Ontology highlight
ABSTRACT: Background
SNP genotyping typically incorporates a review step to ensure that the genotype calls for a particular SNP are correct. For high-throughput genotyping, such as that provided by the GenomeLab SNPstream instrument from Beckman Coulter, Inc., the manual review used for low-volume genotyping becomes a major bottleneck. The work reported here describes the application of a neural network to automate the review of results.Results
We describe an approach to reviewing the quality of primer extension 2-color fluorescent reactions by clustering optical signals obtained from multiple samples and a single reaction set-up. The method evaluates the quality of the signal clusters from the genotyping results. We developed 64 scores to measure the geometry and position of the signal clusters. The expected signal distribution was represented by a distribution of a 64-component parametric vector obtained by training the two-layer neural network onto a set of 10,968 manually reviewed 2D plots containing the signal clusters.Conclusion
The neural network approach described in this paper may be used with results from the GenomeLab SNPstream instrument for high-throughput SNP genotyping. The overall correlation with manual revision was 0.844. The approach can be applied to a quality review of results from other high-throughput fluorescent-based biochemical assays in a high-throughput mode.
SUBMITTER: Huang CY
PROVIDER: S-EPMC406493 | biostudies-literature | 2004 Apr
REPOSITORIES: biostudies-literature
Huang Ching Yu Austin CY Studebaker Joel J Yuryev Anton A Huang Jianping J Scott Kathryn E KE Kuebler Jennifer J Varde Shobha S Alfisi Steven S Gelfand Craig A CA Pohl Mark M Boyce-Jacino Michael T MT
BMC bioinformatics 20040402
<h4>Background</h4>SNP genotyping typically incorporates a review step to ensure that the genotype calls for a particular SNP are correct. For high-throughput genotyping, such as that provided by the GenomeLab SNPstream instrument from Beckman Coulter, Inc., the manual review used for low-volume genotyping becomes a major bottleneck. The work reported here describes the application of a neural network to automate the review of results.<h4>Results</h4>We describe an approach to reviewing the qual ...[more]