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 loss of heterozygosity Regions, Indicator telomeric allelic imbalance Regions and Indicator large scale transitions (LSTs) in one, two, three, four, five, six, seven, eight, nine, ten, eleven, twelve, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22 or 23 pair(s) 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 (a) extends to one of the subtelomeres, (b) does not cross the centromere and (c) is longer than 1.5, 5, 12, 13, 14, 15, 16, 17 or more megabases in length; (c) an Indicator LST 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; and diagnosing a patient in whose sample said number of Indicator LOH Regions, Indicator TAI Regions and Indicator LSTs is greater than a reference number as having an increased likelihood of responding to said cancer treatment regimen. determining, in a sample comprising a cancer cell, the number of Indicator loss of heterozygosity Regions, Indicator telomeric allelic imbalance Regions and Indicator large scale transitions (LSTs) in one, two, three, four, five, six, seven, eight, nine, ten, eleven, twelve, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22 or 23 pair(s) 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 (a) extends to one of the subtelomeres, (b) does not cross the centromere and (c) is longer than 1.5, 5, 12, 13, 14, 15, 16, 17 or more megabases in length; (c) an Indicator LST 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; and (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 (a) extends to one of the subtelomeres, (b) does not cross the centromere and (c) is longer than 1.5, 5, 12, 13, 14, 15, 16, 17 or more megabases in length; (c) an Indicator LST 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; and diagnosing a patient in whose sample said number of Indicator LOH Regions, Indicator TAI Regions and Indicator LSTs is greater than a reference number as having an increased likelihood of responding to said cancer treatment regimen.