Routine - 4 weeks
Urgent - 2 weeks
NOTE: If you have not received a result within the stated TAT, and the results if required for clinical management, please contact the laboratory at
microarray@adhb.govt.nz so that we can expedite analysis.
Illumina Infinium Global Screening Array-24 v3.0 with analysis performed in NxClinical 6.2..
Experimental details and limitations:
1. Microarray analysis performed using the Illumina Infinium Global Screening Array-24 v3.0 with analysis performed in NxClinical 6.2. This platform offers a minimum detection limit of 15 kb with a requirement of at least 15 probes for copy-number detection. Losses smaller than 1 Mb or gains smaller than 2 Mb will not be reported unless associated with a gene/region of known pathogenicity.
2. Regions of homozygosity (ROH) are not reported, however the data is retained by the laboratory. Detection threshold for long contiguous stretches of homozygosity (LCSH) / regions of homozygosity (ROH) is set at 5 Mb.
3. Where a normal female karyotype is reported, using tissue from products of conception, there is a slight chance that it has been obtained from DNA of maternal origin.
4. Microarray analysis will not detect balanced alterations, point mutations, imbalances of regions not represented on the microarray and may not detect low level mosaicism. Microarray may not detect all forms of tetraploidy, and may not distinguish triploidy from triandric tetraploidy.
5. Genome build is GRCh38 (hg38). Nomenclature is according to ISCN (2020).
6. Classification of copy number variants: copy number variants (CNVs) are classified in accordance with the American College of Medical Genetics and Genomics (ACMG) and the Clinical Genome Resource (ClinGen) Technical Standards 2019, into the following five classes: Benign; Likely Benign; Uncertain Significance (3a, 3b, 3c), Likely Pathogenic, Pathogenic.
Benign, likely benign, and VUS 3c copy number variants are NOT reported. VUS 3b may be reported following consultation with Clinical Genetics.
Heterozygous carrier status for recessive conditions is not routinely reported. Data on all CNVs are retained by the laboratory should it be required.
Duplications of the SHOX region are not routinely reported.
Male Y chromosome changes are not reported except in cases of suspected aneuploidy. Supporting documentation regarding the interpretation of variants is available from the Diagnostic Genetics Laboratory; please contact us on
DGen@adhb.govt.nz
.
The classification of copy number variants represents the best interpretation of the data at the time of reporting. We recommend that the status of copy number variants is reviewed by the referring clinician to ensure their continuing validity.
7. The results and interpretations assume that the samples received by the laboratory are correctly identified and that family relationships and clinical diagnosis are as stated.
Consultation with the Genetic Health Service NZ- Northern Hub is recommended when further advice is needed (09-307-4949 ext 25870 or 0800 476-123).
Microarray-based testing screens for genomic imbalance (chromosomal losses and gains) across the entire human genome at a significantly higher genomic resolution (and consequentially higher diagnostic yield) than standard cytogenetic chromosome analysis.
Compared to standard cytogenetic chromosome analysis this technique is unable to detect balanced rearrangements and low level mosaicism of unbalanced rearrangements/aneuploidy. Also, unlike FISH, it cannot be done as a rapid test. Therefore this test should not be used with a family history of a balanced chromosomal rearrangement, couples experiencing infertility/multiple spontaneous pregnancy losses, suspected mosaicism, or patients with a recognizable syndrome where a more rapid test is available.
To contact the Microarray team:
| Auckland City Hospital | (09) 307 4949 |
| Lablink | ext 22000 |
| Microarray Office | ext 22008 |
| Karen Claxton (Section Leader) | ext 22011 |
Transport all bloods between 8C and 24C within 24-48 hours. If necessary specimens can be refrigerated overnight for transport at the temperatures stated above the following day.
For testing of other sample types please contact the laboratory prior to sending.