ArticleThe Journal of molecular diagnostics : JMD2002
Quantification of PCR bias caused by a single nucleotide polymorphism in SMN gene dosage analysis.
Article in The Journal of molecular diagnostics : JMD, 2002. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 9 papers.
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Who cites it
9 citing papers in PubMed, 24 citations in OpenAlex.
- Quantification of disease-associated RNA tandem repeats by nanopore sensing.Nature communications · 2026Article
- Article
- Multi-template polymerase chain reaction.Biomolecular detection and quantification · 2014Review
- Amplification-free Illumina sequencing-library preparation facilitates improved mapping and assembly of (G+C)-biased genomes.Nature methods · 2009Article
- Robust quantification of the SMN gene copy number by real-time TaqMan PCR.Neurogenetics · 2007Article
- Precision and performance characteristics of bisulfite conversion and real-time PCR (MethyLight) for quantitative DNA methylation analysis.The Journal of molecular diagnostics : JMD · 2006Article
- Sensitive sequencing method for KRAS mutation detection by Pyrosequencing.The Journal of molecular diagnostics : JMD · 2005Article
- Rapid detection of single nucleotide polymorphisms associated with spinal muscular atrophy by use of a reusable fibre-optic biosensor.Nucleic acids research · 2004Article
- Evaluation of temperature gradient capillary electrophoresis for detection of the Factor V Leiden mutation: coincident identification of a novel polymorphism in Factor V.Molecular diagnosis : a journal devoted to the understanding of human disease through the clinical application of molecular biology · 2003Article
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Authors and funding
2 authors at 2 institutions in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Approximately 94% of patients with spinal muscular atrophy lack both copies of SMN1 exon 7, and most carriers have only one copy of SMN1 exon 7. We described previously the effect of SMN1/SMN2 heteroduplex formation on SMN gene dosage analysis, which is a multiplex quantitative PCR assay to determine the copy numbers of SMN1 and SMN2 using DraI digestion to differentiate SMN2 from SMN1. We describe herein the quantification of PCR bias between SMN1 exon 7 and SMN2 exon 7, which differ by only one nucleotide that is not present in either primer binding site. Using samples from 272 individuals with various SMN genotypes, we found that the amplification efficiency of SMN2 was consistent only approximately 80% that of SMN1. Thus, even a single nucleotide polymorphism, not in primer binding sites, can cause reproducible PCR bias. The precision and accuracy of our SMN gene dosage analysis are high because our assay design and controls take advantage of the consistency of the PCR bias. As additional clinically significant single nucleotide polymorphisms (SNPs) are discovered, assessment of PCR bias, and judicious selection of standards and controls, will be increasingly important for quantitative PCR assays.
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