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BGI, PentaBase, SD Genomics, BioNanomatrix, International Sheep Genomics Consortium, Meat & Wool New Zealand, AgResearch, Ovita, DuPont, ABI, Illumina

BGI to Add 11 Illumina Analyzers, 3 454 GS FLX; Plans Service in Europe
The Beijing Genomics Institute is expanding its sequencing capacity by adding 14 next-generation sequencers, the institute said last week.
BGI said it has ordered 11 new Illumina Genome Analyzers and three 454 Genome Sequencer FLX instruments. The Institute already owns six Illumina sequencers, as well as 26 ABI 3730xl sequencers and 107 GE Healthcare MegaBace 1000 sequencers.
The purchases will bring BGI’s raw-sequencing data output capacity to at least 16 gigabases per day, and the institute will “significantly increase [its] ability to market new generation sequencing services to the community.”
BGI, which has more than 10,000 customers worldwide, is also planning to expand its service business. The institute has already set a up a US subsidiary and plans to enter the European market. Yang Shuang, general manager of sequencing, said in a statement that BGI is looking for “appropriate agents and cooperators in Europe” to expand there.

BGI, SD Genomics, PentaBase to Develop PCR-Based Dx Kits
The Beijing Genome Institute will collaborate with Danish companies PentaBase and SD Genomics to develop kits for detecting clinical biomarkers, PentaBase said this week.
PentaBase sells “proprietary technologies for genetic diagnostics,” including primers and probes for real-time PCR.

BioNanomatrix Lands $5.1M in Venture Financing
BioNanomatrix has secured $5.1 million in series A venture financing round, lead investor Battelle Ventures said last week.
BioNanomatrix is developing nanoscale single-molecule imaging and analytic platforms with applications in genome analysis and clinical diagnostics.
Besides Batelle, the funding round included investments from Battelle’s affiliate Innovation Valley Partners and KT Venture Group. Ben Franklin Technology Partners and 21 Ventures also participated in the round through debt conversion agreements.
In September, BioNanomatrix and partner Complete Genomics received an $8.8 million grant from the US National Institute of Standards and Technology to develop a high-throughput sequencing technology that they said will be able to sequence a human genome in eight hours for less than $100 (see In Sequence 10/2/2007).

Research Consortium Assembles Sheep Draft Genome Using Next-Gen Sequence Data
Meat & Wool New Zealand, AgResearch, and Ovita said this week that the International Sheep Genomics Consortium has sequenced the sheep genome to three-fold coverage, using next-generation sequencing, and has assembled a draft genome.
The ISGC is a collaboration between scientists from 16 countries, including Australia, New Zealand, the United States, and United Kingdom. So far, the project has generated more than 97 gigabases of sequence data from six sheep. The assembly was created by New Zealand and Australian researchers who are part of the consortium.
The sequence data was generated at Otago University in Dunedin and at the Human Genome Sequencing Center at Baylor College of Medicine within seven months and utilized next-generation sequencing methods.
AgResearch has been involved in sequencing strategy simulations, has generated sequence data using the Otago facility, has developed a database to store the sequences, and is undertaking sequence assembly and subsequent SNP detection in conjunction with Australian researchers.
By late 2009, the researchers want to map production traits to specific regions of the genome.

DuPont Submits Corn Fungus Sequence Data to GenBank
DuPont said this week that it is donating genome sequence data for a fungal pathogen that affects corn to GenBank.
DuPont’s Pioneer Hi-Bred business is releasing sequences of Colletotrichum graminicola. The fungus causes anthracnose leaf blight and stalk rot, which leads to reduced corn yield worldwide due to premature death and weakened stalk strength, the company said.
Making this information publicly available will help researchers complete the genomic sequence of the pathogen, which could help to speed up disease-resistance studies, the company said.
The US Department of Agriculture’s Cooperative State Research, Education, and Extension Service currently is mapping and sequencing a different strain of the pathogen through a collaboration with the Broad Institute.

ABI, Illumina to Compare Next-Gen Sequencers In Subway Rat Genome Project
Researchers at Illumina and Applied Biosystems, in collaboration with New York City's Metropolitan Transit Authority, will compare their next-generation sequencing platforms in a project to sequence the subway rat, Rattus norvegicus indestructibus, a cousin of the common lab rat.
"Those wimpy, pampered lab rats wouldn't survive five minutes in this city," said Rockefeller researcher Duane St. Patrick, a collaborator in the project. "They'd get fried on the third rail of the subway track. But New York rats run up and down those rails."
At a press conference announcing the project, New York Mayor Michael Bloomberg concurred: "One time on 14th Street I saw a rat jump five feet off the platform, grab a whole bagel out of a woman's hand, and run away with the bagel in its mouth — even the cream cheese. This is a serious public health issue for the city."
The project, which will make all sequence data immediately available to the public, will look for SNPs as well as structural variations that may be key to the extremophile-like survival skills of R. norvegicus indestructibus. Among the potentially hereditary behaviors to be probed are the animal's ability to consume and digest large quantities of lead paint chips, to survive underwater for 20 minutes, and to fall over 150 feet without skeletal damage. In addition, females are known for their ability to shorten their gestation period to less than 24 hours if environmental conditions warrant.
The Subway Rat Genome Project will be funded with proceeds from a 50-cent increase in fares for subway riders which, as usual, New Yorkers are expected to accept without protest.
The study is scheduled to take six months, with only the last few weeks set aside for sequencing and data analysis. Says St. Patrick: "The hard part is catching one, and we want to make sure we have several months in which to do that."

— Original version published on GenomeWeb Daily News on April Fool’s Day 2004

The Scan

Genome Sequences Reveal Range Mutations in Induced Pluripotent Stem Cells

Researchers in Nature Genetics detect somatic mutation variation across iPSCs generated from blood or skin fibroblast cell sources, along with selection for BCOR gene mutations.

Researchers Reprogram Plant Roots With Synthetic Genetic Circuit Strategy

Root gene expression was altered with the help of genetic circuits built around a series of synthetic transcriptional regulators in the Nicotiana benthamiana plant in a Science paper.

Infectious Disease Tracking Study Compares Genome Sequencing Approaches

Researchers in BMC Genomics see advantages for capture-based Illumina sequencing and amplicon-based sequencing on the Nanopore instrument, depending on the situation or samples available.

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.