| CPC C12Q 1/6886 (2013.01) [C12Q 2600/106 (2013.01); C12Q 2600/156 (2013.01)] | 18 Claims |
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1. An in vitro method of identifying patient responders to a cancer treatment regimen comprising a DNA damaging agent, anthracycline, topoisomerase I inhibitor, or PARP (poly ADP ribose polymerase) inhibitor comprising:
(i) extracting DNA from a sample comprising a cancer cell;
(ii) contacting the DNA with at least 500 oligonucleotide probes capable of hybridizing to polymorphic regions of human genomic DNA comprising one or more single nucleotide polymorphisms (SNPs);
(iii) genotyping, using a computer, a plurality of SNP loci in the DNA that hybridizes to the oligonucleotide probes in (ii), wherein the SNP loci are spaced about 25 kb to about 100 kb apart on one or more chromosome pairs other than the human X/Y sex chromosome pair; and
(iv) detecting, using a computer, DNA comprising a loss of heterozygosity (LOH) Region and DNA comprising a large scale transition (LST) Region,
wherein each LOH Region is characterized by loss of heterozygosity with a length of about 1.5 or more megabases but shorter than the length of the whole chromosome containing the LOH Region as determined by the presence or absence of SNP loci in corresponding regions on the one or more chromosome pairs, and
wherein each LST region is characterized by copy number transitions along the length of a chromosome located between two regions, each longer than a third length that is at least 5 megabases, after filtering out copy number transitions along the length of the chromosome located between two regions, each shorter than at most 4 megabases, as determined by the presence of absence of SNP loci in corresponding regions on the one or more chromosome pairs.
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