The big advantage of having Hartwig Medical Foundation data available in the cloud
I don’t remember exactly when I first heard about Hartwig Medical Foundation and the whole genome sequencing data it has to offer, but I think it was at some conference. The idea immediately appealed to me and so we decided to ask for access to the data. Once we had that and started to use it for our research, we were not disappointed. The number of WGS samples Hartwig Medical Foundation has is quite unique in the research field and is rapidly growing. It amounted to 3.500 samples when we started and it’s already approaching 5.000 now. We wasted no time in using the data. We needed WGS data to address some of the questions we were interested in, so gaining access to it was very helpful indeed.
WGS using tissue and matched blood samples from cancer patients is the most complete genetic tumor test we can work with for our research. Hartwig Medical Foundation offers this in the cloud, which provides some advantages and has allowed us to run some analysis that wouldn’t have been possible or at least very difficult otherwise. In particular those analyses that you need to do on raw data. If this data wouldn’t be in the cloud, we would have to download it all. That would cost us a valuable amount of time. Besides that, it would mean that we should have to invest in software for all the data storage. The only alternative would be downloading, using and removing the data and that wouldn’t be very constructive. So having the data available in the cloud is much easier. The only thing you pay for is the actual computer time. You can immediately go to work on it.
Of course I’m aware of the fact that some of my colleagues have cold feet when it comes to working with data in the cloud. And I understand their doubt. Working in the cloud means we are dependent on companies like Google and Amazon. And for some, there can be ethical issues about paying such companies money to facilitate your scientific research. To me though this is more a question of governance than money, since running analyses in your own computers also has a cost. I would welcome an alternative, which at this point simply isn’t there. It would be preferable if there was some kind of independent organization, governed on a European level that provides cloud services for scientific computing.
Having said this, this kind of organization simply isn’t there at this point in time. And the way Hartwig Medical Foundation helps our research by providing the WGS data it has in the cloud, is an advantage for some of the analyses we are doing. I’m glad it’s there.
Research professor medical genetics, computational biology and bioinformatics at Catalan Institution for Research and Advances Studies, Pompeu Fabra University and head of the Biomedical Genomics Research Group at the Institute for Biomedicine in Barcelona.U las een blog over het onderwerp Algoritmes. Wellicht bent u ook geïnteresseerd in Behandeling op maat of Betaaltitel.
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We willen het maximum aan informatie uit de tumor van de patiënt halen. Deze DNA-test is daarvoor het best beschikbare instrument. Er is maar één keer weefsel, een biopt, met voldoende tumorcellen nodig. Omdat het hele genoom wordt onderzocht, ook de gebieden in het DNA waarvan we nu nog niet weten of de gevonden afwijkingen belangrijk zijn, is deze DNA-test tumortype onafhankelijk en toekomstbestendig. Deze eigenschappen zijn de twee belangrijkste eigenschappen van WGS.