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Applied Biosystems, NCBI, Northwestern University, US Senate, NIH, Roche NimbleGen, Affymetrix, University of Copenhagen, CLC Bio

ABI Sequences Human Genome with SOLiD, Submits Data to NCBI
Applied Biosystems said last week that it has sequenced a human genome at 12-fold coverage for less than $60,000 in reagent costs and has submitted the data to the National Center for Biotechnology Information.
ABI scientists sequenced the genome of an anonymous African male of the Yoruba people of Ibadan, Nigeria, who participated in the International HapMap Project (see In Sequence 2/26/2008).
They generated 36 gigabases of sequence data in seven runs on the SOLiD system, 3.5 fragment runs and 3.5 paired-end runs, resulting in 12-fold coverage of the genome.
The company said the researchers were able to “confidently identify” millions of SNPs, and to analyze structural variations.
ABI said that it expects the public availability of the data “will help drive innovation and speed the development of new bioinformatics tools.”
In addition to the full human dataset, ABI said it has also submitted subsets of the sequence data to NCBI. The datasets, which are available here, “can be accessed by independent academic and commercial software developers to further enable the development of analytical tools.”
The company has also released an analysis tool through the SOLiD System Software Development Community to help researchers analyze the data.

Northwestern University Center to Buy ABI SOLiD Sequencer
Northwestern University said earlier this month that a benefactor has donated $600,000 to the school’s Robert H. Lurie Comprehensive Cancer Center and the Center for Genetic Medicine so it can purchase a SOLiD sequencer from Applied Biosystems.
According to a statement by the university, Chicago philanthropist Ann Lurie, who is also the widow of Robert Lurie, donated the funds for the ABI SOLiD sequencer. The Center for Genetic Medicine intends to use the system to study genetic variations associated with type-2 diabetes and asthma.

Senate Passes Resolution that Could Raise NIH Budget by $2.1B
The US Senate late last week passed a resolution that would add $2.1 billion to the White House’s proposed National Institutes of Health budget for 2009.
Senators Arlen Specter (R – Pa.) and Tom Harkin (D – Iowa) added the extra funds to the President’s proposed $29.5 billion through an amendment to a budget resolution that will set the limits on the spending frame for an upcoming debate on the 2009 budget.
“The funding for the National Institutes of Health is grossly insufficient,” Specter said in a statement. “This increase in funding will enable the National Institutes of Health to continue to produce remarkable achievements in scientific advances,” he added.
The amendment passed the Senate by a vote of 95 to 4, although the budget resolution itself passed by a smaller margin of 51 to 44.

Roche NimbleGen, Affymetrix Expand Microarray IP Agreement
Roche NimbleGen said last week it has expanded a patent license agreement with Affymetrix to include diagnostic rights to array-based DNA analysis and array-based re-sequencing.
NimbleGen and Affymetrix originally agreed to the patent license, which gave NimbleGen the rights to patents related to the manufacture, use, and sale of nucleic acid microarrays, in October 2006. When Roche purchased NimbleGen last June for $272 million, the licensing rights were transferred to Roche NimbleGen.
Roche NimbleGen makes high-density arrays of long oligo probes used in studying genomic and epigenomics variation.

University of Copenhagen Licenses CLC Bio's Software
The University of Copenhagen has bought a site license for CLC Bio’s Combined Workbench and Educational Suite software platforms, CLC Bio said last week.
Under the agreement, the department of biology at the university has licensed access to the software for five years for “several hundred seats,” the company said.
The university’s genomics projects include retrieving DNA from fossils, gene regulation and SNP cancer research, primate genome evolution, bacterial genome sequencing, and other programs.

The Scan

LINE-1 Linked to Premature Aging Conditions

Researchers report in Science Translational Medicine that the accumulation of LINE-1 RNA contributes to premature aging conditions and that symptoms can be improved by targeting them.

Team Presents Cattle Genotype-Tissue Expression Atlas

Using RNA sequences representing thousands of cattle samples, researchers looked at relationships between cattle genotype and tissue expression in Nature Genetics.

Researchers Map Recombination in Khoe-San Population

With whole-genome sequences for dozens of individuals from the Nama population, researchers saw in Genome Biology fine-scale recombination patterns that clustered outside of other populations.

Myotonic Dystrophy Repeat Detected in Family Genome Sequencing Analysis

While sequencing individuals from a multi-generation family, researchers identified a myotonic dystrophy type 2-related short tandem repeat in the European Journal of Human Genetics.