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Assessment of DNA degradation and the genotyping success of highly degraded samples

NCJ Number
255371
Journal
International Journal of Legal Medicine Volume: 125 Issue: 3 Dated: 2011 Pages: 341-348
Author(s)
S. Hughes-Stamm; K. Ashton; A. van Daal
Date Published
2011
Length
8 pages
Annotation

This article reports the findings and methodology of a comparative study of genotyping that uses STRs, mini-STRs, and single nucleotide polymorphisms (SNPs) with template at different levels of degradation in varying amounts. 

Abstract

DNA becomes progressively more fragmented as biological tissue degrades, resulting in decreasing ability to gain a complete DNA profile. Successful identification of samples that exhibit very high levels of DNA degradation may be complicated by presenting in minute quantities. The industry standard method for human DNA identification using short tandem repeats (STR) may produce partial or no DNA profile with such samples. In the current project, two methods of assessing quantity and quality of a DNA sample prior to genotyping were investigated. The QIAxcel capillary gel electrophoresis system provided a rapid, cost- effective screening method for assessing sample quality. A real-time quantitative PCR (qPCR) assay was able to simultaneously quantify total human DNA, male DNA, DNA degradation and PCR inhibition. The extent of DNA degradation could be assessed with reasonable accuracy to 62.5 pg and genomic targets could be quantified to a lower limit of 15.6 pg. The qPCR assay was able to detect male DNA to a lower limit of 20 pg in a 1:1,000 background of female DNA. By considering the amount of DNA and the degradation ratio of a sample, a general prediction of genotyping success using AmpFlSTR® Profiler Plus®, MiniFiler™ kits and SNP analysis can be made. The results indicate mini-STRs and SNP markers are usually more successful in typing degraded samples. In cases of extreme DNA degradation (≤200 bp) and template amounts below 250 pg., mini-STR and SNP analysis yielded significantly more complete profiles and lower match probabilities than corresponding STR profiles. 23 references (publisher abstract modified)

Date Published: January 1, 2011