Genotyping mitochondrial DNA single nucleotide polymorphisms by PCR ligase detection reactions.
BACKGROUND
The identification of human mitochondrial DNA (mtDNA) sequence variations, especially single nucleotide polymorphisms (SNPs), is important for many applications. The PCR-ligase detection reaction (LDR) method can reduce false-positives and eliminate the need for both post-PCR and post-ligation purifications in SNP analyses. In addition, it has been successfully employed to detect point mutations in various nuclear genes. In this study, we used the PCR-LDR platform to characterize mtDNA SNPs.


METHODS
Multiplex PCR-LDRs were used to genotype 19 mtDNA single nucleotide polymorphic sites from 812 samples. Performance of the method was assessed by direct sequencing of 44 samples.


RESULTS
We established an overall 97.4% success rate with 99.2% accuracy using the multiplex PCR-LDR methodology.


CONCLUSIONS
The PCR-LDR mtDNA genotyping technique is simple, highly accurate, has high-throughput, and is cost-effective. Therefore, this method is applicable to mtDNA haplotyping in various applications.
Luo
Yongjun
Y
Department of Pathophysiology and High Altitude Physiology, Third Military Medical University, Chongqing, PR China.
Tang
Sha
S
Gao
Wenxiang
W
Chen
Li
L
Yang
Xiaohong
X
Huang
Taosheng
T
Gao
Yuqi
Y
D000483:Alleles; D004252:DNA Mutational Analysis; D004272:DNA, Mitochondrial / Q000737:chemistry*; D005838:Genotype; D006801:Humans; D022521:Ligase Chain Reaction; D016133:Polymerase Chain Reaction; D020641:Polymorphism, Single Nucleotide; D015203:Reproducibility of Results; D012680:Sensitivity and Specificity
D004272:DNA, Mitochondrial