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Proceedings Paper

The development of miniplex primer sets for the analysis of degraded DNA
Author(s): Bruce McCord; Kerry Opel; Denise Chung; Jiri Drabek; Nancy Tatarek; Lee Meadows Jantz; John Butler
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Paper Abstract

In this project, a new set of multiplexed PCR reactions has been developed for the analysis of degraded DNA. These DNA markers, known as Miniplexes, utilize primers that have shorter amplicons for use in short tandem repeat (STR) analysis of degraded DNA. In our work we have defined six of these new STR multiplexes, each of which consists of 3 to 4 reduced size STR loci, and each labeled with a different fluorescent dye. When compared to commercially available STR systems, reductions in size of up to 300 basepairs are possible. In addition, these newly designed amplicons consist of loci that are fully compatible with the the national computer DNA database known as CODIS. To demonstrate compatibility with commercial STR kits, a concordance study of 532 DNA samples of Caucasian, African American, and Hispanic origin was undertaken There was 99.77% concordance between allele calls with the two methods. Of these 532 samples, only 15 samples showed discrepancies at one of 12 loci. These occurred predominantly at 2 loci, vWA and D13S317. DNA sequencing revealed that these locations had deletions between the two primer binding sites. Uncommon deletions like these can be expected in certain samples and will not affect the utility of the Miniplexes as tools for degraded DNA analysis. The Miniplexes were also applied to enzymatically digested DNA to assess their potential in degraded DNA analysis. The results demonstrated a greatly improved efficiency in the analysis of degraded DNA when compared to commercial STR genotyping kits. A series of human skeletal remains that had been exposed to a variety of environmental conditions were also examined. Sixty-four percent of the samples generated full profiles when amplified with the Miniplexes, while only sixteen percent of the samples tested generated full profiles with a commercial kit. In addition, complete profiles were obtained for eleven of the twelve Miniplex loci which had amplicon size ranges less than 200 base pairs. These data clearly demonstrate that smaller PCR amplicons provide an attractive alternative to mitochondrial DNA for forensic analysis of degraded DNA.

Paper Details

Date Published: 20 May 2005
PDF: 9 pages
Proc. SPIE 5778, Sensors, and Command, Control, Communications, and Intelligence (C3I) Technologies for Homeland Security and Homeland Defense IV, (20 May 2005); doi: 10.1117/12.603080
Show Author Affiliations
Bruce McCord, Florida International Univ. (United States)
Kerry Opel, Florida International Univ. (United States)
Denise Chung, Ohio Univ. (United States)
Jiri Drabek, Ohio Univ. (United States)
Nancy Tatarek, Ohio Univ. (United States)
Lee Meadows Jantz, Univ. of Tennessee/Knoxville (United States)
John Butler, National Institute of Standards and Technology (United States)

Published in SPIE Proceedings Vol. 5778:
Sensors, and Command, Control, Communications, and Intelligence (C3I) Technologies for Homeland Security and Homeland Defense IV
Edward M. Carapezza, Editor(s)

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