Abstract
For the analysis of degraded DNA in disaster victim identification (DVI) and criminal
investigations, single nucleotide polymorphisms (SNPs) have been recognized as promising
markers mainly because they can be analyzed in short sized amplicons. Most SNPs are
bi-allelic and are thereby ineffective to detect mixtures, which may lead to incorrect
genotyping. We developed an algorithm to find non-binary (i.e. tri-allelic or tetra-allelic)
SNPs in the NCBI dbSNP database. We selected 31 potential tri-allelic SNPs with a
minor allele frequency of at least 10%. The tri-allelic nature was confirmed for 15
SNPs residing on 14 different chromosomes. Multiplex SNaPshot™ assays were developed,
and the allele frequencies of 16 SNPs were determined among 153 Dutch and 111 Netherlands
Antilles reference samples. Using these multiplex SNP assays, the presence of a mixture
of two DNA samples in a ratio up to 1:8 could be recognized reliably. Furthermore,
we compared the genotyping efficiency of the tri-allelic SNP markers and short tandem
repeat (STR) markers by analyzing artificially degraded DNA and DNA from 30 approximately
500-year-old bone and molar samples. In both types of degraded DNA samples, the larger
sized STR amplicons failed to amplify whereas the tri-allelic SNP markers still provided
valuable information. In conclusion, tri-allelic SNP markers are suited for the analysis
of degraded DNA and enable the detection of a second DNA source in a sample.
Keywords
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Article info
Publication history
Published online: March 09, 2009
Accepted:
February 9,
2009
Received in revised form:
February 6,
2009
Received:
November 25,
2008
Identification
Copyright
© 2009 Elsevier Ireland Ltd. Published by Elsevier Inc. All rights reserved.
