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Primeur weekly 2016-02-08

Focus

Reaching towards fully-integrated 3D tomography using new generation of algorithms and high performant scanning equipment and GPU clusters ...

Whole genome sequencing using HPC clusters in project MinE to find a cure for ALS ...

Exascale supercomputing

How to fit ten million computers into a single Supercomputer? The ExaNeSt project paves the way. European consortium becomes the trailblazer in the development of the most challenging architectures ...

Focus on Europe

Europe and Brazil join forces to improve the efficiency of the energy sector with HPC ...

Upcoming e-IRG Workshop will focus on the Progress of the e-Infrastructure Commons ...

CCRT boosts industrial innovation with a petascale supercomputer from Bull ...

Middleware

Ellexus launches tool to load balance shared storage called Mistral ...

Frame unveils powerful new visual supercomputer in the Cloud ...

Hardware

Poznan Supercomputing & Networking Center and Huawei launch HPC cluster, liquid cooled by CoolIT Systems ...

DDN WOS object storage software wins 2016 Storage Visions Award for secure, collaborative Cloud storage ...

Auburn University unveils $1 million supercomputer and initiates new technology acquisition plan ...

AMD reveals world's first hardware-virtualized GPU product line ...

High Performance Computing (HPC) market worth 36.62 billion USD by 2020 ...

Mellanox promotes Amit Katz to Vice President of Ethernet Switch Sales ...

Applications

Ofiice of Naval Research-sponsored technology simulates how legs bleed ...

Anton 2 supercomputer at PSC will increase speed and size of molecular simulations ...

NCSA awarded grant to examine effective practices in industrial HPC ...

A stellar collaboration: Supercomputing and NASA's IRIS Observatory ...

Carnegie Mellon joins IARPA project to reverse-engineer brain algorithms ...

Bionik Laboratories to utilize machine learning and analytics to improve neurological rehabilitation ...

IBM Watson Ecosystem opens for business in India ...

American Heart Association, IBM Watson Health and Welltok team up to transform heart health ...

The Cloud

Nimbix addresses enterprise call for high-performance computing with executive sales hire ...

IBM launches Cloud data and analytics marketplace for developers ...

IBM closes deal to acquire The Weather Company's product and technology businesses ...

Whole genome sequencing using HPC clusters in project MinE to find a cure for ALS


15 Dec 2015 Amsterdam - During the SURFsara Super D Event, recently held at Felix Meritis in Amsterdam, The Netherlands, Primeur Magazine had the opportunity to talk with Jan Veldink, a neurologist and professor in neurogenetics from the University Medical Center (UMC) in Utrecht about Lou Gherig's disease, aslo known as ALS. Jan Veldink is coordinating the project MinE, which is a large genome sequencing project for ALS. ALS is a lethal disease within 3 to 5 years that is typically occurring in people over sixty of age but younger people can be affected as well. Currently, there is no cure so researchers desperately need more insight in its causes and hopefully thereby new treatments.

To do the research you need large cohorts of patients but also matched controls which is only even harder to collect. Jan Veldink's team really needs all of them whole genome sequenced. This amounts to about ninety gigabytes of data per sample. If you want to collect tens of thousands of subjects you need large storage and compute power. The samples are being sent to a company in the US, Illumina. There, they are being whole genome sequenced, 600 per month, which is a high turn-around time. Then, the data comes back over the wire through SURFsara. The data is stored at SURFsara which also allows to provide a local back-up to all the people who collaborate in the project. The SURFsara copy is a working copy of the data. It allows to perform all the calculation at SURFsara on the combined dataset. The investigators (PIs) in the consortium decide whether or not to share the data. They are owner of their own part of the data. If they allow it, you can open up their part of the data so the researchers can do a huge joint analysis.

As of this moment, there are six institutes involved. The partners really want to round this up to maybe ten or fifteen institutes in the coming months. That is really necessary because ALS is a not so common disease and the partners really need international collaborators to get to these numbers of 15.000 patients at least if you want to have whole genome sequences.

Currently, the data is split into two parts: the raw data and the annotated data. The researchers at this moment mainly do the calculations on the annotated data. You could also do it locally. The PIs in the project have local copies of this annotated data. Most analyses now do occur locally on HPC solutions in the US and also here in The Netherlands, at UMC in Utrecht. However, if researchers want to use the raw data where they have some other challenges that they can solve for this disease, they really need SURFsara. Those analyses still need to be run and conducted. That is kind of the set up. The analyses of the raw data are impossible to do locally within the consortium.

For the annotated data, the so-called VCF files, the researchers use the Lisa cluster mainly. The researchers look for this burden of mutations in genes. You kind of summarize all mutations, all variations in a gene and compare those to the healthy controls. Something comes out and the researchers try to replicate it. This is done on Lisa. On grid, the researchers use the roll read information and they can do all sorts of interesting things, for example looking for strange duplications or repeated elements in the genome that are not present in the VCF files. This requires going through all the read information and this is powers of magnitude larger in terms of compute power than the VCF files.

In the end you can calculate a mean genetic number for every subject. You can plot them into 2D space and see whether or not it is a homogeneous sample. This is quite standard in genetics. Other than that, it is not really necessary to have some advanced visualization tools.

Jan Veldink prefers precision medicine to personalized medicine. Precision medicine is all about pinpointing the exact cause of an individual's disease. We know that ALS is a collection of diseases - it is not one disease - so every small group of patients has their own mutation or variants that are responsible for the disease. Nowadays, in molecular biology it is possible to correct or to silence those or to really target those precise aberrations in one patient or in one subgroup of patients. This is going to be of way more benefit than just shooting with a generic drug that will maybe slow the disease a bit. The researchers really hope that this approach will either arrest the disease in the longer term or even better, that remains to be seen.

There are many challenges still ahead: how specific is it really? How efficient is it? Is it safe? If you silence a gene, will that maybe cause some harm because you need the protein of whatever. The researchers are not there yet but at least they have an anchor for future development.

The project collaborates with many foundations over the entire globe. Many patient foundations collect money of course through donations and all sorts of campaigns. The project really tries to bring investigators and foundations together, to help them convince that this is a relevant project so the partners can raise the funds to really complete this project in due course.

More information is available at the MinE project website.

Ad Emmen

Back to Table of contents

Primeur weekly 2016-02-08

Focus

Reaching towards fully-integrated 3D tomography using new generation of algorithms and high performant scanning equipment and GPU clusters ...

Whole genome sequencing using HPC clusters in project MinE to find a cure for ALS ...

Exascale supercomputing

How to fit ten million computers into a single Supercomputer? The ExaNeSt project paves the way. European consortium becomes the trailblazer in the development of the most challenging architectures ...

Focus on Europe

Europe and Brazil join forces to improve the efficiency of the energy sector with HPC ...

Upcoming e-IRG Workshop will focus on the Progress of the e-Infrastructure Commons ...

CCRT boosts industrial innovation with a petascale supercomputer from Bull ...

Middleware

Ellexus launches tool to load balance shared storage called Mistral ...

Frame unveils powerful new visual supercomputer in the Cloud ...

Hardware

Poznan Supercomputing & Networking Center and Huawei launch HPC cluster, liquid cooled by CoolIT Systems ...

DDN WOS object storage software wins 2016 Storage Visions Award for secure, collaborative Cloud storage ...

Auburn University unveils $1 million supercomputer and initiates new technology acquisition plan ...

AMD reveals world's first hardware-virtualized GPU product line ...

High Performance Computing (HPC) market worth 36.62 billion USD by 2020 ...

Mellanox promotes Amit Katz to Vice President of Ethernet Switch Sales ...

Applications

Ofiice of Naval Research-sponsored technology simulates how legs bleed ...

Anton 2 supercomputer at PSC will increase speed and size of molecular simulations ...

NCSA awarded grant to examine effective practices in industrial HPC ...

A stellar collaboration: Supercomputing and NASA's IRIS Observatory ...

Carnegie Mellon joins IARPA project to reverse-engineer brain algorithms ...

Bionik Laboratories to utilize machine learning and analytics to improve neurological rehabilitation ...

IBM Watson Ecosystem opens for business in India ...

American Heart Association, IBM Watson Health and Welltok team up to transform heart health ...

The Cloud

Nimbix addresses enterprise call for high-performance computing with executive sales hire ...

IBM launches Cloud data and analytics marketplace for developers ...

IBM closes deal to acquire The Weather Company's product and technology businesses ...