A test that rapidly identifies which genetic mutations have caused a cancer could pave the way for personalised treatments to improve patients' chances of survival.
Doctors in the US have developed a way to test patients for a wide range of gene variants simultaneously, allowing them to provide more effective, targeted therapy within a matter of weeks.
The test, called SNaPshot, has been used to identify mutations at more than 50 sites in 14 key genes in patients with non-small-cell lung cancer (NSCLC), and is now being offered to patients with a range of other cancers.
Analysis of the genetic makeup of cancers is becoming more common. But it is usually done for specific, single-gene mutations, so this is thought to be the first time such a wide-ranging test has been used clinically.
"Broad genotyping is going to become part of everyday care for lung cancer patients," said Lecia Sequist of the Massachusetts General Hospital, Boston, who co-authored the research published on Wednesday in the Annals of Oncology. "Our study is exciting because it demonstrates it is possible to integrate testing for multiple genetic biomarkers into a busy clinic and steer patients toward personalised therapies."
Sequist and her colleague Dora Dias-Santagata used a form of polymerase chain reaction (PCR), a technique that generates multiple copies of a section of DNA, usually through heating and cooling cycles, to provide more material to test.
The advanced version, known as multiplex PCR, has been used by forensic laboratories for several years to target several genes at once. The recent proliferation of new cancer drugs that target cancers with specific genetic abnormalities is leading to increasing demands for such tests.
"The proportion of patients who can receive these targeted genotype-specific treatments is only going to increase," said Sequist.
Of 589 patients with NSCLC who had the test, 546 had biopsy samples that contained enough tissue to generate results. Just over half, 51%, had one or more cancer gene mutations or an abnormality called a translocation, in which a section of DNA gets incorporated into the wrong chromosome.
The most common genetic variants found in the patients were in a gene called KRAS in 24% of cases, in EGFR for 13%, and in ALK in 5%.
Of 353 individuals with advanced disease, 170 had mutations or rearrangements that could be targeted with potential treatments. These patients could join clinical trials of drugs targeting the specific genetic makeup of their disease.
The test, which costs around £310, is being offered in a network of 14 specialist lung cancer hospitals and clinics across the US.
Tarceva is used to treat lung cancer patients with EGFR gene mutations, while another drug called Xalkori was approved for US patients in August for those who have a mutation that means they produce too much of a protein called ALK.
"Choosing the right therapy can raise response rates in NSCLC patients from around 20-30% to 60-75% and may improve survival," said Sequist.
Later this month, Cancer Research UK will launch its Stratified Medicine Programme, a two-year pilot in which samples from 9,000 patients with breast, bowel, lung, prostate, ovarian and skin cancer will be tested for mutations in 21 genes – known as a "gene panel test".
James Peach, director of the programme, said: "It's great to see the successful delivery of a cancer gene panel test in normal clinical practice. The next step is to build on these studies to develop a national network that can deliver high-quality, universally accessible and cost-effective gene panel testing."
The Foundation for Genomics and Population Health last month published a report calling on the NHS to develop tools to take advantage of advances in genetic testing.
"This test is a prime example of the sort of genomic innovation we can expect to see improving normal cancer care within the next few years by allowing doctors to identify the best treatments for individual patients," said Dr Philippa Brice of the foundation.
"However, moving new technologies into the NHS can be difficult, especially where they are effectively new sorts of test as opposed to improvements on existing tests, so planning is needed now to ensure that UK patients can benefit from the most useful new tests without unnecessary delays."
