Liquid Biopsy

Question 1

What mutations are tumour agnostic?
And what other tumour features?

Answer 1

NTRK fusions, RET, FGFR.
TMB and MSI

Question 2

NTRK fusions are in what percentage of cancers?

Answer 2

<1%

Question 3

Why are NTRK fusions always looked for?

Answer 3

NTRKi on the NHS works very well

Question 4

Give an example of how we limit sequencing to areas of interest?

Answer 4

Only look at EGFR exons 18-21 (TK domain).

Question 5

What’s an important acceptance criteria for genetic testing of solid tumours?

Answer 5

The tumour content. Might be 20 or 30% dependent on test

Question 6

What assay can help increase sensitivity when tumour content is low?

Answer 6

ddPCR

Question 7

What might be looked at on a hotspot panel, comprehensive panel, and WES or WGS.

Answer 7

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.

Question 8

What are some issues with tissue biopsies?

Answer 8

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.

Question 9

What’s good about liquid biopsies?

Answer 9

Easy to obtain, sufficient sample, can do serial sampling, lower cost

Question 10

What can limit ctDNA amount?

Answer 10

The tumour burden of the cancer

Question 11

Liquid biopsy can be used for what?

Answer 11

Diagnosis, prognosis, MRD monitoring, response monitoring etc.

Question 12

What’s the aim of Target National?

Answer 12

To match patients with precision therapies in early phase clinical trials by offering liquid biopsy genomic profiling

Question 13

What are the limitations of liquid based genomic profiling of cancers?

Answer 13

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.

Question 14

What is MSI caused by?

Answer 14

Impaired MMR

Question 15

What is MSI

Answer 15

small tandem repeats change in copy number

Question 16

How can you assess for MSI?

Answer 16

IHC for MMR proteins, PCR assay, or full genomic profiling.

Question 17

What is Tumour mutational burden?

Answer 17

The measure of the total number of genomic alterations per coding area of a tumour genome. Measured by WES or extrapolated from comprehensive panel.

Question 18

What does the Foundation One Liquid CDx do?

Answer 18

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.

Question 19

Why won’t variant allele frequency necessarily equal the tumour/ctDNA content?

Answer 19

A variant could be from a subclone and not the driver of the tumour as a whole.

Question 20

When do you really not trust the VAF?

Answer 20

For Fusions