Chapter 20: Autosomal Short Tandem Repeat Profiling

Forensic DNA analysis relies on established core loci sets such as CODIS, SGM, and ESS systems, which incorporate highly variable markers including TH01, VWA, FGA, and D3S1358 to maximize the probability of differentiation among unrelated populations. Genotyping determination occurs through capillary electrophoresis separation, allowing researchers to visualize allelic patterns and generate categorical conclusions of inclusion, exclusion, or inconclusive findings based on the matching criteria. The chapter extensively addresses the complications arising during STR analysis, including genuine biological variations such as mutations occurring within core repeat regions, point mutations at flanking sequences, and chromosomal duplications that produce triallelic patterns. Additionally, numerous technical artifacts frequently complicate interpretation, such as stuttering phenomena where minor peaks appear one repeat unit smaller than true alleles, nontemplate adenylation creating artificial peaks, heterozygote imbalance affecting relative peak heights, and allelic dropout resulting in false exclusions. Electrophoretic instrumentation can introduce artifacts including pull-up peaks from spectral overlap and electronic spikes requiring careful discrimination from genuine alleles. The final sections address practical challenges encountered in casework, particularly the analysis of degraded DNA samples that may yield incomplete profiles, low copy number DNA testing with its inherent stochastic variation and interpretation difficulties, and the complex problem of analyzing mixed DNA profiles from multiple contributors where allele frequencies, mixture ratios, and contributor numbers create substantial interpretive challenges for forensic practitioners.