Recognizing patterns in genomic data – New visualization software uncovers cancer subtypes from a vast repository of biomedical information by Stephanie Dutchen.
From the post:
Much of biomedical research these days is about big data—collecting and analyzing vast, detailed repositories of information about health and disease. These data sets can be treasure troves for investigators, often uncovering genetic mutations that drive a particular kind of cancer, for example.
Trouble is, it’s impossible for humans to browse that much data, let alone make any sense of it.
…
“It’s [StratomeX] a tool to help you make sense of the data you’re collecting and find the right questions to ask,” said Nils Gehlenborg, research associate in biomedical informatics at HMS and co-senior author of the correspondence in Nature Methods. “It gives you an unbiased view of patterns in the data. Then you can explore whether those patterns are meaningful.”
…
The software, called StratomeX, was developed to help researchers distinguish subtypes of cancer by crunching through the incredible amount of data gathered as part of The Cancer Genome Atlas, a National Institutes of Health–funded initiative. Identifying distinct cancer subtypes can lead to more effective, personalized treatments.
When users input a query, StratomeX compares tumor data at the molecular level that was collected from hundreds of patients and detects patterns that might indicate significant similarities or differences between groups of patients. The software presents those connections in an easy-to-grasp visual format.
“It helps you make meaningful distinctions,” said co-first author Alexander Lex, a postdoctoral researcher in the Pfister group.
Other than the obvious merits of this project, note the the role of software as the assistant to the user. It crunches the numbers in a specific domain and presents those results in a meaningful fashion.
It is up to the user to decide which patters are useful and which are not. Shades of “recommending” other instances of the “same” subject?
StratomeX is available for download.
I first saw this in a tweet by Harvard SEAS.