title: A 34-plex autosomal SNP single base extension assay for ancestry investigations.
abstract: Ancestry inference based on autosomal markers remains a niche approach in forensic analysis: most laboratories feel more secure with a review of the cumulative STR profile frequencies in a range of relevant populations with the possible additional analysis of mitochondrial and/or Y-chromosome variability. However, a proportion of autosomal single nucleotide polymorphisms (SNPs) show very well-differentiated allele frequencies among global population-groups. Furthermore, such ancestry informative marker SNPs (AIM-SNPs) lend themselves to relatively straightforward typing with short-amplicon PCR and multiplexed single base extension reactions using the same capillary electrophoresis detectors required for the sequencing and STR genotyping of mainstream forensic markers. In this chapter, we describe a 34 AIM-SNP multiplex that is robust enough for the analysis of challenging, often highly degraded DNA typical of much of routine forensic casework. We also outline in detail the in-silico procedures necessary for collecting parental population reference data from the SPSmart SNP databases and performing ancestry inference of single AIM-SNP profiles or large-scale population data using the companion ancestry analysis website of Snipper. Two casework examples are described that show, in both cases, that an inference of likely ancestry using AIM-SNPs helped the identification of highly degraded skeletal material.
authors.affiliation: Forensic Genetics Unit, Institute of Legal Medicine, University of Santiago de Compostela, Santiago de Compostela, Spain. c.phillips@mac.com
authors.forename: C
authors.initials: C
authors.lastname: Phillips
authors.forename: M
authors.initials: M
authors.lastname: Fondevila
authors.forename: Maria Victoria
authors.initials: MV
authors.lastname: Lareau
mesh_terms: D020029:Base Pairing / Q000235:genetics*; D001483:Base Sequence; D002877:Chromosomes, Human / Q000235:genetics*; D017931:DNA Primers / Q000378:metabolism; D030541:Databases, Genetic; D005789:Genealogy and Heraldry; D005819:Genetic Markers; D005828:Genetics, Population; D006801:Humans; D008969:Molecular Sequence Data; D016133:Polymerase Chain Reaction / Q000379:methods*; D020641:Polymorphism, Single Nucleotide / Q000235:genetics*; D012015:Reference Standards
chemical_list: D017931:DNA Primers; D005819:Genetic Markers