Auto-validation of fluorescent primer extension genotyping assay using signal clustering and neural networks.
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.


CONCLUSIONS
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.
Huang
Ching Yu Austin
CY
Center for Pharmacogenomics and Complex Disease Research, Newark, NJ 07101, USA. austin.huang@umdnj.edu
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
D001185:Artificial Intelligence; D001331:Automation; D016000:Cluster Analysis; D017931:DNA Primers / Q000235:genetics* / Q000378:metabolism*; D005456:Fluorescent Dyes / Q000378:metabolism*; D005838:Genotype; D006801:Humans; D016133:Polymerase Chain Reaction / Q000379:methods / Q000706:statistics & numerical data; D020641:Polymorphism, Single Nucleotide / Q000235:genetics; D011237:Predictive Value of Tests; D011786:Quality Control; D015203:Reproducibility of Results; D012984:Software / Q000706:statistics & numerical data
D017931:DNA Primers; D005456:Fluorescent Dyes