Next Generation Sequencing

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.

Here you can watch a 6-minute preview of the most ambitious platform for Next Generation Sequencing analyses: CLC Genomics Workbench. This software package is the only to support all current NGS formats: 454, Solexa, SOLiD - and later on Helicos, among more.

This video preview shows a few of the features - more are already implemented in the workbench - and you can learn a bit about the intuitive graphical user-interface to access this extremely powerful Next Generation Sequencing analysis package.

To watch the movie at YouTube.com, click here.

If you’re interested in learning more about CLC Genomics Workbench - or would like to sign up for a trial version - you can click here!

Researchers from Helicos and the universities of Stanford and Ohio have published a genome re-sequencing proof-of-concept paper in the journal Science. The team reports a 100 percent coverage of the 6,407 nucleotide genome which was sequenced with more than 150-fold coverage. Read lengths averaged about 23 bases. A point of interest is that the error rate of the sequencing was quite high, especially in homopolymer regions. However, Helicos reports that a new generation of nucleotides has since been developed that give more accurate homopolymer sequencing, and lower overall error rates. GenomeWeb has more. I have to go get hold of the original paper and read it before I blog on.

Here is the original press release.