Prenatal Diagnostic Genomic Testing
Prenatal Diagnostic Genomic Testing is available at NSW Health Pathology Randwick, VCGS and SA Pathology.
Prenatal trio WES is currently available with WGS to become available in 2022. Please check with laboratories for details on the most appropriate test for your patients (trio, gene panel, singleton).
Prenatal Diagnostic Genomic Testing may be suitable if:
• Fetal imaging anomalies consistent with a clinically significant disorder.
• The underlying condition is likely to have a monogenic or copy number variant basis.
• Perinatal management may be improved if a genetic condition is identified.
Requirements for Prenatal Diagnostic Genomic Testing
Please see here [link] for further information on what is required to order prenatal diagnostic genomic testing
• If CVS/Amnio had already been completed, send information on what prior testing was undertaken (chromosome microarray, karyotype), whether amniotic/chorionic sample used, date of sample and laboratory where sample was analysed.
• If CVS/Amnio had not been completed, send 90ml of amniotic sample to NSWHP Randwick, VCGS or SA Pathology. A chromosome microarray will be run in advance of the WES/WGS.
• 5-10ml EDTA blood for DNA from both parents (trios) for extraction and storage
• Maternal EDTA blood is required for maternal cell contamination studies (all studies).
• If insufficient DNA is available, DNA cell culture or a new amniocentesis will be required.
Prenatal Diagnostic Genomic Testing Documentation Requirements
For requests to NSW Health Pathology Genomic Laboratory Randwick:
• Send test request form to: NSWPATH-RandwickGenomics@health.nsw.gov.au
• Please note where consent is stored
• Please provide a gene list or contact the laboratory for gene choice for gene panels
For requests to VCGS:
• Test request form (https://vcgs.link/genomics-request) with a clinical summary
• Signed informed consent form (https://vcgs.link/genomics-consent)
• Payment authorisation
• Select targeted gene panels for (PanelApp Australia (umccr.org))
• For more information you may contact the laboratory on P: 1300118247 or E: email@example.com
For requests to SA Pathology:
• Enquiries on 8222 3000 or free call 1800 188 077 outside the metropolitan area.
• Prenatal genomic testing enquiries should be discussed with a genetic pathologist (Dr Tristan Hardy or Dr Sui Yu) prior to acceptance by the laboratory.
• Once accepted, please contact the Prenatal Co-ordinator, Wendy Waters (firstname.lastname@example.org)
• SA Pathology request forms and genomic test consents are available on request.
PreGen Inclusion and Exclusion Criteria
General Inclusion criteria
• PreGen is limited to those families who will undergo genomic diagnostic testing as a family trio or where both the mother/egg donor and father/sperm donor are available for testing. Single parent families or those requiring a gene panel or singleton test may access prenatal genomic testing but cannot be included in the translational PreGen project.
Eligible participants must also be able to:
• Provide informed consent
• Speak/read conversational English
Testing in PreGen is limited to:
• Families where the fetus is believed to be alive at the time of enrolment (preterminal imaging findings are exclusion criteria)
Clinical Inclusion Criteria
A fetus with a structural anomaly likely to have a single gene germline aetiology including:
• A significant/ severe brain abnormality
• Facial clefts / facial dysmorphism
• A significant cardiac abnormality
• Renal anomalies (excluding multicystic dysplastic kidney / CAKUT)
• A phenotype consistent with skeletal dysplasia
• Evidence of arthrogryposis (with no obvious structural CNS abnormality)
• Non-immune fetal hydrops
Significantly abnormal biometry:
• Growth restriction (< 1st centile) without placental insufficiency
• The family do not wish to take part in PreGen
• A definite decision already made for pregnancy termination
• Likely non-genetic or undiscoverable aetiologies including teratogenesis, viral infections, and poorly controlled maternal diabetes
• Recognised syndromes/ malformation complexes with no known gene associations (Pentalogy of Cantrell/ limb body wall complex/ cloacal anomalies/ field defects)
Anomalies with a low diagnostic yield including
• Multicystic dysplastic kidney disease / CAKUT
• Apparently isolated unilateral cleft lip +/- palate
• Apparently isolated mild talipes
• Isolated increased nuchal translucency unless associated with features of hydrops or additional malformations
• Apparently isolated agenesis corpus callosum (including corpus callosum dysgenesis and interhemispheric arachnoid cyst as this is considered one anomaly)
• Apparently isolated congenital heart disease (such as ASD, VSD, PDA)
• Isolated unilateral or bilateral ventriculomegaly < 15mm
• Isolated lateral congenital diaphragmatic hernia
Please contact the PreGen team if there are questions about acceptability into the project
Results and anticipated turn-around times (TAT) for prenatal genomic testing
Turn-around Time (TAT)
• TAT is usually within 4 weeks of sample receipt. TAT may be longer if cells need to be cultured to obtain sufficient DNA.
What May or May Not be Reported
• Variants are reported if pathogenic/likely pathogenic with a clear link to a disorder
• Variants of unknown significance (VOUS) will not be reported unless (1) in an autosomal recessive condition where there is a likely pathogenic or pathogenic variant in trans with a VOUS or (2) additional clinical information changes the prior assessment of a variant as a VOUS to pathogenic or likely pathogenic
• Variants associated with an untreatable adult-onset condition in the fetus and/or a parent will not be reported
• Variants associated with a treatable adult-onset condition in a parent will be discussed with the referring clinician prior to reporting
• Carrier status for autosomal recessive conditions outside the clinical phenotype are generally not reported
What is PreGen and how do I refer to them?
PreGen will provide funded genomic testing via WES and WGS trios in 3 national diagnostic genomic laboratories (NSW Health Pathology Randwick, VCGS, SA Pathology) for families who meet imaging inclusion criteria in pregnancy.
Families may be considered for enrolment in PreGen by the clinical genetic and maternal fetal medicine teams from the 14 PreGen-associated major national hospitals after they have been consented for prenatal genomic diagnostic genomic testing. Clinical teams will discuss and consent the family for prenatal genomic testing using their usual counselling and consent processes
To qualify for a PreGen funded prenatal WES or WGS trio, families will need to agree to complete two psychosocial questionnaires with the PreGen Genetic Counsellor and to permit the study to access their MBS and PBS data.
For more information on who you can refer for a PreGen exome or genome and how to refer them, please click here
PreGen is part of the Fetal Sequencing Consortium – read more here