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Cancer Cytogenomic Studies

Chromosome Analysis

Bone marrow cytogenetic evaluation is considered appropriate for patients with neoplastic or pre-neoplastic hematological disorders. Supply 1-2 ml of bone marrow aspirate in sodium heparin vacutainer. Average turnaround time is 3-14 days.

Cytogenetic evaluation of lymph node, spleen, or solid tumor samples is appropriate in patients where neoplastic or pre-neoplastic cells are suspected to be present in the biopsied sample. Supply 0.3-1 cubic centimeter sample submerged in sterile culture medium (or a balanced salt solution). Turnaround time varies by specimen from 5-21 days.

Cytogenetic evaluation of unstimulated blood samples is appropriate in patients with acquired hematologic malignancy where sufficient neoplastic or pre-neoplastic cells (blast cells) are detected in peripheral blood. If the neoplasm is of lymphoid origin, then stimulation is needed for B-cells (IL2/IL4/IL2+DSP30) or T-cells (PHA). If the blast count or mitotic index is low in the blood, chromosome analysis may be infeasible, and interphase FISH or microarray could be an alternative. Supply 5-10 ml of peripheral blood in sodium heparin vacutainer. Average turnaround time is 3-14 days.

NOTE: These studies involve culturing of living cells; therefore, turnaround times given represent average times, which are subject to multiple variables.

Chromosome analysis CPT codes:
Leukemic blood/bone marrow/lymph node: 88237, 88264, 88291
Solid tumor: 88239, 88264, 88291
Note: limited study will use CPT code 88261 instead of 88264; additional codes may be used for extended analyses (additional karyotypes 88280; additional cell counts 88285)

FISH Tests

Fluorescence in Situ Hybridization (FISH) testing extends routine cytogenetic banding methods by resolving ambiguous diagnoses and providing another tool to diagnose submicroscopic and cryptic abnormalities. FISH is a relatively simple, fast, and reliable procedure. FISH testing can be performed independently or concurrently with other cytogenetics studies.

Applications of FISH for hematologic disorders include delineation of chromosomal numerical abnormalities, detection of recurrent translocations and gene rearrangements, and determination of donor cell engraftment following sex-mismatched bone marrow and stem cell transplants. Disease-specific FISH panels for MDS, AML, B-ALL, CLL, MM/MGUS and lymphoma have been standardized to supplement routine chromosome analysis to screen for recurrent chromosome abnormalities. Average turnaround time is 2-7 days.

FISH CPT codes:
FISH analysis may include 88230-88239, 88271-88275 and 88291. Contact lab for specific codes based on specimen type and exact testing being performed.

Fish Panels

ALL, B-cell/pre-B-cell Acute lymphoblastic leukemia/lymphoma
  • ALL panel: ABL1-BCR* t(9;22) │ KMT2A* (MLL) 11q23.3 │ ETV6-RUNX1* t(12;21) │ Trisomy 4*, 10*, 17 (CEP4, CEP10, CEP17)
  • Ph-like panel: ABL2* 1q25.2 │ PDGFRB* 5q33 │ JAK2 9p24.1 │ ABL1* 9q34.1 │ CRLF2 Xp22.3/Yp11.3
  • Available on request/reflex: TCF3-PBX1 (E2A-PBX1) t(1;19) │ MYC 8q24 │ 9p- (CDKN2A (p16) 9p21.3, D9Z3 9q12) │ IGH 14q32
*COG high-risk ALL required testing

ALL, T-cell Acute Lymphoblastic Leukemia/lymphoma
  • T-ALL panel: TLX3 5q35.1 │ TCRB 7q34 │ 9p- (CDKN2A (p16) 9p21.3, D9Z3 9q12) │ ABL1 9q34.1 │ TCRA/D 14q11
Lymphoma, T-cell
  • T-lymphoma panel: TCRB 7q34 │ 9p- (CDKN2A (p16) 9p21.3, D9Z3 9q12) │ TCRA/D 14q11
Lymphoma, B-cell
  • B-lymphoma panel: BCL6 3q27 │ MYC 8q24 │ IGH 14q32
  • Available on request/reflex: ALK 2p23 │ 7q-/-7 (RELN 7q22.1, TES 7q31.2) │ MYC-IGH t(8;14) │CCND1-IGH t(11;14) │ IGH-BCL2 t(14;18) │ BCL2 18q21 │ MALT 18q21
Lymphoma, Cutaneous T-cell, CTCL
  • CTCL panel: MYC 8q24 │ 11q-/17p- (ATM 11q22.3, TP53 17p13.1) │ 13q- (RB1 13q14.2, CDC16 13q34) │ 9p- (CDKN2A (p16) 9p21.3, D9Z3 9q12) │ ARID1A 1p36.11, ZEB1 10p11.22, STAT3 17q21.2 │ DNMT3A 2p23.3, CARD11 7p22.2, FAS 10q23.31
  • Standard panel: 1p-, 1q+ (CDKN2C 1p32, CKS1B 1q21) │ BCL6 3q27 │ 6q- (6cen D6Z1, MYB 6q23) | MYC 8q24 │ Trisomy 9, 15, 17, hyperdiploidy (D9Z3 9q12, PML 15q24.1, TP53 17p13.1) │ 13q- (DLEU1 13q14.3, CDC16 13q34) │ IGH 14q32
Multiple Myeloma (MM), Monoclonal Gammopathy (MGUS), Plasma Cell Neoplasms
  • MM/MGUS panel: 1p-, 1q+ (CDKN2C 1p32, CKS1B 1q21) │ Trisomy 9, 15, 17, hyperdiploidy (D9Z3 9q12, PML 15q24.1, TP53 17p13.1) │ 13q- (DLEU1 13q14.3, CDC16 13q34) │ IGH 14q32
  • IGH partner panel/reflex: FGFR3-IGH t(4;14) | CCND3-IGH t(6;14) | CCND1-IGH t(11;14) | IGH-MAF t(14;16) | IGH-MAFB t(14;20)
CLL, Chronic Lymphocytic Leukemia
  • CLL panel: 11q-/17p- (ATM 11q22.3, TP53 17p13.1) | Trisomy 12/13q- (D12Z3 12cen, DLEU1 13q14.3, CDC16 13q34) | IGH 14q32
  • Available on request/reflex: +3q (BCL6 3q27) | 6q- (6cen D6Z1, MYB 6q23) | +8 (MYC 8q24) | CCND1-IGH t(11;14)
T-cell PLL, Prolymphocytic Leukemia
  • T-PLL panel: MYC 8q24 │ 11q-/17p- (ATM 11q22.3, TP53 17p13.1) | TCRA/D 14q11
B-cell PLL, Prolymphocytic Leukemia
  • B-PLL panel: 13q- (DLEU1 13q14.3, CDC16 13q34) │ IGH 14q32 │ 17p- (TP53 17p13.1, D17Z1 17cen)
MDS, Myelodysplastic Syndrome
  • MDS panel: 5q-/-5 (TAS2R1 5p15.3, EGR1 5q31.2) │ 7q-/-7 (RELN 7q22.1, TES 7q31.2) │ +8/20q- (MYC 8q24.2, PTPRT 20q12)
AML, Acute Myeloid Leukemia
  • AML panel: ABL1-BCR* t(9;22) │ KMT2A* (MLL) 11q23.3 │ RUNX1-RUNX1T1* t(8;21) │ NUP98* 11p15.4 │ PML-RARA t(15;17) │ CBFB-MYH11* inv(16)/t(16;16)
  • Available on request/reflex: MECOM (EVI1) 3q26.2 │ ETV6 12p13.2 │ GLIS2* 16p13.3
*COG AML required testing

CML, Chronic Myeloid Leukemia
  • CML: ABL1-BCR t(9;22)
MPN/MPD (unspecified), Myeloproliferative neoplasm/disorder
  • MPD panel: ABL1-BCR t(9;22) │ +8/20q- (MYC 8q24.2, PTPRT 20q12)
Polycythemia Vera
  • P.Vera panel: +8/20q- (MYC 8q24.2, PTPRT 20q12) │ 13q- (DLEU1 13q14.3, CDC16 13q34) │ 9p- (CDKN2A (p16) 9p21.3, D9Z3 9q12)
Primary Myelofibrosis
  • PMF panel: +8/20q- (MYC 8q24.2, PTPRT 20q12) │ 13q- (DLEU1 13q14.3, CDC16 13q34) │ 1p-, 1q+ (CDKN2C 1p32, CKS1B 1q21)
Mastocytosis/Mast cell disease
  • Mastocytosis: FIPIL1/CHIC/PDGFRA 4q12
  • Eosinophilia panel: FIPIL1/CHIC/PDGFRA 4q12 │ PDGFRB 5q32 │ FGFR1 8p11.2, D8Z2 8cen │ JAK2 9p24.1 │ ABL1 9q34.1 │ ETV6 12p13.2 │ FLT3 13q12.2 │ CBFB-MYH11 inv(16)/t(16;16)
  • Rhabdomyosarcoma panel: PAX7 1p36.13 │ PAX3 2q36.1
  • Neuroblastoma: MYCN 2p24.3, AFF3 (LAF4) 2q11.2
Ewing Sarcoma
  • Ewing Sarcoma: EWSR1 22q12.2
Sex mis-match chimerism
  • XX/XY chimerism: DXZ1 Xcen, DYZ1 Yq12

Microarray Analysis

Chromosomal microarray analysis (CMA) is used to identify somatic copy number aberrations (CNAs) and unbalanced gene rearrangements in cancer-related abnormal clones. CMA has the advantage in identification of cryptic imbalances and detection of clonal aberrations in populations of non-dividing cancer cells and samples with poor chromosome morphology. Microarray analysis can further define the size, precise breakpoints, and gene content of the clonal abnormalities detected by chromosome analysis; characterize marker chromosomes and unknown chromosome materials involving gene amplification; rule out the presence of cryptic imbalance in apparently balanced rearrangements; detect complex genomic imbalances in chromothripsis; and assess regions of copy-neutral loss of heterozygosity, which is common in neoplasia and often masks homozygous mutations involving oncogenes or tumor suppressor genes.

OncoScan microarray assay (OMA), using molecular Inversion Probe (MIP) technology with enhanced resolution of ~900 cancer genes, offers genome-wide CNAs and CN-LOH detection from either fresh, frozen or paraffin-embedded cancer tissues. Average turnaround time is 10-28 days.

NOTE: Microarray turnaround time assumes insurance prior authorization/approval is in place.

Microarray CPT code:
Neoplasia Microarray (Oncoscan): 81277


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