This is a report on NIJ-funded research whose objective is to develop a single nucleotide polymorphism (SNP) panel for the discrimination of species identity from forensic samples of unknown biological origin, using mitochondrial DNA (mtDNA) based markers.
To date the research has demonstrated the proof of concept for the use of degenerate polymerase chain reaction (PCR) and multiplexed single base extension (SBE) for the identification of unknown animal samples using three mini multiplexes; however, the continuing presence of random background noise and baseline anomalies prevents the researchers from suggesting this method for any use other than a research tool. The initial results indicate a presumptive assay with a good deal of promise that needs further development before being ready for widespread use. The proof of concept for the assay was developed by focusing on a small number of ubiquitous species potentially present at North American crime scenes. Using sequence data from NCBI GenBank and just over 100,000 base pairs of sequence generated on-site, researchers created gene alignments across all included taxa and species for three mtDNA genes, including cytochome oxidase I (COI, NADH dehydrogenase subunit 4 (ND4), and cytochrome b (Cytb). The development of canonical SNPs confirmatory for species identity was performed using a neighbor joining phylogenetic algorithm with 10,000 subsequent bootstrap replicates. The resultant SNPs candidates were categorized by gene of origin, species indication, and placement within individual gene sequence. The researchers intend that this assay be used by forensic scientists who encounter an unknown biological specimen as an initial screening tool. The mini multiplexes are plagued by inconsistent representation of species identifying peaks at low template DNA concentration as well as heightened background noise and the presence of random spurious peaks. 9 tables, 13 figures, and a 26-item bibliography
Report (Grant Sponsored)
Date Published: September 1, 2010