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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: - Laboratory Request Form Diagnostic Genetics__blank_copy_id_3256944.pdf

Diagnostic Genetics Request Form


Sterile Container19 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 Container10 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


Microarray (Molecular karyotype) - Prenatal

Microarray will be undertaken on all prenatal samples referred, using the Cytoscan 750K array.

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.


Turnaround Time: Between 2 weeks and 4 weeks


A) Microarray analysis with Prenatal Targeted settings

Used for referrals with NO ultrasound abnormality. Referral indications (as in diagram above) include:-

The Cytoscan 750k Cytogenetics assay is used with analysis settings to detect copy number variants within established clinically significant regions (see table below).

1p36 deletion

Kleefstra

2q37 deletion

Miler Deiker/ 17p13.3 Duplication

3q29 deletion/duplication

Pelizaeus-Merzbacher

8p23.1 deletion

Phelan McDermid

15q24 deletion/duplication

Potocki-Shaffer

16p13.3 deletion/duplication

Rett

17q11.2 deletion

Smith Magensis

17q21.31 Koolen De Vries

Sotos

22q11.2 deletion syndrome/DiGeorge/Velocardiofacial/22q duplication

WAGR

Angelman/Preader Willi

Williams Beuren

Cat Eye

Wolf Hirschhorn

Cri du Chat

B) Microarray with High Resolution analysis settings


Referrals only accepted via the NZ Maternal Fetal Medicine Network

For referrals where an ultrasound abnormality has been observed (further information in diagram above)

The Cytoscan 750k Cytogenetics array is used with analysis settings to detect clinically significant copy number changes across the genome.

Referral Indications include
Ultrasound scan showing abnormality
Nuchal Translucency 3.5mm or greater
Previous abnormal microarray

Limitations of Microarray ( CytoScan 750k Cytogenetics array)

This platform has a mean resolution of 100 kb for copy-number detection.

Microarray analysis will not detect balanced alterations, sequence variants, imbalances of regions not represented on the microarray and may not detect low level mosaicism.

Agenic regions, well established polymorphisms and regions only containing non-coding / pseudogenes are not reported. Duplications of the SHOX region are not routinely reported.

Male Y chromosome changes are not reported except in cases of suspected aneuploidy.

Regions of homozygosity (ROH) on chromosome 15 are reported where there is suspected segmental UPD. ROH for chromosomes 7, 11 and 14 will only be reported where there is clinical suspicion of a related imprinting disorder (specified on the referral). Genomic autosomal ROH % is reported where this is above 6%.

Interpretation is based on GRCh37(hg19) human reference sequence. Nomenclature is according to ISCN (2020).


For clinical queries please contact Genetic Health Service NZ- Northern Hub, on (09) 307-4949 ext 25870 or on 0800 476-123.

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 14:33:49 14/10/2021