Method and system for genotyping samples in a normalized allelic space
OwnerMark Pratt, David Holdeninventors
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Abstract
Aspects of the present invention describe an apparatus and method for generating genotype calls for a sample. The genotyping initially models allelic signal response into an allelic model having one or more model parameters for an identified one or more sources of systematic variation. The model and parameters are then used to transform the allelic signals to a normalized normalized allelic space that serves to compensate for the one or more sources of systematic variation. By compensating for the systematic variation in this manner, the genotype for the sample is readily determined based upon its relationship to the representation of the allelic signals in normalized allelic space and in accordance with the allelic model.
Claims20
A computer implemented method of generating genotype calls for a sample, comprising:
- modeling allelic signal response into an allelic model having one or more model parameters for an identified one or more sources of systematic variation;
- transforming the allelic signals through the one or more model parameters of the allelic model to a normalized allelic space that serves to compensate for the one or more sources of systematic variation;
- and
- determining a genotype for the sample based upon its relationship to the representation of the allelic signals in normalized allelic space and in accordance with the allelic model.
A computer program product for generating genotype calls for a sample, comprising instructions operable to cause a programmable processor to:
- model allelic signal response into an allelic model having one or more model parameters for an identified one or more sources of systematic variation;
- transform the allelic signals through the one or more model parameters of the allelic model to a normalized allelic space that serves to compensate for the one or more sources of systematic variation;
- and
- determine a genotype for the sample based upon its relationship to the representation of the allelic signals in normalized allelic space and in accordance with the allelic model.
An apparatus for generating genotype calls for a sample, comprising:
- means for modeling allelic signal response into an allelic model having one or more model parameters for an identified one or more sources of systematic variation;
- means for transforming the allelic signals through the one or more model parameters of the allelic model to a normalized allelic space that serves to compensate for the one or more sources of systematic variation;
- and
- means for determining a genotype for the sample according to a clustering of allelic data signals as represented in the normalized allelic space.
Dependencies are inferred from the claim text.