Techniques for Identifying, Confirming, Mapping and Categorizing Polymers

Abstract

Systems and methods for identifying, confirming, mapping, and categorizing sample polymers, such as nucleic acid sequences, are provided. An estimation of the fraction of first and second polymers in a sample of polymers can be calculated by inputting a first hybridization value indicative of hybridization affinity of the sample of polymers to polymers probes that are complementary to the first polymer and inputting a second hybridization value indicative of hybridization affinity of the sample of polymers to polymers probes that are complementary to the second polymer. The estimation of the fraction of the first and second polymers in the sample of polymers can then be calculated by dividing the first hybridization value by a sum of the first and second hybridization values. Estimations of the fractions of alleles in a sample can be clustered to form a fraction pattern usable for identifying, confirming, mapping, and genotyping sample nucleic acids.

1 - 25 . (canceled) 
     
     
         26 . A method of estimating relative proportions of a first allele and a second allele for a polymorphism in a sample of nucleic acids, which comprises:
 hybridizing the sample to a plurality of probes to obtain intensity values;   grouping the intensity values for the first allele into at least two divisions including PMa and Ma, wherein PMa is a perfect match and Ma is a single base mismatch;   grouping the intensity values for the second allele into at least two divisions including PMb and Mb, wherein PMb is a perfect match and Mb is a single base mismatch; and   calculating a value MM, wherein the estimated relative proportion of the first allele is:
   (PMa−MM)/[(PMa−MM)+(PMb−MM)], and   (I)
 
   wherein the estimated relative proportion of the second allele is:
   (PMb−MM)/[(PMa−MM)+(PMb−MM)].   (II)
 
   
     
     
         27 . The method of  claim 26 , wherein calculating a value MM comprises:
   MM=min(M*, M*) for center miniblocks, or   (III)
     MM=max(median(Ma, Ma, Ma), median(Mb, Mb, Mb)) for center miniblocks,   (IV)
   
       wherein M* is a single base mismatch to both the first allele and the second allele. 
     
     
         28 . The method of  claim 26 , wherein the genotype of either the first allele or the second allele is associated with an inherited disease in a family of individuals. 
     
     
         29 . The method of  claim 26 , wherein either the first allele or the second allele relates to a gene that is in linkage disequilibrium in an isolated population of individuals. 
     
     
         30 . The method of  claim 26 , wherein the plurality of polymorphisms are selected from the group consisting of insertions, deletions, multi-position polymorphisms, multi-base polymorphisms, and multi-allelic positions. 
     
     
         31 . The method of  claim 26 , wherein:
 (PMa−MM) is assigned a value of 0.00001 if its calculated value is less than zero; and   (PMb−MM) is assigned a value of 0.00001 if its calculated value is less than zero.   
     
     
         32 . The method of  claim 26 , wherein a relative proportion of a third allele is estimated. 
     
     
         33 . The method of  claim 26 , further comprising:
 determining whether the relative proportion estimates pass a quality test designed to detect erroneous values.   
     
     
         34 . The method of  claim 33 , wherein performing the quality test comprises:
 discarding the relative proportion estimate if PMa/max(Ma)<1 and PMb/max(Mb)<1.   
     
     
         35 . The method of  claim 34 , wherein performing the quality test comprises:
 determining whether (PMa−MM) and (PMb−MM) values are above a predetermined threshold.   
     
     
         36 . The method of  claim 35 , wherein the predetermined threshold is 15 photon counts. 
     
     
         37 . The method of  claim 26 , wherein either the first allele or the second allele comprises stretches of DNA that exhibit loss of heterozygosity. 
     
     
         38 . The method of  claim 37 , wherein the stretches of DNA occur in tumors. 
     
     
         39 . The method of  claim 37 , wherein the sample is drawn from a mixture of different cell types. 
     
     
         40 . The method of  claim 38 , wherein the sample is drawn from a mixture of different tumor cell types. 
     
     
         41 . A method of identifying whether a gene comprises stretches of DNA that exhibit loss of heterozygosity, which comprises:
 hybridizing a sample of nucleic acids from the gene to a plurality of probes to obtain intensity values for the gene's first allele and second allele;   grouping the intensity values for the first allele into at least two divisions including PMa and Ma, wherein PMa is a perfect match and Ma is a single base mismatch;   grouping the intensity values for the second allele into at least two divisions including PMb and Mb, wherein PMb is a perfect match and Mb is a single base mismatch;   calculating a value MM, wherein the estimated relative proportion of the first allele is:
   (PMa−MM)/[(PMa−MM)+(PMb−MM)], and   (I)
 
 wherein the estimated relative proportion of the second allele is:
   (PMb−MM)/[(PMa−MM)+(PMb−MM)]; and   (II)
 
 
   evaluating the estimated relative proportions of the first allele and the second allele to identify whether the gene comprises stretches of DNA that exhibit loss of heterozygosity.   
     
     
         42 . A method of estimating relative proportions of a first allele and a second allele for a polymorphism in a sample of nucleic acids, which comprises:
 hybridizing the sample to a plurality of probes to obtain intensity values;   calculating at least a first, a second, and a third hybridization value from the intensity values, wherein the third hybridization value indicates hybridization affinity of mismatches between the sample and the plurality of probes;   calculating a normalized first and a normalized second hybridization value by subtracting the third hybridization value from both the first and the second hybridization values;   estimating the relative proportion of the first allele by dividing the normalized first hybridization value by a sum of the normalized first and the normalized second hybridization values; and   estimating the relative proportion of the second allele by dividing the normalized second hybridization value by a sum of the normalized first and the normalized second hybridization values.