Haematological malignancies in the 100,000 Genomes Project
Haematological malignancies are now eligible for inclusion in the 100,000 Genomes Project. When recruiting a patient the following must be checked:
- Is the patient eligible?
- Has the patient been consented?
- Can an adequate sample of malignant cells be collected?
- Can an adequate sample representative of the germline be collected?
- Has the patient been registered with the project?
- Can data from the patient be uploaded into the Genomics England database?
The eligibility criteria are detailed to ensure that we include patients who are most likely to benefit.
- Acute myeloid leukaemia (AML) patients who are also being recruited to the AML 18/19 trial
- Chronic lymphocytic leukaemia (CLL) patients who are also being recruited to the Flair trial
- Newly diagnosed AML and high-risk MDS outside of clinical trials (n=1,000)
- Myeloma patients who are also being recruited to MUK 9 trial will be eligible when the trial opens for recruitment and after demonstration that collection of sufficient cell numbers for DNA extraction alongside the clinical trial sample requirements is feasible. Further guidance on this will be released.
- Newly diagnosed Myeloma but only if sufficient CD138+ sorted cells can be obtained from bone marrow for DNA extraction. Documented evidence of purity of cell selection has to be provided for each patient (for example, a digital image of an MGG stained slide of sorted cells and a manual differential count of this slide or by Flowcytometry) (n=500). In line with the guidance for germline contamination, the myeloma cell content has to be at least 80%.
- Newly diagnosed aggressive B and T-cell Non-Hodgkin’s Lymphomas including DLBCL, Burkitt Lymphoma, Mediastinal B-cell lymphoma and High Grade lymphoma NOS (i.e. new WHO grey zone category), but only if sufficient fresh biopsy/resection material can be obtained (n=500)
- Patients with an unclassified HM malignancy and unknown diagnosis (for example: MDS/MPD overlap syndromes; uncertain diagnoses where clinical presentation does not fit with pathological diagnosis) (n=500)
- Patients with CML who are extreme responders based on RQ-PCR values after 3 months of treatment (<1% and >10%) and/or have experienced disease progression. Only pre-treatment samples should be submitted and the patient has to be consented retrospectively (n=80)
- Children with ALL who have not obtained MRD levels of less than 5% at day 28 bone marrow examination.
Note: It is recognised that clinical diagnosis and clinical trials for these cancers will still have priority but where it is possible to take sufficient material or an additional sample, this can be submitted through the existing NHS GMC pathways and processes for inclusion in the 100,000 Genomes Project.
Except where explicitly included above, the following patients are excluded:
- Patients who have previously received treatment
- Stage A CLL
- CML and MPDs showing standard or good response to treatment
- FFPE samples from lymphomas
- Stored samples
Locally collected samples would be fine.
AML 19 does include APML but as the genetics of APML is very well worked out these should not be sequenced.
If we over define this category we may miss important cases. These are cases where sequencing may help with the categorizing for diagnostic purposes e.g. MPD/MDS overlap syndromes, triple negative MPDs.
No – not at this stage in the project.
Download the participant information leaflets and consent forms.
Haematological cases present unique difficulties in collecting a germline sample which for other cancers can be a peripheral blood sample. The germline sample is needed for sequencing in order to subtract from the tumour sample and show which mutations are new within the malignancy.
FAQs on sample handling
Are any samples without tumour RNA ineligible?
Particularly for patients where a lower amount of sample is obtained there may not be enough to obtain both high quality DNA and RNA and it would seem more useful to ensure sufficient high quality DNA.
RNA is required where practical, meaning where the DNA would be compromised by this, then DNA should take priority.
Our accredited NHS laboratory pipeline uses RLT buffer (which contains GTC), will this be acceptable?
Yes RLT or any GTC containing buffer is acceptable.
The RNA blood sample should be from the same tube as the tumour DNA so EDTA is fine. There is no requirement for paxgene tubes for RNA. 8.6.1 – states For liquid tumours, the single bone marrow or peripheral blood sample should be used to extract both DNA and RNA. RNA should not be converted into cDNA, but stored in GTC buffer at -80C. Both BM and PB should be collected in EDTA tubes.
A minimum amount of DNA (tumour or bystander cells) is required in order to make a library preparation. 2ug of total DNA from the tumour is adequate (germline samples need more). We have had success with smaller amounts but the chance of failure increases and we do not try and sequence a sample with less than 0.5ug of DNA. As long as there is adequate DNA for the library preparation then a high purity sample would produce a clear sequencing report.
Our older participants tend to have problems producing enough saliva is there flexibility on the minimum amount required?
Saliva samples usually give plenty of DNA, for those who have trouble producing saliva using the OG500 kits, there are assisted collection kits (OG575 and OC175) which may help.
The 10 microgram minimum is based on blood samples. There could be some flexibility here. The Sample Handling Guidance stipulates 4ug as a minimum in exceptional circumstances, where only limited sample volumes were obtained. 4µg – 10µg of DNA is acceptable but this does increase the likelihood of sample QC failure. It is important to meet all the other QC requirements including minimum concentration and volume.
T cells could be used, but there is a risk that any mutations occurring in an early haematopoietic stem cell prior to division into myeloid / lymphoid lineages will be removed during the tumour-normal subtraction. Cultured fibroblasts from a skin biopsy as is recommended for cases in the ‘undiagnosed haem malignancy category’ e.g. for MDS/MPD overlap syndromes and triple negative MPDs would be a more reliable germline although we realise this is logistically harder to set-up
Saliva samples are recommended as the CLL germline and are likely to contain many neutrophils. Theoretically if mutations are in very early stem cells there could be a problem but this is not well recognized in CLL.
In a patient who has shown a good response to treatment, a saliva sample can be used for the germline. In patients who have active disease, potential contamination of saliva with haematological cells means that other sources of germline need to be considered. We have suggested cultures fibroblasts but appreciate the logistical and financial difficulties that this entails. Other sources are being considered and we will update on this in the future.
Is this optional? Also, how is cfDNA distinguished from cellular DNA from the circulating tumour?
cfDNA is optional. It is collected by spinning blood to create acellular plasma /serum. Therefore circulating free DNA can be distinguished from cellular DNA.
Collecting cfDNA in CLL patients is to provide material to allow monitoring once CLL cells are cleared from the blood. DNA in cell free blood has been detected in malignancies prior to other indicators of relapse. It will also allow the detection of new variants which may be associated with relapsing disease or a Richter’s transformation.
Magnetic bead separation (column sort or column enrichment) may be used for this. Samples are incubated with anti-CD138 ab conjugated to magnetic beads, the sample is then passed through a column in a magnetic field meaning the CD138 cells which are attached to the anti-CD138 ab/beads are retained in the column with all other cells passing through, the column is then removed from the magnetic field allowing the CD138 cells to pass through and be collected.
We are not currently able to return results in a clinically meaningful time frame. However, we are working hard to enable this soon.
See an example report.