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Microarray [Chromosome Analysis - Prenatal]
Also known as : [Chromosome Analysis - Prenatal],[Molecular Karyotype [Chromosome Analysis - Prenatal]]

FISH
Test performed by: LabPLUS - Dept. Diagnostic Genetics - Cytogenetics


PRENATAL ANEUSCREEN (FISH)

NOTE: Other FISH or molecular tests for specific genetic conditions can be performed on prenatal specimens as required, clearly indicate on the request form if an additional test is required.

Blood stained amniotic fluid specimens may not be suitable for FISH studies and will require maternal EDTA for MCC.

For results: use ward computer or phone Lablink: 22000 or (09) 307-8995 or 0800 522 7587.

DIAGNOSTIC USE:
The locus specific probes used in this study - X centromeric, Y centromeric, 18 centromeric, 13q14 and 21q13-q22 will detect copy number abnormalities only at the loci specified and will not detect other genetic alterations.

Specimen Collection

Please transport all specimens to the laboratory as soon as possible after collection.

3mls of amniotic fluid are required for FISH testing alone, this is in addition to the 16 mls for karyotyping.

Chorionic villus samples require an additional 1-2mg of villi for the FISH test. There may not be sufficient material for this additional test in some small samples.

Blood stained amniotic fluid specimens will NOT be accepted due to the high risk of maternal contamination.



Test performed by: LabPLUS - Dept. Diagnostic Genetics - Cytogenetics


Results or General Enquiries : use ward computer or contact Lablink: ext 22000, DDI (09) 307-8995 or 0800 522 7587.

Other contacts:

See chromosome analysis Blood (constitutional) for more details.

Turnaround times:

Rapid FISH/Aneuscreen: 2 working days (see FISH section below for more details).

Microarray and G-Banded Karyotype: (CVS and Amniotic Fluid): 14 - 21 days

Turnaround time may vary depending on sample size, gestational age and cell growth rate.

Fetal blood G-banded karyotype results are available in 3-5 days.

Specimen Collection

All samples for Cytogenetics must be collected using sterile technique.
Same day delivery (at room temperature).

Please complete all relevant boxes on the referral form, in order for correct processing of the sample. Essential information includes:-

- Maternal Age (or Date of Birth),

- Gestational Age (or EDD),

- Previous Obstetric History,

- Relevant clinical details / Ultrasound findings,

- Any further tests required (e.g. single gene disorders).

Request Form: - Laboratory Request Form Diagnostic Genetics__blank_copy_id_3256944.pdf

Diagnostic Genetics Request Form

Specimen Collection

Please transport all specimens to the laboratory as soon as possible after collection.

Download: - DG req form - fillable.pdf

Diagnostic Genetics Request Form


Sterile Container

19 mL Adult Sterile Container Amniotic Fluid

and maternal 4mL EDTA blood for maternal cell contamination (MCC) studies.

For Amniotic Fluid samples (AFs) :-

19ml of fluid at 16 weeks + gestation is the optimum size for molecular karyotype analysis, however smaller samples at earlier gestations can be processed but may incur an increased turnaround time. Collect into a sterile 20 ml universal container (obtainable from the laboratory in an emergency).


Sterile Container

10 mg Adult Sterile Container Chorionic Villus

and maternal 4ml EDTA blood for maternal cell contamination (MCC) studies.

For Chorionic Villus samples (CVs) :-

Ideally a minimum of 10-20 mg of tissue is required for microarray analysis, however smaller samples at earlier gestations can be processed but may incur an increased turnaround time. Samples should be collected aseptically into transport media (warmed to room temperature). Transport media is supplied by the Cytogenetics Laboratory and should be stored in the refrigerator for no longer than three weeks (or six months if frozen) before being discarded.


DNA
Test performed by: LabPLUS - Dept. Diagnostic Genetics - Cytogenetics

Turnaround Time: Between 2 weeks and 3 weeks

Microarray (Molecular karyotype) - Prenatal


Referrals only accepted via the NZ Maternal Fetal Medicine Network

Microarray will be undertaken on all prenatal samples referred, using the Infinium Global Screening Array-24 v3.0.
Where the primary request is not for microarray (e.g. single gene testing for a specific disorder) please specify on the referral if microarray is not required.
Conventional G-banded karyotype studies (chromosomes) will only be performed if specific criteria are met (details below).
Supporting clinical information (including ultrasound abnormalities) must be provided on the referral form to assist analysis (resolution of analysis and for the interpretation of findings).
Maternal EDTA blood should also be sent for maternal cell contamination (MCC) studies for all cases.

Microarray details and limitations (Infinium Global Screening Array-24 v3.0)
1. Microarray analysis performed using the 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 200 kb, and gains smaller than 400 kb will not be reported unless associated with a gene/region of known pathogenicity. Detection threshold for long contiguous stretches of homozygosity (LCSH) / regions of homozygosity (ROH) is set at 5 Mb.
2. It is beyond the scope of this assay to confirm UPD (uniparental disomy) and imprinting disorders. Long contiguous stretches of homozygosity (LCSH) are not routinely reported in prenatal cases unless relevant to the clinical phenotype, delineated by the referring clinicians. We will however report LCSH spanning chromosome 15 in view of the risk of UPD15 associated with Angelman syndrome and Prader-Willi syndrome. The finding of LSCH over imprinted 15q11.2-q13 region, terminal LSCH (>=5 Mb) and interstitial LCSH (>=10 Mb) will be reflexed to methylation studies to clarify the risk of UPD15 for timely results that may guide informed decisions.
3. Microarray analysis will not detect balanced alterations, point mutations, imbalances of regions not represented on the microarray and may not detect low level mosaicism.
4. Genome build is GRCh38 (hg38). Nomenclature is according to ISCN (2020).
5. 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 Benign; Likely Benign; Uncertain Significance (VUS 3c, 3b,3a), 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.
6. 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.

G-banded Karyotype (chromosome) Analysis

Only undertaken if meeting specific criteria:

1) Positive Trisomy 13 or 21 (?Robertsonian)

2) Known familial rearrangement (stated on the referral form)

3) Possible familial rearrangement (detected on microarray)

4) Large copy number imbalance on microarray (~10 Mb) detectable by G-banding

5) Mosaicism on FISH or microarray

6) Discordance between FISH and microarray

7) Unresolved genotype/phenotype mismatch


PRODUCTS OF CONCEPTION (POC)
See POC main page for more information.


Last updated at 12:19:51 04/03/2024