2012 LEGACY SITE:
Chinese Hamster
Genome Database

Visit www.esact2013.com for more details.

The CHOgenome.org workshop was titled "The www.CHOgenome.org Resource for the International CHO Biotechnology Community?" The workshop included presentations on current applications of genome scale information, where it is useful, and how has it helped in different research efforts, followed by discussion on the next steps for the cell culture community surrounding the CHO Genome effort.

Additional information can be found here.

The international community's effort was recognized at the 2012 Bioprocess International Awards ceremony in Providence, RI, held on October 9th, 2012. CHOgenome.org was nominated as one of three finalists for the Upstream Collaboration of the Decade Award. "The Collaboration of the Decade Award recognizes industry alliances and collaborations whose innovative partnerships dramatically transformed stand-alone technologies. These collaborations result in overall process cost reduction while creating new, effective approaches to biopharmaceutical design, development, and manufacturing."

We are grateful and would like to recognize the support and engagement of the broad international community in the sequencing of CHO and related genomes to improve bioprocessing.

Functional genomics in cell culture technology: from sequence to function and application

An update regarding recent advances in genomics and functional genomics in cell culture technology, including transcriptomics, proteomics, metabolomics and other innovative technologies.

Visit www.esf.org/conferences/12405 for more information.

An update on the community's efforts at CHOgenome.org and an interactive workshop to demonstrate the web tools.

Visit www.ibclifesciences.com/CellLine/overview.xml for more information.

Visit www.engconfintl.org/12ac.html for more information.

Omics Workshop Summary

Over 170 participants attended the workshop led by Susan Sharfstein, Kelvin Lee, and Mike Betenbaugh. The workshop opened with an overview of genome-scale technologies applicable to CHO cells such as expression profiling, proteomics, and metabolomics. This was followed by an overview of the tools being developed at www.CHOgenome.org and presentation of case study examples of how to use these tools. The workshop concluded with an interactive discussion of next steps for the CHO community.

Visit www.esact2011.com for more information.

CHO Genome Workshop Summary

The CHO genome workshop, with more than 220 participants, opened with three talks describing the generation of draft genome sequences for several CHO cell lines and the Chinese hamster followed by three talks demonstrating how this information can be leveraged in metabolic and transcriptomic studies to aid in cell line engineering.

The talks included:

• Bernhard Palsson described the draft genome of CHO-K1 and a comparative genomic analysis of six additional CHO cell lines.
• Bernard Loo presented a draft genome assembly and annotation of the Chinese hamster and outlined efforts to identify transcriptional start sites and regulatory elements.
• Nicole Borth described a draft genome assembly of the Chinese hamster by integrating multiple NGS technologies and efforts to identify and annotate splice variants.
• Iman Famili described the application of a metabolic model for CHO cells in media optimization and development of novel vector systems.
• Colin Clarke presented a model to predict CHO cell productivity based on gene expression profiles of temperature-shifted CHO cell lines.
• Jeoffrey Schageman described a comparative transcriptomic analysis of CHO cells lines under varying culture conditions that can identify gene co-expression patterns.

After the workshop, Mike Betenbaugh and Kelvin Lee led a discussion of the development of and the next steps for the CHO community-based website, www.CHOgenome.org.

Visit www.genomeconference.org for more information.

November 17, 2010 was the day that the Chinese hamster ovary cell community entered the genome era!

CHO Genome Workshop Summary

The workshop opened with remarks from Kelvin Lee who gave a history of how the community came together and Bernhard Palsson who provided context on the use of CHO cells in the biotechnology industry.

The talks included:

• Xu Xun gave the first ever detailed description of the CHO K1 genome and described many features of the CHO genome.
• Takeshi Omasa provided an overview of physical mapping and karyotyping efforts on CHO, highlighting the dynamic nature of the chromosomes.
• Steve Quake discussed efforts to characterize the CHO exome using a variety of techniques and assembly of these data in the context of mouse data.
• Nicole Borth presented an analysis of CHO microRNA including some possibly new microRNAs that have not been reported previously.
• Gyun-Min Lee gave a detailed overview of the use of proteomic methods to characterize CHO cells and particular CHO phenotypes of interest.
• Lars Nielsen provided an important description of how genome-scale flux analysis models can be developed - something that is now possible with a CHO genome.
• Bernhard Palsson then discussed specific aspects of the CHO K1 genome included a coarse-grained analysis (relative to mouse, rat, human), a functional analysis (glycosyltransferases and viral susceptibility genes), and individual genes (p53 and EGFR).

Finally, Mike Betenbaugh and Kelvin Lee led a discussion of next steps for our community. These include the importance of sequencing the hamster and other cell lines as well as having a simple framework for the community to interact with these data.

Pictures from the Conference