of multiplex pyrosequencing-based SNP assays (mtSNPlex) that interrogate 10 coding region SNPs.  These are particularly useful for differentiating Caucasian individuals.