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Cytogenetics / Molecular Cytogenomic 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 integrated computerised karyotyping workstations. All reports include a description of the cytogenetic findings in accordance to the International System for Human Cytogenomic 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, lung cancer panel, lymphoma panel, and other FISH tests for solid tissue sarcomas. The laboratory recently introduced Cytogenomic Microarray Analysis (CMA) as an adjuvant test to detect gains/losses of genes / chromosomal regions. 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.
    • For CMA-Solid Tumours: 8-10 sections of 5µm FFPE tumour sections, accompanied by a copy of H&E section with tumour region marked out.
  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 SG

1p36 / 19q13

Oligodendroglioma & mixed oligoastroglioma

ALK BA

2p23

Anaplastic Large Cell Lymphoma, non-small cell lung cancers (NSCLC)

ATM

11q22.3

B-CLL

BCL2 BA

18q21

DLBCL, 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, p16

Cen 3 /Cen 7 / Cen 17 / p16

Cholangiocarcinoma

CEP 8

Cen 8

AML, CML, MDS

CEP 9, 11, 15

Cen 9 / Cen 11 / Cen 15

Multiple Myeloma

CEP X and CEP Y

Cen X and Cen Y

Sex-mismatched Bone Marrow Transplant

CKS1B

1q21

Multiple Myeloma or Plasma Cell Disorders

c-MYC BA

8q24.1

Burkitt's Lymphoma (include variants), ALL, DLBCL

D13S25

13q14.3

B-CLL

D20S108

20q12

MDS, AML, polycythemia vera, chronic neutrophilic leukemia

D7S486

7q31

MDS, AML

DDIT3 BA

12q13

Myxoid Liposarcoma, Round cell and Mixed Liposarcoma

DUSP22

6p25.3

ALK negative Anaplastic Large Cell Lymphoma

EGR1

5q31

MDS, AML

EWSRI BA

22q12

Ewing's sarcoma (include variants)

FOXO1 BA

13q14

Alveolar Rhabdomyosarcoma

FUS BA

16p11.2

Fibromyxoid 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 DF

14q32 / 16q23

Multiple Myeloma

MALT1 BA

18q21

MALT lymphoma, DLBCL

MAML2 BA

11q21

Mucoepidermoid Carcinoma

MDM2

12q15

Well-differentiated liposarcoma / Dedifferentiated liposarcoma

MET SR

7q31.2

NSCLC

MLL BA

11q23

ALL, AML

PIK3CA

3q26.32

NSCLC

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 BA

10q11.2

NSCLC

ROS1BA

6q22

NSCLC

RUNX1T1/RUNX1 DF

8q21.3 / 21q22

AML

SS18 (SYT) BA

18q11.2

Synovial sarcoma

TFE3 BA

Xp11.23

Alveolar 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-MM IGH/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

Last Modified Date :25 Oct 2018