Cancer is in constant combat with the body.
Hostile cells can trigger an intricate network of interactions,
alerting the immune system.
But many cancer cells fly under the radar.
Now, advanced sequencing techniques are helping researchers
unravel these complex interactions with the potential to
boost the immune system and provide life-saving treatments.
Cancer cells have mutations that cause them to relentlessly divide
but these mutations can be different between patients and even between neighbouring cancer cells.
And not all mutations are created equal.
To come up with treatments 
researchers first need to know
which mutations will sound the immune system's alarm.
Cancer cell mutations can lead to abnormal proteins.
In cells, proteins are constantly broken up into peptides.
Foreign peptides can only be spotted if they're displayed on the surface of a cell.
The immune system uses Major Histocompatibility Complex or MHC molecules to bind to the peptides
and carry them to the cell surface.
But MHCs vary a lot between patients and can't always bind to the mutant peptides.
Mutant peptides that can trigger an immune response, and are specific to the tumour, are called neoantigens.
And to find out which mutations lead to neoantigens, researchers can use sequencing.
Comparing the DNA from cancer cells with healthy cells shows which mutations the cancer has.
And sequencing RNA can then show which abnormal proteins might be produced.
Sequencing can also reveal what what the MHC molecules will look like
and, together with the mutant protein sequences,
this can predict which neoantigens cells will display.
But this is only half the story because
even when neoantigen MHC complexes are produced,
the immune system might still miss them and fail to respond to the threat.
T cells are the body's way of spotting foreign molecules .
Only T cells with the right receptors will be able to spot a cancer's neoantigens
and there are vast numbers of different receptors.
Understanding all this variation is also important for providing treatments.
Researchers can sequence the T cells that have infiltrated a tumour.
Because T cells vary so much,
each has to be sequenced individually using cutting edge techniques.
This can reveal whether any have the right receptors
and looking at which genes are active can show which cells are fit enough to attack.
The interaction between T cells, neoantigens and MHCs is one of the most complex in biology.
But quicker and cheaper sequencing is helping researchers understand this interaction
and put together the pieces of this complex puzzle.
And this information is already helping tailor treatments to patients' own unique immune systems.
Vaccines put the body on high alert for a threat,
so a cancer vaccine could boost the concentration of a tumour's neoantigens,
switching on the immune system.
And flooding a tumour with the right T cells can ramp up the immune system's fight against a tumour.
With treatments like these, researchers are hoping to help the body win more of its battles against cancer.
