Next Generation Sequencing

Leaders of the 1000 Genomes Project announced today that three firms that have pioneered development of new sequencing technologies have joined the international effort to build the most detailed map to date of human genetic variation as a tool for medical research. The new participants are: 454 Life Sciences/Roche, SOLiDApplied Biosystems and Solexa/Illumina Inc..

The three companies each have agreed to sequence the equivalent of 75 billion DNA bases in the program’s pilot phase, generating the equivalent of 25 human genomes each over the coming year, according to GenomeWeb.

Update: There is a nice piece on this over at the Genetic Future blog

Boston, USA — April 29, 2008 — Today at the Bio-IT World Conference & Expo in Boston, USA, CLC bio announced collaboration with Microsoft Corp. on integrating CLC bio’s extensive bioinformatics solutions with Microsoft’s software platform, for the benefit of companies, corporations, and institutions in the biotech, pharmaceutical, and life science sectors. CLC bio has already added support for Microsoft SQL Server in its database solution, CLC Bioinformatics Database, as well as support for Microsoft’s high-performance computing solutions, Windows Compute Cluster Server 2003 and Windows HPC Server 2008.

Dr. Rudy Potenzone, worldwide pharmaceutical industry technology strategist at Microsoft Corp. and director of the Bio IT Alliance, states

We are delighted to work together with CLC bio, a member of the Bio IT Alliance and one of the world’s leading bioinformatics solution providers. This collaboration will ultimately help life sciences firms transition to the Microsoft platform throughout their research and development departments. CLC bio’s tools, fully integrated with the Microsoft Office System, increase ease of use and expand the number of potential users, while reducing administrative overhead and creating a lean workflow. Furthermore, CLC bio’s internationally renowned experts are available for consulting and customized development.

Jan Lomholdt, Vice President at CLC bio, continues

With our support for Microsoft’s server solutions, the first step in the process has already been taken. The second step is to further advance our collaboration in areas such as Next Generation Sequencing and high-performance computing, which ultimately can help realize the potential of personalized medicine. As a former member of Microsoft’s World Wide Advisory Council, I have first hand experience of the strength and potential Microsoft brings to the table with a collaboration like this, which of course is interesting for a company like ours.

Windows HPC Server 2008, the successor to Windows Compute Cluster Server 2003, includes a common set of High Performance Computing productivity tools that reaches across desktop and clusters, including a new Parallel Computing Initiative for multicore development. CLC bio’s high-performance computing solution for servers and clusters, CLC Bioinformatics Cell, supports Microsoft’s Message Passing Interface (MPI) in order to run bioinformatics algorithms such as HMMER, ClustalW, and Smith-Waterman on Windows HPC Server 2008 installations.

All CLC bio’s solutions are cross-platform, running on Windows 2000, Windows XP, Windows Vista, as well as Mac OS X and Linux.

Aarhus, Denmark — April 9, 2008 – CLC bio, several prominent Danish research institutions, and three crop-enhancing companies have joined forces in a project which aims to develop potatoes into a high-efficient, low-maintenance and multipurpose crop, which cannot only be used for animal and human food, but also for energy and chemical production, like biofuel and starch. The project will make extensive use of Next Generation Sequencing technology and Digital Gene Expression - also known as Tag-based Transcriptomics - to generate the knowledge for developing next generation crops.

Head of the project and Associate Professor at the Department of Life Sciences at Aalborg University, Dr. Kåre Lehmann Nielsen, states

With this project we want to discover the central biochemical pathways involved in the production of starch and storage proteins, and to identify the genes and genetic variants involved in the plants’ response to drought and diseases. CLC bio will develop the bioinformatics platform for all the Next Generation Sequencing analyses, and will ultimately be the instrumental part in developing the thousand Digital Gene Expression profiles, which will be used for developing the new super potato crop.

The Potato plant was chosen for this project as it produces twice the amount of energy per area, compared to maize and wheat, which makes it ideal for energy and food production. The project will draw on information gained from gene expressions of 40 different growth conditions for 15 selected cultivars, which subsequently has been analyzed.

A significant number of new or optimized bioinformatics algorithms will be developed in this project. They will all be bundled into a comprehensive bioinformatics package based on CLC bio’s present platform, the workbench, facilitating analysis of new sequencing technology data by research groups in companies and large corporations, as well as public and private research institutions.

The partners of this project are Institute of Food and Resource Economics and Department of Plant Biology, LIFE, Copenhagen University; Genetics and Biotechnology, Aarhus University; Department of Biotechnology, Chemistry and Environmental Engineering, Aalborg University; Landbrugets Kartoffelfond (LKF); Andelskartoffelmelsfabrikken Vendsyssel (AKV); Kartoffelmelscentralen (KMC); and CLC bio.

Daniel Macarthur over at Genetic Future has an interesting comment about the first two customers who have signed op to get their genome sequenced by personal genomics company Knome.

Sequencing will be done by our collaborator, BGI and supposedly has a price tag of around 350.000$ per genome.

Aarhus, Denmark and Pretoria, South Africa — February 12, 2008 — The world’s leading bioinformatics solution provider, CLC bio, has joined forces with the first center for High Throughput DNA Sequencing in Africa, Inqaba Biotechnical Industries (Pty) Ltd., in an effort to help fight tuberculosis on the African continent. Together CLC bio and inqaba biotec will assemble and analyze data from multiple tuberculosis strains, sequenced on inqaba biotec’s Genome Sequencer FLX system.

CLC bio, is in the final stage of development of their upcoming CLC Genomics Workbench, which is a new workbench aimed at next generation sequencing and whole genome assembly. The new workbench will support all next generation sequencing platforms, such as Roche GS FLX (454), Illumina Gene Analyzer System (Solexa), and SOLiD Analyzer from Applied Biosystems from the start - with Helicos and others to be included in the near future.

Dr. Oliver Preisig, Executive Director at Inqaba Biotechnical Industries, states,

The consortium’s goal is to find the genetic differences between different strains of Mycobacterium tuberculosis. We target our genome sequencing on XDR (Extreme Drug Resistant) and MDR (Multi Drug Resistant) strains of the bacterium. Having assembled the genomes of these strains we can find the strains’ specific markers and develop a PCR test that could bring much faster diagnosis for proper treatment. This means we have an urgent need for whole genome sequencing, and look forward to CLC bio’s upcoming workbench, which will provide an intuitive and fast solution.

Senior Scientific Officer at CLC bio, Dr. Roald Forsberg, continues,

We are really exited to join forces with inqaba biotec in their Tubercolosis research program. The large amount of genomic data inqaba biotec produces offers us an exciting opportunity to test and fine tune our algorithms on real and challenging data - and at the same time it allows us to contribute to the ongoing fight against Tuberculosis. This is a great motivation to our developer team.

The South African Mycobacterium tuberculosis genome sequencing project is funded by BioPAD, a biotechnology investment trust funded by the Department of Science and Technology of South Africa and includes as consortium members the Chris Hani Baragwanath business unit of the National Health Laboratory Services, the Respiratory and Meningeal Pathogens Research Unit at the University of Witwatersrand and inqaba biotec.

The upcoming CLC Genomics Workbench will among other things feature an SIMD accelerated genome assembler, and will take full advantage of “paired ends” data. CLC bio will release CLC Genomics Workbench in the spring.

About CLC bio

CLC bio is the world’s leading full-service bioinformatics solution provider, solely focusing on the development of bioinformatics: software, hardware, data analysis, and custom-designed bioinformatics algorithms. CLC bio is an Apple value added reseller.

CLC bio’s mission is to be among the most innovative bioinformatics companies in the 21st century. This is realized through:

• Development of bioinformatics software and hardware based on the latest scientific findings
• User-friendly, integrated and intuitive cross-platform software solutions
• Continuous focus on customer needs and superior customer service
• Frequent product updates including the latest IT technologies and bioinformatics algorithms
• A flexible IT architecture, enabling customers to buy or develop individualized solutions at a reasonable price

About inqaba biotec

Inqaba Biotechnical Industries (Pty) Ltd, trading as inqaba biotec, is a private South African genomics company founded in 2002. inqaba biotec was initiated and funded by a few scientists from South Africa, the USA, Germany and Switzerland. inqaba biotec is based in Pretoria, South Africa. A Swiss government loan with the aim of facilitating investments in developing and emerging countries was crucial in the start-up years. At the end of 2005 BioPAD (www.biopad.org.za), a biotechnology investment trust funded by the Department of Science and Technology of South Africa, joined inqaba biotec as a shareholder and strategic partner. inqaba biotec’s customer base covers the whole of South Africa as well as other Sub-Saharan countries. In March 2007, inqaba biotec started offering a genome sequencing service using first a GS 20 and later a GS FLX from Roche as part of an infrastructure investment by BioPAD.
For further information, please visit inqaba biotec’s website www.inqababiotec.co.za