Systems and Methods for SNP Characterization and Identifying off Target Variants
AssigneeAffymetrix, Inc.
InventorsHong Gao, Ali Pirani, Teresa Webster, Mei-Mei Shen
Life of this patent
Estimating the term…
Abstract
Methods for processing data using information gained from examining biological materials identifies and characterized probes for Single Nucleotide Polymorphisms and identifies Off Target Variants.
Claims47
A method of genotyping polymorphisms using a computer system comprising:
- accessing genotype clustering data from a plurality of polymorphism (e.g., SNPs and indels) probeset locations from a plurality of samples, the genotype clustering data comprising genotype cluster calls of samples, cluster centers, and variance;
- accessing polymorphisms probeset sample data that indicates contrast and intensity detected at a probeset location across a number of samples;
- determining one or more quality metrics for each probeset;
- using said quality metrics and said computer system, choosing a selected probeset from two or more probesets available for a polymorphisms;
- and
- outputting the selected probeset.
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A method of genotyping single nucleotide polymorphisms (SNPs) by identifying off-target variants (OTVs) using a computer system comprising:
- accessing genotype clustering data from a number of samples from a probeset location, the genotype clustering data comprising genotype cluster calls of samples;
- cluster centers, and variance;
- accessing sample data that indicates contrast and intensity detected at a probeset location across a number of samples;
- searching for optimal clustering of said sample data in both contrast and intensity dimensions, allowing for an OTV genotype cluster;
- iteratively updating sample assignments to clusters and cluster centers until convergence;
- and
- outputting genotyping cluster results for said samples.
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33-34. (canceled)
A method using a computer system to select a preferred SNP probeset from a plurality of SNP probesets comprising:
- determining a plurality of first SNP probeset quality control metrics that characterize genotype clusters for an SNP probeset;
- classify each probeset for an SNP using the first and second SNP probeset quality control metrics;
- select a probeset with the highest priority classification.
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A computer program stored on a non-transitory computer readable medium, the computer program comprising code to perform:
- accessing genotyping data comprising intensity and contrast data for one or more probesets for a polymorphism;
- determining a plurality of probeset quality control metrics for said one or more probesets;
- when said genotyping data includes two or more of said probesets of said polymorphism, selecting at least one of said two or more probesets for providing an improved genotyping result for said polymorphism;
- outputting data indicating said quality control metrics or said at least one probeset or said genotyping result or any combination thereof.
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Dependencies are inferred from the claim text.