What test options are available?

  • You can request genome-wide sequencing (GWS) for your patient as a trio (preferred), or as part of a singleton, duo, or quad testing strategy, with samples from relevant biological family members.
Test Structure Example
Singleton Patient only
Duo Patient + one biological parent or another affected family member
Trio Patient + both biological parents
Quad Patient + parents and another affected family member
  • Please contact your catchment laboratory prior to ordering to discuss different ordering strategies.

What is the test eligibility review process?

  • Once the completed requisition, supporting documents, and the patient/family specimens are submitted to the CHEO Genetics Diagnostic Laboratory or the SickKids Genome Diagnostics Laboratory, the request for testing will be reviewed by the laboratory.
  • Incomplete applications may delay the review and adjudication of the request for genome-wide sequencing, as well as overall turnaround time.
  • The checklist outlining the clinical criteria for testing is included in the test requisition. Review the clinical criteria for testing checklist.
    For more details on the approval process, please see the Review and Approval Process page.

What are the eligibility criteria for testing?

  • GSO will continue to use the “Clinical Whole Exome Sequencing (WES) Checklist” developed by the Ontario Ministry of Health, to ensure GWS is provided to the most appropriate patients in Ontario. See the testing eligibility criteria.

What are the specimen requirements?

What paperwork do I need to include with each specimen?

  • One requisition is required for each individual submitted for testing, including the proband and other biological family members. The requisitions can be found here.
  • The proband requisition includes the following sections, which must all be completed for genome-wide sequencing (GWS) to proceed:
    • Clinical data sheet
    • Clinical GWS Testing Criteria and Provider Attestation
    • Signed consent forms
  • The family history and relevant clinic notes detailing the proband’s phenotype and evolution must also be provided

For more details, please see the How to Order page.

Does GSO accept family member samples for GWS if the proband has OHIP coverage but the family members do not?

  • Yes. There is no GSO cost for family member samples. However, some phlebotomy clinics may have fees associated with specimen collection and/or shipping to the GSO laboratory. This should be checked with the facility that will handle sample collection and shipping.

What is the turnaround time for genome-wide sequencing (GWS)?

  • A report will be issued within approximately 12 weeks.

What is randomization and which cases are randomized?

  • Beginning April 1st, 2022, trio cases (proband + two parents) will be randomized to receive either whole exome sequencing (WES) or whole genome sequencing (WGS). Singletons, duos, quads and trio cases that do not include both parents will receive WES. The genetic test report will include information on the type of sequencing that was performed for the case.
  • Cases are randomized as part of the clinical quality improvement pilot (approved by the SickKids Quality Management Quality Improvement Projects approvals team and CHEO GDL leadership), which will generate evidence for the Ministry of Health on the clinical outcomes and cost effectiveness of WES and WGS.

Does GSO offer expedited whole exome sequencing (WES)?

Are Copy Number Variants (CNV) analyzed?

  • Yes, CNV analysis will be included in the genome-wide sequencing analysis. However, it is not intended to replace chromosomal microarray at this time.

Is mitochondrial DNA (mtDNA) analyzed?

  • No, mtDNA is currently not analyzed.

Will reanalysis of the GWS data be available?

  • Full or variant-specific reanalysis may be requested by the ordering provider after 18 months, or if a new phenotype or new pregnancy emerges in the family within 1 year.

Can targeted variant testing be requested in extended family members of the proband?

  • Diagnostic, predictive, or carrier testing of relatives for variants identified in a patient by genome-wide sequencing (GWS) can be ordered at a clinical laboratory that offers clinical testing for the gene of interest.
  • In some situations, testing of specific family members may help to clarify the significance of a variant identified in a patient; if segregation testing is indicated in a case, it will be specified on the proband’s test report, and will be available at the GSO laboratory that performed the GWS.

Does GSO offer fetal whole exome sequencing?

How will I, as the provider, receive the results?

  • For providers at institutions in the GSO catchments, the final report will be sent to the fax number provided by the ordering physician on the requisition form.
  • Providers at CHEO will receive the result report via their Epic InBasket.
  • Providers at SickKids will receive the result report via digital fax.

What findings will be reported?

  • The report will include a short overall summary of the result interpretation as it relates to the reason or indication for testing. Variants that are pathogenic, likely pathogenic, or of uncertain significance in known disease genes related to the reason or indication for testing will be reported.
  • Secondary findings will be reported if patients have opted to receive secondary findings. Learn more about the reporting of secondary findings.
  • View example test reports.

Will secondary findings be reported?

Are there any findings that will NOT be reported?

  • Variants not associated with disease, such as harmless variants commonly seen in healthy individuals and variants in genes not known at this time to cause disease
  • Variants thought to cause small increases or decreases in the risk of developing common conditions (i.e., multifactorial/polygenic disorders)
  • Variants associated with unrelated adult-onset conditions for which there is no prevention, early detection, or treatment
  • Carrier status for recessive genetic disorders unrelated to the condition for which testing has been offered
  • Pharmacogenomic variants

What research opportunities are available for my patients?

  • There may be additional research opportunities for your patient’s specific genetic condition identified through GWS. Patients who wish to be contacted for opportunities to participate in research or clinical knowledge bases may indicate their preference on the Acknowledgement form in the “Contact for Research” section.

Will my patient’s data be available for research studies?

  • If the patient has consented to a research study that requires use of the patient’s sequence data, please contact us to request patient data with a copy of the study protocol and the patient’s signed consent form.

What is GSO’s policy on sample storage and future use?

  • Following GWS, any remaining sample will be stored at the CHEO and/or SickKids laboratories as per their policy. The sample may be available for additional clinical genetic testing for the patient, upon request from a provider. Samples may also be used for test development/validation and quality assurance procedures in the laboratory once they have been de-identified.
  • The patient may request that their remaining sample be destroyed at any time, by contacting their physician.
  • The patient may request that their complete GWS data be shared with their health care provider or a research program with Research Ethics Board approval.

How will GSO share data?

  • Analysis of the patient’s GWS data will be completed using a secure external IT platform. The external IT platform provider will have access to a limited set of anonymized data for the purpose of quality assurance and improvement of the platform as a whole. The external IT platform has been reviewed and approved for use by CHEO and SickKids Privacy and Legal.
  • To help healthcare providers and laboratories deliver better care to patients, laboratories share their interpretation of genetic results. Anonymized (i.e., information that can identify the patient has been permanently removed) genetic results and diagnoses may be shared with healthcare providers, genetic testing laboratories, and/or submitted to public databases, including those outside of Canada, for these purposes.
  • With consent coded (i.e., information that can identify the patient will be replaced by a code) GWS data and clinical features will be shared through Ontario’s Clinical Knowledge Base to ensure that GSO is providing the best possible test for all patients. This data may also be shared with institutionally approved Clinical Knowledge Bases within Canada. Coded data shared in Clinical Knowledge Base(s) can include: demographic information (sex, age, and ethnicity), details of the patient’s clinical presentation, diagnoses, and genetic variants. This data will only be accessible to professionals working in diagnostic laboratories in Canada.
  • Coded or anonymous results and data may also be used for education, publication and metric reporting.
  • Results of GWS will only be reported to the health care provider(s) who ordered the test. The laboratory will not give test results to other individuals without the patient’s written permission, or unless required by law. The written report will become part of the patient’s permanent medical record.