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Short Reads: Mar 3, 2009


Febit Joins READNA Consortium

Febit said this week that it is joining the Revolutionary Approaches and Devices for Nucleic Acid, or READNA, project, a consortium funded with €12 million ($15 million) from the European Union (see In Sequence 12/9/2009).

The company plans to use its HybSelect sequence capture technology in READNA projects.

Specifically, Febit plans to adapt HybSelect for specific applications in next-generation sequencing for a research group at the Centre National de Génotypage near Paris that participates in READNA.

The company also said it will "soon" launch its HybSelect technology "in several markets."

Complete Genomics to Analyze Glioblastoma, Melanoma Samples for Broad Institute

Complete Genomics will sequence glioblastoma and melanoma samples for the Broad Institute as part of a pilot study the company announced last month (see In Sequence 2/10/2009).

For the project, Complete Genomics will use its DNA sequencing technology to sequence five samples provided by the Broad Institute. The first genome will be a sample that has already been studied extensively by the scientific community. The other four genomes will be a glioblastoma and a melanoma sample and their matched normal controls.

EnGenCore Offering 454 Titanium Sequencing Services

Service provider EnGenCore said last week that it is now offering 454 sequencing services using the Titanium long-read chemistry.

EnGenCore said it will begin offering amplicon sequencing, 16S RNA sequencing, and barcoding using Titanium this summer. In the interim, the company will continue to offer these applications using the old GS FLX chemistry.

EnGenCore was founded last September as a spin-off from the University of South Carolina to provide additional sequencing capacity for the Environmental Genomics Core facility, which is located within the Public Health Research Center at the Columbia, SC, campus.

The sequencing laboratory is a public-private partnership between the Arnold School of Public Health and EnGenCore. It provides sequencing services for academic and commercial research as well as for regulated environments. EnGenCore has received a university start-up assistance grant from SC Launch.

Evolutionary Genetics Conference to Focus on Impact of Next-Gen Sequencing

This year's spring meeting of the German Genetics Society will focus on the impact of next-generation sequencing technologies.

The meeting, organized by Diethard Tautz at the Max-Planck-Institute for Evolutionary Biology and Wolfgang Stephan at the University of Munich will take place April 2-4 in Wittenberg, Germany.

More information about the meeting can be found here.

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Einstein College Licenses CLC Bio Software for Analyzing Sequence Data

Researchers at Albert Einstein College of Medicine will use two CLC Bio software platforms in its epigenomics and other research programs under a new site license agreement, the Danish company said this week.

CLC Bio said that the College's Einstein Center for Epigenomics will use its Genomics Workbench and its Genomics Server to handle data it generates in its high-throughput sequencing programs.

John Greally, director of the Bronx, NY-based Einstein Center for Epigenomics, said in a statement that the software will enhance the researchers' ability to explore massively parallel sequencing data being generated at the center. He added that using the software platforms is "a way of lowering barriers for scientists who have not previously performed these high-throughput epigenomics assays, allowing them to explore their data and explore hypotheses."

The two CLC Bio platforms can be used to analyze and visualize data from Applied Biosystems' SOLiD, Illumina's Genome Analyzer, Roche 454's Genome Sequencer, and Helicos' HeliScope system.

Boehringer Ingelheim to Use Genomatix Software for Sequencing Studies

Genomatix said this week that Boehringer Ingelheim has installed a Genomatix Mining Stations (GMS) and a Genomatix Genome Analyzer at its Pharma Research Center in Biberach, Germany.

The company said the two systems combine hardware, databases, and software for next-generation sequencing studies.

The GMS provides mapping of sequencing of any length, "with no practical limits on the number of point mutations, insertions, or deletions," and can be used for SNP detection and genotyping, copy number analysis, small RNA analysis, ChIP-Seq, and RNA-Seq. The package includes a GenomeThesaurus for splice junction analysis and identifying new transcriptional units.

The GGA is used to perform a number of deep biological analysis functions on data coming from the GMS, and annotates genomic coordinates and surrounding areas derived using the GMS or other mapping procedures.

Methylation Patterns Provide Hints about Cancer Expansion

In a paper scheduled to appear online this week in PNAS, scientists used DNA methylation patterns to gauge what happens during cancer-related cellular expansions, as a lone cancerous cell progresses to become a tumor containing billions of cells.

Researchers from the University of Southern California and the University of Cambridge used bisulfite sequencing to measure methylation in colorectal cancers taken from a dozen men, and compared methylation patterns at two genomic sites in samples taken from different regions of each patient's tumor. They saw similar methylation patterns from opposite sides of the same tumors, suggesting they arose via so-called isotropic or "flat" clonal expansion — in a rapid burst — rather than by sequential expansion.

The overall approach is based on the idea that methylation and demethylation errors arise during cell division, similar to DNA point mutations. "Although this assumption has not been directly tested, DNA methylation appears to require cell division," the researchers explained, "and methylation patterns in the normal human colon are consistent with such replication errors."

The researchers also did computer simulations to try to figure out how many long-lived cancer stem cell lineages there are in the tumors. Their results suggest that the tumors tested likely didn't spring from rare cancer stem cells, but rather from several more common stem cell lineages.

At the moment, the scientists are looking at metastatic colorectal cancers to see whether there are similarities or differences in methylation patterns, compared to those observed in tumors in this study. Such work could provide new insights into tumor characteristics and diversity and could improve researchers' understanding of what makes chemotherapy effective in some cases and ineffective in others.

By Andrea Anderson; originally published on GenomeWeb Daily News