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PGP, Google, COUQ Foundation, OrbiMed, Stowers Institute for Medical Research, GeneWorks, 454, Applera, ABI, Celera, Genomatix

Personal Genome Project Receives Donations from Google, COUQ Foundation, OrbiMed
George Church’s Personal Genome Project has received undisclosed amounts of funding “in the form of unrestricted gifts” from Google, the COUQ Foundation, and OrbiMed, according to the project’s website.
The project does not disclose the funding amounts “in large part because we appreciate all donations and don’t want to discourage small ones by comparing them with large ones,” Church told In Sequence last week.
The PGP has also received “unrestricted royalty donations via Harvard and George Church” from Applied Biosystems, Agencourt, Helicos BioSciences, Lynx (now part of Illumina), and Complete Genomics, according to the website.
Further, it has received grant funding from the Broad Institute, the US Department of Energy, and the National Human Genome Research Institute.

Stowers Researcher Founds Google User Group for Solexa Sequencing
A scientists at the Stowers Institute for Medical Research has started a Google group for customers of Illumina’s Genome Analyzer.
The group, which is independent of Illumina, serves for “the exchange of information regarding the Solexa sequencing platform offered by Illumina,” according to its website. Possible discussion topics include sample preparation protocols, data analysis pipelines, quantification schemes for expression data, normalization, ChIP-seq, data display, data storage, data standards, and track files.
Chris Seidel, director of the microarrays group at the Stowers Institute, which is based in Kansas City, founded the group “because I wasn't aware of any public resource for discussing the technology,” he told In Sequence via e-mail. The reason he chose to focus on Illumina’s technology, rather than all next-gen sequencing technologies, is that “each technology will have its own issues.”

GeneWorks Offers Next-Gen Sequencing on Illumina GA in Australia
GeneWorks has started offering next-generation sequencing services on ILlumina’s Genome Analyzer platform, In Sequence has learned.
The company, which is based in Adelaide in South Australia, provides molecular biology research products and associated services.
GeneWorks Managing Director Peter Guilhaus told In Sequence by e-mail that the company acquired a Genome Analyzer last October, which he claims is the first in Australia.
In late January, the company started offering sequencing services on the instrument and has so far successfully completed two small contract re-sequencing projects.
“We did consider other technologies, specifically 454 GS FLX, but felt the cost of their system as well as running [and] infrastructure costs were somewhat prohibitive,” Guilhaus said.

Study Uses 454 to Find that H. pylori Changes Genetically in Progression from Gastritis to Stomach Cancer
Researchers from Washington University in St. Louis, the United Arab Emirates University, Sweden’s Karolinska Institute, and the Swedish Institute for Infectious Disease Control used 454 sequencing and array-based transcriptional profiling to compare the dominant Helicobacter pylori strain in one patient before and after he developed stomach cancer.
Their findings, which appear online this week in the early edition of the Proceedings of the National Academy of Sciences, suggest H. pylori gene expression and cellular interactions change with disease progression.
“The degree of sequence change between the two strains was very modest,” senior author Jeffrey Gordon, director of the Center for Genome Studies at Washington University in St. Louis, told In Sequence’s sister publication GenomeWeb Daily News. Still, they were able to pinpoint several differences in the cancer-associated isolate.
His team sequenced the dominant H. pylori strain found in a patient’s stomach when he first underwent endoscopy as well as the strain present four years later when he had developed gastric cancer.
When they sequenced the coding regions of these isolates using a 454 GS 20 and compared them with three published H. pylori genomes, the researchers discovered subtle differences between the pre- and post- cancer genomes. Also, both lacked genes present in the reference strains.
They also looked at the effect of the gastric cancer H. pylori isolate on a mouse model of chronic atrophic gastritis. The H. pylori strain isolated when the patient had cancer did not colonize these mice as well. But it did invade mouse progenitor cells, something the pre-cancerous strain did not seem to do.
Using custom-designed Affymetrix microarrays, the team also compared gene expression between the H. pylori strains during mouse progenitor cell infection.
Taken together, it is still unclear whether H. pylori is casually or causally involved in cancer development.
— Abridged version of an article from GenomeWeb Daily News by Andrea Anderson

Applera Files to Separate ABI, Celera
Applera said last week that it has filed with the US Securities and Exchange Commission for the separation of Celera from the Applera Group.
The move, which was expected following recent comments from the management of both Applera and Celera that the board of directors of Applera favored separating the firms, is subject to a number of conditions. Applera must gain final board approval, SEC clearance of the registration statement, and receipt of an opinion of tax counsel as to the tax-free nature of the separation, before it closes the transaction. Applera shareholders are not required to approve the deal.
Under the terms of the separation, shareholders of the Applera Group-Celera Group tracking stock would receive one share of new Celera Corporation shares for each share of the tracking stock they currently own. Upon completion of the deal, Celera would become an independent, publicly traded company.
The firms expect Celera to trade on the Nasdaq under its current ticker symbol, CRA, while its current tracking stock would be delisted from the New York Stock Exchange. Celera President Kathy Ordoñez is expected to serve as CEO of the firm, which will be based in Alameda, Calif.
Applera Group-Applied Biosystems Group common stock will continue to trade on the New York Stock Exchange.
Last August, Applera announced that it had hired investment bank Morgan Stanley to conduct a review and advise the company on its options for restructuring the groups, including a possible split.
Speaking early this year at the JPMorgan Healthcare Conference, Ordoñez said that although a final decision had not yet been reached, Applera’s board of directors had recently stated its preference that the sister companies be split into two independent entities rather than remaining tracking stocks of Applera.
Ordoñez said that Applera’s goal would be to finalize the split by the end of its current fiscal year, which ends June 30. “We’re grown up now and prepared to go out on our own,” Ordoñez said, pointing to Celera’s guidance that it will be profitable for the second half of 2008.

Genomatix Tests Annotation Technology On Next-Gen Sequencing Dataset
Genomatix Software, a bioinformatics company based in Munich, Germany, said last week that it has tested its annotation software on a next-generation sequencing data set and has made the results available on its website.
Company researcher took Illumina sequencing data from a recent study that was published in Cell in January. The study, entitled “High-Resolution Mapping and Characterization of Open Chromatin across the Genome,” identified DNase I hypersensitive sites from primary human white blood cells, using both Illumina’s and 454’s sequencing platforms.
Genomatix applied its next-generation sequencing analysis pipeline to the Illumina data, which it retrieved from the Gene Expression Omnibus database, and published the results of its analysis on its website.

The Scan

Expanded Genetic Testing Uncovers Hereditary Cancer Risk in Significant Subset of Cancer Patients

In Genome Medicine, researchers found pathogenic or likely pathogenic hereditary cancer risk variants in close to 17 percent of the 17,523 patients profiled with expanded germline genetic testing.

Mitochondrial Replacement Therapy Embryos Appear Largely Normal in Single-Cell 'Omics Analyses

Embryos produced with spindle transfer-based mitochondrial replacement had delayed demethylation, but typical aneuploidy and transcriptome features in a PLOS Biology study.

Cancer Patients Report Quality of Life Benefits for Immune Checkpoint Inhibitors

Immune checkpoint inhibitor immunotherapy was linked in JAMA Network Open to enhanced quality of life compared to other treatment types in cancer patients.

Researchers Compare WGS, Exome Sequencing-Based Mendelian Disease Diagnosis

Investigators find a diagnostic edge for whole-genome sequencing, while highlighting the cost advantages and improving diagnostic rate of exome sequencing in EJHG.