Cytogenetics / Molecular Cytogenetics

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.

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

Special Instructions on 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 should be collected under sterile conditions. Send only fresh samples to the Laboratory, and as soon as possible.
3. 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.
4. 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
• 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 test, 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
ALK BA	2p23	Anaplastic Large Cell Lymphoma, non-small cell lung cancers
1p36 / 19q13	1p36 / 19q13	Oligodendroglioma & mixed oligoastroglioma
BCL6 BA	3q27	DLBCL, FL
IGH/FGFR3 DF	4p16.3 / 14q32	Multiple Myeloma
EGR1	5q31	MDS, AML
EGFR (HER-1)	7p12	Solid tumours: head and neck, ovarian, cervical, bladder, oesophageal, non-small cell lung cancer, breast
D7S486	7q31	MDS, AML
CEP 8	Cen 8	AML, CML, MDS
c-MYC BA	8q24	Burkitt's Lymphoma (include variants), ALL, DLBCL
IGH/c-MYC DF	8q24.1 / 14q32	Burkitt's Lymphoma, ALL
RUNX1T1/RUNX1 DF	8q22 / 21q22	AML
BCR/ABL1 DF	9q34 / 22q11.2	ALL, AML, CML
CEP 9, 11, 15	Cen 9 / Cen 11/ Cen 15	Multiple Myeloma
MLL BA	11q23	ALL, AML
ATM	11q22.3	B-CLL
API2/MALT1 DF	11q21 / 18q21	MALT lymphoma, DLBCL
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
ETV6/RUNX1	12p13 / 21q22	B-ALL
RB1	13q14	Multiple Myeloma, CLL, AML, MDS, CLD
D13S25	13q14	B-CLL
IGH BA	14q32	Multiple Myeloma, ALL, CLL, NHL
IGH/BCL2 DF	14q32 / 18q21	DLBCL, FL
PML/RARA DF	15q22 / 17q21.1	AML-M3
CBFB BA	16q22	AML-M4Eo
TP53	17p13.1	Multiple Myeloma, B-CLL, ALL, AML, MDS, NHL
HER-2/neu (ERBB2)	17q11.2q12	Breast Cancer, gastric cancers and GEJ carcinomas
MDM2	12q15	Well-differentiated liposarcoma
RARA BA	17q21.1	AML-M3 (include variants)
MALT1 BA	18q21	MALT lymphoma, DLBCL
SS18 (SYT) BA	18q11.2	Synovial sarcoma
D20S108	20q12	MDS, AML, polycythemia vera, chronic neutrophilic leukemia
EWSRI BA	22q12	Ewing's sarcoma (include variants)
DDIT3 BA	12q13	Liposarcoma
FUS BA	16p11.2	Fibromyxoid sarcoma/myxoid liposarcoma
FOXO1 BA	13q14	Rhabdomyosarcoma

Probe Constructions:
1. BA- Breakapart
2. DF- Dual Fusion
3. ES- Extra Signal

Table 2. Haematological 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

MM Hyperdiploidy Panel	CEP 9
	CEP 11
	CEP 15

CLL Panel	ATM
	CEP 12
	D13S25
	TP53

MDS Panel	EGR1
	D7S486
	CEP 8
	D20S108

Table 3. Normal cut-off level for haematological and oncology FISH probes

Probes	Abnormal Signal Pattern based on probe construction	Cut-off level %
ALK	1F1R1G	3.77
1p36 (1q25) (paraffin)	Loss	17.2
	Ratio	<0.80
19q13 (19p13) (paraffin)	Loss	17.2
	Ratio	<0.80
BCL6	1F1R1G	3.08
EGFR (HER-1) / CEP 7 (paraffin)	³4 copies	21.65
c-MYC	1F1R1G	1.48
IGH/c-MYC/CEP 8	2F1R1G	1.48
RUNX1T1 / RUNX1	2F1R1G	1.48
BCR/ABL1	2F1R1G	1.48
MLL	1F1R1G	2.34
ATM	Loss	7.39
API2/MALT1	2F1R1G	1.48
ETV6 / RUNX1	1F2R1G	1.48
IGH	1F1R1G	5.67
IGH/BCL2	2F1R1G	1.48
PML/RARA	2F1R1G	1.48
CBFB	1F1R1G	2.34
HER-2/neu (ERBB2) Breast cancer	Negative	Ratio <1.8
	Equivocal	Ratio 1.8-2.2
	Positive	Ratio >2.2
HER-2/neu (ERBB2) Gastric-Oeosophageal Junction (GEJ)	Positive	Ratio ≥2.0
MDM2	Positive	Ratio ≥2.0
RARA	1F1R1G	3.08
MALT1	1F1R1G	2.33
SS18 (SYT)	1F1R1G	5.66
EWSRI	1F1R1G	7.39
DDIT3	1F1R1G	6.8
FUS	1F1R1G	5.7
FOXO1	1F1R1G	4.4

Expanded MM Panel	Abnormal Signal Pattern based on probe construction	Cut-off level %
IGH/FGFR3	2F1R1G	1.48
CCND1 XT/IGH	2F1R1G	1.48
RB1	Loss	5.06
TP53	Loss	10.5
IGH/MAF	2F1R1G	1.48

MM Hyperdiploidy Panel	Abnormal Signal Pattern based on probe construction	Cut-off level %
CEP 9	Gain	2.33
CEP 11	Gain	1.48
CEP 15	Gain	3.08

CLL Panel	Abnormal Signal Pattern based on probe construction	Cut-off level %
ATM	Loss	7.39
CEP 12	Gain	4.43
D13S25	Loss	1.49
TP53	Loss	10.5

MDS Panel	Abnormal Signal Pattern based on probe construction	Cut-off level %
EGR1	Loss	7.39
D7S486	Loss	8.48
CEP 8	Gain	3.77
D20S108	Loss	8.48

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