This Small Business Innovation Research (SBIR) Phase I project proposes to develop a next generation forensic human DNA typing system. DNA profiling has gained broad popularity since its first use 25 years ago. Its application has expanded from criminal and parentage issues to mass disasters and battlefield forensics. In addition, the desire to rapidly analyze degraded and minimal samples has also increased exponentially. While DNA analysis of Short Tandem Repeats (STR) is considered routine, scientists continue to explore ways to identify smaller segments of DNA for identification purposes. Mitochondrial sequencing is presently the test of last resort but lacks the discrimination power of nuclear STR typing. As DNA profiling has increased, so has the need for quicker, more robust and less costly tests. This project proposes the use of a microfluidic platform with redesigned primers for the Alu family of Mobile Interspersed Genetic Elements. Alu primer sets producing amplicons in the 100-200 bp range will be typed for Alu insertion polymorphism. Due to the large number of Alus available in the human genome and their known ancestral state, these genetic elements can be a valuable tool for typing degraded DNA samples and in their ability to infer geographic origin.
The broader impact and commercial potential of this project is to provide a complete, robust, next generation DNA typing system for human identification. Successful development of a rapid Alu-based DNA typing system would provide the human identity testing market with additional and potentially transformational tools to identify biological samples containing degraded DNA as well as provide clues to the geographic ancestry of a specimen. Supplemental and next generation DNA typing systems will result in the production of more genetic information that can aid society in its search for the truth and justice for victims of violent crimes. Mass disasters, battlefield forensics, as well as routine DNA analysis for crime scene and parentage testing will benefit from a next generation rapid DNA identification system. For forensic applications, a microfluidic platform in conjunction with an Alu-based DNA typing system will address the commercial needs of this industry and at minimum could provide additional information to existing testing methods. Based upon the current human DNA identification testing market the commercial potential of a supplemental Alu-based DNA typing system is in excess of 100 million dollars, thus making a significant commercial impact and positive contribution to the field of human DNA profiling.
This research project evaluated the feasibility of developing a second generation genetic marker system for human identification purposes. Current human identification DNA markers have been well characterized, generally accepted by the scientific community and widely utilized for forensic DNA applications as well as in relationship testing. Despite this widespread acceptance, there still is a need for additional genetic markers that can identify unknown, degraded, human DNA fragments. Events such as mass disasters, battlefield explosions and missing person cases often result in human remains that are extremely decomposed, degraded and present in minute amounts. The unidentified forensic samples, that are a result of these catastrophic events, are not amenable to identification with current DNA test systems because DNA in the sample is degraded to fragments of less than 100 base pairs in size. Current, available tests target fragment sizes in the 100-350 base pair size range. To analyze highly degraded samples, there is a definite need for a DNA marker system that targets small DNA fragments of less than 100 base pairs. Utilizing a proprietary primer design, a new method has been developed resulting in the creation of additional genetic markers which specifically target the less than100 base pair DNA fragment sizes. These genetic markers have been extensively evaluated in the laboratory. Of the 77 different markers tested, twenty five have been identified as satisfying the criteria set forth for sensitivity, robustness and ability to discriminate between individuals, based upon database studies performed on three different population sets. This Phase I investigation also identified a set of markers which can be used to determine the bio-ancestry of an unknown DNA sample. Further research is planned to develop a prototype DNA test kit(s) where a combination of markers can be tested simultaneously to provide a high power of discrimination for use in human DNA identification laboratories. The broader impact of this project and the subsequent test kit(s) developed will result in the ability to identify human remains that cannot be identified utilizing current test kits and systems. This new DNA test kit(s) will be an additional tool useful in the fields of forensic identification, relationship testing, population genetics as well as anthropological and medical research. The resulting contribution to scientific research and society is immeasurable.