Methods and materials for assessing loss of heterozygosity

Abstract

This document provides methods and materials involved in assessing samples (e.g., cancer cells) for the presence of a loss of heterozygosity (LOH) signature. For example, methods and materials for determining whether or not a cell (e.g., a cancer cell) contains an LOH signature are provided. Materials and methods for identifying cells (e.g., cancer cells) having a deficiency in homology directed repair (HDR) as well as materials and methods for identifying cancer patients likely to respond to a particular cancer treatment regimen also are provided.

What is claimed is: 
     
         1 . A method of predicting the response of cancer patients to a cancer treatment regimen comprising a PARP inhibitor, said method comprising:
 (1) assaying a patient tumor sample to detect the number of indicator LOH regions in at least 15 pairs of human chromosomes of a cancer cell of said patient tumor sample, wherein an indicator LOH region is longer than a first length but shorter than the length of the whole chromosome containing the indicator LOH region, and wherein said first length is 10 megabases;   (2) calculating a test response score comprising the number of said indicator LOH regions detected in (1);   (3) comparing said test response score to a reference response score; and   (4) classifying a patient in whose sample said test response score exceeds said reference response score as having an increased likelihood over a reference patient cohort of response to said cancer treatment regimen.   
     
     
         2 . The method of  claim 1 , wherein said assaying step comprises targeted sequencing of a plurality of polymorphic loci. 
     
     
         3 . The method of  claim 2  comprising enriching genomic DNA from said patient tumor sample for a plurality of DNA fragments each containing one or more of said polymorphic loci. 
     
     
         4 . The method of  claim 3 , wherein said enriching comprises amplifying via PCR said plurality of DNA fragments. 
     
     
         5 . The method of  claim 1 , wherein detecting the number of said indicator regions comprises:
 (a) analyzing said patient tumor sample to determine in at least 15 pairs of human chromosomes the heterozygous or homozygous nature of a plurality of polymorphic loci;   (b) identifying indicator LOH regions at least 10 megabases in length wherein each polymorphic locus in said region is determined in (a) to be homozygous; and   (c) calculating the number of indicator LOH regions identified in (b).   
     
     
         6 . The method of  claim 5 , wherein an indicator LOH region is identified in (b) if the number of consecutive analyzed loci found to be homozygous within said at least 10 megabases is at least 3. 
     
     
         7 . The method of  claim 5 , wherein an indicator LOH region is identified in (b) if the number of consecutive analyzed loci found to be homozygous within said at least 10 megabases is at least 5. 
     
     
         8 . The method of  claim 5 , wherein an indicator LOH region is identified in (b) if the number of consecutive analyzed loci found to be homozygous within said at least 10 megabases is at least 7. 
     
     
         9 . The method of  claim 5 , wherein an indicator LOH region is identified in (b) if the number of consecutive analyzed loci found to be homozygous within said at least 10 megabases is at least 10. 
     
     
         10 . The method of  claim 5 , wherein said polymorphic loci cover the human genome in a somewhat evenly spaced manner 
     
     
         11 . The method of  claim 5 , wherein said polymorphic loci are in the human genome at least one every about 25 kb to about 100 kb. 
     
     
         12 . The method of  claim 5 , wherein said polymorphic loci are in the human genome at least one every about 25 kb to about 500 kb. 
     
     
         13 . The method of  claim 1 , wherein said first length is 12 megabases. 
     
     
         14 . The method of  claim 1 , wherein said first length is 15 megabases. 
     
     
         15 . The method of  claim 1 , wherein said reference response score incorporates a threshold number of indicator LOH regions shown in a reference patient cohort to classify those reference patients in said reference patient cohort in whose sample the number of indicator LOH regions exceeds said threshold number as having a higher rate of response to said cancer treatment than those reference patients in said reference patient cohort in whose sample the number of indicator LOH regions does not exceed said threshold number. 
     
     
         16 . The method of  claim 15 , wherein said threshold number is 6 or greater. 
     
     
         17 . The method of  claim 15 , wherein said threshold number is 6. 
     
     
         18 . The method of  claim 15 , wherein said threshold number is 7 or greater. 
     
     
         19 . The method of  claim 15 , wherein said threshold number is 7. 
     
     
         20 . The method of  claim 15 , wherein said threshold number is 8 or greater. 
     
     
         21 . The method of  claim 15 , wherein said threshold number is 8. 
     
     
         22 . The method of  claim 15 , wherein said threshold number is 9 or greater. 
     
     
         23 . The method of  claim 15 , wherein said threshold number is 9. 
     
     
         24 . The method of  claim 15 , wherein said threshold number is 10 or greater. 
     
     
         25 . The method of  claim 15 , wherein said threshold number is 10. 
     
     
         26 . The method of  claim 15 , wherein said threshold number is 11 or greater. 
     
     
         27 . The method of  claim 15 , wherein said threshold number is 11. 
     
     
         28 . The method of  claim 15 , wherein said threshold number is 12 or greater. 
     
     
         29 . The method of  claim 15 , wherein said threshold number is 12. 
     
     
         30 . The method of  claim 15 , wherein said threshold number is 13 or greater. 
     
     
         31 . The method of  claim 15 , wherein said threshold number is 13. 
     
     
         32 . The method of  claim 15 , wherein said threshold number is 15 or greater. 
     
     
         33 . The method of  claim 15 , wherein said threshold number is 15. 
     
     
         34 . The method of  claim 15 , wherein said threshold number is 20 or greater. 
     
     
         35 . The method of  claim 15 , wherein said threshold number is 20. 
     
     
         36 . The method of  claim 2 , wherein said plurality of polymorphic loci is at least 10,000 polymorphic loci. 
     
     
         37 . The method of  claim 3 , wherein said plurality of polymorphic loci is at least 10,000 polymorphic loci. 
     
     
         38 . The method of  claim 5 , wherein said plurality of polymorphic loci is at least 10,000 polymorphic loci. 
     
     
         39 . The method of  claim 2 , wherein said plurality of polymorphic loci is at least 25,000 polymorphic loci. 
     
     
         40 . The method of  claim 3 , wherein said plurality of polymorphic loci is at least 25,000 polymorphic loci. 
     
     
         41 . The method of  claim 5 , wherein said plurality of polymorphic loci is at least 25,000 polymorphic loci. 
     
     
         42 . The method of  claim 2 , wherein said plurality of polymorphic loci is at least 50,000 polymorphic loci. 
     
     
         43 . The method of  claim 3 , wherein said plurality of polymorphic loci is at least 50,000 polymorphic loci. 
     
     
         44 . The method of  claim 5 , wherein said plurality of polymorphic loci is at least 50,000 polymorphic loci. 
     
     
         45 . The method of  claim 2 , wherein said plurality of polymorphic loci is at least 75,000 polymorphic loci. 
     
     
         46 . The method of  claim 3 , wherein said plurality of polymorphic loci is at least 75,000 polymorphic loci. 
     
     
         47 . The method of  claim 5 , wherein said plurality of polymorphic loci is at least 75,000 polymorphic loci. 
     
     
         48 . The method of  claim 2 , wherein said plurality of polymorphic loci is at least 100,000 polymorphic loci. 
     
     
         49 . The method of  claim 3 , wherein said plurality of polymorphic loci is at least 100,000 polymorphic loci. 
     
     
         50 . The method of  claim 3 , wherein said plurality of polymorphic loci is at least 100,000 polymorphic loci. 
     
     
         51 . The method of  claim 36 , wherein said plurality of polymorphic loci is no more than 100,000 polymorphic loci. 
     
     
         52 . The method of  claim 37 , wherein said plurality of polymorphic loci is no more than 100,000 polymorphic loci. 
     
     
         53 . The method of  claim 38 , wherein said plurality of polymorphic loci is no more than 100,000 polymorphic loci. 
     
     
         54 . The method of  claim 39 , wherein said plurality of polymorphic loci is no more than 100,000 polymorphic loci. 
     
     
         55 . The method of  claim 40 , wherein said plurality of polymorphic loci is no more than 100,000 polymorphic loci. 
     
     
         56 . The method of  claim 41 , wherein said plurality of polymorphic loci is no more than 100,000 polymorphic loci. 
     
     
         57 . The method of  claim 42 , wherein said plurality of polymorphic loci is no more than 150,000 polymorphic loci. 
     
     
         58 . The method of  claim 43 , wherein said plurality of polymorphic loci is no more than 150,000 polymorphic loci. 
     
     
         59 . The method of  claim 44 , wherein said plurality of polymorphic loci is no more than 150,000 polymorphic loci. 
     
     
         60 . The method of  claim 45 , wherein said plurality of polymorphic loci is no more than 200,000 polymorphic loci. 
     
     
         61 . The method of  claim 46 , wherein said plurality of polymorphic loci is no more than 200,000 polymorphic loci. 
     
     
         62 . The method of  claim 47 , wherein said plurality of polymorphic loci is no more than 200,000 polymorphic loci. 
     
     
         63 . The method of  claim 48 , wherein said plurality of polymorphic loci is no more than 500,000 polymorphic loci. 
     
     
         64 . The method of  claim 49 , wherein said plurality of polymorphic loci is no more than 500,000 polymorphic loci. 
     
     
         65 . The method of  claim 50 , wherein said plurality of polymorphic loci is no more than 500,000 polymorphic loci.