Method and System for Genotyping Samples in a Normalized Allelic Space

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 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.

What is claimed: 
     
         1 . A method for generating genotype calls using an allele signal detection system that comprises a fluorescent probe having at least one of an associated discrete marker and a reporter dye responsive to an allele to be detected, the method comprising:
 generating, by a processor, an allelic model having one or more parameters source of systematic variation;   detecting, by the allele signal detection system, an allelic signal response from a plurality of biological samples;   determining, by the processor, a Cartesian distance from a sample to an expected one or more genotype coordinates in a normalized allelic space, the normalized allelic space being compensated for systemic variation based on a plurality of data points stored within a memory coupled to the processor, the data points being gathered from at least one of a plurality of runs and a plurality of samples;   displaying, by the allele signal detection system, a genotype call for the sample based on the shortest measured Cartesian distance between the sample and one of the expected one or more genotype coordinates.   
     
     
         2 . The method of  claim 1 , wherein the expected one or more genotype coordinates is selected from a set of genotype coordinates including: a homozygous allele A, a heterozygous allele AB and a homozygous allele B having corresponding coordinates (1, 0), (½, ½) and (0, 1) respectively. 
     
     
         3 . The method of  claim 1 , wherein the systematic variation comprises at least one of variability arising from different samples, and variability arising from different run. 
     
     
         4 . The method of  claim 1 , wherein the allele signal detection system records a measured fluorescent intensity to determine an allelic composition of the sample. 
     
     
         5 . The method of  claim 1 , wherein the parameter associated with each source of systematic variation is modified, by the processor, to minimize overall variation in the allelic signals and a model of the alleles in a training population. 
     
     
         6 . The computer implemented method of  claim 5 , wherein the model of the alleles in the training population arc assigned a unit probability, by the processor, of occurrence in the allele space of homozygous and heterozygous alleles. 
     
     
         7 . A non-transitory machine-readable storage device comprising instructions executable by a programmable processor within an allele signal detection system, the instructions operable to cause the programmable processor to cause the allele signal detection system to:
 detect an allelic signal response from a sample using a fluorescent probe having at least one of an associated discrete marker and a reporter dye responsive to an allele to be detected;   generate an allelic model using the allelic signal response, by the processor, the model having one or more parameters of systematic variation;   determine a genotype for the sample based upon its relationship to the representation of the allelic signal in a normalized allelic space and in accordance with the allelic model, the normalized allelic space being configured to compensate for systemic variation based on a plurality of data points gathered from at least one of a plurality of runs and a plurality of samples;   display the genotype for the sample based on the shortest measured Cartesian distance between the sample and one of the expected one or more genotype coordinates within the normalized allelic space.   
     
     
         8 . The non-transitory machine-readable storage device of  claim 7 , wherein the systematic variation comprises at least variability arising from different samples, and variability arising from different runs. 
     
     
         9 . The non-transitory machine-readable storage device of  claim 7 , wherein the expected one or more genotype coordinates is selected from a set of genotype coordinates including: a homozygous allele A, a heterozygous allele AB and a homozygous allele B having corresponding coordinates (1, 0), (½, ½) and (0, 1) respectively. 
     
     
         10 . The non-transitory machine-readable storage device of  claim 7 , wherein the instructions further comprises instructions when executed that cause the processor to cause the allele signal system to,
 create a fixed prior probability distribution of normalized allele signals from a statistically significant training set of genotype data by fitting, by the processor, a normalized training set of genotype data to probability distributions that reflect a set of allowed genotypes in the normalized allelic space;   and   display the genotype call for the sample, the call determined upon a greatest prior probability as reflected by the fitted probability distribution and applied to the sample normalized in the normalized allelic space.   
     
     
         11 . The non-transitory machine-readable storage device of  claim 10 , wherein the probability distributions are based upon elliptical Gaussian probability distributions. 
     
     
         12 . A system for generating genotype calls for a sample, comprising
 an allele signal detection system configured to detect an allelic signal response, the detection system comprising a fluorescent probe having at least one of an associated discrete marker and a reporter dye responsive to an allele to be detected;   a computer processor operable to:
 model the allelic signal response, by a processor, into an allelic model having one or more parameters sources of systematic variation; 
 transform the allelic signals through the one or more parameters of the allelic model to a normalized allelic space, by the processor, the normalized allelic space configured to compensate for systemic variation based on a plurality of data points gathered from at least one of a plurality of runs and a plurality of samples; 
 determine a genotype for the sample, by the processor, according to a clustering of the normalized allelic data signals in the normalized allelic space; 
 measure a relative angular offset of values for the normalized allelic data signals, by the processor, in the normalized allelic space; and 
 call, by the processor, a genotype for the sample based upon its proximity to the different angular offsets of values and their corresponding genotype classifications; and 
   a display operable to display the genotype call for the sample.   
     
     
         13 . The system of  claim 12 , wherein the expected one or more genotype coordinates is selected from a set of genotype coordinates including: a homozygous allele A, a heterozygous allele AB and a homozygous allele B having corresponding coordinates (1, 0), (½, ½) and (0, 1) respectively. 
     
     
         14 . The system of  claim 12 , wherein determining the genotype for the sample further comprises,
 presenting the cluster of allelic data signals in a diagram along with a confidence factor for the sample and genotype classification.   
     
     
         15 . The system of  claim 12 , wherein the allele signal detection system records a measured fluorescent intensity to determine an allelic composition of the sample. 
     
     
         16 . The system of  claim 12 , wherein the normalized allelic space is further configured to transform a relative measure of an allelic signal response into a unit-less scalar measure. 
     
     
         17 . The system of  claim 12 , wherein the systematic variation comprises at least one of variability arising from different samples, and variability arising from different runs. 
     
     
         18 . The system of  claim 17 , wherein the systematic variation further comprises variability arising from signal response imbalance from pairs of complementary alleles.