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NCGR, Solexa, Daphnia Genomics Consortium, LI-COR, Aloka, Washington University, Philips Research, GeneGo

NCGR Begins Offering Solexa Sequencing Services
The National Center for Genome Resources said this week that it is now offering Solexa sequencing on Illumina's Genome Analyzer, as well as pipelining analysis services based on its next-gen sequencing analysis and visualization software, called Alpheus.
In addition to Solexa sequencing, NCGR will offer pipelining services that are designed for "very large" next-generation sequencing projects and enable clients to view and analyze sequence alignments, nucleotide variants, and splice isoforms, as well as compare samples securely over the web.
NCGR purchased the system with a $600,000 grant from the state of New Mexico to create a sequencing facility under a collaboration with the New Mexico Institute of Mining and Technology (see In Sequence 1/9/2007).
As In Sequence reported last month, NCGR considered purchasing Roche’s 454 FLX, ABI’s SOLiD, and Illumina’s Genome Analyzer before opting for the Illumina system (see In Sequence 6/26/2007)
Greg May, a program leader at NCGR who is in charge of building the sequencing facility, told In Sequence at the time that NCGR sent the companies a brain RNA sample to sequence.
“For our needs [with regard to] timeframe and availability, we have chosen the Solexa [sequencer] as our technology platform for our first instrument purchase,” May said.
Financial terms of the agreement with Illumina were not released.
According to literature on the NCGR website, the turnaround time for sequencing a human genome is two weeks. NCGR did not disclose pricing.
Further information about the services offering is available here.  

Daphnia Genomics Consortium Releases Initial Data
The Daphnia Genomics Consortium has released an early-access version of the genome of the arthropod crustacean Daphnia pulex, or water flea, via the Joint Genome Institute’s Genome Portal
The DGC said last month it plans to publish the genome data and submit it in Genbank between fall 2007 and spring 2008.
The JGI portal provides gene predictions and homology reports, with services for Blast searches and bulk data downloads.
The terms of pre-publication use of the genome data are available here.  

LI-COR, Aloka End Japanese Distribution Pact; LI-COR Taps M&S for New Agreement
LI-COR Biosciences and Aloka said this week that their distribution agreement for LI-COR’s sequencers and other products in Japan ends as of Aug. 31, 2007. The companies began the partnership in 1993.
“This decision reflects the strategic direction of both companies and enables Aloka to concentrate on its own product line,” the firms said in a statement.
LI-COR said that has appointed M&S TechnoSystems to distribute its products and provide all customer service and support in Japan effective Sept. 1.

Wash U Researcher Gains Funding from National Geographic Society to Study Coconut Genetics
Kenneth Olsen, an assistant professor of biology at Washington University, has received a $20,000 grant from the National Geographic Society to study the genetics of the coconut (Cocos nucifera L.).
The work will be done in collaboration with Bee Gunn, a research specialist at the Missouri Botanical Garden.
"Our preliminary DNA sequence data show genetic variation within the coconut, and this is key to delineating historical relationships among different populations,” Olsen said in a statement.
"Fossil data indicate that the coconut underwent an ancient dispersal event that predates human activity. This early dispersal is expected to have created a genetic signature that can be traced by examining the genetic structure of plants sampled across the species range."
Olsen will study the phylogeography of C. nucifera and its ancient dispersal; the geographical origins of domestication; the impact of human activities in homogenizing population structure across the species range; and the possible geographical location of the undomesticated wild progenitor populations.

Philips Research Licenses GeneGo's MetaCore Platform
Philips Research has licensed GeneGo’s MetaCore pathway analysis software platform, GeneGo said last week.
The MetaCore suite is used for functional analysis of experimental data, including information from serial analysis of gene expression, SNP and comparative genomic hybridization arrays, proteomics, metabolomics, and other interactions.
Financial terms of the agreement were not disclosed.

The Scan

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.

Analysis of Endogenous Parvoviral Elements Found Within Animal Genomes

Researchers at PLOS Biology have examined the coevolution of endogenous parvoviral elements and animal genomes to gain insight into using the viruses as gene therapy vectors.

Saliva Testing Can Reveal Mosaic CNVs Important in Intellectual Disability

An Australian team has compared the yield of chromosomal microarray testing of both blood and saliva samples for syndromic intellectual disability in the European Journal of Human Genetics.

Octopus Brain Complexity Linked to MicroRNA Expansions

Investigators saw microRNA gene expansions coinciding with complex brains when they analyzed certain cephalopod transcriptomes, as they report in Science Advances.