D9S1120, a Simple STR With a Common Native American-Specific Allele: Forensic Optimization, Locus Characterization and Allele Frequency Studies

• NCJ Number: 225660
• Journal: Forensic Science International: Genetics Volume: 3 Issue: 1 Dated: December 2008 Pages: 7-13
• Author(s): C. Phillips; A. Rodriquez; A. Mosquera-Miguel; M. Fondevila; L. Porras-Hurtado; F. Rondon; A. Salas; A. Salas; A. Carracedo; M. V. Lareu
• Date Published: December 2008
• Length: 7 pages
• Grant Number(s): PGIDTIT06PXIB228195PR; BIO2006-06178
• Sponsoring Agency: Ministerio de Ciencia e Innovacion; Xunta de Galicia
• Publication Format: Article
• Publication Type: Report (Study/Research)
• Language: English
• Country: Ireland

Annotation

This article reports on the redesign of PCR primers that reduce the amplified product sizes reported in NCBI UniSTS by more than a third and have characterized the repeat structure of D9S1120, which exhibits a common population-specific allele of nine repeats (9RA) reported to have an average frequency of 0.36 in Native Americans from both North and South of the continent.

Abstract

This study indicates that 9RA will be a useful supplement to Y-chromosome and mtDNA typing for the analysis of Native American populations and their origins. In addition, the 9RA allele shows informative levels of American specificity for inferring Native American ancestry in approximately 53 percent of individuals from this population group. Comparison with the authors’ set of most informative American indicative AIM-SNPs show D9S1120 will be a useful additional locus, particularly for differentiating American and East Asian ancestries. One less useful characteristic of D9S1120 is that variation in 9RA frequencies among American populations is high, making estimation of Native American admixture proportions based on this marker alone imprecise; however, the 9RA allele is generally frequent enough across the American continent to allow the detection of a minor Native American component when examining admixed populations using a large enough sample set. The authors are currently analyzing all three loci plus autonomic AIM-SNPs in parallel in assessing the extent to which D9S1120 helps to resolve complicated patterns of admixture previously characterized by mtDNA alone. A survey was made of six American (Maya, three native Colombian, and two American-African-European admixed populations from Colombia) and three non-American populations. Descriptions of materials and methods address the PCR primer design and amplification conditions, as well as the sequence analysis and construction allelic ladder. 3 tables, 3 figures, and 10 references