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The bioinformatics centre takes up the challenge

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The “ICGC-TCGA DREAM Genomic Mutation Calling Challenge” was launched in 2014 by DREAM* to bioinformatics researchers all over the world. It focuses on the detection of somatic mutations using high throughput sequencing data: punctual mutations of a nucleotide, small insertions and deletions (several nucleotides) and chromosomal rearrangements (duplications, large deletions). “The stakes underlying the challenge are considerable: the analysis pipelines selected will become the standards for the coming years”, points out Anne-Sophie-Sertier, bioinformatics researcher at the bioinformatics centre of Synergie Lyon Cancer. “In fact, they will be used for the Pan-Cancer project of the International Cancer Genome Consortium (ICGC) and the Cancer Genome Atlas (TCGA), the two most important international consortiums in the study of cancer genomes. What’s more, the pipelines/algorithms will be published in Nature **!”

Synergie Lyon Cancer, the only French team active in the challenge

The competition has been divided into several sub-challenges on synthetic data (the mutations are created artificially) and real data (experimental validation trials are performed). Teams from the United States, Canada, Japan, China, Spain and Italy confront each other in this “ICGC-TCGA DREAM Genomic Mutation Calling Challenge”. And in the battle, we allow ourselves a brief hooray : the bioinformatics centre is the only French team to have submitted its lists of variants to the organiser.  
 
To date, the first 4 “synthetic” challenges have terminated and submissions for the real data are in progress. The results of the bioinformatics centre of Synergie Lyon Cancer are already excellent, and improving! Classed 5th out of the 8 participating teams for the first sub-challenge on punctual mutations, it is now 3rd out of the 12 participating teams (just after the prestigious Cancer Genome Analysis at the Broad Institute of Harvard and the Genome Institute at the Washington University School of Medicine), on the podium ! Make a date in 2015 for the final result of this scientific challenge.

Find out more: ICGC-TCGA DREAM Genomic Mutation Calling Challenge 

* DREAM (Dialogue for Reverse Engineering Assessments and Methods) organises challenges raising fundamental issues in systems biology to stimulate research on specific problems and consolidates interactions between theory and experiments.

** Nature is an English scientific journal, a reference, and one of the most reputed in the world.