Considerations for Ultra-Rapid WGS include, but are not limited to, the following:
If a child’s clinical course is entirely explained by 1 or more of the following, they are unlikely to benefit from Rapid or Ultra-rapid WGS:
It is recommended that samples from biological parents be sent whenever they are available, but they are not required for RCIGM-CGC to perform genomic analysis. Even when ordering Proband-only rWGS, we request that you send parental samples which may inform variant classification/phasing and inheritance.
Ultra-rapid WGS is best performed when a biological trio is sequenced concurrently, but may be performed with duos or singletons. Please note that RCIGM-CGC’s commitment to provisional time reporting does require trios. Whole blood is required for this testing.
Whenever possible, please send parental samples along with patient’s, but do not delay in sending patient samples. If parents are not immediately available, their samples can be sent in a subsequent shipment.
RCIGM-Clinical Genome Center is validated to report on the following:
Benign and Likely Benign variants are not reported. In addition, RCIGM-CGC does not report on carrier status, pharmacogenetic markers, polygenic risk scores, or genome wide association studies (GWAS) risk variants.
Also not reported: variants of uncertain significance that are unrelated to the patient's phenotype or are weak/leaning LB.
Selected Variants of Uncertain Significance will be reported according to RCIGM-CGC Policy:
A VUS is a variant that lacks sufficient evidence to allow for diagnosis of genetic disease due to limited or conflicting evidence of pathogenicity
A VUS may be reported in primary finding table or in a separate VUS table based on current gene-disease evidence.
RCIGM-CGC will report out a VUS when one or more of the following criteria are met:
The policy for reporting Incidental Findings is as follows:
We do not run a separate pipeline to interrogate the ACMG 73 genes. However, should a pathogenic variant in one of the ACMG 73 genes be revealed during genomic analysis for proband, and parents opt in to receive incidental findings, it will be added to the proband's report. Each parent will have the option to receive or not to receive this information for her/himself, if they opt in for proband.
If a pathogenic variant in a gene unrelated to phenotype is revealed, and that gene is not included on the ACMG 73 list, it will be evaluated by our interpretation and clinical teams for reporting. If the variant is classified as pathogenic per ACMG guidelines, is in alignment with the known inheritance pattern for the genetic condition, associated with a well established gene-disease relationship, and medically actionable, it meets criteria as an incidental finding. The finding will be included on the proband's report if parents opt in. Each parent will have the option to receive or not to receive this information for her/himself if they opt in for proband. Approximately 2% of patients sequenced in our laboratory are found to have an incidental finding.
Please see the How to Order page.
At present, our laboratory is validated to run whole genome sequencing on whole blood or DNA isolated from whole blood when collected in an EDTA tube. Saliva specimens may be used for phasing, classification, or inheritance of variants for informing proband’s WGS testing or for custom variant analysis testing.
Please contact RCIGM_rWGS@rchsd.org for information about specimen collection kits.
Clinicians may call (858) 966-8127 if inquiry is taking place Monday-Friday 9am-5pm PT.
After hours or weekend inquiries, call (858) 900-5979.
If you have questions regarding data, record, or sample transfers please contact RCIGM_rWGS@rchsd.org.
Please email ask@RadyGenomics.org and a member of our Business Development team will reach out to you promptly.