Optimal genotype determination in highly multiplexed SNP data.
Eur J Hum Genet
; 14(2): 207-15, 2006 Feb.
Article
in En
| MEDLINE
| ID: mdl-16306880
ABSTRACT
High-throughput genotyping technologies that enable large association studies are already available. Tools for genotype determination starting from raw signal intensities need to be automated, robust, and flexible to provide optimal genotype determination given the specific requirements of a study. The key metrics describing the performance of a custom genotyping study are assay conversion, call rate, and genotype accuracy. These three metrics can be traded off against each other. Using the highly multiplexed Molecular Inversion Probe technology as an example, we describe a methodology for identifying the optimal trade-off. The methodology comprises a robust clustering algorithm and assessment of a large number of data filter sets. The clustering algorithm allows for automatic genotype determination. Many different sets of filters are then applied to the clustered data, and performance metrics resulting from each filter set are calculated. These performance metrics relate to the power of a study and provide a framework to choose the most suitable filter set to the particular study.
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Collection:
01-internacional
Database:
MEDLINE
Main subject:
Research Design
/
Algorithms
/
Molecular Probe Techniques
/
Polymorphism, Single Nucleotide
Type of study:
Prognostic_studies
Language:
En
Journal:
Eur J Hum Genet
Journal subject:
GENETICA MEDICA
Year:
2006
Document type:
Article
Affiliation country:
United States