title: Inference of human geographic origins using Alu insertion polymorphisms.
abstract: The inference of an individual's geographic ancestry or origin can be critical in narrowing the field of potential suspects in a criminal investigation. Most current technologies rely on single nucleotide polymorphism (SNP) genotypes to accomplish this task. However, SNPs can introduce homoplasy into an analysis since they can be identical-by-state. We introduce the use of insertion polymorphisms based on short interspersed elements (SINEs) as a potential alternative to SNPs. SINE polymorphisms are identical-by-descent, essentially homoplasy-free, and inexpensive to genotype using a variety of approaches. Herein, we present results of a blind study using 100 Alu insertion polymorphisms to infer the geographic ancestry of 18 unknown individuals from a variety of geographic locations. Using a Structure analysis of the Alu insertion polymorphism-based genotypes, we were able to correctly infer the geographic affiliation of all 18 unknown human individuals with high levels of confidence. This technique to infer the geographic affiliation of unknown human DNA samples will be a useful tool in forensic genomics.
authors.affiliation: Department of Biological Sciences, Biological Computation and Visualization Center, Louisiana State University, 202 Life Sciences Building, Baton Rouge, LA 70803, USA.
authors.forename: David A
authors.initials: DA
authors.lastname: Ray
authors.forename: Jerilyn A
authors.initials: JA
authors.lastname: Walker
authors.forename: Ashley
authors.initials: A
authors.lastname: Hall
authors.forename: Barbara
authors.initials: B
authors.lastname: Llewellyn
authors.forename: Jack
authors.initials: J
authors.lastname: Ballantyne
authors.forename: Allen T
authors.initials: AT
authors.lastname: Christian
authors.forename: Kenneth
authors.initials: K
authors.lastname: Turteltaub
authors.forename: Mark A
authors.initials: MA
authors.lastname: Batzer
mesh_terms: D020087:Alu Elements; D016172:DNA Fingerprinting / Q000379:methods*; D005006:Ethnicity / Q000235:genetics*; D005260:Female; D005838:Genotype; D006801:Humans; D020071:Interspersed Repetitive Sequences; D008297:Male; D016133:Polymerase Chain Reaction; D011110:Polymorphism, Genetic