ArticleNucleic acids research2008
Predicting failure rate of PCR in large genomes.
Article in Nucleic acids research, 2008. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 19 papers.
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Who cites it
19 citing papers in PubMed.
- ExonSurfer: a web-tool to design primers at exon-exon junctions.BMC genomics · 2024Article
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- PRIMEval: Optimization and screening of multiplex oligonucleotide assays.Scientific reports · 2019Article
- MFEprimer-3.0: quality control for PCR primers.Nucleic acids research · 2019Article
- ThermoAlign: a genome-aware primer design tool for tiled amplicon resequencing.Scientific reports · 2017Article
- TipMT: Identification of PCR-based taxon-specific markers.BMC bioinformatics · 2017Article
- Onchocerciasis transmission in Ghana: the human blood index of sibling species of the Simulium damnosum complex.Parasites & vectors · 2016Article
- Multivariate test power approximations for balanced linear mixed models in studies with missing data.Statistics in medicine · 2016Article
- Article
- The truth about metagenomics: quantifying and counteracting bias in 16S rRNA studies.BMC microbiology · 2015Article
- Quantifying RNA allelic ratios by microfluidic multiplex PCR and sequencing.Nature methods · 2014Article
- URPD: a specific product primer design tool.BMC research notes · 2012Article
- Sequence dependence of isothermal DNA amplification via EXPAR.Nucleic acids research · 2012Article
- Article
- pcrEfficiency: a Web tool for PCR amplification efficiency prediction.BMC bioinformatics · 2011Article
- Optimization of turn-back primers in isothermal amplification.Nucleic acids research · 2011Article
- MPprimer: a program for reliable multiplex PCR primer design.BMC bioinformatics · 2010Article
- RExPrimer: an integrated primer designing tool increases PCR effectiveness by avoiding 3' SNP-in-primer and mis-priming from structural variation.BMC genomics · 2009Article
- Automatic identification of species-specific repetitive DNA sequences and their utilization for detecting microbial organisms.Bioinformatics (Oxford, England) · 2009Article
Corrections and comments
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Authors and funding
3 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
We have developed statistical models for estimating the failure rate of polymerase chain reaction (PCR) primers using 236 primer sequence-related factors. The model involved 1314 primer pairs and is based on more than 80 000 PCR experiments. We found that the most important factor in determining PCR failure is the number of predicted primer-binding sites in the genomic DNA. We also compared different ways of defining primer-binding sites (fixed length word versus thermodynamic model; exact match versus matches including 1-2 mismatches). We found that the most efficient prediction of PCR failure rates can be achieved using a combination of four factors (number of primer-binding sites counted in different ways plus GC% of the primer) combined into single statistical model GM1. According to our estimations from experimental data, the GM1 model can reduce the average failure rate of PCR primers nearly 3-fold (from 17% to 6%). The GM1 model can easily be implemented in software to premask genome sequences for potentially failing PCR primers, thus improving large-scale PCR-primer design.
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