A LDR-PCR approach for multiplex polymorphisms genotyping of severely degraded DNA with fragment sizes <100 bp.
Reducing amplicon sizes has become a major strategy for analyzing degraded DNA typical of forensic samples. However, amplicon sizes in current mini-short tandem repeat-polymerase chain reaction (PCR) and mini-sequencing assays are still not suitable for analysis of severely degraded DNA. In this study, we present a multiplex typing method that couples ligase detection reaction with PCR that can be used to identify single nucleotide polymorphisms and small-scale insertion/deletions in a sample of severely fragmented DNA. This method adopts thermostable ligation for allele discrimination and subsequent PCR for signal enhancement. In this study, four polymorphic loci were used to assess the ability of this technique to discriminate alleles in an artificially degraded sample of DNA with fragment sizes <100 bp. Our results showed clear allelic discrimination of single or multiple loci, suggesting that this method might aid in the analysis of extremely degraded samples in which allelic drop out of larger fragments is observed.
Department of Forensic Serology, China Medical University, Shenyang, China.
Zhen
Z
Zhang
Bao-Jie
BJ
Wang
Hong-Yu
HY
Guan
Hao
H
Pang
Jin-Feng
JF
Xuan
D000483:Alleles; D053836:DNA Degradation, Necrotic; D016172:DNA Fingerprinting / Q000379:methods*; D053938:DNA Fragmentation; D017931:DNA Primers; D015342:DNA Probes; D005838:Genotype; D006801:Humans; D022521:Ligase Chain Reaction; D016133:Polymerase Chain Reaction; D020641:Polymorphism, Single Nucleotide
D017931:DNA Primers; D015342:DNA Probes