Liquid Biopsy Flashcards
What mutations are tumour agnostic?
And what other tumour features?
NTRK fusions, RET, FGFR.
TMB and MSI
NTRK fusions are in what percentage of cancers?
<1%
Why are NTRK fusions always looked for?
NTRKi on the NHS works very well
Give an example of how we limit sequencing to areas of interest?
Only look at EGFR exons 18-21 (TK domain).
What’s an important acceptance criteria for genetic testing of solid tumours?
The tumour content. Might be 20 or 30% dependent on test
What assay can help increase sensitivity when tumour content is low?
ddPCR
What might be looked at on a hotspot panel, comprehensive panel, and WES or WGS.
Hotspot panel - 20-30 genes, SNVs, Indels.
Comprehensive panel - 200-350 genes, SNVs, indels, CNVs, fusions, MSI, TMB
WES/WGS - All of it. Mainly used as a research tool or seeing if someone is eligible for a clinical trial.
What are some issues with tissue biopsies?
Difficult to obtain, and there can be tissue heterogeneity depending on what you biopsy. Serial biopsies are even tougher. Might have insufficient material after histopathology.
What’s good about liquid biopsies?
Easy to obtain, sufficient sample, can do serial sampling, lower cost
What can limit ctDNA amount?
The tumour burden of the cancer
Liquid biopsy can be used for what?
Diagnosis, prognosis, MRD monitoring, response monitoring etc.
What’s the aim of Target National?
To match patients with precision therapies in early phase clinical trials by offering liquid biopsy genomic profiling
What are the limitations of liquid based genomic profiling of cancers?
Requires highly sensitive tech. variants won’t always be detectable. Cautious about detecting CNVs and fusions. Need to be able to differentiate high frequency somatic mutations from germline variants.
What is MSI caused by?
Impaired MMR
What is MSI
small tandem repeats change in copy number
How can you assess for MSI?
IHC for MMR proteins, PCR assay, or full genomic profiling.
What is Tumour mutational burden?
The measure of the total number of genomic alterations per coding area of a tumour genome. Measured by WES or extrapolated from comprehensive panel.
What does the Foundation One Liquid CDx do?
Looks at a range of variation from 324 genes from a liquid biopsy. It will tell you about MSI, TMB, and the tumour fraction too.
Why won’t variant allele frequency necessarily equal the tumour/ctDNA content?
A variant could be from a subclone and not the driver of the tumour as a whole.
When do you really not trust the VAF?
For Fusions
