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ACGT, National Genomics for Biodiversity Laboratory, The South Korean Research Institute of Bioscience and Biotechnology, Genome Structural Variation Consortium, NimbleGen

MWG Biotech/Eurofins Medigenomix Installs GS FLX Upgrade
MWG Biotech/Eurofins Medigenomix has installed a 454 Genome Sequencer FLX, upgrading from its GS 20, the company said last week.
Ebersberg, Germany-based MWG, which installed its GS 20 last fall, said it has used the system to complete sequencing service projects for academic, industrial and pharmaceutical research institutions worldwide.
"Based on the experience with the GS 20 in the last months and in combination with
additional software tools and processes developed in-house, it is now possible to serve our customers in an even more cost effective and time-efficient way," said Georg Gradl, MWG’s sales manager for sequencing in Europe, in a company statement.

Indiana University to Install GS FLX This Month
The Center for Genomics and Bioinformatics at Indiana University Bloomington said last week that it will acquire a 454 GS FLX this month.
The center plans to use the new sequencer for de novo sequencing of genomes, re-sequencing of known genomes, genotyping, cDNA sequencing for gene discovery, and microRNA sequencing, said CGB Deputy Director Jennifer Steinbachs in a statement.
"Not only will the new sequencer allow us to do current projects faster and more effectively, but we will be able to take on new projects in collaboration with other scientists from around the world," she said.
The instrument, which CGB said costs about $500,000, was purchased with a grant from the Indiana METACyt Initiative that also covers maintenance and operational costs.
CGB was created in 2000 by the Office of the Vice President for Research and the College of Arts and Sciences with seed funding from the Indiana Genomics Initiative.

Synthetic Genomics, ACGT to Sequence Oil Palm Genome
Synthetic Genomics and the Asian Center for Genome Technology plan to sequence the genome of the oil palm, and ACGT’s parent company has made an undisclosed equity investment in SG, SG said last week.
ACGT, based in Kuala Lumpur, is owned by an oil palm plantation, Asiatic Development Berhad, which is listed on the Malaysian Stock Exchange.
SG, located in Rockville, Md., and La Jolla, Calif., called oil palm “one of the most productive oil crops,” but said its “promise as a clean energy source has not been fully realized.”
SG and ACGT plan to use the genomic data to pursue ways to “enable palm oil to be a better source of renewable fuel by breeding plants with useful traits,” SG said. The researchers would like to hunt for the genomic mechanisms behind traits that allow for growth in arid locations, and for those linked to higher oil yield and low height.
SG said the first phase of the agreement will focus on oil palm, and in later studies the groups will study the palm’s root and microbial communities “to identify biomarkers and metabolic pathways that affect the plant's growth and viability.”
Financial terms of the agreement were not released.

Mexican Scientists Create Draft Sequence of Corn Genome
Researchers at the National Genomics for Biodiversity Laboratory in Mexico City have generated a rough draft of the corn genome, Bloomberg reported last week.  
The scientist sequenced the genome of a Mexican corn variety at 4X coverage at a cost of about 600 million pesos ($55.3 million).
The researchers will share their map, which may help develop corn varieties that are resistant to pests, diseases, or dry climates, with a network of Mexican researchers working on crop improvements.

South Korean Bioscience Institute Uses Integrated Genomics' ERGO Software
The South Korean Research Institute of Bioscience and Biotechnology has licensed Integrated Genomics’ ERGO software, the company said last week.
Daejeon-based KRIBB, which is funded by the South Korean government, will use the tools for metabolic reconstruction, enzyme-data mining, and comparative genomics studies, Chicago-based IG said.  
The ERGO software “combines pattern-based analyses with a repertoire of comparative genomics tools for gene visualization,” and is optimized for analyzing microorganisms and for integrating data from genomic studies, biochemistry, gene expression, genetics, and literature.
The platform contains more than 1,236 genomes at various stages of completion, and a collection of networked cellular pathways.
Financial terms of the agreement were not released.

Genome Structural Variation Consortium to Use NimbleGen Arrays To Create High-Res CNV Map
The Genome Structural Variation Consortium, an international research collaboration involving scientists from the US, UK, and Canada, said last week that it will develop a comprehensive, high-resolution copy number variation map for the human genome using microarrays from NimbleGen Systems.
The project constitutes phase 2 of the research. In 2006, the group, along with other international collaborators, generated a first-generation map of copy number variants covering the human genome. The data suggested that thousands more CNVs exist, but technological limitations precluded the discovery of these.
The consortium has now designed a set of whole-genome oligo tiling arrays for the genome-wide detection of CNVs using 42 million probes, spaced at intervals of 50 bases of DNA.
The arrays will be used to scan DNA samples from dozens of individuals of diverse geographic background in order to capture all CNVs with a frequency of five percent or greater in the world.
Stephen Scherer at the Center for Applied Genomics at the Hospital for Sick Children in Toronto; Nigel Carter, Matthew Hurles, and Chris Tyler-Smith of the Wellcome Trust Sanger Institute; and Charles Lee from Brigham and Women's Hospital and Harvard Medical School lead the consortium.
"The first data from the 42 million probe set has confirmed the ability of this approach to identify copy number variants at least as small as 500 base pairs in size," said Carter, senior investigator at the Sanger Institute, in a statement.

The Scan

Study Links Genetic Risk for ADHD With Alzheimer's Disease

A higher polygenic risk score for attention-deficit/hyperactivity disorder is also linked to cognitive decline and Alzheimer's disease, a new study in Molecular Psychiatry finds.

Study Offers Insights Into Role of Structural Variants in Cancer

A new study in Nature using cell lines shows that structural variants can enable oncogene activation.

Computer Model Uses Genetics, Health Data to Predict Mental Disorders

A new model in JAMA Psychiatry finds combining genetic and health record data can predict a mental disorder diagnosis before one is made clinically.

Study Tracks Off-Target Gene Edits Linked to Epigenetic Features

Using machine learning, researchers characterize in BMC Genomics the potential off-target effects of 19 computed or experimentally determined epigenetic features during CRISPR-Cas9 editing.