ArticleNucleic acids research2007
A bioinformatic filter for improved base-call accuracy and polymorphism detection using the Affymetrix GeneChip whole-genome resequencing platform.
Article in Nucleic acids research, 2007. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 12 papers.
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Who cites it
12 citing papers in PubMed.
- How industrial bacterial cultures can be kept stable over time.Letters in applied microbiology · 2020Review
- Development of a high-throughput resequencing array for the detection of pathogenic mutations in osteogenesis imperfecta.PloS one · 2015Article
- High-throughput retina-array for screening 93 genes involved in inherited retinal dystrophy.Investigative ophthalmology & visual science · 2011Article
- Large scale mtDNA sequencing reveals sequence and functional conservation as major determinants of homoplasmic mtDNA variant distribution.Mitochondrion · 2011Article
- Insights into N-calls of mitochondrial DNA sequencing using MitoChip v2.0.BMC research notes · 2011Article
- Mitochondrial genome sequence analysis: a custom bioinformatics pipeline substantially improves Affymetrix MitoChip v2.0 call rate and accuracy.BMC bioinformatics · 2011Article
- Monitoring the long-term molecular epidemiology of the pneumococcus and detection of potential 'vaccine escape' strains.PloS one · 2011Article
- Identification of rare DNA variants in mitochondrial disorders with improved array-based sequencing.Nucleic acids research · 2011Article
- Large-scale evolutionary surveillance of the 2009 H1N1 influenza A virus using resequencing arrays.Nucleic acids research · 2010Article
- High-throughput detection of mutations responsible for childhood hearing loss using resequencing microarrays.BMC biotechnology · 2010Article
- Whole genome single nucleotide polymorphism based phylogeny of Francisella tularensis and its application to the development of a strain typing assay.BMC microbiology · 2009Article
- VarDetect: a nucleotide sequence variation exploratory tool.BMC bioinformatics · 2008Article
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Authors and funding
11 authors.
Funding
Abstract
DNA resequencing arrays enable rapid acquisition of high-quality sequence data. This technology represents a promising platform for rapid high-resolution genotyping of microorganisms. Traditional array-based resequencing methods have relied on the use of specific PCR-amplified fragments from the query samples as hybridization targets. While this specificity in the target DNA population reduces the potential for artifacts caused by cross-hybridization, the subsampling of the query genome limits the sequence coverage that can be obtained and therefore reduces the technique's resolution as a genotyping method. We have developed and validated an Affymetrix Inc. GeneChip(R) array-based, whole-genome resequencing platform for Francisella tularensis, the causative agent of tularemia. A set of bioinformatic filters that targeted systematic base-calling errors caused by cross-hybridization between the whole-genome sample and the array probes and by deletions in the sample DNA relative to the chip reference sequence were developed. Our approach eliminated 91% of the false-positive single-nucleotide polymorphism calls identified in the SCHU S4 query sample, at the cost of 10.7% of the true positives, yielding a total base-calling accuracy of 99.992%.
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