Implementation-effectiveness Trial of Mainstreaming of Clinical Genomic Sequencing for Rare Disease in Ontario, Canada

The proportion of causative, pathogenic or likely pathogenic genotypes in known disease genes. This will be reported as the proportion of cases for whom diagnostic and partially diagnostic, and non-optional medically actionable secondary findings are identified at the time of primary analysis and re-analysis. Proportion of cases for whom optional medically actionable secondary findings will also be reported, relative to the number of cases who opted to receive them.

Satisfaction with Genome-wide Sequencing Ontario (GSO) intervention and implementation among ordering providers (geneticists and non-geneticists), GSO leadership, laboratory, patients and families. This outcome will be measured using a team-developed questionnaire with a 5-point Likert scale with 1 indicating strongly disagree and 5 indicating strongly agree.

Fit and suitability for regular use by ordering providers. This outcome will be measured using a team-developed questionnaire with a 5-point Likert scale with 1 indicating strongly disagree and 5 indicating strongly agree.

Sustainability is defined as the extent to which the Genome-wide Sequencing Ontario (GSO) service can be maintained within a clinical practice. This outcome will be measured using a team-developed questionnaire with a 5-point Likert scale with 1 indicating strongly disagree and 5 indicating strongly agree.

Timeliness is defined as the time needed to reach a molecular diagnosis. For routine cases, this will be reported as the proportion of cases for whom laboratory turnaround time is less than 12 weeks. From a laboratory perspective timeliness will be measured as the number of weeks elapsed from sample accessioning to laboratory reporting, reported as the proportion of cases for whom laboratory turnaround time is less than 12 weeks. The study team will also assess timeliness from the patient perspective using a patient experience questionnaire that addresses this dimension of care.

The cost per case of community-based genetic service delivery will be measured. This will include sessions with physicians and genetic counselors and laboratory sequencing costs. Laboratory costs will be determined by updating existing microcost estimates of the laboratory workflow components for sequencing approaches. If a comparative design is possible, a cost analysis will compare service delivery cost for non-geneticist clinicians compare to geneticist clinicians.

Adoption is defined as the total number of non-geneticist clinicians ordering Genome-wide Sequencing Ontario (GSO) for their patients, and total number of submitted cases per clinician, assessed through the GSO REDCap database.

Fidelity is defined as adherence to the Genome-wide Sequencing Ontario (GSO) workflow (including form completion, use of appeal process), measured by time (in days) between when the GSO order is accessioned in the lab and when the order is processed and sent for sequencing.

Penetration is defined as the degree of integration within a service delivery system (i.e., proportion of eligible clinicians who offer genome-wide sequencing (GWS)). This outcome will be measured by iteratively assessing the rate of requests for GWS based on total eligible clinicians. This outcome will be reported based on practice characteristics of the requesting clinician (specialty, geography, years in practice, etc.).

Acceptability (to patients/families) is defined as the experiences of patients or their family members during their participation in the mainstreamed model of care. This outcome will be measured using a team-developed questionnaire with a 5-point Likert scale with 1 indicating strongly disagree and 5 indicating strongly agree.