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  <title>Publication Announcements</title>
  <link>http://www.bcgsc.ca</link>

  <description>
    
      Recent scientific publications and software releases from the Michael Smith Genome Sciences Centre. For a more complete list of  publications by principal investigator, please visit the individual Faculty pages.
    
  </description>

  

  
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            <syn:updateBase>2010-04-28T22:54:07Z</syn:updateBase>
        

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        <rdf:li rdf:resource="http://www.bcgsc.ca/about/pubann/published-july-27th-in-nature"/>
      
      
        <rdf:li rdf:resource="http://www.bcgsc.ca/about/pubann/human-t-cell-repertoire-analysis-1"/>
      
      
        <rdf:li rdf:resource="http://www.bcgsc.ca/about/pubann/moving-the-field-of-clinical-genomics-toward-a-future-of-more-effective-diagnosis-and-treatment-of-cancers"/>
      
      
        <rdf:li rdf:resource="http://www.bcgsc.ca/about/pubann/alternative-expression-analysis-by-rna-sequencing"/>
      
      
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        <rdf:li rdf:resource="http://www.bcgsc.ca/about/pubann/regression-of-castrate-recurrent-prostate-cancer-by-a-small-molecule-inhibitor-of-the-amino-terminus-domain-of-the-androgen-receptor"/>
      
      
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        <rdf:li rdf:resource="http://www.bcgsc.ca/about/pubann/the-completion-of-the-mammalian-gene-collection-mgc"/>
      
      
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  <item rdf:about="http://www.bcgsc.ca/about/pubann/published-july-27th-in-nature">
    <title>Published July 27th in Nature</title>
    <link>http://www.bcgsc.ca/about/pubann/published-july-27th-in-nature</link>
    <description>BC Cancer Agency Researchers from the Michael Smith Genome Sciences Centre and The Centre for Lymphoid Cancer published recent results from the NIH-funded research project: Sequencing for Discovery of Candidate Mutations in Lymphoma Transcriptomes</description>
    <content:encoded xmlns:content="http://purl.org/rss/1.0/modules/content/"><![CDATA[<h1>Sequencing for Discovery of Candidate Mutations in Lymphoma Transcriptomes</h1>
<p>This research project is led by Drs. <a href="../../faculty/mmarra">Marco Marra</a>, <a href="http://www.bccrc.ca/dept/cflr/personnel/randy-gascoyne">Randy Gascoyne</a> and <a href="http://www.bccrc.ca/dept/cflr/personnel/joseph-m.-connors">Joseph Connors</a>.</p>
<p><a href="../../project/lymphoma-transcriptome-sequencing-and-analysis">The project</a> involves identifying and characterizing the range of  mutations found in lymphoma tumours. Once identified, specific mutations  may be shown to effect or be associated with response to treatment,  patient outcome and survival, or be useful as a target for anti-cancer  drug development.</p>
<p>The most recent publication by this large research team can be found on-line in the prestigious journal Nature.  The full citation and link to the published journal article is below:</p>
<p><b>Frequent mutation of histone-modifying genes in non-Hodgkin lymphoma</b>. 2011. <a href="http://www.nature.com/nature/journal/vaop/ncurrent/full/nature10351.html"><b>Nature</b> (Published online 27 July 2011; doi:10.1038/nature10351)</a> Ryan D. Morin, Maria Mendez-Lago, Andrew J. Mungall, Rodrigo Goya, Karen L. Mungall, Richard D. Corbett, Nathalie A. Johnson, Tesa M. Severson, Readman Chiu, Matthew Field, Shaun Jackman, Martin Krzywinski, David W. Scott, Diane L. Trinh, Jessica Tamura-Wells, Sa Li, Marlo R. Firme, Sanja Rogic, Malachi Griffith, Susanna Chan, Oleksandr Yakovenko, Irmtraud M. Meyer, Eric Y. Zhao, Duane Smailus, Michelle Moksa, Suganthi Chittaranjan, Lisa Rimsza, Angela Brooks-Wilson, John J. Spinelli, Susana Ben-Neriah, Barbara Meissner, Bruce Woolcock, Merrill Boyle, Helen McDonald, Angela Tam, Yongjun Zhao, Allen Delaney, Thomas Zeng, Kane Tse, Yaron Butterfield, Inanç Birol, Rob Holt, Jacqueline Schein, Douglas E. Horsman, Richard Moore, Steven J. M. Jones, Joseph M. Connors, Martin Hirst, Randy D. Gascoyne &amp; Marco A. Marra</p>]]></content:encoded>
    <dc:publisher>No publisher</dc:publisher>
    <dc:creator>Stephanie McInnis</dc:creator>
    <dc:rights></dc:rights>
    <dc:date>2011-07-28T01:46:46Z</dc:date>
    <dc:type>News Item</dc:type>
  </item>


  <item rdf:about="http://www.bcgsc.ca/about/pubann/human-t-cell-repertoire-analysis-1">
    <title>Human T-cell repertoire analysis</title>
    <link>http://www.bcgsc.ca/about/pubann/human-t-cell-repertoire-analysis-1</link>
    <description></description>
    <content:encoded xmlns:content="http://purl.org/rss/1.0/modules/content/"><![CDATA[<p><span>T-cell receptors, like antibodies, are encoded by genes that undergo random somatic recombination to generate sequence diversity and consequently structural diversity.  The structural diversity of the T-cell receptor allows T-cells to recognize an enormous number of foreign antigens. In this study, scientists at the Genome Sciences Centre have profiled to an unprecedented depth the repertoire of rearranged T-cell receptor beta chain sequences in the peripheral blood of three healthy individuals. They obtained over one million distinct T-cell receptor nucleotide sequences from a single individual which establishes a new, directly measured lower limit on individual T-cell repertoire size and provides a useful reference set of sequences for repertoire analysis.  A key observation is that there is much higher sharing of specific T-cell receptor sequences among individuals than expected by chance, and these shared sequences show a strong signature of selection, where a given amino acid sequence may be encoded by multiple different nucleotide sequences. The study also presents an analysis of the impact of sequencing error on repertoire analysis, and reports an error handling strategy that will be important for understanding future deep sequencing studies of immune repertories.  Ongoing work involves characterization of immune repertoire changes in response to immune challenges from, for example, cancer, autoimmune disease, and bone marrow transplant and vaccination.</span></p>
<p><span><br />René L. Warren<sup>1</sup>, J. Douglas Freeman<sup>1</sup>, Thomas Zeng<sup>1</sup>, Gina Choe<sup>1</sup>, Sarah Munro<sup>1</sup>, Richard Moore<sup>1</sup>, John R. Webb<sup>2</sup>, Robert A. Holt<sup>1,3</sup>.  2011. Exhaustive T-cell repertoire sequencing of human peripheral blood samples reveals signatures of antigen selection and a directly measured repertoire size of at least 1 million clonotypes.  Genome Research. doi:10.1101/gr.115428.110<br /><sup>1</sup>BC Cancer Agency, Michael Smith Genome Sciences Centre, 675 West 10th Avenue, Vancouver, BC V5Z 1L3 Canada </span></p>
<p>
<p><sup>2</sup>BC Cancer Agency, Deeley Research Centre, 2410 Lee Ave, Victoria, BC V8R 6V5 Canada</p>
<p><sup>3</sup>Department of Molecular Biology and Biochemistry, Simon Fraser University, Burnaby, British Columbia, Canada</p>
<p> </p>
<p>Further details of this publication can be found online at:</p>
<p> </p>
<p> <a href="http://genome.cshlp.org/content/early/2011/02/23/gr.115428.110.abstract">http://genome.cshlp.org/content/early/2011/02/23/gr.115428.110.abstract</a></p>
<p> </p>
</p>]]></content:encoded>
    <dc:publisher>No publisher</dc:publisher>
    <dc:creator>Kandyce Betts</dc:creator>
    <dc:rights></dc:rights>
    <dc:date>2011-03-08T00:25:00Z</dc:date>
    <dc:type>News Item</dc:type>
  </item>


  <item rdf:about="http://www.bcgsc.ca/about/pubann/moving-the-field-of-clinical-genomics-toward-a-future-of-more-effective-diagnosis-and-treatment-of-cancers">
    <title>Moving the field of clinical genomics toward a future of more effective diagnosis and treatment of cancers.</title>
    <link>http://www.bcgsc.ca/about/pubann/moving-the-field-of-clinical-genomics-toward-a-future-of-more-effective-diagnosis-and-treatment-of-cancers</link>
    <description>Scientists and engineers from BC Cancer Agency’s Genome Sciences Centre (GSC) have developed two new approaches for characterizing how the information in genes is expressed. Details of each method, known as ALEXA-Seq and Trans-ABySS, were recently published in separate papers in the journal Nature Methods. Each approach uses state-of-the-art sequencing technology to characterize transcriptomes—collections of all expressed genes. Both methods represent significant steps towards cost-effective surveying of all genetic information in a tumour.</description>
    <content:encoded xmlns:content="http://purl.org/rss/1.0/modules/content/"><![CDATA[
<p>The paper <a href="http://www.nature.com/nmeth/journal/v7/n10/full/nmeth.1503.html">“Alternative expression analysis by RNA sequencing”</a>, published in September, describes the <a href="http://www.alexaplatform.org/">ALEXA-seq analysis system</a>. Most genes can be expressed as RNA in several different ways or ‘isoforms’, each of which makes a distinct version of a protein. ALEXA-seq sensitively detects isoforms within individual genes. The researchers proved the method’s value by identifying isoforms that were specific to chemotherapy-resistant colon cancer cells. This type of highly detailed information will provide a roadmap of the cancer, pointing to distinct proteins involved in the growth and development of its cells.</p>
<div class="photo right">
<a href="http://www.alexaplatform.org/"><img src="../alexa_icon.jpg//image_preview" alt="ALEXA icon" height="195" /></a>
<p><strong>ALEXA</strong>: <strong>Al</strong>ternative <strong>Ex</strong>pression <strong>A</strong>nalysis</p>
</div>
<p>“Cancer is an umbrella term for thousands of distinct diseases, “ says <a href="../../faculty/mmarra">Marco Marra</a>, PhD, director, BC Cancer Agency Genome Sciences Centre. “Now we have entered an era where we can economically characterize all of the types and sub-types that fall under this massive cancer umbrella.” Marra adds, “We are already applying the ALEXA-seq approach to characterize breast cancer, multiple myeloma, lymphoma, leukemia, and other cancer types. With the knowledge gained we can propel development of personalized treatment.”</p>
<p>The research paper <a href="http://www.nature.com/nmeth/journal/vaop/ncurrent/abs/nmeth.1517.html">“De novo assembly and analysis of RNA-seq data”</a>, published today in Nature Methods, describes <a href="../../platform/bioinfo/software/trans-abyss">Trans-ABySS</a>, an approach that is highly effective in identifying novel RNA molecules—the coding mechanism for proteins. The challenge was to develop a method that could correctly reconstruct thousands of RNA sequences from short sequence reads. “With Trans-ABySS, we showed how to use assembly to reconstruct a challenging genetic jigsaw puzzle accurately from millions of tiny pieces,” says <a href="../../faculty/inanc-birol">Inanc Birol</a>, PhD, bioinformatics group leader, BC Cancer Agency Genome Sciences Centre. The team has shown that Trans-ABySS can detect known isoform irregularities in non-Hodgkin lymphoma, and are now applying the approach to survey a wider range of cancer types.</p>
<p>Both methods are able to detect isoforms that do not normally occur in human tissues, but, are found in cancerous tissue. If isoforms could be described efficiently in large numbers of patients, in particular types and subtypes of cancers, the resulting knowledge could be used to develop new drugs, and to predict how an individual patient should respond to particular drugs.</p>
<p>The rapid evolution of sequencing and computer systems have made it practical to comprehensively and efficiently produce a snapshot of entire transcriptomes, and is allowing the field of ‘clinical genomics’ to emerge. Because the human genome is large and transcriptomes are complex, developing efficient computational analysis methods remains central to progress in this area. ALEXA-seq and Trans-ABySS represent advances towards more cost-effective and efficient methods for surveying the isoforms in a tumor in order to identify those that are specific to a cancer or are associated with a particular clinical outcome.</p>
<h3>Research Paper Citations:</h3>
<p><strong>Alternative expression analysis by RNA sequencing.</strong> Griffith M, Griffith OL, Mwenifumbo J, Goya R, Morrissy AS, Morin RD, Corbett R, Tang MJ, Hou YC, Pugh TJ, Robertson G, Chittaranjan S, Ally A, Asano JK, Chan SY, Li HI, McDonald H, Teague K, Zhao Y, Zeng T, Delaney A, Hirst M, Morin GB, Jones SJ, Tai IT, Marra MA. <a href="http://www.nature.com/nmeth/journal/v7/n10/full/nmeth.1503.html">Nat Methods. 2010 Oct;7(10):793-5.</a></p>
<p><strong>De novo assembly and analysis of RNA-seq data.</strong>Robertson G, Schein J, Chiu R, Corbett R, Field M, Jackman SD, Mungall K, Lee S, Okada HM, Qian JQ, Griffith M, Raymond A, Thiessen N, Cezard T, Butterfield YS, Newsome R, Chan SK, She R, Varhol R, Kamoh B, Prabhu AL, Tam A, Zhao Y, Moore RA, Hirst M, Marra MA, Jones SJ, Hoodless PA, Birol I. <a href="http://www.nature.com/nmeth/journal/vaop/ncurrent/full/nmeth.1517.html">Nat Methods. 2010 Oct 10.</a> [Epub ahead of print]</p>
<h3>Acknowledgements:</h3>
<p>ALEXA-seq research team acknowledges the financial support received from the <a href="http://www.ubc.ca/">University of British Columbia</a>, <a href="http://www.msfhr.org/">the Michael Smith Foundation for Health Research</a>, <a href="http://www.nserc-crsng.gc.ca/index_eng.asp">the Natural Sciences and Engineering Research Council</a>, <a href="http://www.genomebc.ca/">Genome British Columbia</a>, <a href="http://www.terryfox.org/Foundation/">the Terry Fox Foundation</a>, <a href="http://www.cihr-irsc.gc.ca/e/193.html">the Canadian Institutes of Health Research</a>, <a href="http://www.cancer.ca/Canada-wide/Cancer%20research.aspx?sc_lang=en">the National Cancer Institute of Canada</a> and the <a href="http://www.bccancerfoundation.com/cms/index.cfm">BC Cancer Foundation</a>.</p>
<p>Trans-ABySS research team acknowledges the support received from <a href="http://www.genomecanada.ca/">Genome Canada</a>, <a href="http://www.genomebc.ca/">Genome British Columbia</a> and the <a href="http://www.cihr-irsc.gc.ca/e/193.html">Canadian Institute of Health Research (CIHR)</a>, including the <a href="http://bioinformatics.bcgsc.ca/">CIHR Bioinformatics Training Program for Health Research.</a></p>
<h3>About the BC Cancer Agency</h3>
<p>The BC Cancer Agency, an agency of the Provincial Health Services Authority, is committed to reducing the incidence of cancer, reducing the mortality from cancer, and improving the quality of life of those living with cancer. It provides a comprehensive cancer control program for the people of British Columbia by working with community partners to deliver a range of oncology services, including prevention, early detection, diagnosis and treatment, research, education, supportive care, rehabilitation and palliative care. The <a href="http://www.bccancerfoundation.com/cms/index.cfm">BC Cancer Foundation</a> raises funds to support research and enhancements to patient care at the <a href="http://www.bccancer.bc.ca/default.htm">BC Cancer Agency</a>.</p>
<h3>About the Genome Sciences Centre</h3>
<p>Operating under the BC Cancer Agency, the Genome Sciences Centre is Canada’s first high-throughput sequencing facility. The centre provides state-of-the-art DNA sequencing technology to support genetic research focused on improving the diagnosis and treatment of cancer. The ultimate goal of this research is to develop methods for controlling the human genes affecting the growth and suppression of cancer.</p>
<p>For more information, please contact:
Papinder Rehncy
Communications Leader
BC Cancer Agency
604.877.6261
prehncy@bccancer.bc.ca</p>
]]></content:encoded>
    <dc:publisher>No publisher</dc:publisher>
    <dc:creator>Stephanie McInnis</dc:creator>
    <dc:rights></dc:rights>
    <dc:date>2010-10-15T00:15:00Z</dc:date>
    <dc:type>News Item</dc:type>
  </item>


  <item rdf:about="http://www.bcgsc.ca/about/pubann/alternative-expression-analysis-by-rna-sequencing">
    <title>Alternative expression analysis by RNA sequencing.</title>
    <link>http://www.bcgsc.ca/about/pubann/alternative-expression-analysis-by-rna-sequencing</link>
    <description>ALEXA-Seq is a method for using massively parallel paired-end transcriptome sequencing for 'alternative expression analysis.'  

</description>
    <content:encoded xmlns:content="http://purl.org/rss/1.0/modules/content/"><![CDATA[
<p>&nbsp;</p>
<p>In alternative expression analysis by sequencing (ALEXA-seq), we developed a method to analyze massively parallel RNA sequence data to catalog transcripts and assess differential and alternative expression of known and predicted mRNA isoforms in cells and tissues. As proof of principle, we used the approach to compare fluorouracil-resistant and -nonresistant human colorectal cancer cell lines. We assessed the sensitivity and specificity of the approach by comparison to exon tiling and splicing microarrays and validated the results with reverse transcription-PCR, quantitative PCR and Sanger sequencing. We observed global disruption of splicing in fluorouracil-resistant cells characterized by expression of new mRNA isoforms resulting from exon skipping, alternative splice site usage and intron retention. Alternative expression annotation databases, source code, a data viewer and other resources to facilitate analysis are available at&nbsp;<a class="external-link" href="http://www.alexaplatform.org/alexa_seq/">http://www.alexaplatform.org/alexa_seq/</a></p>
<p><strong>Alternative expression analysis by RNA sequencing.</strong> Malachi Griffith, Obi L. Griffith, Jill Mwenifumbo, Rodrigo Goya, A. Sorana Morrissy, Ryan D. Morin, Richard Corbett, Michelle J. Tang, Ying-Chen Hou, Trevor J. Pugh, Gordon Robertson, Suganthi Chittaranjan, Adrian Ally, Jennifer K. Asano, Susanna Y. Chan, Haiyan I. Li, Helen McDonald, Kevin Teague, Yongjun Zhao, Thomas Zeng, Allen Delaney, Martin Hirst, Gregg B. Morin, Steven J. M. Jones, Isabella T. Tai &amp; Marco A. Marra. <a href="http://www.ncbi.nlm.nih.gov/pubmed/20835245">Nat Methods. 2010 Oct;7(10):843-7.</a></p>
<p>&nbsp;</p>
<p>&nbsp;</p>
]]></content:encoded>
    <dc:publisher>No publisher</dc:publisher>
    <dc:creator>Kandyce Betts</dc:creator>
    <dc:rights></dc:rights>
    <dc:date>2010-10-01T23:25:00Z</dc:date>
    <dc:type>News Item</dc:type>
  </item>


  <item rdf:about="http://www.bcgsc.ca/about/pubann/locus-co-occupancy-nucleosome-positioning-and-h3k4me1-regulate-the-functionality-of-foxa2-hnf4a-and-pdx1-bound-loci-in-islets-and-liver">
    <title>Locus co-occupancy, nucleosome positioning, and H3K4me1 regulate the functionality of FOXA2-, HNF4A-, and PDX1-bound loci in islets and liver </title>
    <link>http://www.bcgsc.ca/about/pubann/locus-co-occupancy-nucleosome-positioning-and-h3k4me1-regulate-the-functionality-of-foxa2-hnf4a-and-pdx1-bound-loci-in-islets-and-liver</link>
    <description>A MORGEN project publication available online June 15, 2010.</description>
    <content:encoded xmlns:content="http://purl.org/rss/1.0/modules/content/"><![CDATA[
<p>Because most eukaryotic transcription factors bind thousands of loci, many of which are thought to be inactive, methods that can discriminate functionally active binding events are essential for interpreting genome-wide transcription factor binding data. By analyzing our binding data for FOXA2, PDX1 and HNF4A and H3K4me1 ChIP-seq data for mouse adult liver and pancreas islets, in combination with comprehensive gene expression data, we show that H3K4me1 enrichment profiles discriminate transcription factor occupied loci into three classes: those that are functionally active, those that are poised for activation, and those that reflect pioneer-like transcription factor activity.</p>
<p><strong>Locus co-occupancy, nucleosome positioning, and H3K4me1 regulate the functionality of FOXA2-, HNF4A-, and PDX1-bound loci in islets and liver.</strong>

Hoffman BG, Robertson G, Zavaglia B, Beach M, Cullum R, Lee S, Soukhatcheva G, Li L, Wederell ED, Thiessen N, Bilenky M, Cezard T, Tam A, Kamoh B, Birol I, Dai D, Zhao Y, Hirst M, Verchere CB, Helgason CD, Marra MA, Jones SJ, Hoodless PA.

<a href="http://genome.cshlp.org/content/early/2010/06/15/gr.104356.109.full.pdf+html">Genome Res. 2010 Jun 15.</a> [Epub ahead of print]   <em>(full text is available online)</em></p>
<p>This research is part of the <a href="../../project/mammalian-organogenesis-morgen"><strong>MORGEN project</strong></a> which is focused on dissecting gene expression networks during mammalian organogenesis.</p>
]]></content:encoded>
    <dc:publisher>No publisher</dc:publisher>
    <dc:creator>Stephanie McInnis</dc:creator>
    <dc:rights></dc:rights>
    <dc:date>2010-06-16T05:00:00Z</dc:date>
    <dc:type>News Item</dc:type>
  </item>


  <item rdf:about="http://www.bcgsc.ca/about/pubann/regression-of-castrate-recurrent-prostate-cancer-by-a-small-molecule-inhibitor-of-the-amino-terminus-domain-of-the-androgen-receptor">
    <title>Regression of Castrate-Recurrent Prostate Cancer by a Small-Molecule Inhibitor of the Amino-Terminus Domain of the Androgen Receptor</title>
    <link>http://www.bcgsc.ca/about/pubann/regression-of-castrate-recurrent-prostate-cancer-by-a-small-molecule-inhibitor-of-the-amino-terminus-domain-of-the-androgen-receptor</link>
    <description>Dr. Marianne Sadar publishes the latest results from her studies into prostate cancer  treatments in the journal Cancer Cell, Vol. 17, Issue 6, 535-546, 15 June 2010.</description>
    <content:encoded xmlns:content="http://purl.org/rss/1.0/modules/content/"><![CDATA[
<p>Androgen receptor (AR) is a transcription factor that plays an important role in prostate cancer. We identified EPI-001 as a small molecule that inhibits transactivation of the AR amino-terminal domain (NTD). The advantages of EPI-001 are: (1) its mechanism is unique from antiandrogens that target the C-terminal ligand-binding domain (LBD) and fail presumably due to gain-of-function mutations in the LBD, or expression of constitutively active splice variants; (2) it does not appear to be toxic in the therapeutic dose range in vivo; and (3) currently there are no curative treatment options for castration- recurrent prostate cancer (CRPC). These findings suggest that the AR NTD is a promising target to develop therapeutics for the treatment of CRPC.</p>
<p><em>Regression of Castrate-Recurrent Prostate Cancer by a Small-Molecule Inhibitor of the Amino-Terminus Domain of the Androgen Receptor.</em>   Raymond J. Andersen, Nasrin R. Mawji, Jun Wang, Gang Wang, Simon Haile, Jae-Kyung Myung, Kate Watt, Teresa Tam, Yu Chi Yang, Carmen A. Bañuelos, David E. Williams, Iain J. McEwan, Yuzhou Wang, <a href="../../faculty/msadar"><strong>Marianne D. Sadar</strong></a>
  <a href="http://download.cell.com/cancer-cell/pdf/PIIS153561081000200X.pdf?intermediate=true">Cancer Cell, Volume 17, Issue 6, 535-546, 15 June 2010</a></p>
<p>This research was supported by grants from the Canadian Institutes of Health Science, National Cancer Institute of Canada (R.J.Andersen), and the U.S. Army Medical Research and Materiel Command Prostate Cancer Research Program (M.D.Sadar). We are grateful to Country Meadows Senior Men’s Golf Charity Classic and the FORE PAR Prostate Awareness Research Charity Golf Classic for their financial support to purchase essential equipment. The article is dedicated to men who have fought but succumbed to CRPC (castrate-resistant prostate cancer).</p>
<p>In the same issue of Cancer Cell, A Previews Article by Timothy C. Thompson highlights the importance of this research (<a href="http://www.cell.com/cancer-cell/fulltext/S1535-6108(10)00205-9">Cancer Cell 17, June 15, 2010 525-526</a>) pointing out "it is a rare occasion in prostate cancer research when such a unique and promising therapeutic agent for advanced prostate cancer is developed. We all wait with interest the further preclinical and possible clinical testing of EPI-001 or its derivative(s).</p>
]]></content:encoded>
    <dc:publisher>No publisher</dc:publisher>
    <dc:creator>Stephanie McInnis</dc:creator>
    <dc:rights></dc:rights>
    <dc:date>2010-06-15T11:00:00Z</dc:date>
    <dc:type>News Item</dc:type>
  </item>


  <item rdf:about="http://www.bcgsc.ca/about/pubann/a-quality-management-system-application-to-investigate-and-troubleshoot-process-failures">
    <title>A quality management system application to investigate and troubleshoot process failures</title>
    <link>http://www.bcgsc.ca/about/pubann/a-quality-management-system-application-to-investigate-and-troubleshoot-process-failures</link>
    <description></description>
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<p>&nbsp;This
study describes how the cause for the poor quality sequence data, as indicated
from the quality score, involving high molecular weight follicular lymphoma DNA
samples for a study of tumour-associated genome rearrangements was successfully
identified and confirmed through the application of a well structured FI
(Failure Investigation) process. <br /></p>
<p>Through this FI process the
underlying causes were effectively identified, immediate corrective actions
were executed and a preventative action to avoid or minimize reoccurrences was
also implemented and monitored for effectiveness.</p>
<h3>Citation<br /></h3>
<p>Balasundaram,
M., Tsai, M., Clarke, A., Leung, D., Munro, S., Wagner, S., Michael, M., Moore,
R., Holt, R.A., (2010), “A Quality Management System Application to Investigate
and Troubleshoot Process failures: A Case Study of BC Cancer Agency”, <em>Clinical
Governance</em>: An International Journal, Vol. 15 No. 2.<em> </em><a href="http://www.emeraldinsight.com/Insight/viewContentItem.do;jsessionid=953E2EA19756B63B6895D68AA9509255?contentType=Article&amp;contentId=1858303">http://www.emeraldinsight.com/Insight/viewContentItem.do;jsessionid=953E2EA19756B63B6895D68AA9509255?contentType=Article&amp;contentId=1858303</a><em></em></p>
<p>&nbsp;</p>
<p>&nbsp;</p>
]]></content:encoded>
    <dc:publisher>No publisher</dc:publisher>
    <dc:creator>Kevin Teague</dc:creator>
    <dc:rights></dc:rights>
    <dc:date>2010-05-05T17:43:42Z</dc:date>
    <dc:type>News Item</dc:type>
  </item>


  <item rdf:about="http://www.bcgsc.ca/about/pubann/predicted-mutational-epitopes-suitable-for-immunological-cancer-control">
    <title>Predicted mutational epitopes suitable for immunological cancer control</title>
    <link>http://www.bcgsc.ca/about/pubann/predicted-mutational-epitopes-suitable-for-immunological-cancer-control</link>
    <description>In this meta-analysis, scientists at the Genome Sciences Centre have evaluated all known somatic mutations in human tumors for their antigenic potential. </description>
    <content:encoded xmlns:content="http://purl.org/rss/1.0/modules/content/"><![CDATA[
<p>The approach consisted in quantifying somatic tumor mutations and any corresponding predicted, candidate epitopes that would be expected to be of utility in immunological cancer control. This allows, for the first time, estimation of the potential impact of preventative cancer vaccination.</p>
<p>&nbsp;</p>
<p>Full citation<br />
<br />
René L. Warren and Robert A. Holt. &nbsp;2010. A census of predicted
mutational epitopes suitable for immunological cancer control. &nbsp;Human
Immunology. &nbsp;10.1016/j.humimm.2009.12.007.&nbsp; 71:245-254</p>
<p><br />
Further details of this <a class="external-link" href="http://www.sciencedirect.com/science?_ob=ArticleURL&amp;_udi=B6T3B-4Y46JFK-1&amp;_user=1022551&amp;_rdoc=1&amp;_fmt=&amp;_orig=search&amp;_sort=d&amp;_docanchor=&amp;view=c&amp;_acct=C000050484&amp;_version=1&amp;_urlVersion=0&amp;_userid=1022551&amp;md5=b56f1996338fbb4e12db0e2618215901">publication can be found online</a>.</p>
<p>&nbsp;</p>
]]></content:encoded>
    <dc:publisher>No publisher</dc:publisher>
    <dc:creator>Rene Warren</dc:creator>
    <dc:rights></dc:rights>
    <dc:date>2010-02-25T23:27:28Z</dc:date>
    <dc:type>News Item</dc:type>
  </item>


  <item rdf:about="http://www.bcgsc.ca/about/pubann/de-novo-assembly-of-a-fungus-genome">
    <title>De novo assembly of a fungus genome</title>
    <link>http://www.bcgsc.ca/about/pubann/de-novo-assembly-of-a-fungus-genome</link>
    <description></description>
    <content:encoded xmlns:content="http://purl.org/rss/1.0/modules/content/"><![CDATA[
<p>Scientist at Genome Sciences Centre were able to successfully produce a high quality draft genome for a filamentous fungus using Sanger, 454 and Illumina sequence data in a cost effective way. This method demonstrate that eukaryotic genome can be accurately assembled using our method.</p>
<p>&nbsp;</p>
<p>&nbsp;</p>
<p>Further details of this publication can be found online at:</p>
<p>&nbsp;</p>
<a class="external-link" href="http://genomebiology.com/2009/10/9/R94/abstract/"><u>http://genomebiology.com/2009/10/9/R94/abstract/</u></a>
<p>For more information please contact <a href="mailto:info@bcgsc.ca"><u>info@bcgsc.ca</u></a></p>
]]></content:encoded>
    <dc:publisher>No publisher</dc:publisher>
    <dc:creator>Reception Admin</dc:creator>
    <dc:rights></dc:rights>
    <dc:date>2009-11-12T20:13:23Z</dc:date>
    <dc:type>News Item</dc:type>
  </item>


  <item rdf:about="http://www.bcgsc.ca/about/pubann/the-issake-short-read-sequence-assembly-approach-for-profiling-t-cell-metagenomes">
    <title>The iSSAKE short read sequence assembly approach for profiling T cell metagenomes </title>
    <link>http://www.bcgsc.ca/about/pubann/the-issake-short-read-sequence-assembly-approach-for-profiling-t-cell-metagenomes</link>
    <description></description>
    <content:encoded xmlns:content="http://purl.org/rss/1.0/modules/content/"><![CDATA[
<p>The iSSAKE short read sequence assembly approach for profiling T cell metagenomes and developed by Rene Warren and Rob Holt is featured in the June edition of <em>The Scientist (</em>Volume 23 | Issue 6 | Page 53<em>).</em> <br /><br /><a class="external-link" href="http://www.the-scientist.com/templates/trackable/display/article1.jsp?a_day=1&amp;index=1&amp;year=2009&amp;page=53&amp;month=06&amp;o_url=2009/06/1/53/1"><u>http://www.the-scientist.com/templates/trackable/display/article1.jsp?a_day=1&amp;index=1&amp;year=2009&amp;page=53&amp;month=06&amp;o_url=2009/06/1/53/1</u></a></p>
<p>&nbsp;</p>
<p>For more information please contact <a href="mailto:info@bcgsc.ca"><u>info@bcgsc.ca</u></a></p>
]]></content:encoded>
    <dc:publisher>No publisher</dc:publisher>
    <dc:creator>Reception Admin</dc:creator>
    <dc:rights></dc:rights>
    <dc:date>2009-11-10T23:11:23Z</dc:date>
    <dc:type>News Item</dc:type>
  </item>


  <item rdf:about="http://www.bcgsc.ca/about/pubann/visualization-system-for-comparative-genomics">
    <title>Visualization system for comparative genomics.</title>
    <link>http://www.bcgsc.ca/about/pubann/visualization-system-for-comparative-genomics</link>
    <description></description>
    <content:encoded xmlns:content="http://purl.org/rss/1.0/modules/content/"><![CDATA[
<p>Martin Krzywinski, Jacqueline Schein, Inanc Birol1, Joseph Connors, Randy Gascoyne, Doug Horsman, Steven J. Jones, Marco A. Marra. Circos: An information aesthetic for comparative genomics. Genome Research. Published in Advance June 18, 2009.</p>
<p>&nbsp;</p>
<p>SHORT DESCRIPTION</p>
<p>Scientists at Canada's Michael Smith Genome Sciences Centre announce today the publication of the visualization tool Circos. Circos facilitates the identification and analysis of similarities and differences arising from comparisons of genomes and is effective in displaying variation in genome structure and, generally, any other kind of positional relationships between genomic intervals. Circos can be automated for incorporation into data analysis pipelines.</p>
<p>&nbsp;</p>
<p>Further details of this publication can be found online at:</p>
<p><a class="external-link" href="http://genome.cshlp.org/content/early/2009/06/15/gr.092759.109.abstract"><u>http://genome.cshlp.org/content/early/2009/06/15/gr.092759.109.abstract</u></a></p>
<p>&nbsp;</p>
<p>For more information please contact <a href="mailto:info@bcgsc.ca"><u>info@bcgsc.ca</u></a></p>
<p>&nbsp;</p>
<p>&nbsp;</p>
]]></content:encoded>
    <dc:publisher>No publisher</dc:publisher>
    <dc:creator>Reception Admin</dc:creator>
    <dc:rights></dc:rights>
    <dc:date>2009-11-10T23:07:20Z</dc:date>
    <dc:type>News Item</dc:type>
  </item>


  <item rdf:about="http://www.bcgsc.ca/about/pubann/de-novo-genome-sequence-assembly-of-a-filamentous-fungus-using-sanger-454-and-illumina-sequence-data">
    <title>De novo genome sequence assembly of a filamentous fungus using Sanger, 454 and Illumina sequence data</title>
    <link>http://www.bcgsc.ca/about/pubann/de-novo-genome-sequence-assembly-of-a-filamentous-fungus-using-sanger-454-and-illumina-sequence-data</link>
    <description></description>
    <content:encoded xmlns:content="http://purl.org/rss/1.0/modules/content/"><![CDATA[
<p><strong>Scott DiGuistini</strong>* ,<strong> Nancy Y Lia</strong>o* &nbsp;<strong>, Darren Pla</strong>tt <strong>, Gordon Roberts</strong>on <strong>, Michael Seid</strong>el <strong>, Simon K Ch</strong>an <strong>, T Roderick Docki</strong>ng <strong>, Inanc Bir</strong>ol <strong>, Robert A Ho</strong>lt <strong>, Martin Hir</strong>st <strong>, Elaine Mard</strong>is <strong>, Marco A Mar</strong>ra <strong>, Richard C Hamel</strong>in <strong>, Jörg Bohlma</strong>nn <strong>, Colette Breu</strong>il &nbsp;an<strong>d Steven JM Jon</strong>es <br /><br /><br /></p>
<p>For more information please contact <a href="mailto:info@bcgsc.ca"><u>info@bcgsc.ca</u></a></p>
]]></content:encoded>
    <dc:publisher>No publisher</dc:publisher>
    <dc:creator>Reception Admin</dc:creator>
    <dc:rights></dc:rights>
    <dc:date>2009-11-10T23:04:48Z</dc:date>
    <dc:type>News Item</dc:type>
  </item>


  <item rdf:about="http://www.bcgsc.ca/about/pubann/the-completion-of-the-mammalian-gene-collection-mgc">
    <title>The completion of the Mammalian Gene Collection (MGC)</title>
    <link>http://www.bcgsc.ca/about/pubann/the-completion-of-the-mammalian-gene-collection-mgc</link>
    <description></description>
    <content:encoded xmlns:content="http://purl.org/rss/1.0/modules/content/"><![CDATA[
<p>Martin Hirst, Thomas Zeng, Kane Tse, Michelle Moksa, Merinda Deng, Kevin Ma, Diana Mah, Johnson Pang, Greg Taylor, Eric Chuah, Athena Deng, Keith Fichter, Anne Go, Stephanie Lee, Jing Wang, Malachi Griffith, Ryan Morin, Richard A. Moore, Michael Mayo, Sarah Munro, Susan Wagner, Steven J.M. Jones, Robert A. Holt, Marco A. Marra</p>
<p>Since its start, the Mammalian Gene Collection (MGC) has sought to provide at least one full-CDS cDNA clone for every human and mouse gene with a RefSeq transcript, and at least 6200 rat genes. The MGC cloning effort initially relied on random EST-screening of cDNA libraries. Here we summarize our recent progress using directed RT-PCR cloning and DNA synthesis. The MGC now contains clones with the entire protein-coding sequence for 92% of human and 89% of mouse genes with curated RefSeq (NM-accession) transcripts, and for 97 % of human and 96% of mouse genes with curated RefSeq transcripts that have one or more PubMed publications, in addition to clones for more than 6300 rat genes. These high-quality MGC clones and their sequences are accessible without restriction to researchers worldwide.</p>
<p>For more information please contact <a href="mailto:info@bcgsc.ca"><u>info@bcgsc.ca</u></a></p>
]]></content:encoded>
    <dc:publisher>No publisher</dc:publisher>
    <dc:creator>Reception Admin</dc:creator>
    <dc:rights></dc:rights>
    <dc:date>2009-11-10T23:00:51Z</dc:date>
    <dc:type>News Item</dc:type>
  </item>


  <item rdf:about="http://www.bcgsc.ca/about/pubann/abyss-explorer-visualizing-genome-sequence-assemblies">
    <title>"ABySS-Explorer: Visualizing Genome Sequence Assemblies"</title>
    <link>http://www.bcgsc.ca/about/pubann/abyss-explorer-visualizing-genome-sequence-assemblies</link>
    <description></description>
    <content:encoded xmlns:content="http://purl.org/rss/1.0/modules/content/"><![CDATA[
<p>Cydney B. Nielsen, Shaun D. Jackman, Inanç Birol, Steven J.M.&nbsp; Jones</p>
<p>To appear in the Nov-Dec 2009 issue of IEEE Transactions on Visualization and Computer Graphics</p>
<p>&nbsp;</p>
<p>The paper was awarded one of two Best Paper Awards at this year's IEEE Information Visualization conference (October 2009) which is "the premier forum for visualization advances in science and engineering for academia, government, and industry".</p>
<p>&nbsp;</p>
<p>For more information please contact <a href="mailto:info@bcgsc.ca"><u>info@bcgsc.ca</u></a></p>
]]></content:encoded>
    <dc:publisher>No publisher</dc:publisher>
    <dc:creator>Reception Admin</dc:creator>
    <dc:rights></dc:rights>
    <dc:date>2009-11-10T22:56:01Z</dc:date>
    <dc:type>News Item</dc:type>
  </item>


  <item rdf:about="http://www.bcgsc.ca/about/pubann/genetic-variants-associated-with-susceptibility-to-fl">
    <title>Genetic variants associated with susceptibility to FL</title>
    <link>http://www.bcgsc.ca/about/pubann/genetic-variants-associated-with-susceptibility-to-fl</link>
    <description></description>
    <content:encoded xmlns:content="http://purl.org/rss/1.0/modules/content/"><![CDATA[
<p>We conducted genome-wide association studies of non-Hodgkin lymphoma using Illumina HumanHap550 BeadChips to identify subtype-specific associations in follicular, diffuse large B-cell and chronic lymphocytic leukemia/small lymphocytic lymphomas. We found that rs6457327 on 6p21.33 was associated with susceptibility to follicular lymphoma (FL; N = 189 cases, 592 controls) with validation in another 456 FL cases and 2,785 controls (combined allelic P = 4.7 x 10(-11)). The region of strongest association overlapped C6orf15 (STG), located near psoriasis susceptibility region 1 (PSORS1).</p>
<p class="rprtbody">Skibola CF, Bracci PM, Halperin E, Conde L, Craig DW, Agana L, Iyadurai K, Becker N, Brooks-Wilson A, Curry JD, Spinelli JJ, Holly EA, Riby J, Zhang L, Nieters A, Smith MT, Brown KM.</p>
<p class="aux"><span class="jrnl">Nat Genet</span><span class="src">. 2009 Aug;41(8):873-5. Epub 2009 Jul 20.</span></p>
<p class="aux"><span class="src">Further details of this publication can be found online at:</span></p>
<span class="src">
<p class="title"><a class="external-link" href="http://www.ncbi.nlm.nih.gov/pubmed/19620980?itool=EntrezSystem2.PEntrez.Pubmed.Pubmed_ResultsPanel.Pubmed_RVDocSum&amp;ordinalpos=1"><u>Genetic variants at 6p21.33 are associated with susceptibility to follicular lymphoma.</u></a></p>
<p>For more information please contact <a class="external-link" href="mailto:info@bcgsc.ca"><u>info@bcgsc.ca</u></a></p>
</span>]]></content:encoded>
    <dc:publisher>No publisher</dc:publisher>
    <dc:creator>Josie Audet</dc:creator>
    <dc:rights></dc:rights>
    <dc:date>2009-11-10T22:39:08Z</dc:date>
    <dc:type>News Item</dc:type>
  </item>





</rdf:RDF>

