skip navigation

Test Identifier Information

Registration CodeCTGN

High density array comparative genomic hybridization detects copy number variants (CNVs) in patient DNA. This chromosomal microarray (CMA) provides a genome-wide analysis of DNA copy number changes, with targeted probe coverage in disease-associated regions. It can detect microduplications and microdeletions around 100 times smaller than 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.

For further technical details about the method and platform design see technical information sheet
Diagnostic Use / Indications

The microarray can be used to diagnose any genetic disorder resulting from copy number change greater than ~50kb, or an imprinting disorder, providing the corresponding region of interest is represented on the array.  

Indications for testing:
1.    One or more structural fetal anomalies detected by ultrasound (including IUGR or NT >3.5mm)
2.    Structural chromosome imbalance identified by G-band karyotyping
3.     Family history of chromosome rearrangement. Liaise with Genetic Health NZ or the laboratory to determine the most appropriate investigation  
4.    On a case by case basis following consultation with a Clinical Geneticist, a Pathologist or Fetal Medicine
External Price$941.12(Exclusive of GST)

Specimen Collection

Pre-Testing Requirements

Appropriate counselling where the implications for this test and expected results can be discussed. It may be useful to discuss testing with a Clinical Geneticist or Genetic Pathologist prior to requesting this test. 

It is necessary to complete a patient consent form before requesting this test, as well as the additional information form.For more information contact: and add 'Prenatal Microarray query' in subject line

Solid specimens (CVS, Fetal Tissues or POC) should be collected in  RPMI Tissue Transport Medium in a universal container. To order the transport medium phone CHL Patient and client services 03 364 0484 between 09.00-17.00, Mon-Fri and allow at least one working day for delivery. In emergency the specimen can be collected into sterile saline. 


Specimen Collection Protocols

Amniotic fluid (AF):   >18mL of clear fluid from >15 weeks gestation (ideally >16 weeks). Rapid aneuploidy screening and back-up cultures are performed. Limitations:  samples <16 wks gestation, <18mL, or visibly blood-stained fluid, will be cultured prior to DNA extraction. This will delay results by up to 2 weeks. 

Send parental bloods together with the prenatal specimen if possible, to avoid a delayed result.  2-3mL of EDTA (purple top) and 2-3mL of lithium heparin (green top) from each parent, well mixed and at ambient temperature, is required. 

Chorionic villus (CVS):   >15mg of clean villus material, from 11 weeks gestation onwards. Rapid aneuploidy screening and back-up cultures are performed. Limitations: small samples (<10mg) will be cultured prior to DNA extraction in order to obtain sufficient cells. This will delay results by up to 2 weeks.
Send parental bloods together with the prenatal specimen if possible to avoid a delayed result.  2-3mL of EDTA (purple top) and 2-3mL of lithium heparin (green top) from each parent, well mixed and at ambient temperature, is required. 
Products of Conception (POC)/Fetal Tissue
1.       At least 15mg of fetal tissue(s) (preferably not muscle) + 15mg placental villi
2.       From POC – a small piece of placental villi and membrane (at least 1cm2)
For POC referrals, please send a maternal blood (2ml EDTA purple top) together with the sample for maternal cell exclusion testing.  A paternal specimen will only be requested if required.
Patient SpecimenAmniotic fluid; CVS; Products of conception; Fetal
Sample Delivery to LabSame day or overnight by courier, room temperature

Instructions for Referral to CHLabs

Aliquot InstructionsKeep at room temperature

CHLabs Laboratory

DepartmentHaematology - Cytogenetics
Contact Details Email Email
This e-mail address is being protected from spam bots, you need JavaScript enabled to view it
Contact Phone Number03 364 1425
Test Availability8am-5.30pm Monday to Friday
Turnaround TimeAF or CVS <15 days. POC/Fetal tissue <28 days
Referred toCytogenetics

Multiple databases and current literature from NCBI are used to aid determination of the clinical significance of any copy number changes identified during CMA analysis. Associations between patient phenotype and gene content/function of the affected region(s), or the known syndrome inferred, are also considered when determining pathogenicity. 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


Uncertainty of Measurement

 Comment on report

Additional Information

Microarray testing does not detect balanced rearrangements and very small imbalances, regions of homozygosity <5Mb and some uniparental disomy. It may not detect mosaicism <20%.  

The effective screening resolution is approximately 50 kb in known clinically significant regions and 200kb elsewhere in the genome.

Interpretation is based on current knowledge. Copy number changes of uncertain or unknown signficance are reported after consultation with Genetic Health NZ. Copy number changes that are considered benign or likely benign will not be 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.

Delphic Number Test Number8047

CHL Follow us on Facebook