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Making sense out of the genome sequencing

When reading this news I was reminded of an old wisdom thought saying: "be careful on what you ask because you might get it".
Indeed, we have been looking for faster and cheaper ways to sequentialise the genome, and now we are getting real close to be able to the affordability of genome sequencing for a growing part of the population. Along with that we are flooded with data (the codons representation A-C-G-T) and we have the problem of what to do with that.
Extracting meaning from the genome sequence is tough. Hence the shift of focus, from the sequencing to the analyses of the sequences. And here is where the news from the Nationwide Children’s Hospital comes up.
Investigators at NCH have developed a method (with related algorithms and software), called Churchill, that allows the extraction of (few) meaningful information from a sequenced genome in a matter of hours, rather than weeks. It is a bit like searching a needle in the haystack. Only, in this case, you don’t know that you are searching for a needle, you are searching for something you don’t know what it might be.
In case you have doubt, this is not about medicine (although medicine/doctors are the clients) but about ICT. The problem is to find a way for parallel processing of data so that the "discovery" time can be slashed down to few hours, rather than the several weeks it takes today.
This is what the team at NCH has managed to do. Come up with a parallel computation algorithm that can scale, reaching an amazing sensitivity of 99.7% and an accuracy of 99.99%.  They have tested their method on the 1000 genome project, using the Amazon Cloud services (AWS) and managing to analyse 1088 genomes samples in just seven days identifying millions of significative variants. Impressive.
And a further proof (if ever one was needed) that ICT is pervasive, so pervasive indeed to go inside the nuclei of our cells to unravel the code of life.

About Roberto Saracco

Roberto Saracco fell in love with technology and its implications long time ago. His background is in math and computer science. Until April 2017 he led the EIT Digital Italian Node and then was head of the Industrial Doctoral School of EIT Digital up to September 2018. Previously, up to December 2011 he was the Director of the Telecom Italia Future Centre in Venice, looking at the interplay of technology evolution, economics and society. At the turn of the century he led a World Bank-Infodev project to stimulate entrepreneurship in Latin America. He is a senior member of IEEE where he leads the Industry Advisory Board within the Future Directions Committee and co-chairs the Digital Reality Initiative. He teaches a Master course on Technology Forecasting and Market impact at the University of Trento. He has published over 100 papers in journals and magazines and 14 books.