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Max Planck Institutes, NIEHS, NCGR, Personal Genome Project, Applied Biosystems, Keygene, Illumina, University of Minnesota, Mayo Clinic, Tumor Sequencing Project, Baylor College of Medicine, Foundry Networks, Rutgers University, Translational Genomics Re

Two Max Planck Institutes Add Illumina GA, SOLiD Systems to Sequencing Stable
Illumina said last week that two Max Planck Institutes recently ordered a total of six Genome Analyzers to add to their existing base.
A researcher at the Max Planck Institute for Evolutionary Anthropology in Leipzig told In Sequence this week that the institute currently has five Illumina GAs on site, of which four were installed during the last month.
The Max Planck Institute for Molecular Genetics in Berlin currently has four Illumina GAs installed and has a fifth instrument on order, according to a researcher at that institute. In addition, he told In Sequence, his institute has two Applied Biosystems SOLiD systems installed and has ordered a third one.

NIEHS to Tap NCGR for ChIP Sequencing Services
The National Institute for Environmental Health Sciences intends to use chromatin immunoprecipitation sequencing services provided by the National Center for Genome Reseources in Santa Fe.
According to a presolicitation notice published on the Federal Business Opportunities website last week, NIEHS “intends to negotiate on a sole source basis” with NCGR for genome sequencing services.
These services will include ChIP sequencing antibody studies, using Illumina’s Genome Analyzer, with 200 megabases of coverage per 27 samples, Alpheus project set-up and website, and an Alpheus alignment pipeline analysis run of up to one gigabase worth of reads from approximately five samples. 
If NIEHS does not receive a response to its notice within eight days to determine “whether a qualified source is more advantageous to the government,” it will order the services from NCGR.
The notice did not include financial terms of the proposed service agreement.

Personal Genome Project Posts Some Data from First 10 Participants
The Personal Genome Project, a research project led by George Church at Harvard Medical School, last week posted on its website certain medical, phenotypic, and genomic data from its first 10 participants.
As of early this week, four of the 10 datasets included files containing “preliminary exon data.”
Last month, Church said that these data represent 50,000 exons, generated on the Illumina Genome Analyzer and the Polonator (see In Sequence 9/23/2008).
The datasets are available here.

ABI to Grant SOLiD Services Under Competitive Grant Program
Applied Biosystems will provide sequencing services on its SOLiD system to eleven researchers representing an academic laboratory of institution as part of a new competitive grant program, the company said this week.
The program intends to “inspire new genomic sequencing studies on next-generation sequencing technology,” according to a company statement.
The $10K Genome Grant Program will give one first-place winner up to 60 gigabases or 750 million tags of sequencing data, and ten second place winners one two-slide run each. For the first-place winner, ABI will perform the sequencing, primary data generation, and analysis on its SOLiD 3 system. The second place winners will receive sequencing services on the SOLiD 3 either from ABI, or from a member of the SOLiD service provider program, such as SeqWright.
ABI said it aims to support genomics, epigenomics, and transcriptome studies. Grant applications, which are due by Dec. 31, will be reviewed by an international panel of scientists with next-generation sequencing knowledge and ABI officials. The winners will be announced in February 2009.
The panel includes Sean Grimmond, leader of the genomics and computational group at the Institute of Molecular Bioscience at the University of Queensland in Australia; Yoshihide Hayashizaki, director of the Omics Science Center at the Institute for Physical and Chemical Research, RIKEN, in Japan; John McPherson, cancer genomics director at the Ontario Institute of Cancer Research; Stan Nelson, professor and vice-chair of human genetics and professor of psychiatry at the David Geffen School of Medicine at the University of California at Los Angeles; Stefan Schreiber, professor of medicine and gastroenterology at the Christian-Albrechts University in Kiel in Germany; Chung-I Wu, professor in the department of ecology and evolution at the University of Chicago and director of the Beijing Institute of Genomics; Francisco de la Vega, vice president of SOLiD applications and bioinformatics at ABI; Kevin McKernan, senior director of SOLiD scientific operations at ABI; Michael Rhodes, senior manager of SOLiD product applications at ABI; and Bob Setterquist, director of scientific operations for transcriptome analysis at ABI.
ABI said it is encouraging scientists to submit a proposal that includes a statement of their underlying project goals, the type and status of the project samples, and availability of bioinformatics resources.

Keygene Adds Second 454 Sequencer for Plant Genome Studies
Plant breeding company Keygene said last week that it has added a second 454 GS FLX sequencer from Roche to its lab, and has started to use the Titanium reagents and consumables, which enable longer reads and higher throughput.
Keygene, based in Wageningen, the Netherlands, said it will use its increased sequencing capacity to try to meet demand for whole-genome crop plant projects. The company also said it has made “new investments” in its bioinformatics infrastructure to handle large-scale data storage and analyses such as mining SNPs, mutant alleles, gene identification, and genome assembly.
Keygene will use SNPs it identifies for “cost-effective genotyping and molecular breeding of field, vegetable, and flower crops,” the firm said.
Mark van Haaren, Keygene’s vice president of business development, said in a statement that its sequencing and informatics enhancements have allowed the company to “develop new applications such as a novel whole-genome sequencing procedure of smaller to mid-sized plant genomes as well as SNP mining and mutant screening technologies.”
The company bought its first GS FLX and an Illumina Genome Analyzer in April 2007.

Illumina to Repurchase Up to $120M of Stock
Illumina said last week that its board of directors has approved the repurchase of up to $120 million of its common stock.
"Given the underlying strength of Illumina's business and the recent turbulence in the equity markets, we think our current stock price is undervalued,” said Illumina President and CEO Jay Flatley. “Therefore, we believe the stock buy-back program is in the best interests of our stockholders.”
Illumina said that the purchases would be made on the open market or through privately negotiated transactions. It will fund the purchases with existing cash balances.

U of Minnesota, Mayo Land $1.2M State Grant to Develop Next-Gen Sequence Analysis Tools
A bioinformatics research project at the University of Minnesota and Mayo Clinic has won $1.2 million under a Minnesota state grant program funding biotechnology and genomics studies.
The project, called High Throughput Sequence Analysis Infrastructure Technology Investigation, or HAITI, is led by Jean-Pierre Kocher of Mayo Clinic and Sushmita Singh of the University of Minnesota. Its goal is to “streamline management and analysis of large amounts of genetic data produced by new medical genomics research,” Mayo Clinic said last week.
Other awards under the program, made by the Minnesota Partnership for Biotechnology and Medical Genomics — collaboration between the University of Minnesota, Mayo Clinic, and the State of Minnesota — went to a High-throughput, Nanovolume, Crystallization Facility, which will receive $1.8 million to offer analysis of around 400 different conditions and diseases; an Advanced Molecular Neuroimaging center that will receive $3.5 million to adapt new imaging technologies for psychiatric diseases; and the Minnesota Congenital Heart Network, which will receive $500,000 to generate and manage research data on children born with congenital heart defects.

TSP Consortium Uses Genomic Approaches to Uncover Lung Cancer Genes
An international team of researchers has integrated gene sequencing, SNP array, and gene expression data to begin characterizing lung adenocarcinoma, the most common form of lung cancer.
Prior to this study, which is the largest such study on lung adenocarcinoma to date, just a handful of genes had been linked to lung adenocarcinoma. In an effort to flesh out that list and start deciphering the biological changes associated with the lung cancer, the Tumor Sequencing Project consortium sequenced 623 genes that were known or suspected to contribute to cancer formation in 188 lung cancer patients and matched controls.
By combining mutation information with copy number and expression data for 41 lung adenocarcinomas, they were also able to determine whether specific mutations affected gene activity or copy number.
The work appeared online last week in Nature.
“Integrative approaches like these allow us to more clearly pinpoint important genes than a single method alone would,” co-senior author Matthew Meyerson, a researcher affiliated with the Broad Institute and the Dana-Farber Cancer Institute, said in a statement.
The researchers detected 1,013 non-synonymous somatic mutations in 163 of these lung tumors. Most of these — more than 900 — were point mutations, though the researchers also detected insertions, deletions, and dinucleotide mutations.
Overall, the researchers found 26 genes that were most often mutated in lung adenocarcinoma. Among them were genes that had not previously been tied to lung cancer, but which had been linked to other types of cancer.
“Generally we found that each mutation only occurs in a small percentage of the tumor samples,” co-senior author Richard Wilson, co-director of the Genome Center at Washington University St. Louis, said in a statement, “but when we looked at all the mutations that intersect a particular signaling pathway, we were surprised to find a lot of overlap in only a handful of pathways. This gives us a much better idea of what goes wrong in cells when they become cancerous.”
In the future, researchers say, applying such approaches to larger patient groups and a broader range of cancers could provide even more information about lung cancer and other cancers — and eventually guide more personalized cancer treatment.
“Clearly much still remains to be discovered,” co-author Richard Gibbs, director of Baylor College of Medicine’s Human Genome Sequencing Center, said in a statement. “We have just begun to realize the tremendous potential of large-scale, genomic studies to unravel the many mysteries of cancer.”
The TSP, which began as an NHGRI-funded pilot project for characterizing cancer genomes, is intended to complement another NHGRI-funded project, the Cancer Genome Atlas. Last month, TCGA reported that it had characterized a type of brain cancer called glioblastoma (see In Sequence 9/9/2008). That group is also working on unraveling the genetics of squamous cell lung cancer and ovarian cancer.

Foundry Network Sells Baylor Equipment for Its Sequencing Data Center
Foundry Networks said this week that it has sold Baylor College of Medicine network equipment for its Human Genome Sequencing Center data center.
Baylor selected Foundry's NetIron MLX Series 10 gigabit Ethernet routers, and its FastIron Edge X Series and FastIron LS Series Layer 2/3 switches for its new data center.
The equipment will help the center to manage and support the transfer of large data sets between researchers, supercomputers, and storage facilities with line-rate, non-blocking performance, reliability and cost-effectiveness, according to Foundry Networks.

Rutgers Rakes in $58M of NIMH, NIDDK Funding for Genomics Studies
Rutgers University has reeled in nearly $58 million from the National Institutes of Health to fund two research programs to conduct genomics studies of mental disorders and of metabolic and digestive diseases, the university said this week.
Rutgers said it will use a $42.4 million five-year grant, and a supplemental award of $1.2 million, to create a Center for Genomic Studies on Mental Disorders at the university. The funding for the genomics center will support maintenance of a comprehensive lab, clinical databases, and computational infrastructure to fund national and international research focused on autism, bipolar disorder, depression, obsessive-compulsive disorder, and schizophrenia.
That grant also includes subcontracts to the Washington University School of Medicine to establish clinical and genetic databases, and to the Information Sciences Institute of the University of Southern California, which will study computational technology.
Rutgers also will use a five-year, $14 million contract from the National Institute of Diabetes and Digestive and Kidney Diseases to fund services and infrastructure costs for a cellular and molecular biology lab used for studying digestive, liver, and kidney diseases, and diabetes.

TGen Spins Out Online Oncology Data Resource Company
Arizona’s Translational Genomics Research Institute said last week that it has spun out a new company that will offer a data resource for clinical oncologists that will include genetic information discovered at TGen.
Based in Scottsdale, MedTrust Online will be a web-based resource that will serve as a “one-stop medical information resource” for oncologists, the company said.
The new company will offer information about potential drug therapies and a consultation service allowing doctors to discuss difficult cases with experts.
MedTrust said that cancer care provider South Texas Oncology and Hematology is helping to develop the MedTrust website, which is expected to launch in December.
MedTrust spun out of TGen Accelerator Management, which is aimed at translating TGen’s genetics research into medical treatments and services, TGen said.
TGen said it signed a licensing and services agreement with MedTrust Online in early August that covered the use of TGen’s technologies and personnel.

The Scan

Study Tracks Responses in Patients Pursuing Polygenic Risk Score Profiling

Using interviews, researchers in the European Journal of Human Genetics qualitatively assess individuals' motivations for, and experiences with, direct-to-consumer polygenic risk score testing.

EHR Quality Improvement Study Detects Demographic-Related Deficiencies in Cancer Family History Data

In a retrospective analysis in JAMA Network Open, researchers find that sex, ethnicity, language, and other features coincide with the quality of cancer family history information in a patient's record.

Inflammatory Bowel Disease Linked to Gut Microbiome Community Structure Gradient in Meta-Analysis

Bringing together data from prior studies, researchers in Genome Biology track down microbial taxa and a population structure gradient with ties to ulcerative colitis or Crohn's disease.

Ancient Greek Army Ancestry Highlights Mercenary Role in Historical Migrations

By profiling genomic patterns in 5th century samples from in and around Himera, researchers saw diverse ancestry in Greek army representatives in the region, as they report in PNAS.