Investigation into the use of Single Nucleotide Polymorphisms for forensic identification purposes

Major limitations of the short tandem repeat (STR) loci that form the basis of criminal DNA databases are the 'partial' profiles that result from degradation of the longer repeat sequences. In contrast, Single Nucleotide Polymorphisms (SNPs) can be encompassed in smaller amplicons increasing the chance of amplification in degraded and limited samples. To aid SNP analysis a range of studies were performed including creation of the ASGOTH (Automated SNP Genotype Handler) software for rapid and accurate sample genotyping on microarrays. A multiplex assay for simultaneous detection of 20 SNPs plus a sex-determining locus by single-tube PCR amplification and electrophoretic detection was also developed. All loci conformed to Hardy- Weinberg equilibrium and showed independent inheritance. Computer simulations characterised the effects of inbreeding and supported the use of current STR Fst correction factors. Both paternity testing and kinship analysis were compared to STR DNA profiling results. Interpretation criteria were formulated for correct genotyping of the 21-SNP multiplex to control for stochastic variation at low DNA inputs. Each locus was individually characterised for allele dropout, homozygous thresholds and heterozygous balance. The performance of the 21-SNP multiplex on degraded samples was compared with the AMPF/STR SGMplus (SGM+) STR method currently used for the UK National DNA Database and other DNA profiling techniques used across Europe. Applying the 21-SNP multiplex to casework samples previously profiled using low copy number (LCN) SGM+ amplification indicated that partial SNP profiles could be generated in samples that had given partial LCN SGM+ profiles, but samples failing to amplify using LCN PCR parameters would also fail with SNPs. This study demonstrated the use of SNPs for human forensic identification purposes as an adjunct to current STR methods and has formed the basis of further work on degraded DNA and the design of the next generation of DNA profiling systems