Background

Traditional mainstays of forensic science that depend on qualitative expert opinion, such as hair and fingerprint analysis, are being challenged as lacking a scientific and statistical basis. These challenges, leading to questions of admissibility of this type of evidence in current cases and validity of previous convictions, are casting doubt on current forensic practices. The shortcomings of these qualitative methods not only undermine the criminal justice system, but also increase resistance to their use in the broader national security community. DNA typing stands out as an exception because it is quantifiable and has sound scientific footing. Use of DNA, however, is limited when the sample has degraded or when there are multiple contributors. Protein can serve as a surrogate for DNA in these cases and provide an alternative quantifiable analysis strategy.

LLNL has developed the scientific and statistical basis for forensic use of genetically variant peptides (GVP) analysis and to extend the concept into other forensic and intelligence contexts. LLNL has also developed strategies to track individuals, even against a complex background of many individuals, using GVPs related to ultra-rare variants.

Description

LLNL has developed specific technical approaches and methods to obtain proteomic information from various human tissue types (hair, skin, teeth, bone). These processes have been developed to maximize proteomic information recovery using liquid chromatography/mass spectrometry methods. LLNL has also developed software tools and processes to mine genetic databases and human genetic sequence data for specific mutations related to human identity that can be observed in the proteome. Finally, LLNL has established several advanced methods including biochemical processes that allow significant proteomic data to be obtained from short segments of single hairs as well as biochemical processes that enable both mitochondrial DNA (mtDNA) as well as proteomic information to be obtained from a single hair sample.

There are 3 main inventions included in LLNL’s GVP technology platform:

  1. Chemical and biochemical processes for single-hair processing and GVP analysis
  2. Processes for concomitant determination of mitochondrial DNA and GVPs from single hairs
  3. Discovery and selection of GVPs through genetically driven analysis
Advantages

The current 'gold' standard, DNA typing, has a solid scientific and statistical basis and now constitutes the bulk of biological forensic evidence. However, DNA typing has its limitations and when DNA is not available the options for identification are extremely limited.

As an alternative to DNA, genetic information that is reflected in the primary structure of protein (amino acid sequence) can be used for forensic investigations. Protein is more stable than DNA and can persist in the environment for periods of hundreds or thousands of years. Protein is often present when DNA is not present, such as in hair and in degraded tissues, and can persist in heated samples, after explosive events, or in other harsh environmental conditions. There is a significant scientific opportunity to use the genetic information in protein to complement, or if necessary replace, the identifying information available from DNA analysis.

  • GVP analysis technology platform provides a new approach to human identification.
  • Optimized processing conditions allow for a single hair (2.5 cm) to be fully dissolved, the protein concentrated and then digested and made compatible with LC-MS/MS proteomic analysis.
  • Validated single-hair processing method is able to provide usable mitochondrial DNA (mtDNA) from single hair samples and both mtDNA and proteomic data can be obtained from the resulting sample preparations.
  • Multiple novel bioinformatic software tools allow for a "top-down" approach to GVP discovery that is driven by exome data. These tools serve a number of functions that enable the identification of candidate GVPs based on the specific genetic mutations contained in individual or pooled genomes.
Potential Applications

Uses of LLNL's GVP methods, software tools and processes include:

  • Human identification for forensic and other purposes
  • Determining relatedness of individuals
  • Determining expression of genes through proteomic analysis; and
  • Determining biogeographic origin
Development Status

LLNL has demonstrated that genetically useful information can be obtained using GVPs extracted from protein samples. For example, hair protein can be used to determine the profile of single nucleotide polymorphisms (SNPs) in an individual. As a result, analysis of GVPs allows calculation of measures of identity and biogeographic background.

LLNL has filed U.S. Provisional Patent 60/555001; LLNL internal case number (IL13212) for its Genetically Variant Protein Analysis to Maximize Proteomic Information Recovery intellectual property platform.

Reference Number
35517