What sample types can be processed?
Our tests are designed to be performed on a range of processed histology and cytology specimens, including resections, Fine Needle Aspirates (FNAs), core biopsies etc. Generally these are received in the format of formalin-fixed paraffin-embedded (FFPE) blocks, although we are happy to also accept slides (stained/unstained) or curls pre-cut from such blocks, as well as air-dried or alcohol fixed direct smears from FNA samples or even pre-extracted DNA.
Please note that when submitting curls or extracted DNA, either a H&E stained slide must be submitted with the material or a pathologist must have reviewed the material prior to dispatch and confirmed that it meets our minimum assay requirements, see below. For somatic mutation requests, any cases where the tumour content cannot be verified prior to analysis will be returned untested.
How much is enough?
For virtually all of our tests, the relative proportion of tumour cells to nucleated non-tumour cells is the single most important sample characteristic. Requirements based upon physical amounts of tissue are of less value, as even large pieces of certain samples type (e.g. fat and blood) may contain very few nucleated cells. Alternatively, other sample types, like lymph nodes may be large with many tumour cells, but be so heavily infiltrated with normal lymphocytes that they do not reach the minimum relative tumour content. Nevertheless, as a very rough guide, a sample with a combined tumour area greater than 4 square millimetres that meets or exceed the minimum tumour contents specified below would be expected to be sufficient. However, even for samples which have been accepted on the basis of relative tumour content, the final decision upon whether to proceed with analysis will be based upon the quality and quantity of nucleic acid (DNA and/or RNA) recovered.
Multi-gene (NGS) tests require that tumour cells comprise >5% of all nucleated cells
Single-gene tests (KRAS, NRAS, BRAF & EGFR) require that tumour cells comprise >10% of all nucleated cells
MLH1 methylation & MSI analyses require regions where tumour cells comprise >30% of all nucleated cells, ideally with additional non-involved regions for comparative purposes
Endopredict analysis requires regions where tumour comprises >30% by area (also see below)
For any samples received that are below the above cut offs, we will perform macro-dissection whenever possible in order to selectively harvest high tumour content sub-areas. However should this not be technically possible, samples will unfortunately have to be rejected and returned untested.
To avoid unnecessary sample rejection, we strongly suggest that either all available material is sent or that a pathologist reviews all such material locally first and selects that which is likely to yield the most DNA with the highest relative tumour content.
Please note: If sending more than a single sample per case, please ensure that you make it clear whether you wish us to select and analyse only the most suitable sample or analyse them all regardless. This will prevent results being delayed and/or analyses being charged incorrectly.
Clonality specific comments
For B & T-cell clonality testing, we can receive a range of tissue types in varying states. Those in the format of cut curls or a cell suspension they will be extracted ‘as received’, though a majority of cases come as FFPE (Formalin Fixed Paraffin embedded) and include lymph nodes, bone marrow trephines, fluids (cell blocks), bowel biopsies and skin samples.
Skin samples are assessed for suitability prior to testing by a histopathologist (as the lymphocyte distribution in skin is highly variable). If the majority of lymphocytes are located in a specific area (e.g. subepidermis, peri-adnexal…) then this will be macro-dissected to enable enrichment.
Blocks containing very little total tissue will also be assessed for suitability prior to testing by a histopathologist.
Note: The currently used CE-IVD Invivoscribe assays cannot reliably detect less than 5 positive (TCR or Immunoglobulin gene rearrangement) cells per 100 normal cells.
Blood (ctDNA) based EGFR specific comments
This test is primarily intended for use in non-small cell lung cancer patients who are progressing on EGFR TKI therapy. Blood must be drawn into the correct stabilisation tubes (Roche, Cell free DNA collection, REF:0778566601) and be shipped at ambient temperature for receipt by the laboratory within 96 hours of the draw time. Users who are unfamiliar with the process and/or the potential advantages & disadvantages of circulating tumour DNA based analysis are strongly advised to contact the laboratory for advice before proceeding.
Endopredict specific comments
As this test is based on RNA expression rather than DNA sequencing, tumour requirements (>30%) are by area as opposed to the proportion nucleated cells. For eligibility, cases must also be ER+ve/HER2 -ve with known tumour size and not more than 3 positive lymph nodes. To avoid any unnecessary delays please provide a full histopathology report(s) with the specimen and completed request form.