An in vitro method of predicting patient response to a cancer treatment regimen comprising a DNA damaging agent, anthracycline, topoisomerase I inhibitor, or PARP inhibitor, the method comprising: determining, in a sample comprising a cancer cell, the number of Indicator CA Regions comprising Indicator LOH Regions, Indicator TAI Regions, and Indicator LST Regions in at least one pair of human chromosomes of a cancer cell of said cancer patient; wherein (a) an Indicator LOH Region is an LOH Region that is longer than 1.5, 5, 12, 13, 14, 15, 16, 17 or more megabases in length but shorter than the entire length of the respective chromosome within which the LOH Region is located; (b) an Indicator TAI Region is a TAI Region with allelic imbalance that (i) extends to one of the subtelomeres, (ii) does not cross the centromere and (iii) is longer than 1.5, 5, 12, 13, 14, 15, 16, 17 or more megabases in length; (c) an Indicator LST Region is a somatic copy number breakpoint along the length of a chromosome that is between two regions of at least 10 megabases in length after filtering out regions shorter than 3 megabases in length; combining said Indicator CA Regions to provide a test value as follows: Test Value = (number of Indicator LOH Regions)+(number of Indicator TAI Regions)+(number of Indicator LST Regions); and providing a reference value for comparison against said test value, wherein said reference value is greater than 32. determining, in a sample comprising a cancer cell, the number of Indicator CA Regions comprising Indicator LOH Regions, Indicator TAI Regions, and Indicator LST Regions in at least one pair of human chromosomes of a cancer cell of said cancer patient; wherein (a) an Indicator LOH Region is an LOH Region that is longer than 1.5, 5, 12, 13, 14, 15, 16, 17 or more megabases in length but shorter than the entire length of the respective chromosome within which the LOH Region is located; (b) an Indicator TAI Region is a TAI Region with allelic imbalance that (i) extends to one of the subtelomeres, (ii) does not cross the centromere and (iii) is longer than 1.5, 5, 12, 13, 14, 15, 16, 17 or more megabases in length; (c) an Indicator LST Region is a somatic copy number breakpoint along the length of a chromosome that is between two regions of at least 10 megabases in length after filtering out regions shorter than 3 megabases in length; (a) an Indicator LOH Region is an LOH Region that is longer than 1.5, 5, 12, 13, 14, 15, 16, 17 or more megabases in length but shorter than the entire length of the respective chromosome within which the LOH Region is located; (b) an Indicator TAI Region is a TAI Region with allelic imbalance that (i) extends to one of the subtelomeres, (ii) does not cross the centromere and (iii) is longer than 1.5, 5, 12, 13, 14, 15, 16, 17 or more megabases in length; (c) an Indicator LST Region is a somatic copy number breakpoint along the length of a chromosome that is between two regions of at least 10 megabases in length after filtering out regions shorter than 3 megabases in length; combining said Indicator CA Regions to provide a test value as follows: Test Value = (number of Indicator LOH Regions)+(number of Indicator TAI Regions)+(number of Indicator LST Regions); and providing a reference value for comparison against said test value, wherein said reference value is greater than 32.