BigData@Chalmers seminar with Jens Nielsen

"Big Data in Life Science : Cancer and gut microbiome research" by Jens Nielsen, Professor of System Biology, at the Department of Biology and Biological Engineering, Chalmers.
Abstract:

With the development of novel technologies for sequencing DNA the costs have been reduced, and it is now possible to obtain a complete human genome sequence for around 1000 USD. Furthermore it is possible to read the activity of each gene by quantifying the so-called mRNAs, also through next generation sequencing. This many studies in life sciences are today generating very large datasets, which are often used to answer simple questions, e.g. is a specific mutation associated with a certain cancer type, and the data are rarely being analyzed in details due to the difficulties with handling large data. Thus, in the field of cancer there are now data available for >3,000 individuals where the whole genome has been sequenced (billions of base-pairs) and where the activity of >20,000 genes have been quantified by sequencing of up to 1,000 of mRNA reads for each gene. Often mRNA data are available for both the tumor and from healthy tissue, which results in a further doubling of the amount of data. It is clearly challenging to analyze this kind of data, but as will be demonstrated here, it allows for identification of completely new biological findings that can lead to novel diagnostic tools and novel treatment strategies.

Also in the field of the gut microbiome next generation sequencing has allowed for gaining much new insight, and it has been shown by us and others that the gut microbiome composition is associated with the development of a number of diseases, including type-2-diabetes, obesity and arteriosclerosis. Here there is also a challenge of very large data being generated. Thus, a typical study involves analysis of fecal samples from >100 subjects for which there is each generated 3 billion base pairs. These sequencing reads have to be assembled and aligned with catalogs of genes present in the 1,000 of different bacteria living in the human gut. Such catalogs involves >10 million of genes and analysis of sequences against these catalogs is a major computational challenge. Here it will be shown how analysis of this kind of data can be used to gain new insight into obesity related diseases, but also how analysis of the gut microbiome can potentially be used to solve problems of malnutrition in Asia and Africa.
Welcome to this Area of Advance ICT and Big Data@Chalmers seminar. We encourage you all to stay for coffee and further discussion after the seminar. Welcome!

Please register here, so that we can estimate the number of participants.
Category Seminar
Location: Room Catella, Chalmers Student Union Building (Kårhuset), Chalmersplatsen 1, Campus Johanneberg
Starts: 11 December, 2015, 15:00
Ends: 11 December, 2015, 16:00

Published: Mon 02 Nov 2015. Modified: Mon 23 Nov 2015