Cytogenetics Test List 1

Cytogenetics Hematopathology

Whole-Genome Oncology Microarray (SNP-Array) for Hematological Malignancies (CytoScan HD)*

The CytoScan HD microarray provides high resolution whole-genome interrogation of newly diagnosed or relapse neoplastic specimens,
including genome-wide copy number and copy-neutral loss of heterozygosity (CN-LOH) analyses.

Enumeration Probes

FISH probes are available to detect aneuploidy of chromosomes 1-22, X and Y.

* Currently available to City of Hope patients only. Please contact lab outreach for non-City of Hope availability status.

  • City of Hope Cytogenetics Laboratory is a Children’s Oncology Group (COG)-approved lab for conventional cytogenetic and FISH analyses.
  • Most commonly known designations are used here to indicate each abnormality identified by the FISH probes.

G-banded Chromosome Analysis

Conventional cytogenetic studies to detect chromosomal gains, losses and rearrangements such as inversions and translocations for a variety
of neoplasms including hematological malignancies and solid tumors

Fluorescence In Situ Hybridization (FISH) Panels

Molecular cytogenetic FISH assays to detect or confirm previous or applicable abnormalities for a variety of neoplasms. Available FISH probes
and panels are listed below.

  • Chronic Lymphocytic Leukemia (CLL): del(11q) ATM, Trisomy 12 DDIT3, -13/del(13q) D13S319/LAMP1, del(17p) TP53; t(11;14) IGH::CCND1
  • Targeted Plasma Cell FISH: 1q/1p (CKS1B/CDKN2C), +5/+9/+15 (for hyperdiploidy), MYC, -13/del(13q) D13S319/LAMP1, del(17p)
    TP53, IGH break-apart [with reflex to t(4;14),t(11;14) and t(14;16)]

Individual FISH Probes for Myeloid and Lymphoid Lineage Abnormalities

  • 1q/1p (CKS1B/CDKN2C) gain/loss
  • ABL2 (1q25.2) rearrangement
  • 2p/ALK rearrangements (lymphoma)
  • inv(3)/t(3;3) MECOM
  • 3q/BCL6 rearrangement
  • +4/+10 (CEP 4/10)
  • 4q12 rearrangement
  • CHIC2 deletion/FIP1L1::PDGFRA fusion
  • t(4;14) IGH::FGFR3 fusion
  • -5/5q- (EGR1)
  • PDGFRB (5q32) rearrangement
  • del(6q21) FOXO3
  • t(6;9) DEK::NUP214 fusion
  • -7/7q- (CEP 7/D7S486)
  • +8 (CEP 8/MYC)
  • 8q24.21/MYC rearrangement
  • +8, del(20q) (CEP 8/D20S108)
  • t(8;21) RUNX1::RUNX1T1 fusion
  • t(8;14) IGH::MYC fusion

Cytogenetics Hematopathology Specimen Requirements


  • ABL1 (9q34.1) rearrangement
  • t(9;22) BCR::ABL1/ASS1
  • del(9p) CDKN2A/CDKN2B
  • t(11;14) IGH::CCND1 fusion
  • del(11q22.3) ATM/CEP 11
  • 11q23/KMT2A rearrangement
  • 12p/ETV6 rearrangement
  • t(12;21) ETV6::RUNX1 fusion
  • Trisomy 12 (DDIT3)
  • -13/del(13q) (D13S319/LAMP1)
  • 14q32.33/IGH rearrangement
  • t(14;16) IGH::MAF fusion
  • t(14;18) IGH::BCL2 fusion
  • t(15;17) PML::RARA fusion
  • inv(16)/t(16;16) CBFB
  • del(17p) TP53/CEP 17
  • 17q/RARA rearrangement, e.g., t(15;17)
  • 18q21.3/MALT1 rearrangement
  • 19p/TCF3 rearrangement, e.g., t(1;19)
  • CRLF2 (Xp22.33/Yp11.32)
  • P2RY8 (Xp22.33/Yp11.32)

Cytogenetics Solid Tumor

Individual Probes

  • MYCN amplification (neuroblastoma)
  • FOXO1 rearrangement (alveolar rhabdomyosarcoma)
  • SS18 rearrangement (synovial sarcoma)
  • EWSR1 rearrangement (Ewing sarcoma/PNET)

Cytogenetics Solid Tumor Specimen Requirements


  • ERBB2 (HER2) amplification (breast, gastroesophageal and other cancers)*
  • MYC amplification/rearrangement
  • del(9p) CDKN2A/CDKN2B, del(10q) PTEN, del(17p) TP53/CEP 17
    (various tumor types; fresh tissue is required for deletion probes)