Cancer Research UK hope that the project will analyse the tumours of up to 6,000 patients a year for a range of genetic defects.
The results will guide doctors in choosing the most effective therapy for that patient.
The charity predicts such tests could become routine within five years.
Due to be launched in the autumn, the project will examine how best to roll out genetic testing across the NHS.
Six centres will be set up around the country where scientists will classify a patient’s tumour according to the specific genetic mutations it carries.
Patients will then be offered drug treatment based on the genetic make-up of their cancer.
Potentially, such an approach could save the NHS money by cutting prescribing of expensive treatments which are unlikely to work.
Harpal Kumar, chief executive of Cancer Research UK, said scientists have now discovered enough genetic markers and drugs for such testing to make a real difference.
Cancer drugs which have been developed in recent years to specifically target a genetic mutation, include the breast cancer treatment Herceptin.
Some genetic testing is already done in NHS cancer patients, but provision is patchy and tumours are often tested for just one mutation.
James Peach, the charity’s director of stratified medicine, said they wanted to build a national programme to allow cancer patients in the UK to benefit from global genetic discoveries.
“Patients will have their tumours genetically tested, and will receive treatments based on the evidence of what does and doesn’t work for their type of tumour.
“The benefits for patients are clear: better treatments and avoiding unnecessary side-effects. But this would also allow us to drive research in stratified medicines by recording the effectiveness of certain treatments against each type of tumour.”
He said the first phase of the project would be set up in partnership with the NHS, business and government.
Once they have proven the approach works, the plan is to roll out the scheme to all patients.
The charity is looking to similar initiatives in the US to determine which mutations to test for in which cancers.
Professor Mike Stratton, director of the Cancer Genome Project at the Wellcome Trust Sanger Institute, said: “Discoveries of new cancer genes, of new drug targets and of new ways to predict whether patients will respond to particular therapies are accelerating, but a major challenge is how to obtain the benefits of these advances for patients in the NHS.
“This initiative will form the basis for doing just that.”