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Eurofins, Operon, MWG, Medigenomix, Knome, George Church's Personal Genome X-Team, Norwegian Functional Genomics Program, Broad Institute, UK Biotechnology and Biological Sciences Research Council, University of Miami, NHLBI

Eurofins to Close Three Facilities as Operon, MWG, and Medigenomix Subsidiaries Form Genomics Joint Venture
The Eurofins Group, an international bioanalytical testing provider, said this week that it has formed a genomics business unit called Eurofins Genomics that will consolidate the operations of Operon Biotechnologies, which it recently acquired, and two existing Eurofins subsidiaries.
As a result, Eurofins Genomics is planning to close two European facilities and one US site, GenomeWeb Daily News, In Sequence’s sister publication, has learned.
The closures are part of Eurofins Genomics’ plan to consolidate and align assets after its recent purchase of Operon Biotechnologies, said Jutta Huber, head of marketing at Eurofins’ MWG Biotech subsidiary.
Eurofins Group said two weeks ago that it had acquired three genomics companies with facilities in the US, Germany, and Japan, although the company did not disclose the names of the companies at the time. 
Patrick Weiss, Operon’s managing director, confirmed today that the acquisitions comprised Operon, based in Huntsville, Ala., and two of its subsidiaries in Köln, Germany, and Tokyo, Japan.
Weiss has been tapped to serve as CEO of Eurofins Genomics, a joint venture between three Eurofins subsidiaries: Operon, MWG Biotech, and Medigenomix.
MWG Biotech is based in Munich, but it had a facility in Highpoint, NC, that will be now closed. Those operations will move to Operon’s headquarters in Huntsville.
In addition, MWG Biotech may lay off some of its staff as it consolidates resources regionally, Huber said, though she said it was too early to provide further details.
Operon’s Köln facility will, in turn, be closed and moved to MWG’s headquarters in Ebersberg, Germany.
Eurofins’ sequencing services subsidiary Medigenomix, which is based in Munich, also will relocate to Ebersberg. 
Huber said that the consolidation is partly in response to a competitive but, in terms of organic growth, “not very dynamic” oligonucleotide synthesis market. 
Operon’s Weiss said in a statement that “overcapacity in the market has put a lot of pressure on oligonucleotide synthesis service suppliers,” and that “very few companies are able to keep up with the level of investment and innovation needed to meet the market demand.”
“It is a very competitive market,” Weiss said, “[but] with every competitor that we take out there is less competition.”
Weiss said Operon expects growth in the oligo and custom DNA markets, but noted that the company is under competitive pressure to keep prices low.
Weiss added that there may be more restructuring to come, but could not anticipate whether that would mean trimming staff, more relocations, or more consolidation with the Eurofins Group’s other subsidiaries.

Knome to Offer $350K Genome Sequencing Using ‘Commercially Available’ Platforms
Cambridge, Mass.-based Knome will offer its personal genome sequencing service using platforms that are already commercially available, In Sequence has learned. Last week, the company officially launched its service, offering it initially to approximately 20 individuals for a price “starting at” $350,000.
Clarifying a statement made in an earlier interview (see In Sequence 10/30/2007), Knome CEO Jorge Conde said the company will “not be working with a technology that has not been launched yet.” Rather, it will be using “the newest available technologies today.”
ABI’s SOLiD sequencer is “one of the [platforms] that we are considering working with,” Conde said, adding that the company is “technology agnostic.”
Knome will outsource the sequencing to commercial service providers, Conde said, but is not disclosing its partners yet.
The $350,000 cost will be “primarily driven by the cost of sequencing.”
The company, which was co-founded by Harvard geneticist George Church, said in a statement that it will allow select customers a “historic opportunity” to be among the first to follow the trail blazed by Craig Venter and James Watson by offering whole-genome sequencing and specialized analysis services.
Knome said whole-genome sequencing will allow for the analysis of up to 2,000 common and rare conditions and over 20,000 genes. The entire service will include whole-genome sequencing and “comprehensive” analysis from geneticists, clinicians, and bioinformaticians, who “will also provide continued support and counseling.”

George Church's Personal Genome X-Team Joins X Prize Race
Harvard geneticist George Church and his Personal Genome X-Team have joined the $10 million Archon X Prize for Genomics competition, the X-Prize Foundation said this week.
The prize will go to the first research team that can sequence 100 human genomes within ten days for less than $10,000 per genome (see GenomeWeb Daily News 10/23/2006).
Church was an important player in the Human Genome Project and is a co-founder of startup Knome (see above), which offers whole-genome sequencing and analysis services.
Church said in a statement that the Personal Genome Project “was founded in recognition that second-generation DNA sequencing has arrived and along with it, affordable personal genomics in which anyone will be able to access their own genetic information."
The Church-led Personal Genome X-Team will employ a combination of multiplex polony sequencing and haplotyping.
"We feel that the Archon X Prize for Genomics will help raise consciousness, encourage cost reductions, and standardize comparisons, all of which will allow for the creation of truly personalized medicine," Church said.
Church’s team includes Rich Terry, senior engineer for device R&D and integration; Greg Porreca, a co-developer of multiplex polony sequencing; Jay Shendure, a genome sciences professor at the University of Washington; and Kevin McCarthy, who is chief technology officer of the Dover business of Danaher Motion, the company commercializing Church’s sequencing technology (see feature story in this issue).

PGP to Enroll New Participants in Early 2008
George Church’s Personal Genome Project will enroll new participants in early 2008, according to the project’s redesigned website.
The open-ended research study “aims to improve our understanding of genetic and environmental contributions to human traits,” according to the website.
The project is looking for “members of the public who are willing to share their genome sequence and other personal information with the scientific community and the general public.”
The new website is “a preliminary attempt to describe how participation in the PGP works and to outline important topics for volunteers to consider, such as benefits, risks, and privacy.”
More information is available here.

Norwegian Functional Genomics Program Installs 454 FLX
The Norwegian Functional Genomics Program said last week that it has acquired a Roche 454 Genome Sequencer FLX.
The instrument is installed at the Center for Ecological and Evolutionary Synthesis at the University of Oslo, one of the program’s key sequencing facilities.
The program will use the instrument to expand its existing service platform and provide genome analyses and annotations for evolutionary and phylogenetic research.
Tom Gilbert from the University of Copenhagen mentioned in a statement that his university has already used 454 sequencing to investigate the taxonomic relationship of extinct woolly mammoths and rhinoceroses.

New Study from Broad Institute Lowers Human Gene Count to 20,500
A study published online last week in the Proceedings of the National Academy of Sciences indicates that the number of protein-coding genes in the human genome may be significantly lower than the current estimate of around 24,500 genes.
According to the study, published by Michele Clamp and colleagues at the Broad Institute, human gene catalogs such as Ensembl, RefSeq, and Vega include many open reading frames that are actually “random occurrences” rather than protein-coding regions — a finding that cuts the number of protein-coding genes in the genome to around 20,500.
The Broad team analyzed ORFs for which there is no evidence of evolutionary conservation with mouse or dog. According to the researchers, it has been “broadly suspected” that many of these ORFs are “functionally meaningless,” but there has been no scientific evidence to prove they are not valid genes.
“As a result,” they note in the PNAS paper, “the human gene catalog has remained in considerable doubt.”
Clamp and colleagues developed a method to characterize the properties of putative genes that lack cross-species counterparts. By analyzing these nonconserved ORFs alongside the genomes of two primates, the researchers found that they are neither the result of gene innovation in the primate lineage nor the result of gene loss in mouse or dog.
This offers “strong evidence” that these nonconserved ORFs are indeed “spurious,” and should be removed from the gene catalogs, according to the paper.
The Broad team did acknowledge that the study has “certain limitations” that could impact the final gene count. For example, they note, they did not consider 197 putative genes that lie in regions that were omitted from the finished assembly of the human genome.
In addition, the authors explain in the paper, the nonconserved ORFs that they studied were included in current gene catalogs “because they have the potential to encode at least 100 amino acids.” Therefore, they note, “we thus do not know whether our conclusions would apply to much shorter ORFs.”
They also concede that it’s likely there are additional protein-coding genes yet to be found, but note that “the final total is likely to remain under 21,000.”

UK Research Groups Wins $3.5M to Sequence Genome of Potato Parasite
Researchers in the UK, led by the University of Leeds, will use funding from the UK’s Biotechnology and Biological Sciences Research Council to sequence the genome of a tiny worm that damages potato plants, the university said last week.
The groups will use £1.7 million ($3.5 million) to sequence the potato cyst nematode’s genome in order to find out how the parasite, Globodera pallida, functions and how to prevent it from damaging crops.
Along with Leeds, researchers from the Wellcome Trust Sanger Institute, Rothamstead Research, and the Scottish Crop Research Institute will contribute to the genomics project, which is expected to be completed in 2012.
G. pallida invades a potato plant’s root system and injects it with a substance that causes the plant to create a cell that serves as a sort of “feeding tube” that allows the worm to feed on the plant, the university said. This stunts the growth of the roots and reduces the yield and quality of potato crops.
Another problem is that the worm can remain viable in soil for as long as twenty years and has a hatching process that is triggered by its sensing of nearby potato roots.
Leeds said that G. pallida is found in 55 countries worldwide. Farmers in the UK spend as much as £50 million per year to combat the worm with chemicals that can kill other organisms in the soil.

University of Miami Opens Genomics Center
The University of Miami opened a new genomics institute on the school’s South Campus last week that will focus on researching Alzheimer’s, Parkinson’s, multiple sclerosis, macular degeneration, cardiovascular disease and other common diseases.
Backed by an undisclosed amount of funding from UM’s Miller School of Medicine and $37 million in federal funds, the Miami Institute for Human Genomics includes several research centers but has two main components: the Center for Genomic Medicine and the Center for Genome Technology.
The institute will be led by Margaret Pericak-Vance, who formerly was director of Duke University’s Center for Human Genetics. Jeffrey Vance, who was assistant director at the Duke center, will direct the Center for Molecular Genetics and Genomic Medicine.
The Center for Genomic Medicine is anchored by a biorepository of blood, tissue, and fluid samples representing DNA from more than 25,000 individuals. This facility is made available to all researchers and collaborators at the university.
The Center for Genome Technology will conduct genotyping, sequencing, variant detection, and microarray analysis.
The institute, which already employs a staff of around 100, is currently conducting a study of 800 families with autism spectrum disorder that is aimed at identifying genes that contribute to the disease.
The institute also houses the Morris K. Udall Parkinson Disease Research Center of Excellence, which is focused on genetic screening for Parkinson’s and so far has identified “close to half of the confirmed susceptibility genes in Parkinson’s disease to date,” Vance said in a statement.
The MIGH also expects to conduct research collaborations with other UM researchers, as well as those at other schools, including the University of Florida, Florida International University, and Florida Atlantic University.

NHLBI to Link Genetic Data with Health Information as Part of 10 Year Strategic Plan
The National Heart, Lung, and Blood Institute announced a new strategic plan this week that will guide its next decade of research, training, and education.
The plan sets forth three major goals: to increase understanding of the molecular and physiological basis of health and disease; to enhance knowledge of the clinical mechanisms of disease; and to improve the translation of research into practice.
“Powerful new research approaches in the fields of genetics, genomics, and imaging provide unprecedented opportunities to achieve” the first goal, NHLBI said in a statement.
As an example, the institute cited a new program that will link genetic data from “long-standing groups of clinical study participants” with data about their health and characteristics, and make these data available to researchers.
The NHLBI, which was founded in 1948, provides $2.9 billion in research funding per year into cardiovascular, lung, blood, and sleep diseases and disorders.

The Scan

Drug Response Variants May Be Distinct in Somatic, Germline Samples

Based on variants from across 21 drug response genes, researchers in The Pharmacogenomics Journal suspect that tumor-only DNA sequences may miss drug response clues found in the germline.

Breast Cancer Risk Gene Candidates Found by Multi-Ancestry Low-Frequency Variant Analysis

Researchers narrowed in on new and known risk gene candidates with variant profiles for almost 83,500 individuals with breast cancer and 59,199 unaffected controls in Genome Medicine.

Health-Related Quality of Life Gets Boost After Microbiome-Based Treatment for Recurrent C. Diff

A secondary analysis of Phase 3 clinical trial data in JAMA Network Open suggests an investigational oral microbiome-based drug may lead to enhanced quality of life measures.

Study Follows Consequences of Early Confirmatory Trials for Accelerated Approval Indications

Time to traditional approval or withdrawal was shorter when confirmatory trials started prior to accelerated approval, though overall regulatory outcomes remained similar, a JAMA study finds.