Sequencing Cancer Mutations? There's an App for That

The Development of Gene Sequencing Methods for Cancer Mutations

Using precise information about an individual’s genetic makeup is becoming increasingly routine for developing tailored treatments for breast, lung, colon and other cancers. But techniques used to identify meaningful gene mutations depend on analyzing sequences of both normal and mutant DNA in tumor samples—a process that can yield ambiguous results.

In the mid-1990s, Swedish researchers invented pyrosequencing as an alternative to the traditional method of gene sequencing. Pyrosequencing is an automated process in which solutions of the four DNA-building nucleotides, or “bases” (G, C, T, A) are added, one at a time, to single strands of DNA from sampled cells, in order to build up a complementary matching strand. A match with the next available base causes a chemical reaction with a special enzyme, which in turn emits a light pulse, resulting in a “peak” on the pyrogram–effectively indicating the next base in the DNA sequence.

Pyrosequencing works on shorter stretches of DNA than does the traditional method, known as “Sanger,” named for Frederick Sanger who invented the process. But pyrosequencing is also more sensitive in registering the presence of mutant DNA in a tumor sample, which is a mix of tumor and normal cells. That sensitivity makes it very useful for tumor sequencing because the mutant genes that drive a tumor’s abnormal growth typically are less prevalent in a tumor sample, compared with normal versions of those genes.

Because a tumor pyrogram is an overlay of both healthy and mutant DNA, identifying the correct sequence may be difficult and further studies to sort it all out can delay diagnosis and add significantly to costs. And while most pyrograms correspond precisely to a person’s unique mutation or set of mutations, some mutations can be more difficult to interpret than others.

That’s been the challenge until this year. Now, a team of Johns Hopkins researchers has developed an easy-to-use online computer software application that can clear up any confusion faster and cheaper than other methods. Called "Pyromaker,” the tool is the June Featured Free Solution available here for download on MX. Pyromaker’s value is in rapidly sorting through each of several simulated pyrograms, until there is a clear match with the actual tumor pyrogram.

This enables researchers to do in minutes, essentially at no cost, what otherwise would take days of further, expensive tests.

Download the Pyromaker for free now.