Chromosome microarray in haematological malignancies

About the test:

Chromosome microarray (also known as molecular karyotyping) is an advanced whole genome investigation used to detect sub-microscopic DNA abnormalities that are not readily detectable by conventional karyotype and/or fluorescence in-situ hybridisation (FISH). This technique can be used in the diagnostic investigation of haematological malignancies to detect loss and/or gain of DNA, and copy neutral loss of heterozygosity (CNLOH). This test will provide information about the genes involved in regions of copy number alteration. The information provided will assist in patient management.

Why order a chromosome microarray?

Molecular karyotyping provides additional and clinically useful genomic information, assisting in diagnostic, prognostic and therapeutic decisions. In the clinical setting the information gained can be applied to monitoring of disease progression and response to therapy.

Duplications and deletions of oncogenes which play a role in leukemogenesis, such as CDKN2A, ETV6, RUNX1, cMYC are detectable by microarray technology at a greater resolution than conventional techniques. Additionally, copy neutral loss of heterozygosity, which has been reported in association with poor prognosis in myeloid malignancies is readily detected by SNP microarray, but is not detectable by conventional karyotyping.

Microarray platform:

Our DNA microarray platform contains high density probe coverage to assess copy number and single nucleotide polymorphisms, specifically targeting 526 cancer genes with a resolution 2000-4000 DNA basepairs (2-4 kb). In comparison, the resolution of FISH is ~500 kb.

Each haematological disorder requires an individual approach to investigation with microarrays; in some as a primary investigation (e.g. CLL), or as an adjunct investigation in others (e.g AML, ALL, MDS). The high resolution and genome-wide coverage combined with minimal DNA requirements, and relatively short turnaround time allows chromosomal microarray analysis to be advantageous for use in a clinical setting.


Test Molecular karyotyping
Genes  Whole genome – high resolution, 2000-4000 DNA basepairs (2-4 kb)
Method  Single Nucleotide Polymorphism (SNP) Microarray

 Indications for ordering:

Chromosomal microarray is most useful as an adjunct test in the investigation of the following haematological malignancies:

Acute Lymphoblastic Leukaemia (ALL)

  • Acute Myeloid Leukaemia (AML)
  • Myelodysplastic syndrome (MDS)
  • Chronic Lymphocytic Leukaemia (CLL)

The test is regarded as a complementary investigation and may be beneficial where no genomic alterations have been detected by conventional techniques such as karyotype and FISH, or where a cytogenetic result has not been achieved due to the failure of cell culture. The additional genetic information provided in this setting may assist in patient management.

Chromosomal microarray does not detect balanced rearrangements; thus for haematological malignancies where exclusion of a balanced rearrangement or known fusion partners is required, conventional karyotype or FISH is recommended.

How to order chromosomal microarray testing:

 To request this test, please include “microarray analysis” or “molecular karyotype” on the initial patient request form. Alternatively, the test can be added to an existing request by calling the added tests department.

Acceptable samples include:
 1x Lithium Heparin (5-9mls) and
 1x EDTA bone marrow aspirate (1ml)

Turn Around Time  Routine: 28 business days
 Urgent: 10 business days
Turn Around Time  Routine: 18 working days
 Urgent: 5 working days
Required Documents
(Downloadable documents are supplied within each kit dispatched)

 Standard Test Request Form

Price  No out of pocket fees apply