NCJ Number
228341
Journal
Forensic Science International: Genetics Volume: 3 Issue: 4 Dated: September 2009 Pages: 233-241
Date Published
September 2009
Length
9 pages
Annotation
This article reports on the development of an algorithm to find nonbinary (i.e., tri-allelic or tetra-allelic) single nucleotide polymorphisms (SNPs) in the NCBI dbSNP database.
Abstract
The study concluded that tri-allelic SNP markers are suited for the analysis of degraded DNA and enable the detection of a second DNA source in a sample. Fifteen tri-allelic SNPs on 14 different chromosomes were detected in DNA samples from Dutch and Netherlands Antilles donors. The study showed that such nonbinary SNPs have the ability to reveal the presence of a second DNA donor in mixed samples with a ratio of up to 1:8. Indications for a mixture are the presence of a third allele on one locus, unexpected peak height ratios, and uncalled peaks above the detection threshold. Several of the tri-allelic SNP markers may not only be useful for identification purposes, but also as ancestry informative markers. In addition, degraded (UV irradiated, TURBO DNase treated, and 500-year-old bone and molar) DNA samples show that when the higher molecular weight STR markers fail to amplify, tri-allelic SNP markers can still provide valuable information. Multiplex SNaPshot assays were developed, and the allele frequencies of 16 SNPs were determined for 152 Dutch and 111 Netherlands Antilles reference samples. The descriptions of materials and methods address sample characteristics, SNP selection, PCR, SNaPshot (single base extension), SNP detection and analysis, allele frequencies and statistics, and sequencing. 2 tables, 4 figures, and 35 references