Information for Laboratory and Bioinformatics Staff
The SGFS will annotate your existing research exome/genome sequence data for the presence of possible actionable secondary variants in a list of genes that the SGFS will develop, curate, and update. The current list is based on the genes and variant types specified by the most recent ACMG clinical ES/GS secondary findings report Kalia et al., 2017. This list will be re-evaluated and updated at least annually by the SGFS with notification of any changes in the list to currently participating PIs and all IRP IRBs.
Sequence Data Submission
Please ensure that your data do not include any participant identifiers. Contact the SGFS team at 301-435-6689 to discuss the best way to submit your data to the SGFS. Please note the following important information about data submission:
- Genomic coordinates for each of the SGFS genes will be provided for data submission.
- Files should be submitted in either variant call (.vcf) or VarSifter (.vs) format and should be restricted to the coding/splice regions of the genes included in the ACMG list of genes for return of secondary variants.
- Data should be aligned to GRCh37 (hg19).
A Data Submission Portal is in development. Please contact SGFS staff to discuss how best to submit your data.
Confirmation of Secondary Variants
- If a pathogenic or likely pathogenic variant is identified in one of the SGFS genes then confirmation by Sanger sequencing will be offered.
- A new DNA sample will be required which can be collected via a saliva sample kit mailed to the patient or a blood draw performed at the NIH Clinical Center.
- Direct submission of previously isolated DNA may be acceptable but submission of a saliva sample is strongly preferred.
- Direct submission of previously isolated DNA can only be accepted for confirmation of secondary findings if:
- There is documentation that the new sample and the original sample were collected at different times (i.e. independently of one another).
- The new sample was processed in a CLIA certified lab. DNA from any other source cannot be processed for confirmation of secondary findings.
SGFS Guidance Memo
- Start here, describes SGFS processes in detail
- Complete the attached application, print and send to SGFS staff
Last Updated: November 9, 2018