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.

Whole genome computational comparative genomics: A fruitful approach for ascertaining Alu insertion polymorphisms

“…The remaining 46 CHGS polymorphic elements were likely from the public human BAC sequences that may have not been used for the assembly of PHGS. To determine how many of the 800 polymorphic Alu elements had been previously identified and published, we compiled a database containing 1051 non-redundant polymorphic Alu insertions (http://falcon.roswellpark.org:9090; Wang et al, in press) from the over 1500 polymorphisms reported in the literature (Batzer et al, 1994Bennett et al, 2004;Callinan et al, 2003;Carroll et al, 2001;Carter et al, 2004;Garber et al, 2005;Mamedov et al, 2005;Otieno et al, 2004;Ray et al, 2005;Roy-Engel et al, 2001;Watkins et al, 2003;Xing et al, 2003). A comparison of the genomic locations of our 800 polymorphic Alu insertions with the list revealed that only 266 of the 800 Alu elements correspond with previously reported Alu repeats, suggesting that the remaining 534 insertions represent newly identified polymorphisms.…”

A new set of markers for human identification based on 32 polymorphic Alu insertions

“…In the past decade, a new type of MGMs based on RE insertion polymorphism has become popular in population studies. [28][29][30][31][32] These markers belong to a biallelic indel (insertion/deletion) polymorphism type and are characterized by several features making them good candidates for human genetic identification. Multiple studies intended to identify new polymorphic RE insertions resulted in an increasing number of candidate MGMs scattered across the whole human genome.…”

Mobile element-based forensic genomics

“…In a study conducted in collaboration with law enforcement officials, forensic DNA specimens were evaluated using the dataset of 100 Alu insertion polymorphisms and Structure 2.0. The system demonstrated accurate assignment of each specimen to the correct geographic affiliation [109].…”