Microarray, Peripheral blood

Diagnostic Use

A chromosomal microarray (CMA) is used to detect very small genomic changes. It is recommended as the first-tier genetic test for unexplained developmental delay or intellectual disability, autism spectrum disorders or multiple congenital anomalies. The diagnostic yield for such disorders is around 15%–20%.

Turnaround times: Routine: 28 days; Neonate/urgent: 10 days; Family follow-up: 6 weeks

The CMA provides a genome-wide analysis of DNA copy number changes, with targeted probe coverage in disease-associated regions. It detects microduplications and microdeletions around 100 times smaller than those seen by conventional G-band chromosome analysis (karyotype). The inclusion of single nucleotide polymorphism (SNP) probes in the microarray design enables the detection of large regions of homozygosity, which can indicate uniparental disomy or recessive disease.
This test does not detect Fragile X or sequence-based changes, low level mosaicism, or balanced chromosome rearrangements.

Department

Genetics - Cytogenetics

Delphic Registration Code

CTGN

Laboratory Handling

Phlebotomy

Please ensure a separate tube is taken for this test. EDTA is ESSENTIAL for this testing. Lith hep is optional

Registration

EDTA is ESSENTIAL for this testing - send to MOLP. Lith hep is OPTIONAL - send to CTGN if received

Synonyms

Array CGH/SNP
Chromosomal microarray
Microarray
Molecular karyotype

Turnaround Time

28 days

Test Code

8046

Specimen Type

• Whole Blood
• Saliva

Specimen Requirements

Tube/Container Type:

Preferred

• EDTA (Lavender Cap)

Acceptable

• Lithium Heparin - Non-gel (Green Cap)

Preferred Sample Volume (ml)

5

Paediatric Specimen Requirements

Tube/Container Type:

Preferred

• EDTA (Lavender Cap)

Acceptable

• Lithium Heparin - Non-gel (Green Cap)

Preferred Sample Volume (ml)

2

Minimum Sample Volume (ml)

1

Additional Specimen Information

Appropriate counselling and patient consent to testing prior to requesting this test. Consult with a clinical geneticist should be considered.
Urgent requests - phone the laboratory on 03 364 1425. It may be useful to discuss potential testing with a Clinical Geneticist or Genetic Pathologist. For more information contact: genelab.test@cdhb.health.nz and add 'Microarray query' in subject line.

Aliquot Instructions

Sample Type

• Whole Blood

Transport to Lab

Ambient (8 - 24 degrees Celsius)

Additional Referral/Aliquot Information

Biological sex information MUST be provided to allow selection of the correct reference material for this assay. If the incorrect reference is used, repeat processing is required which will delay the result and increase the cost of testing.

Same day or overnight courier, ambient.
This test needs fresh, whole blood cells - do not freeze or centrifuge. The specimen must be well mixed.
Do NOT centrifuge or freeze the sample(s).

Genomic DNA is extracted prior to testing, and this incurs an additional charge. Laboratories may submit DNA for testing, although this in not preferred. Please send at least 2 micrograms of DNA at 200 ng/mL.

Interpretation

The clinical significance of any copy number change identified during CMA analysis is assessed by interrogation of multiple databases and current literature, association between patient phenotype and gene content/function of the affected region(s) or suspected syndrome. Interpretation is based on current knowledge at the time of assessment.
Results are reported as:
1. No clinically relevant copy number change
2. Copy number change of uncertain or unknown significance
3. Clinically significant copy number change
4. Clinically significant homozygosity, indicative of UPD

Reporting policy: copy number changes that are considered benign or unlikely to be clinically significant are not reported. Regions of homozygosity totalling <3% of the genome are not routinely reported. Further detailed analysis of regions of homozygosity can be performed on request if a specific recessive disorder is suspected. A list of all unreported findings is available on request.

Test Method

Microarray specifications: Perkin Elmer designed 180k CGX SNP-HD, manufactured by Agilent with 110,000 copy number probes and 60,000 SNP probes. Genome build hg19. This is a targeted array with genomic coverage which includes over 245 syndromes, at least 980 functionally significant genes and subtelomeric and pericentric regions. Copy number resolution: approximately 160kb (backbone) and 40kb at clinically significant regions. SNP resolution: regions of homozygosity greater than 5MB.
Analysis Software: Cytogenomics (Agilent) and Genoglyphix (Perkin Elmer)
Method: patient DNA and a reference DNA are labelled with different fluorescent dyes. Both the reference DNA and patient DNA are hybridised overnight to probes on the array. The array slide is scanned to compare fluorescence at each DNA probe. Gains and losses of genomic material are detected by a change in fluorescence intensity ratio between the patient and the reference. A duplication is indicated by a Log2 ratio of close to 0.58, while a deletion is indicated by a log 2 ratio close to -1.

Non-Funded Test Cost

$1015.14 (Exclusive of GST)

Billing Code

8046

Resources

• Microarray consent form

Contact Information

Enquiry Form