Internal quality assessment and genotyping error investigation in SNP microarray testing: Lessons from the ESWG-ISFG forensic proficiency trial

In 2024, the English Speaking Working Group of the International Society for Forensic Genetics (ESWG-ISFG) introduced single nucleotide polymorphism (SNP) genotyping into its annual proficiency trial, providing DNA testing laboratories with their first opportunity to evaluate performance in this area. Twelve laboratories participated using a range of sequencing and microarray platforms. AttoLife Limited, a UKAS-accredited laboratory, contributed results using the Infinium HTS iSelect custom ‘Rita’ microarray containing 4366 SNP markers. Blood samples from a child and alleged father were supplied on FTA cards, extracted with the QIAamp DNA Mini Kit, quantified using the Quantifiler Trio kit, and genotyped following the Infinium HTS protocol with GenomeStudio analysis. SNP call rates exceeded 99 % (excluding Y-SNPs in the female child), confirming high-quality data. Three discrepancies were identified, rs10108270 in both samples and rs10513300 in the child, which subsequent Sanger sequencing attributed to probe-binding site variation and potential copy number imbalance. These findings illustrate the value of proficiency testing in detecting locus-specific challenges, reinforce the need for cautious interpretation of uncertain results, and highlight the importance of cross-platform comparison to strengthen confidence in forensic SNP genotyping.