In the laboratory, Next generation sequencing (NGS) is confirmed via Sanger sequencing for pathogenic and likely pathogenic variants. Sanger is also conducted on variants that are not clearly defined as artefact or genuine on IGV due to low read depth. Currently, sanger confirmations largely impedes the reporting TAT in the laboratory.
The purpose of this project is to collate data that can allow clinical scientists in AWMGS to make an informed decision of whether sanger confirmation should be discontinued.
Note: Project discontinued
An attempt has been made to collate data from shire of all TSO variants that have been confirmed/not confirmed by sanger.
Project has been discontinued as currently there isn't a standard process implemented in the labarotary to record variants not confirmed by sanger.
Furthermore, data in shire is not clearly linked to ensure samples that have had both TSO and sanger test was for the purpose of sanger confirmation e.g. some patient may have had a sanger test pre-dating introduction of TSO in service or samples could be family members that might have had a TSO test with no sanger confirmation but was later called to do sanger test to confirm variant of another member of their family.
Therefore, it would be difficult to confidently drop sanger confirmation with only anectdotal evidence.
With the new LIMS system soon to be implemented, there should be a record of all variants confirmed/not confirmed by sanger. Once this record is collated, this project may be revisited in the future.