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Primeur weekly 2014-10-27

Special

European research prominently addressed in ISC Big Data'14 Conference ...

Focus

CloudFlow to leverage HPC and Cloud-based simulation services to manufacturing and engineering SMEs  ...

The Cloud

NIST's Cloud Computing Roadmap details research requirements and action plans ...

IBM and Microsoft to offer greater choice in the hybrid Cloud ...

IBM expands global Cloud footprint with first SoftLayer Cloud centre in France ...

German Public Transportation Co. adopts IBM Software Defined Storage to tackle Big Data ...

Desktop Grids

Crowd computing Project seeks better understanding of DNA and improved quality of life ...

World Community Grid to launch 'Uncovering Genome Mysteries' Project ...

Crowd computing power to solve microbe mysteries ...

EuroFlash

SysFera and Kitware integrate HPC products for improved scientific data analysis ...

ADVA Optical Networking and BT show real value of transport SDN at SDN and OpenFlow World Congress ...

Major oil and gas software providers integrate with Altair PBS Professional ...

New computational method allows the identification of genetic alterations in cancer patients within hours ...

DANTE and TERENA join forces to become the GÉANT Association ...

ISC High Performance'15 team to issue Call for Workshops ...

Mellanox InfiniBand powers top European high performance computing centres ...

'CT scan' of distant universe reveals cosmic web in 3D ...

Brain simulation raises questions ...

PRACE in search of two Peer-review Officers ...

USFlash

ESnet extends 100G connectivity across Atlantic ...

Mellanox Ethernet solutions selected for new HP 64-bit ARM data centre platform ...

Take a tour of high performance computing with "Optimizing HPC Applications with Intel Cluster Tools" ...

SGI supercomputer places DownUnder GeoSolutions at the forefront of oil and gas exploration ...

Supercomputers link proteins to drug side effects ...

HP supercomputer at NREL garners top honour ...

UTA engineer uses advanced sensing, crowdsourcing to predict urban water flow, city needs ...

GLOBALFOUNDRIES to acquire IBM's Microelectronics business ...

Mellanox Technologies announces third quarter 2014 financial results ...

New computational method allows the identification of genetic alterations in cancer patients within hours

26 Oct 2014 Barcelona - A new computational method has made it possible to detect genetic changes responsible for the onset and progression of tumours in a simple, quick and precise way. The SMUFIN - Somatic Mutations Finder - method is capable of analyzing the complete genome of a tumor and identifying its mutations in a few hours. In addition, it is able to identify alterations which had previously not been revealed, even using methods which require the use of supercomputers over several weeks.

Today's issue of the prestigious journalNature Biotechnologyfeatures an article describing the characteristics of SMUFIN, which has been developed by the computational genomics group at Barcelona Supercomputing Center (BSC). The team is led by David Torrents, ICREA Research Professor ICREA at the BSC, in collaboration with research groups at Barcelona's Hospital Clínic and the August Pi i Sunyer Biomedical Research Institute (IDIBAPS), the University Institute of Oncology of Asturias at the University of Oviedo (IUOPA), the European Molecular Biology Laboratory (EMBL, Heidelberg) and the Spanish National Genome Analysis Centre (CNAG, Barcelona).

One of SMUFIN's main innovations is that it represents a radical change in the method by which genomes are analyzed. To date, identifying mutations responsible for the appearance of tumours has involved comparing genomes taken from the tumour with genomes obtained from healthy cells from the same patient via a reference human genome, which is used as a guide. This lengthy and complex process results in the loss of a considerable amount of information and makes it difficult to identify many mutations which have an impact on the tumor. This analysis is also executed on different computer programs in succession, each one of which is only capable of detecting certain types of variations.

SMUFIN, meanwhile, undertakes a direct comparison between the genome of healthy cells and cells from a tumour in the same patient and determines the location of almost all types of mutations at once, without requiring the use of several programs. This results in a much quicker and more complete analysis.

The article published inNature Biotechnologyexplains how SMUFIN, in addition to making the analysis faster and more cost-effective, is able to reveal hard-to-detect genetic alterations in aggressive tumours. Using SMUFIN to analyze two types of aggressive cancer samples, a blood tumour - mantle cell lymphoma - and one of the nervous system - paediatric medulloblastoma, has allowed the discovery of almost all the types of mutations occurring in their genomes for the first time and with over 90% accuracy. This includes alterations in the organisation of chromosomes, which have not been revealed by methods used to date. This represents the first step necessary to understanding how these chromosome alterations affect the evolution and aggressiveness of the tumour.

SMUFIN makes it possible for a large number of research groups to study their patients' genomes in a way previously unavailable to them. In addition, when used by supercomputing centres, SMUFIN allows mutations to be identified in hundreds or thousands of cancer genomes in just a few days. In this regard, BSC is already participating in the largest global cancer genome initiative through the International Cancer Genome Consortium (ICGC), which aims to analyze the genomes of thousands of patients in order to study the genetic bases of the onset and evolution of a large number of tumour types.

SMUFIN represents a decisive step towards personalized medicine, where the genome analysis of each patient will enable faster and more accurate diagnosis. It will also allow the development and application of personalized treatments which are less invasive than those currently used. While methods which have existed up until now are complex, limited and require days or even weeks to undertake the full analysis of a tumour genome, SMUFIN is a practical way to incorporate genome analysis into the health system, as it is capable of analyzing a tumour genome in a few hours accurately and simply.

Development work on SMUFIN began at Barcelona Supercomputing Center in 2011 by the genomics team, which is part of the Barcelona Supercomputing Center, Genomic Regulation Centre and Institute for Research in Biomedicine Barcelona (BSC-CRG-IRB) Joint Programme in Computational Biology.

SMUFIN was developed in two research environments in which the center participates. One is the Chronic Lymphocytic Leukemia Genome Project, of which the scientific directors are Elías Campo, Hospital Clínic, IDIBAPS, and Carlos López Otín, University of Oviedo, and which aims to research leukemia by analyzing the genome of more than 500 patients. The development also forms part of the National Severo Ochoa Programme, with which Barcelona Supercomputing Center is driving forward the creation of bioinformatics tools capable of managing and analyzing big amounts of biomedical data which are necessary to make personalized medicine possible, among other tools.

Source: Barcelona Supercomputing Center - BSC

Back to Table of contents

Primeur weekly 2014-10-27

Special

European research prominently addressed in ISC Big Data'14 Conference ...

Focus

CloudFlow to leverage HPC and Cloud-based simulation services to manufacturing and engineering SMEs  ...

The Cloud

NIST's Cloud Computing Roadmap details research requirements and action plans ...

IBM and Microsoft to offer greater choice in the hybrid Cloud ...

IBM expands global Cloud footprint with first SoftLayer Cloud centre in France ...

German Public Transportation Co. adopts IBM Software Defined Storage to tackle Big Data ...

Desktop Grids

Crowd computing Project seeks better understanding of DNA and improved quality of life ...

World Community Grid to launch 'Uncovering Genome Mysteries' Project ...

Crowd computing power to solve microbe mysteries ...

EuroFlash

SysFera and Kitware integrate HPC products for improved scientific data analysis ...

ADVA Optical Networking and BT show real value of transport SDN at SDN and OpenFlow World Congress ...

Major oil and gas software providers integrate with Altair PBS Professional ...

New computational method allows the identification of genetic alterations in cancer patients within hours ...

DANTE and TERENA join forces to become the GÉANT Association ...

ISC High Performance'15 team to issue Call for Workshops ...

Mellanox InfiniBand powers top European high performance computing centres ...

'CT scan' of distant universe reveals cosmic web in 3D ...

Brain simulation raises questions ...

PRACE in search of two Peer-review Officers ...

USFlash

ESnet extends 100G connectivity across Atlantic ...

Mellanox Ethernet solutions selected for new HP 64-bit ARM data centre platform ...

Take a tour of high performance computing with "Optimizing HPC Applications with Intel Cluster Tools" ...

SGI supercomputer places DownUnder GeoSolutions at the forefront of oil and gas exploration ...

Supercomputers link proteins to drug side effects ...

HP supercomputer at NREL garners top honour ...

UTA engineer uses advanced sensing, crowdsourcing to predict urban water flow, city needs ...

GLOBALFOUNDRIES to acquire IBM's Microelectronics business ...

Mellanox Technologies announces third quarter 2014 financial results ...