Provider Resources

Whole Exome Sequencing (WES) or Whole Genome Sequencing (WGS)

This is a list of resources that could help to support the delivery of MBS Items 73358-73363 for-whole exome sequencing (WES) or whole genome sequencing (WGS) to identify childhood syndromes in affected individuals. Claims may not be able to be made against the Medicare Benefits Schedule for public patients. For more information about Medicare Billing, please see Department of Health | Medicare Billing in Public Hospitals.

Please contact your local genetic service or diagnostic genomic laboratory for more detailed information.

To submit a correction or other content, please contact [email protected] or [email protected].

 

Laboratories

Some laboratories offer testing under the new MBS Items 73358-73363 for-whole exome sequencing (WES) or whole genome sequencing (WGS) to identify childhood syndromes in affected individuals with the following requirements. Providers should contact the laboratory directly for forms, sample requirements, and turn around times.

To find Australian laboratories offering Whole Exome Sequencing, please visit the National Association of Testing Authorities (NATA) directory of accredited laboratories https://www.nata.com.au/accredited-facility. Search by your state with the keyword “exome” and contact the laboratory directly for more information. In New Zealand, please contact International Accreditation New Zealand (IANZ) https://www.ianz.govt.nz/.

  1. Eligibility criteria
    The patient is aged 10 years or younger and is strongly suspected of having a monogenic condition, based on the presence of:
  • dysmorphic facial appearance and one or more major structural congenital anomalies; OR
  • intellectual disability or global developmental delay of at least moderate severity, as determined by a specialist paediatrician; AND
  • the results of chromosome analysis by genome-wide micro-array (including targeted assessment of specific regions for constitutional genetic abnormalities) were non-informative.
  1. Consultation with a clinical geneticist. The item numbers may be ordered by a specialist paediatrician or clinical geneticist, but require consultation with a clinical geneticist before ordering. Contact details for local genetic services are available at the HGSA-Find a Genetic Counsellor or the Centre for Genetics Education.
  1. Informed consent. For copies of required consent forms, please contact the laboratory or your local Genetic Service.
  1. Signed pathology request form. Contact the laboratory for the appropriate form.
  1. Detailed clinical history and phenotype. A phenotype description form and/or copy of clinical letter detailing the clinical history (preferably with Human Phenotype Ontology (HPO) terms) is critical for analysis and interpretation of results. The lab may require a specific form.
  1. Trio samples. Wherever possible, samples should be submitted from both biological parents as well as the affected child to assist with analysis and interpretation of the results. Contact the laboratory directly for sample requirements.

Supporting Resources-Public Access

This is an NPAAC Level 2 test, and therefore requires that the family or patient receives pre-test counselling about what the test can offer and its limitations, as well post-test counselling to discuss the result and any implications for family members. The following resources are available for providers and patients.

Resources for Providers
(last updated: 15 July 2021)

Australasian Association for Clinical Biochemistry and Laboratory Medicine (AACB)

Lab Tests Online

Public facing website to facilitate understanding of pathology tests. “Whole Genome or Whole Exome Testing For Childhood Syndromes” https://www.labtestsonline.org.au/learning/test-index/whole-genome-or-whole-exome-testing-for-childhood

Australian Genomics

National Approach to Clinical Consent for Genetic and Genomic Testing

-Adult consent form

-Parent/Guardian consent form

-Supporting Information “Genomic Testing Fact Sheet”

National clinical consent forms — Australian Genomics

Public facing genomics resources

Fact sheets/resource links

https://www.genomicsinfo.org.au/

Laboratory resources

PanelApp Australia

-A publicly available knowledge base and tool to allow gene panels to be shared, downloaded, viewed and evaluated by experts, providing an opportunity for the standardisation of gene panels, and a consensus on which genes have sufficient evidence for disease association.

https://panelapp.agha.umccr.org

 

Shariant

-A controlled access variant hub and communication platform for real-time sharing of expertise and detailed scientific evidence about clinically curated variants between Australian laboratories and clinical services.

https://www.australiangenomics.org.au/resources/tools/shariant/

Australian Health Minister's Advisory Council (AHMAC) Project Reference Group on Health Genomics

National Model of Consent for Clinical Genomic Testing

https://www.health.nsw.gov.au/services/Pages/genomic-testing-national-model.aspx

 

 

 

ANU National Centre for Indigenous Genomics

NCIG: an introduction (video)

General video about genomics research.

https://ncig.anu.edu.au/about and

https://youtu.be/wftujBV2LPs

Centre for Genetics Education

Online resources

Listing of Genetic Services https://www.genetics.edu.au/SitePages/Genetic-Services.aspx

Landing page “Genomic Testing for Childhood Syndromes and Intellectual Disability” (http://www.genetics.edu.au/SitePages/Genomic-testing-Intellectual-disability-childhood-syndromes.aspx), with links to other resources:

General genomic testing resources:

Melbourne Genomics

Learn Genomics webpage and resources

Free educational resources on genetic and genomic testing for health professionals, and resources that can support consultations with patients about genomic testing and can inform consent.

http://learn-genomics.org.au/

Video, general to genomic tests for patients, what to consider before consent, with some VIC-specific content.

http://learn-genomics.org.au/animation-genomic-testing/ also at https://vimeo.com/421337094/9dfaf9ef0f

 

Email Elly Lynch [email protected] or Amy Nisselle [email protected] if used outside HGSA so they can track it's impact.

Paediatric Epilepsy Network New South Wales (PENNSW)

Web content for families and clinicians

Web content for clinicians with considerations for ordering genetic testing, including exomes. http://www.pennsw.org.au/clinicians/Genetic-Epilepsy/why-genetic-testing

 

Web content for families about types of genetic testing (including exomes) and things to consider. http://www.pennsw.org.au/families/epilepsy/genetic-epilepsies

QIMR-Berghofer Indigenous Genomics Health Literacy Project

Video and brochures

General video/brochures about genomics research, specific to QLD. https://www.qimrberghofer.edu.au/ig-help/

Royal Australasian College of Physicians (RACP), Continuous Learning Division

RACP genomics module

https://elearning.racp.edu.au/mod/page/view.php?id=10851 (requires login/registration)

Royal Children's Hospital Melbourne

RCH genomics credentialing course

https://learn.rch.org.au/course/view.php?id=12

 

Users will need to create a free account for The Royal Children's Hospital Online Learning Platform to access the content. The course takes about 15 minutes to complete.

Victorian Clinical Genetics Services (VCGS), Murdoch Children’s Research Institute (MCRI)

Information and resources about genomic sequencing for patients and providers, with links to other reliable resources.

https://www.vcgs.org.au/tests/genomics

Royal College of Pathologists of Australia (RCPA)

 

General Consent fact sheet

https://www.rcpa.edu.au/getattachment/f5f2a32d-4910-482e-a0de-bb11d6c36093/FctSht-3-Consent.aspx.

 

Individual labs can update their service contact and test listings by contacting RCPA https://www.rcpa.edu.au/Manuals/RCPA-Manual/Contact

 

Contributing members (alphabetical):

  • Alan Ma (CG, NSW)
  • Amy Pearn (WA)-Project Officer
  • Amy Nisselle (Melbourne Genomics)
  • Ben Lundie (ASDG rep to HGSA Council, QLD)
  • Cliff Meldrum (NSW Health Pathology)
  • Corinna Cliffe (NSW)
  • Drago Bratkovic (SA, HOD/CG)
  • Edwin Kirk (NSW Health Pathology)
  • Gareth Baynam (AACG, WA)
  • Gayathri Parasivam (Centre for Genetics Education, NSW)
  • Ivan Macciocca (ASGC ex-Officio Chair, VIC)
  • Janice Fletcher (NSW Health Pathology)
  • John Bielby (PathWest HOD, WA)
  • Julie McGaughran (GHQ, QLD)
  • Justine Elliot (VCGS)
  • Kevin Carpenter (NSW)- HGSA Executive
  • Krista Recsei (RACP)
  • Lesley McGregor (AACG, SA)
  • Mary Louise Freckman (CG, ACT)
  • Matthew Wallis (CG, TAS)
  • Meg Wall (VCGS)
  • Mike Field (CG, NSW)
  • Monica Armstrong (ASDG, ACT, HGSA Council)
  • Natalie Grainger (Project Officer, CGE)
  • Rani Sachdev (CG, NSW)
  • Rebecca Macintosh (ASGC Secretary, NSW)
  • Sebastian Lunke (VCGS)
  • Sue White (AACG, VIC)
  • Tiffany Boughtwood (Australian Genomics, VIC)
  • Vanessa Fitzgerald (NSW Ministry of Health)
  • Vanessa Tyrrell (HGSA President, NSW)
  • Yemima Berman (NSW)-Chair