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Cytogenetics / Molecular Cytogenetics / Chromosome Microarray Analysis (CMA)

Introduction

The Cytogenetics Laboratory offers a comprehensive array of chromosome investigations for cancers, constitutional abnormalities, and prenatal and postnatal diagnosis. Analyses are performed with the aid of dedicated computerised karyotyping workstations. All reports include a description of the cytogenetic findings in accordance to the International System for Human Cytogenetic Nomenclature, and an interpretation of the results. The Laboratory also offers a wide array of metaphase and interphase Fluorescence In Situ Hybridization (FISH) tests, including rapid aneuploidy screening, microdeletion syndromes, and a host of specific malignancy tests for gene fusion / break-apart such as BCR/ABL1, PML/RARA and MLL. The FISH section also offers HER2 gene (ERBB2) amplification detection assay on breast cancer and other FISH tests for solid tissue sarcomas. The laboratory recently introduced Chromosome Microarray Analysis (CMA) as an adjuvant test to detect gains/losses. Cost effective CLL package (karyotyping plus CMA), MM package (FISH plus CMA), and standalone CMA for MDS, AML, ALL and other haematological disorders, are able to detect chromosomal gains/losses which are submicroscopic or located outside the regions of available FISH probes.

Please refer to Tables 1 and 2 for the list of available FISH probes.

Special Instructions on Fresh Specimen Collection and Handling

  1. Please contact the Cytogenetics Laboratory for an appointment before despatching the specimen over for processing (Tel: 63214678/4650).
  2. All samples for Cytogenetics studies should be collected under sterile conditions. Send only fresh samples to the Laboratory as soon as possible.
  3. Please note:
    • For the test package of Kary & CMA for CLL, collect 2-3ml peripheral blood/bone marrow specimen each in 2 lithium heparinized vacutainers.
    • For the test package of FISH & CMA for MM, collect 2ml bone marrow (2nd aspirate) specimen in 1 lithium heparinized vacutainer, or 2ml bone marrow (3rd aspirate onwards) specimens in 2 lithium heparinized vacutainers.
    • For CMA-Haematological, collect 2ml bone marrow (2nd aspirate preferred) specimen in 1 lithium heparinized vacutainer.
  4. Do not freeze the specimen. A cool pack may be used to ensure that the samples are not exposed to temperatures in excess of 30ºC.
  5. Please ensure that all samples arrive at the laboratory at least two (2) hours before closing time.

Operating Hours:
Monday – Friday: 8.00am – 5.30pm
Saturday: 8.00am – 1.00pm

Provide all necessary information on the cytogenetics request form or CPOE, including:

  • Patient’s name, NRIC number, sex, age, date of birth
  • Clinical diagnosis, relevant clinical information
  • Specimen type
  • Block number (for FFPE FISH)
  • Fixation time (for FFPE FISH)
  • Name of referring doctor, clinic, telephone/fax number
  • Date and time of specimen collection
For prenatal specimens, also include the following:
  • Gestational age
  • Volume / weight of specimen
  • LMP
  • EDD

For FISH tests, also indicate the type of FISH DNA probes required.

Tables

Table 1: Haematology/Oncology Fluorescence In Situ Hybridization (FISH) available probes

FISH Probes Probe Location Clinical Indications
1p36 SO/ 19q13 SG1p36 / 19q13 Oligodendroglioma & mixed oligoastroglioma
ALK BA 2p23 Anaplastic Large Cell Lymphoma, non-small cell lung cancers (NSCLC)
ATM 11q22.3 B-CLL
BCL2 BA18q21DLBCL, FL
BCL6 BA 3q27 DLBCL, FL
BCR/ABL1 DF 9q34 / 22q11.2 ALL, AML, CML
BIRC3/MALT1 DF 11q21 / 18q21 MALT lymphoma, DLBCL
CBFB BA 16q22 AML-M4Eo
CCND1 XT/IGH DF 11q13 / 14q32 Mantle Cell Lymphoma, B-Prolymphocytic Leukaemia, Plasma Cell Leukaemia, Splenic Lymphoma, CLL, Multiple Myeloma, B-lineage lymphocyte
CEP 12 Cen 12 B-CLL
CEP 3, 7, 17, p16Cen 3 / Cen 7 / Cen 17 / p16Cholangiocarcinoma
CEP 8 Cen 8 AML, CML, MDS
CEP 9, 11, 15 Cen 9 / Cen 11 / Cen 15 Multiple Myeloma
CEP X and CEP YCen X and Cen YSex-mismatched Bone Marrow Transplant
CKS1B1q21Multiple Myeloma or Plasma Cell Disorders
c-MYC BA 8q24.1Burkitt's Lymphoma (include variants), ALL, DLBCL
D13S25 13q14.3B-CLL
D20S108 20q12 MDS, AML, polycythemia vera, chronic neutrophilic leukemia
D7S486 7q31 MDS, AML
DDIT3 BA12q13Myxoid Liposarcoma, Round cell and Mixed Liposarcoma
DUSP226p25.3ALK negative Anaplastic Large Cell Lymphoma
EGR1 5q31 MDS, AML
EWSRI BA 22q12 Ewing's sarcoma (include variants)
FOXO1 BA13q14Alveolar Rhabdomyosarcoma
FUS BA16p11.2Fibromyxoid sarcoma/myxoid liposarcoma
HER-2/neu (ERBB2) 17q11.2q12 Breast Cancer, gastric cancers and GEJ carcinomas, Colonic cancer
IGH BA 14q32 Multiple Myeloma, ALL, CLL, NHL, DLBCL
IGH/BCL2 DF 14q32 / 18q21 DLBCL, FL
IGH/c-MYC DF 8q24.1 / 14q32 Burkitt's Lymphoma, ALL
IGH/FGFR3 DF 4p16.3 / 14q32 Multiple Myeloma
IGH/MAF DF14q32 / 16q23  Multiple Myeloma
MALT1 BA 18q21 MALT lymphoma, DLBCL
MAML2 BA11q21Mucoepidermoid Carcinoma
MDM212q15Well-differentiated liposarcoma / Dedifferentiated liposarcoma
MET SR7q31.2 NSCLC
MLL BA 11q23 ALL, AML
PIK3CA 3q26.32NSCLC
PML/RARA DF 15q22 / 17q21.1 AML-M3
RARA BA 17q21.1 AML-M3 (include variants)
RB1 13q14 Multiple Myeloma, CLL, AML, MDS, CLD
RET BA10q11.2NSCLC
ROS1 BA6q22 NSCLC
RUNX1T1/RUNX1 DF 8q21.3 / 21q22 AML
SS18 (SYT) BA 18q11.2 Synovial sarcoma
TFE3 BAXp11.23Alveolar Soft Part Sarcoma, Renal Cell Carcinoma
TP53 17p13.1 Multiple Myeloma, B-CLL, ALL, AML, MDS, NHL

Probe Constructions:
1. BA- Breakapart
2. DF- Dual Fusion

Table 2. Haematological/Oncology Fluorescence In Situ Hybridization (FISH) Panel Tests

Panel FISH Tests FISH Probes Used
Expanded MM Panel IGH/FGFR3 DF
CCND1 XT/IGH DF
RB1
TP53
IGH/MAF DF
 CKS1B 1q21
MM Hyperdiploidy Panel CEP 9
CEP 11
CEP 15
CLL Panel ATM
CEP 12
D13S25
TP53
MDS Panel EGR1
D7S486
CEP 8
D20S108
​Combined MM Panel​IGH/FGFR3 DF




CCND1 XT/IGH DF
RB1
TP53
IGH/MAF DF
CKS1B 1q21
CEP 9
CEP 11
CEP 15
Cholangiocarcinoma Panel CEP 3 
CEP 7
CEP 17
p16
Lung Cancer Panel ALK  BA
MET SR
ROS1 BA
 RET BA
Lymphoma Panel BCL2 BA
MYC BA 
BCL6 BA
FISH & CMA-MMIGH/FGFR3 DF
CCND1 XT/IGH DF
IGH/MAF DF


Click here to view all Cancer/Cancer FISH tests
Click here to view all CMA tests
Click here to view all Postnatal tests
Click here to view all PP FISH tests
Click here to view all Prenatal tests