Chapter 22: Single Nucleotide Polymorphism Profiling

The foundation of SNP analysis in forensic science developed through historical methodologies such as allele-specific oligonucleotide hybridization assays targeting the HLA-DQA1 locus, including commercially available systems like the DQα AmpliType and Polymarker kits that established early protocols for genetic profiling. Contemporary forensic applications have evolved to incorporate autosomal SNPs for human identification purposes, enabling investigators to distinguish individuals with increasing precision. A significant advancement involves ancestry informative markers, which function to estimate the biogeographical origin of individuals based on allele frequency patterns specific to different populations, providing investigative leads regarding geographic ancestry. An emerging and powerful application involves forensic phenotyping, wherein SNPs associated with specific genes such as MC1R and P are analyzed to make predictive inferences about observable physical traits including hair color, eye color, and other externally visible characteristics that may help generate investigative leads. The chapter details multiple SNP detection methodologies, with particular emphasis on the SNaPshot assay, a primer extension technique that allows simultaneous genotyping of multiple loci. Additionally, array-based detection methods are discussed as scalable approaches to analyzing large numbers of SNP markers simultaneously. Modern advances in Next-Generation Sequencing technologies form a substantial focus, encompassing the complete workflow from DNA sample preparation through sequencing library construction, including the preparation of fragment libraries and incorporation of index tags for sample multiplexing. The chapter addresses the specialized sequencing chemistry platforms used in NGS and emphasizes the importance of achieving adequate coverage depths necessary to ensure the reliability and reproducibility of forensic SNP data across casework samples and reference populations.