Oncology Fluorescence in situ Hybridization (FISH)

Diagnostic gene rearrangements at or below the resolution of cytogenetics may be defined by FISH protocol. Disease-specific translocations can be detected in nondividing (interphase) cells by implementing multicolor fluorescence probes specific for the involved genes that reciprocally merge to form a third color. Oncogenes that have multiple reciprocal translocation sites can be sensitively evaluated by “break-apart” probes in which the neoplastic splitting of the critical sequence separates the normal fusion color into distinct colors regardless of the variant reciprocal site. Disease-causing deletions relating to the loss of known or putative tumor suppressor genes (TSGs) are readily identified by the detection of cells with only a single signal, as in loss of the 5q31 locus-specific probe characteristic of 5q- syndrome in myelodysplasia.

Specially designed profiles targeting the most common genetic changes can effectively detect indolent CLL and myeloma clones that are often normal in cytogenetic analysis due the slow cell division of the clones. MDS and AML profiles can effectively be used as an interphase adjunct to cytogenetic analysis with no mitotic activity. The ALL profile not only detects the submicroscopic t(12;21) but is not affected by the poor chromosome morphology problems that often beset this type of leukemia. The CML probeset now includes the argininosuccinate synthetase (ASS) gene probe as a control to confirm any ABL deletions thought to be associated with poor prognosis CML by some investigators. A CML FISH+chromosome analysis profile is available for monitoring residual disease in marrow samples (FISH alone is better for blood samples since therapy usually blocks peripheral leukemia cell division). A new Aggressive B-Cell Lymphoma Profile, FISH (510344) with three break-apart probes can reliably identify double/triple “hit” NHL.

Opposite sex bone marrow transplants can be monitored by either sex chromosome-specific probes or (cases of same-sex transplants) a leukemia clone-specific probe previously identified by cytogenetics, eg, a centromere 8 probe for trisomy 8 or BCR/ABL fusion probes for CML. Engraftment Monitoring, Pre (168138) is also available.

Clone specific probes may also monitor residual disease. These studies offer the advantage of not requiring mitotic cells in the often hypocellular posttreatment aspirates. Newly available dual fusion and break-apart probes more accurately rule out low level residual disease by dramatically reducing background.

FISH is also readily applicable to blood smears; touch preps; formalin-fixed, paraffin-embedded samples; and frozen sections.

See table for available probes and test numbers.

SNP Microarray—Oncology (Reveal®) (510146)

Cancer microarray analysis has the resolution to identify significant acquired genetic alterations that would remain undefined by routine chromosome analysis and not targeted by the DNA probes employed in routine FISH analysis, as well as better defining existing abnormalities. Chromosome studies can only detect copy number abnormalities (ie, deletions or duplications), in the size range of 5 to 10 megabases. Contrary to FISH analysis that is limited to specific target sites; the dense whole genome microarray coverage substantially increases the potential detection rate. MDS analysis can be performed from blood, as opposed to standard chromosome analysis that requires mitotic activity.

The Reveal SNP (2.69 million probe) microarray analysis has the resolution to detect copy number changes about 200 times (50-100 kb range) better than cytogenetics, while detecting copy-neutral loss of heterozygosity (CN-LOH). CN-LOH is a common form of clonal evolution that results in homozygosity of a gene mutation, biallelic loss of a tumor suppressor, or doubling of a gene fusion. The precise whole-genome high-resolution detection of copy number changes combined with the dynamic resolution of CN-LOH provided by SNP arrays is revolutionizing DNA-based clonal analysis in cancer diagnostics.

In general, array analysis is recommended for an initial diagnosis (and after clinical progression) to determine whether new abnormalities are present. It cannot be used for the detection of balanced rearrangements and should not be used for detection of residual disease. FISH (see above for FISH test numbers), Chromosome Analysis, Leukemia/Lymphoma (510999), and possibly qPCR (eg, BCR/ABL1) should be used for MRD (minimal residual disease).

Any FISH or chromosome testing suggested as a result of the array will be added upon receiving authorization from the physician. Array testing may be added at the request of the client within one week of initial test resulting or may be ordered as a standalone test. Array may also be ordered as a reflex from a normal chromosome analysis, ie, Chromosome Analysis, Leukemia/Lymphoma With Reflex to Chromosome Microarray (CMA) (511040).

Diagnosis Required

Frozen Gel Packs. To ensure specimen integrity during warm weather, follow these Instructions for Use of frozen gel packs and specimen lockboxes.