Cancer and the Cloud
As GeneTalk grows, the network is looking to expand into other areas of study, such as cancer—where it hopes to offer solid assessments of variants and discussions about mutations that also play key roles as risk alleles for cancer predisposition syndrome.
GeneTalk is hosted on Illumina’s BaseSpace genomics analysis cloud computing platform, which directly integrates with the sequencing giant’s MiSeq and HiSeq instruments. BaseSpace automatically transfers data to the cloud in real time during a sequencing run. A 10-person lab, each user gets 1 terabyte of data free, with the second costing $250.
“For us, it’s a big advantage to address all the BaseSpace users’ need for a filtering tool. That’s a big opportunity,” Dr. Krawitz said. “There are really hundreds of users every hour analyzing data. For BaseSpace users, we hope to offer a good solution for doing the analysis.”
And like your smartphone, BaseSpace has its own growing number of apps. BaseSpace’s two dozen bioinformatics apps, developed by Illumina or third parties have been launched by individual users some 15,000 times. Apps include alignment, amplicon analysis, annotation of data, de novo assembly, library QC, metagenomics, resequencing, small RNA analysis, tertiary analysis, tumor profiling, variant calling, and visualization.
“We have about 12,000 overall BaseSpace users signed up. And we see around 2,000 people using it in any particular week,” Alex Dickinson, Illumina’s svp, cloud genomics, told GEN.
GeneTalk has its origins in Dr. Krawitz and colleagues at IMG being one of the first centers at Charité to apply next-generation sequencing in a clinical context. The researchers saw they could only solve cases for which they had access to an expert in their clinical discussion round— namely, a geneticist who could explain why a particular mutation was actually the one that caused a disease, and not others that were so rare that they could not be ruled out based on any database.
“From that experience, we concluded that you have to go global with your discussion round,” Dr. Krawitz recalled. “You need to be able to contact any geneticist in the world that’s an expert for a specific gene. So we wanted to make use of all the social web technology that’s out there, and to build such a network for our geneticists. That was the idea three years ago, and it got GeneTalk started.”