ArticleNucleic acids research1998
Automated detection of point mutations using fluorescent sequence trace subtraction.
Article in Nucleic acids research, 1998. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 27 papers, 1 of them a synthesis that pooled it.
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Who cites it
27 citing papers in PubMed, 1 synthesis or guideline pooled it.
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- The novel mouse mutation Oblivion inactivates the PMCA2 pump and causes progressive hearing loss.PLoS genetics · 2008Article
- Mutational analysis of the breast cancer susceptibility gene BRIP1 /BACH1/FANCJ in high-risk non-BRCA1/BRCA2 breast cancer families.Journal of human genetics · 2008Article
- High frequency of missense mutations in glycogen storage disease type VI.Journal of inherited metabolic disease · 2007Article
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- Polymorphism discovery and association analyses of the interferon genes in type 1 diabetes.BMC genetics · 2006Article
- Direct detection of methylation in genomic DNA.Nucleic acids research · 2005Article
- SeqDoC: rapid SNP and mutation detection by direct comparison of DNA sequence chromatograms.BMC bioinformatics · 2005Article
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Authors and funding
3 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
The final step in the detection of mutations is to determine the sequence of the suspected mutant and to compare it with that of the wild-type, and for this fluorescence-based sequencing instruments are widely used. We describe some simple algorithms forcomparing sequence traces which, as part of our sequence assembly and analysis package, are proving useful for the discovery of mutations and which may also help to identify misplaced readings in sequence assembly projects. The mutations can be detected automatically by a new program called TRACE_DIFF and new types of trace display in our program GAP4 greatly simplify visual checking of the assigned changes. To assess the accuracy of the automatic mutation detection algorithm we analysed 214 sequence readings from hypermutating DNA comprising a total of 108 497 bases. After the readings were assembled there were 1232 base differences, including 392 Ns and 166 alignment characters. Visual inspection of the traces established that of the 1232 differences, 353 were real mutations while the rest were due to base calling errors. The TRACE_DIFF algorithm automatically identified all but 36, with 28 false positives. Further information about the software can be obtained from http://www.mrc-lmb.cam.ac.uk/pubseq/
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