Microarray, Parental follow up

Diagnostic Use

Parental (or other clinically relevant family member) follow up testing is performed on occasion to further characterise a variant identified in a young adult, child or pregnancy. and/or establish recurrence risk.
Testing is usually by chromosomal microarray, however FISH, karyotype or molecular studies may be applied depending on the variant detected in their child/pregnancy.

Department

Genetics - Cytogenetics

Delphic Registration Code

CTGN

Synonyms

Parental follow up: microarray
Family study

Turnaround Time

6 weeks

Test Code

8048

Specimen Type

• Whole Blood

Specimen Requirements

Tube/Container Type:

Preferred

• EDTA (Lavender Cap)

Acceptable

• Lithium Heparin - Non-gel (Green Cap)

Preferred Sample Volume (ml)

5

Additional Specimen Information

Appropriate counselling where the implications for the test and expected results can be discussed. A patient consent form must be completed before requesting this test. 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 'Family study, microarray query' in subject line.

Aliquot Instructions

Transport to Lab

Ambient (8 - 24 degrees Celsius)

Additional Referral/Aliquot Information

Send same day or overnight courier
This test needs fresh, whole blood cells. The specimen must be well mixed.
Do NOT centrifuge or freeze the blood tubes and keep at ambient temperature.
Genomic DNA is extracted from the specimen prior to testing. This incurs an additional charge. Laboratories may submit DNA for testing, although it is not preferred. Please provide a minimum of 2µg of DNA at 200ng/mL.

Interpretation

Multiple databases and current literature from NCBI are used to determine the clinical significance of the any copy number variants (CNV) identified by the cytogenetics microarray. Associations between the patient phenotype and the gene content/function of the affected region(s), or the known syndrome inferred, are also necessary to link pathogenicity.

Limitations: Cytogenetic microarray will not detect balanced rearrangements, very small imbalances, low level mosaicism or regions of homozygosity <5Mb, and some uniparental disomy. The screening resolution of this test is 50 kb in known clinically significant regions and 160kb elsewhere in the genome.

Reporting policy: copy number changes of uncertain or unknown significance are reported after consultation with a genetic pathologist or Genetic Health NZ. Copy number changes that are considered benign or likely benign 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

$716.86 (Exclusive of GST)

Billing Code

8048

Contact Information

Enquiry Form