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Center for the Advancement of Genomics, HP, Aventis, US Department of Energy, the Joint Genome Institute, Stanford University, Invitrogen, University of California, Sequenom, Lynx Therapeutics, Amersham, General Electric


Can Venter’s TCAG and HP Improve Genomics Tools?

The Center for the Advancement of Genomics and HP will collaborate to improve genome-sequencing technology, the groups said last week.

Initially, the partners plan to create a “genome-sequencing pipeline” based on TCAG software and HP hardware; reduce the cost and increase the throughput of genome sequencing and proteomics techniques; and collaborate with other research organizations to establish standards for data and tools and to develop open source technologies.

Specific terms of the agreement call for HP to provide TCAG with technology to support its IT infrastructure. In addition, engineers and researchers from HP Cambridge Research Lab will contribute to the collaboration, and HP Services will provide certain undisclosed technical support.

Australian Gov’t to Add AU$3 Million To Tammar Wallaby Sequencing Project

The government of Victoria, Australia, will add an additional AU$3 million ($2.2 million) to the sequencing project of the tammar wallaby, according to several Australian news outlets.

Victoria has already promised AU$1.5 million to fund the project, which is being managed by the Australian Genome Research Facility and the US National Institutes of Health.

Ardais Expands Aventis Agreement

Ardais has extended a research collaboration with Aventis that the companies began in 2002.

Terms of the original collaboration called for Aventis to grant access to Ardais’ BIGR library of clinical data and biomaterials. Under the expanded agreement, Ardais will use this platform in combination with immunohistochemistry profiling “to assess the potential of certain biological targets in the pharmaceutical company’s R&D pipeline.”

Ardais said it would use its technology to optimize validation assays and assist in the characterization of targets in panels of normal and diseased human tissues. Financial terms of the agreement were not disclosed.

DOE, JGI, Stanford Sequence Human Chromosome 19

The US Department of Energy, the Joint Genome Institute, and Stanford University have completed the sequencing of human chromosome 19, the groups said last week.

Among the genes encoded in chromosome 19 are genes for the diseases of insulin-dependent diabetes, myotonic dystrophy, migraines, and familial hypercholesterolemia.

The sequence of the chromosome, which was described in the April 1 issue of Nature, represents 2 percent of the genome’s base pairs but contains almost 1,500 genes. It is 500 times better in terms of contiguity and accuracy than previous draft human genome sequences, according to Stanford.

The DOE originally began the sequencing project in the 1990s because it contained DNA repair genes that could be useful in the agency’s bid to study the link between DNA damage from radiation and cancer. The project was transferred to the JGI and Stanford in 1999.

Genaissance Completes Acquisition of Lark

Genaissance Pharmaceuticals has completed its acquisition of Lark Technologies, the companies said last week.

As part of the terms of agreement, each outstanding share of Lark’s common stock will be exchanged for 1.81 shares of Genaissance stock. Genaissance last December announced its plan to acquire Lark for $19.9 million [see 1/1/04 SNPtech Pharmacogenomics Reporter].

Invitrogen Buys Protein Chip Maker Protometrix

Invitrogen has acquired protein microarray company Protometrix, the companies said last week.

Invitrogen said it will offer Protometrix’s first product, a yeast proteome chip, this summer. Protometrix started selling its Yeast ProtoArray chip last fall.

In addition, Invitrogen plans to introduce protein microarrays for analyzing human kinase interactions and activity in the second half of the year. Furthermore, the company intends to develop arrays for diagnostics, biomarkers and biodefense research, and testing drug interactions and side effects. Invitrogen hopes the acquisition will add $3 million to $5 million to its revenues this year.

Researchers to Study Genetic Variation in Drosophila Using Affy Resequencing Arrays

A consortium of researchers led by the University of California, Davis, has received a $4.9 million grant from the National Human Genome Research Institute to study genetic variation in 50 Drosophila melanogaster strains.

The consortium includes scientists from UC Davis, Johns Hopkins University, Children’s Hospital Oakland Research Institute, Emory University, and Affymetrix. Its researchers plan to re-sequence two large regions of the Drosophila genome using re-sequencing arrays from Affymetrix, and to develop methods to analyze the data.

All sequencing data will be made publicly available as it is generated, and all software developed for the project will be open-source. Affymetrix is providing its CustomSeq arrays, which it plans to commercialize, for the project under an early technology access program.

Sequenom Tech Used in Identification Of Novel Gene-Diabetes Association

An international team of researchers used Sequenom’s MassArray system to identify a novel association between the HNF4A gene and type 2 diabetes, the company said last week.

The study, published in the April 2004 issue of Diabetes, was conducted by a team from the United States, the United Kingdom, and Finland. It was led by National Human Genome Research Institute director Francis Collins as part of the Finland-United States Investigation of NIDDM Genetics study. In this study, also known as FUSION, researchers study sibling pair families from Finland in an effort to identify genetic variants that predispose to type 2 diabetes.

The group surveyed a set of families and found a high degree of linkage on chromosome 20, at 20q13. The group then used the MassArray to genotype SNP markers in this area in pools of case and controls. The strongest association proved to be with a SNP 1.3 kb downstream of the primary ß-cell promoter P2 of HNF4A. The researchers also found nine additional associated SNPS over 64 kb.

Lynx’s Revenues Fall, Loss Widens in Q4

Lynx Therapeutics last week posted falling revenues and increased losses for the last quarter of 2003.

Revenues for the period ended Dec. 31 fell to $2 million from $4.7 million one year ago.

R&D costs decreased to $2.4 million from $4.2 million during the year-ago period, as net loss increased to $3.5 million, or $.65 per share, from $3 million, or $.69 per share, during the fourth quarter of 2002. As of Dec. 31, Lynx had cash and cash equivalents of $5.6 million, including $700,000 million in restricted cash.

Amersham Will Become Part of GE on April 8; GE Plans Strategy Conference

General Electric will finalize its acquisition of Amersham on April 8, and will hold a teleconference on that day discussing how the British company will fit into GE’s new healthcare unit, the companies said last week.

Filed under

The Scan

New Study Investigates Genomics of Fanconi Anemia Repair Pathway in Cancer

A Rockefeller University team reports in Nature that FA repair deficiency leads to structural variants that can contribute to genomic instability.

Study Reveals Potential Sex-Specific Role for Noncoding RNA in Depression

A long, noncoding RNA called FEDORA appears to be a sex-specific regulator of major depressive disorder, affecting more women, researchers report in Science Advances.

New mRNA Vaccines Offer Hope for Fighting Malaria

A George Washington University-led team has developed mRNA vaccines for malaria that appear to provide protection in mice, as they report in NPJ Vaccines.

Unique Germline Variants Found Among Black Prostate Cancer Patients

Through an exome sequencing study appearing in JCO Precision Oncology, researchers have found unique pathogenic or likely pathogenic variants within a cohort of Black prostate cancer patients.