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LABORATORY & STATISTICAL SCIENCE
Method improved for finding genetic mistakes
A computer tool for fi nding the genetic missteps that fuel cancer has been developed by US researchers working on children’s cancers. At the beginning of 2010, St Jude Children’s Research Hospital in Memphis, Tennessee, and Washington University School of Medicine in St Louis, Missouri, embarked on a research programme to identify the genetic changes that give rise to some of the world’s deadliest childhood cancers. The teams joined forces to decode the genomes of more than 600 patients with childhood cancer, who contributed tumour samples. The researchers are now using the new algorithm to help identify the chromosomal rearrangements and DNA insertions or deletions unique to cancer. The new computational method, known as CREST (Clipping Reveals Structure), enabled the
identifi cation of 89 new structural differences in the cancer genomes of fi ve St Jude patients with a subtype of acute lymphoblastic leukaemia (ALL) known as T-lineage ALL. CREST revealed complex chromosomal rearrangements, including one that involved four chromosomes. Investigators also used the tool to fi nd 50 new variations in melanoma cells. The study appeared in the 12 June advance online edition of scientifi c journal Nature Methods. ‘CREST is signifi cantly more accurate and sensitive than existing methods of fi nding structural variations in next-generation sequencing data. It fi nds differences between a patient’s normal and cancer genomes other tools cannot fi nd,’ said Jinghui Zhang, an associate member of the St Jude Department of Computational Biology, and the study’s senior author.
Software partnership to drive research
ACD/Labs has deployed its analytical component collection on the Accelrys Pipeline Pilot R&D platform in the latest development in the continuing partnership between the two companies. This software integration accelerates the dissemination of informatics solutions in spectroscopic data processing and prediction, property prediction, analytical knowledge
management and interactive reporting of scientifi c data. Integration with Pipeline Pilot’s scientifi c information processing, automation, analysis and integration functionality helps organisations using ACD/Name, ACD/PhysChem Suite, ACD/ADME Suite, ACD/Tox Suite and ACD/Labs’ tools move new products from lab to market more quickly and effi ciently.
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In the bank – data management within biobanking
www.scientific-computing.com/news 10 SCIENTIFIC COMPUTING WORLD
Biotech project gets new member
Genedata, which provides software for research in biotechnology, life science, and drug discovery, has joined the Integrated Phenotype- Genotype (IPG) project. The IPG is an industry- led research consortium of biotechnology companies, including Evonik Industries and GATC, as well as the Bielefeld University Centre of Biotechnology. The project is co-funded by the German Federal Ministry of Education and Research (BMBF). Consortium members will contribute intellectual property and technologies to develop a high- throughput phenotype-genotype platform, which will identify complex genetic effects infl uencing
phenotypes relevant to industrial biotechnology production. Genedata Selector will be used for data analysis and management of these production strains and processes.
‘Correlating the productivity of our proprietary microbial production strains with their genotypes in the IPG project is extremely challenging, in particular matching the synergistic combinations of mutations against a high background of random mutations,’ said Stephan Hans, senior scientist, Evonik. The IPG integrates two complementary high-throughput (HT) platforms: phenotyping and genotyping. The main applications are in industrial biotech strain and process development.
ACQUISITIONS ANNOUNCED
The acquisitions of two major Electronic Laboratory Notebook (ELN) providers have recently been announced: Accelrys’ subsidiary, Accelrys Software, has acquired privately-held Contur Software (Stockholm, Sweden), while PerkinElmer has acquired Labtronics (Ontario, Canada). The Labtronics acquisition follows the recent purchases of informatics companies CambridgeSoft and ArtusLabs by PerkinElmer earlier this year. The addition of Labtronics’ solutions extends PerkinElmer’s ELN and data integration software offerings into laboratories following strict routine procedures, such as regulated and non-regulated QA/ QC, late stage product or method development laboratories, and environmental and food testing labs. Founded in 1986, Labtronics’ products include its Nexxis ELN for quality control (QC) and R&D,
and its Nexxis iLAB laboratory automation platform.
Launched in 2003, Contur ELN’s primary customer base is outside of large pharmaceutical companies, and the product has achieved success in the food and beverage, chemicals and biotechnology sectors, as well as academia. ‘We are excited about expanding
Accelrys’ portfolio with Contur’s ELN and view this as an important addition to our evolving Enterprise R&D Platform,’ said Accelrys president and chief executive offi cer Max Carnecchia. ‘With the addition of Contur’s software solutions, Accelrys now offers cost-effective ELNs to meet the range of needs of various scientifi c research and development teams — from R&D organisations transitioning from paper to an electronic notebook to those requiring a fully-integrated electronic lab environment.’
www.scientific-computing.com
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