Methods and apparatus for genotyping

Abstract

A method for establishing the genotype of the locus is provided in which a series of calibration samples are analysed, the results being one of three indication types, a window being defined relative to the indication for each of the indication types, unknown samples being similarly analysed with the window that they fall within being taken to determine the indication type for the unknown sample and hence the genotype of the relevant locus. The technique provides a robust, reliable and accurate method of genotyping which is suited to automation.

1 . A method of establishing the genotype at each of a plurality of loci, the genotype at each locus being one of two possible identities, the method including: 
 analysing a plurality of replicates of each of a plurality of calibration samples to provide an indication of the genotype at each of the loci for each replicate of each sample, the indication being a ratio of a measure of the presence of the first possible identity relative to a measure of the second possible identity for a given locus, the indication for a sample at a given locus being one of three indication types;    generating an average indication for each of the three indication types from the indications in each of those indication types;    providing a window relative to the average indication for each of the three indication types for each of the loci;    analysing a plurality of replicates of an unknown sample to provide an indication of the genotype at each of the loci for which a window is provided, the indication being a ratio of a measure of the presence of the first possible identity relative to a measure of the second possible identity for that given locus;    generating an average indication from each of the indications for the replicates of that unknown sample for each of the loci;    comparing the average indication for the unknown sample at a locus with the windows provided for that locus, the analysis of the unknown sample being accepted if the indication is within a window and/or the analysis of the unknown sample being rejected if the indication is outside the window, the genotype for a locus being derivable from the average indication.    
     
     
         2 . A method according to  claim 1  in which at least 10 replicates are analysed for each of at least 8 calibration samples, the genotype being established for at least 8 loci, the indication being the level of one or more dyes, one indication type relating to one homozygous possibility for the genotype, the second of the indication types relating to the heterozygous possibility genotype, and the third indication type relating to the other homozygous possibility for the genotype.  
     
     
         3 . A method of establishing the genotype at a locus, the genotype being one of two possible identities, the method including: 
 analysing one or more calibration samples to provide an indication of the genotype at one or more loci, the indication for a given locus including a measure of the presence of the first possible identity and a measure of the second possible identity;    providing a window relative to the indication for a given locus;    analysing an unknown sample to provide an indication of the genotype at a locus for which a window is provided, the indication including a measure of the presence of the first possible identity and a measure of the second possible identity for that given locus;    the indication for a locus for the unknown sample being compared with the window for that locus, that analysis of the unknown sample for that locus being accepted if the indication is within the window and/or that analysis of the unknown sample for that locus being rejected if the indication is outside the window, the genotype for a locus being derivable from the indication.    
     
     
         4 . A method according to  claim 3  in which the method establishes the genotype for at least 12 loci in respect of the calibration samples and unknown samples.  
     
     
         5 . A method according to  claim 3  in which the method includes analysing at least 10 calibration samples.  
     
     
         6 . A method according to  claim 3  in which at least 10 replicates are considered for each sample.  
     
     
         7 . A method according to  claim 3  in which the indication is the level of one or more distinctive components introduced into the results of the amplification of the sample.  
     
     
         8 . A method according to  claim 3  in which the indication is the ratio of the measured amount of one distinctive component relative to another distinctive component.  
     
     
         9 . A method according to  claim 3  wherein the indication is one of three indication types, one indication type relating to one homozygous possibility for the genotype, a second indication type relating to the heterozygous possibility for the genotype, the third indication type relating to the other homozygous possibility.  
     
     
         10 . A method according to  claim 3  in which a plurality of indications for a sample and/or an indication type are used to generate an average indication, the average being expressed as a mean or as a median.  
     
     
         11 . A method according to  claim 3  in which the window is defined in terms of a multiple, including fractions, of a standard deviation.  
     
     
         12 . A method according to  claim 3  in which the window has defined upper and lower limits for heterozygous genotypes.  
     
     
         13 . A method according to  claim 3  in which the window is open ended in one direction for homozygous genotypes.  
     
     
         14 . A method according to  claim 3  in which a plurality of indications for an unknown sample are used to generate an average indication.  
     
     
         15 . A method according to  claim 3  in which the indication for the unknown sample is compared with a window by comparing the value of the indication with the range of values defining the window.  
     
     
         16 . A method according to  claim 15  in which if the value of the indication for the unknown sample is within the range of a window that analysis of the unknown sample is accepted, if the value of the indication falls within the range for two windows then that analysis is rejected.  
     
     
         17 . A method according to  claim 15  in which if the value of the indication falls outside the range of any window then that analysis is rejected.  
     
     
         18 . A method according to  claim 3  in which the genotype is derivable from the indication or average indication based on the measure.  
     
     
         19 . A method according to  claim 3  in which the method is automated.  
     
     
         20 . A method according to  claim 3  in which the method is performed on a micro-fabricated array.  
     
     
         21 . A method according to  claim 3  in which the method includes analysing one or more control samples to obtain a control indication, the control indication including a measure of the suggestion of the first possible identity and a measure of the suggestion of the second possible identity in the form of a ratio between those suggestions, the control indication being used to ensure the indication is of a sufficient level for the analysis to be considered, the control indication being used to set a threshold, a sample or replicate falling below the threshold being discounted from further consideration.