HaemOnc Germline Confirmation Pathway
Germline HaemOnc variants can be associated with underlying cancer predisposition. When NGS sequencing has been performed using a tumour sample only, further testing is required to determine whether a variant is somatic or germline in origin.
In line with a national consensus statement (Speight et al., 2023 British Journal of Haematology), with input from NE&Y GLH Clinical Genetics and Haematology Clinical Teams, we have implemented a NE&Y GLH pathway for managing HaemOnc germline predisposition variants.
The pathway is focused on specific clinically actionable genes where the VAF (variant allele frequency) and age of the patient are suggestive of a possible germline cause. For these cases, the somatic NGS report will incorporate a germline variant classification (classified using rare disease ACMG/CanVIG guidance) with a recommendation whether or not to perform germline follow-up testing.
Germline testing is conducted by Sanger sequencing on DNA extracted from cultured fibroblasts requiring a punch skin biopsy sample.
The variants on which the haemonc germline pathway is followed
A variant in one of the following genes:
RUNX1, ETV6, GATA2, CEBPA, ANKRD26, DDX41 & TP53
Where:
- a) VAF >30%
- b) age of the patient at diagnosis is <45yrs
- c) DDX41 variants represent an exception. Germline follow-up is recommended based on a VAF >30% only (i.e. any age).
Germline follow up for any other gene/variant should be discussed on a case by case basis.
Instructions for taking skin biopsies
Punch Skin Biopsy for Fibroblast Culture Standard Operating Procedure (leedsth.nhs.uk)
**It is strongly recommended that skin punches are received in culture medium or sterile saline to ensure a greater success rate in culturing.** Please contact the laboratory (Leeds) for culture medium if required ([email protected])
How to complete a referral form for germline confirmation requests
Please use the Rare disease test request form
Please annotate this form to state:
- Diagnostic test; R443
- ‘Skin sample for culture and DNA extraction for germline confirmation of HaemOnc finding – FAO Inherited Cancer Team’
- Details of the GENE & VARIANT(s) requiring confirmation
Please send on the routine transport to your local genomics laboratory (see request form for address)
When to expect results?
- Somatic panHaemOnc diagnostic test – 21 days
- Skin punch fibroblast culture & gDNA extraction – 14-21 days
- Germline confirmation – 14 days from when gDNA available
- Allow 28-35 days for the complete confirmation pathway.
Contact details:
In the first instance please contact the initial reporting laboratory for germline confirmation enquiries/queries regarding the pan-HaemOnc/Haematology report.
| HMDS Leeds | [email protected] |
| Sheffield | [email protected] |
| Newcastle | [email protected] |
For cases where germline confirmation is in progress contact:
| Germline confirmation enquiries | [email protected] |
| Cell culture enquiries (Leeds) | [email protected] |