A method of conducting a fluorescence in situ hybridization-based assay for deletion of a tumor suppressor gene comprising: (a) performing fluorescence in situ hybridization (FISH) with a probe set on a cellular sample comprising a plurality of cells, wherein the probe set comprises at least one first flanking probe that hybridizes to a position centromeric to the tumor suppressor gene, at least one second flanking probe that hybridizes to a position telomeric to the tumor suppressor gene, and at least one target probe that hybridizes to the tumor suppressor gene; (b) enumerating FISH signals from the at least one first and at least one second flanking probes and the at least one target probe in the plurality of cells; (c) providing at least one artifactual deletion frequency from a control sample for a deletion that affects only the target probe, a deletion that affects the target probe and the centromeric flanking probe closest to the target probe, a deletion that affects the target probe and the telomeric flanking probe closest to the target probe, or a deletion that affects the target probe, the centromeric flanking probe closest to the target probe, and the telomeric flanking probe closest to the target probe, the artifactual deletion frequency being chosen from (i) an artifactual hemizygous deletion frequency and (ii) an artifactual homozygous deletion frequency; (d) determining at least one apparent deletion frequency from the enumerated FISH signals of step (b), for the same type of deletion event as at least one artifactual deletion frequency of step (c), the apparent deletion frequency being chosen from (i) an apparent hemizygous deletion frequency and (ii) an apparent homozygous deletion frequency, wherein the at least one apparent deletion frequency comprises an apparent hemizygous deletion frequency if an artifactual homozygous deletion frequency was not provided in step (c), and wherein the at least one apparent deletion frequency comprises an apparent homozygous deletion frequency if an artifactual hemizygous deletion frequency was not provided in step (c); and (e) determining whether the sample comprises cells with a hemizygous deletion of the tumor suppressor gene based on whether the apparent hemizygous deletion frequency is significantly greater than the artifactual hemizygous deletion frequency, or determining whether the sample comprises cells with a homozygous deletion of the tumor suppressor gene based on whether the apparent homozygous deletion frequency is significantly greater than the artifactual homozygous deletion frequency. (a) performing fluorescence in situ hybridization (FISH) with a probe set on a cellular sample comprising a plurality of cells, wherein the probe set comprises at least one first flanking probe that hybridizes to a position centromeric to the tumor suppressor gene, at least one second flanking probe that hybridizes to a position telomeric to the tumor suppressor gene, and at least one target probe that hybridizes to the tumor suppressor gene; (b) enumerating FISH signals from the at least one first and at least one second flanking probes and the at least one target probe in the plurality of cells; (c) providing at least one artifactual deletion frequency from a control sample for a deletion that affects only the target probe, a deletion that affects the target probe and the centromeric flanking probe closest to the target probe, a deletion that affects the target probe and the telomeric flanking probe closest to the target probe, or a deletion that affects the target probe, the centromeric flanking probe closest to the target probe, and the telomeric flanking probe closest to the target probe, the artifactual deletion frequency being chosen from (i) an artifactual hemizygous deletion frequency and (ii) an artifactual homozygous deletion frequency; (d) determining at least one apparent deletion frequency from the enumerated FISH signals of step (b), for the same type of deletion event as at least one artifactual deletion frequency of step (c), the apparent deletion frequency being chosen from (i) an apparent hemizygous deletion frequency and (ii) an apparent homozygous deletion frequency, wherein the at least one apparent deletion frequency comprises an apparent hemizygous deletion frequency if an artifactual homozygous deletion frequency was not provided in step (c), and wherein the at least one apparent deletion frequency comprises an apparent homozygous deletion frequency if an artifactual hemizygous deletion frequency was not provided in step (c); and (e) determining whether the sample comprises cells with a hemizygous deletion of the tumor suppressor gene based on whether the apparent hemizygous deletion frequency is significantly greater than the artifactual hemizygous deletion frequency, or determining whether the sample comprises cells with a homozygous deletion of the tumor suppressor gene based on whether the apparent homozygous deletion frequency is significantly greater than the artifactual homozygous deletion frequency.