16 results on '"Caleb Choo"'
Search Results
2. Supplemental Data from Uncovering Clinically Relevant Gene Fusions with Integrated Genomic and Transcriptomic Profiling of Metastatic Cancers
- Author
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Jonathan M. Loree, Steven J.M. Jones, Marco A. Marra, Janessa Laskin, Stephen Yip, Daniel J. Renouf, David F. Schaeffer, Howard J. Lim, Sophie Sun, Tony Ng, Basile Tessier-Cloutier, Yongjun Zhao, Andrew J. Mungall, Richard A. Moore, Eric Chuah, Laura M. Williamson, Daniel MacMillan, Joanna M. Karasinska, Reanne Bowlby, Marcus Carreira, Caleb Choo, Caralyn Reisle, Karen Mungall, James T. Topham, Erin Pleasance, Cameron J. Grisdale, and Erica S. Tsang
- Abstract
Supplemental Data
- Published
- 2023
3. Supplemental Table 2 from Uncovering Clinically Relevant Gene Fusions with Integrated Genomic and Transcriptomic Profiling of Metastatic Cancers
- Author
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Jonathan M. Loree, Steven J.M. Jones, Marco A. Marra, Janessa Laskin, Stephen Yip, Daniel J. Renouf, David F. Schaeffer, Howard J. Lim, Sophie Sun, Tony Ng, Basile Tessier-Cloutier, Yongjun Zhao, Andrew J. Mungall, Richard A. Moore, Eric Chuah, Laura M. Williamson, Daniel MacMillan, Joanna M. Karasinska, Reanne Bowlby, Marcus Carreira, Caleb Choo, Caralyn Reisle, Karen Mungall, James T. Topham, Erin Pleasance, Cameron J. Grisdale, and Erica S. Tsang
- Abstract
Supplemental Table 2
- Published
- 2023
4. Supplemental Table 1 from Uncovering Clinically Relevant Gene Fusions with Integrated Genomic and Transcriptomic Profiling of Metastatic Cancers
- Author
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Jonathan M. Loree, Steven J.M. Jones, Marco A. Marra, Janessa Laskin, Stephen Yip, Daniel J. Renouf, David F. Schaeffer, Howard J. Lim, Sophie Sun, Tony Ng, Basile Tessier-Cloutier, Yongjun Zhao, Andrew J. Mungall, Richard A. Moore, Eric Chuah, Laura M. Williamson, Daniel MacMillan, Joanna M. Karasinska, Reanne Bowlby, Marcus Carreira, Caleb Choo, Caralyn Reisle, Karen Mungall, James T. Topham, Erin Pleasance, Cameron J. Grisdale, and Erica S. Tsang
- Abstract
Supplemental Table 1
- Published
- 2023
5. Data from Uncovering Clinically Relevant Gene Fusions with Integrated Genomic and Transcriptomic Profiling of Metastatic Cancers
- Author
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Jonathan M. Loree, Steven J.M. Jones, Marco A. Marra, Janessa Laskin, Stephen Yip, Daniel J. Renouf, David F. Schaeffer, Howard J. Lim, Sophie Sun, Tony Ng, Basile Tessier-Cloutier, Yongjun Zhao, Andrew J. Mungall, Richard A. Moore, Eric Chuah, Laura M. Williamson, Daniel MacMillan, Joanna M. Karasinska, Reanne Bowlby, Marcus Carreira, Caleb Choo, Caralyn Reisle, Karen Mungall, James T. Topham, Erin Pleasance, Cameron J. Grisdale, and Erica S. Tsang
- Abstract
Purpose:Gene fusions are important oncogenic drivers and many are actionable. Whole-genome and transcriptome (WGS and RNA-seq, respectively) sequencing can discover novel clinically relevant fusions.Experimental Design:Using WGS and RNA-seq, we reviewed the prevalence of fusions in a cohort of 570 patients with cancer, and compared prevalence to that predicted with commercially available panels. Fusions were annotated using a consensus variant calling pipeline (MAVIS) and required that a contig of the breakpoint could be constructed and supported from ≥2 structural variant detection approaches.Results:In 570 patients with advanced cancer, MAVIS identified 81 recurrent fusions by WGS and 111 by RNA-seq, of which 18 fusions by WGS and 19 by RNA-seq were noted in at least 3 separate patients. The most common fusions were EML4-ALK in thoracic malignancies (9/69, 13%), and CMTM8-CMTM7 in colorectal cancer (4/73, 5.5%). Combined genomic and transcriptomic analysis identified novel fusion partners for clinically relevant genes, such as NTRK2 (novel partners: SHC3, DAPK1), and NTRK3 (novel partners: POLG, PIBF1).Conclusions:Utilizing WGS/RNA-seq facilitates identification of novel fusions in clinically relevant genes, and detected a greater proportion than commercially available panels are expected to find. A significant benefit of WGS and RNA-seq is the innate ability to retrospectively identify variants that becomes clinically relevant over time, without the need for additional testing, which is not possible with panel-based approaches.
- Published
- 2023
6. Uncovering Clinically Relevant Gene Fusions with Integrated Genomic and Transcriptomic Profiling of Metastatic Cancers
- Author
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James T. Topham, Caralyn Reisle, Cameron J. Grisdale, Jonathan M. Loree, Reanne Bowlby, Sophie Sun, Karen Mungall, Basile Tessier-Cloutier, Laura Williamson, Marco A. Marra, Erin Pleasance, Caleb Choo, Andrew J. Mungall, Richard A. Moore, Daniel J. Renouf, Tony Ng, David F. Schaeffer, Stephen Yip, Joanna M Karasinska, Eric Chuah, Yongjun Zhao, Daniel MacMillan, Janessa Laskin, Marcus Carreira, Steven J.M. Jones, Erica S Tsang, and Howard John Lim
- Subjects
0301 basic medicine ,Cancer Research ,Oncogene Proteins, Fusion ,Colorectal cancer ,Computational biology ,Biology ,Transcriptome ,03 medical and health sciences ,0302 clinical medicine ,Neoplasms ,Exome Sequencing ,medicine ,Humans ,RNA-Seq ,Neoplasm Metastasis ,Gene ,Retrospective Studies ,Contig ,Gene Expression Profiling ,Breakpoint ,Structural variant ,Genomics ,medicine.disease ,Advanced cancer ,3. Good health ,Treatment Outcome ,030104 developmental biology ,Oncology ,030220 oncology & carcinogenesis ,Gene Fusion - Abstract
Purpose:Gene fusions are important oncogenic drivers and many are actionable. Whole-genome and transcriptome (WGS and RNA-seq, respectively) sequencing can discover novel clinically relevant fusions.Experimental Design:Using WGS and RNA-seq, we reviewed the prevalence of fusions in a cohort of 570 patients with cancer, and compared prevalence to that predicted with commercially available panels. Fusions were annotated using a consensus variant calling pipeline (MAVIS) and required that a contig of the breakpoint could be constructed and supported from ≥2 structural variant detection approaches.Results:In 570 patients with advanced cancer, MAVIS identified 81 recurrent fusions by WGS and 111 by RNA-seq, of which 18 fusions by WGS and 19 by RNA-seq were noted in at least 3 separate patients. The most common fusions were EML4-ALK in thoracic malignancies (9/69, 13%), and CMTM8-CMTM7 in colorectal cancer (4/73, 5.5%). Combined genomic and transcriptomic analysis identified novel fusion partners for clinically relevant genes, such as NTRK2 (novel partners: SHC3, DAPK1), and NTRK3 (novel partners: POLG, PIBF1).Conclusions:Utilizing WGS/RNA-seq facilitates identification of novel fusions in clinically relevant genes, and detected a greater proportion than commercially available panels are expected to find. A significant benefit of WGS and RNA-seq is the innate ability to retrospectively identify variants that becomes clinically relevant over time, without the need for additional testing, which is not possible with panel-based approaches.
- Published
- 2021
7. Pan-cancer analysis of advanced patient tumors reveals interactions between therapy and genomic landscapes
- Author
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Cameron J. Grisdale, Scott D. Brown, Kevin Y. Fan, Wei Zhang, Caralyn Reisle, Zoltan Bozoky, Robert A. Holt, Tariq Vira, Richard Corbett, Melika Bonakdar, My Linh Thibodeau, Kathleen Wee, Dean Cheng, Luka Culibrk, Marcus Carreira, David F. Schaeffer, Deirdre Weymann, Anna V. Tinker, Eric Y. Zhao, Michael K.C. Lee, Karen A. Gelmon, Karen Mungall, Richard A. Moore, Dean A. Regier, Daniel J. Renouf, Zusheng Zong, Reva Shenwai, Stephen Chia, Jahanshah Ashkani, Ana Fisic, Stephen Yip, Darryl D’Souza, Yussanne Ma, Daniel MacMillan, Erin Pleasance, Steve Bilobram, Alexandra Fok, Amir Muhammadzadeh, Jean-Michel Lavoie, Martin R. Jones, Hillary Pearson, Simon K. Chan, Balvir Deol, Steven J.M. Jones, Andrew J. Mungall, Mya Warren, Gregory A. Taylor, Elisa Majounie, Harwood H. Kwan, Eric Chuah, Howard John Lim, Sara Sadeghi, Dustin Bleile, Emma Titmuss, Reanne Bowlby, Anna Davies, Laura Williamson, Jessica Nelson, Caleb Choo, Jasleen K. Grewal, Katherine Dixon, Yongjun Zhao, Shehara Mendis, Yaoqing Shen, Janessa Laskin, Joanna M. Karasinska, Veronika Csizmok, Tina Wong, Sophie Sun, Kasmintan A. Schrader, and Marco A. Marra
- Subjects
Cancer Research ,Mutation ,DNA repair ,medicine.medical_treatment ,Cancer ,Context (language use) ,Computational biology ,Immunotherapy ,Biology ,medicine.disease ,medicine.disease_cause ,Transcriptome ,Oncology ,medicine ,DPYD ,Gene - Abstract
Advanced and metastatic tumors with complex treatment histories drive cancer mortality. Here we describe the POG570 cohort, a comprehensive whole-genome, transcriptome and clinical dataset, amenable for exploration of the impacts of therapies on genomic landscapes. Previous exposure to DNA-damaging chemotherapies and mutations affecting DNA repair genes, including POLQ and genes encoding Polζ, were associated with genome-wide, therapy-induced mutagenesis. Exposure to platinum therapies coincided with signatures SBS31 and DSB5 and, when combined with DNA synthesis inhibitors, signature SBS17b. Alterations in ESR1, EGFR, CTNNB1, FGFR1, VEGFA and DPYD were consistent with drug resistance and sensitivity. Recurrent noncoding events were found in regulatory region hotspots of genes including TERT, PLEKHS1, AP2A1 and ADGRG6. Mutation burden and immune signatures corresponded with overall survival and response to immunotherapy. Our data offer a rich resource for investigation of advanced cancers and interpretation of whole-genome and transcriptome sequencing in the context of a cancer clinic. Marra and colleagues describe POG570, a pan-cancer, whole-genome, transcriptome and clinical dataset stressing the molecular interactions in advanced and post-therapy cancer patients.
- Published
- 2020
8. FeatureStack: Perl module for comparative visualization of gene features.
- Author
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Christian Frech, Caleb Choo, and Nansheng Chen
- Published
- 2012
- Full Text
- View/download PDF
9. MAVIS: merging, annotation, validation, and illustration of structural variants
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Daniel Paulino, Richard A. Moore, Karen Mungall, Yussanne Ma, Dustin Bleile, Andrew J. Mungall, Amir Muhammadzadeh, Steven J.M. Jones, Inna Shlafman, Stephen Pleasance, Caleb Choo, Caralyn Reisle, and Robin J.N. Coope
- Subjects
Statistics and Probability ,0303 health sciences ,Computer science ,Process (engineering) ,030302 biochemistry & molecular biology ,Computational Biology ,Structural variant ,Context (language use) ,Genomics ,Computational biology ,Biochemistry ,Genome ,Computer Science Applications ,Transcriptome ,03 medical and health sciences ,Computational Mathematics ,Annotation ,Computational Theory and Mathematics ,Neoplasms ,Key (cryptography) ,Humans ,Molecular Biology ,Software ,030304 developmental biology - Abstract
Summary Reliably identifying genomic rearrangements and interpreting their impact is a key step in understanding their role in human cancers and inherited genetic diseases. Many short read algorithmic approaches exist but all have appreciable false negative rates. A common approach is to evaluate the union of multiple tools increasing sensitivity, followed by filtering to retain specificity. Here we describe an application framework for the rapid generation of structural variant consensus, unique in its ability to visualize the genetic impact and context as well as process both genome and transcriptome data. Availability and implementation http://mavis.bcgsc.ca Supplementary information Supplementary data are available at Bioinformatics online.
- Published
- 2018
10. Pan-cancer analysis of advanced patient tumors reveals interactions between therapy and genomic landscapes
- Author
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Erin, Pleasance, Emma, Titmuss, Laura, Williamson, Harwood, Kwan, Luka, Culibrk, Eric Y, Zhao, Katherine, Dixon, Kevin, Fan, Reanne, Bowlby, Martin R, Jones, Yaoqing, Shen, Jasleen K, Grewal, Jahanshah, Ashkani, Kathleen, Wee, Cameron J, Grisdale, My Linh, Thibodeau, Zoltan, Bozoky, Hillary, Pearson, Elisa, Majounie, Tariq, Vira, Reva, Shenwai, Karen L, Mungall, Eric, Chuah, Anna, Davies, Mya, Warren, Caralyn, Reisle, Melika, Bonakdar, Gregory A, Taylor, Veronika, Csizmok, Simon K, Chan, Zusheng, Zong, Steve, Bilobram, Amir, Muhammadzadeh, Darryl, D'Souza, Richard D, Corbett, Daniel, MacMillan, Marcus, Carreira, Caleb, Choo, Dustin, Bleile, Sara, Sadeghi, Wei, Zhang, Tina, Wong, Dean, Cheng, Scott D, Brown, Robert A, Holt, Richard A, Moore, Andrew J, Mungall, Yongjun, Zhao, Jessica, Nelson, Alexandra, Fok, Yussanne, Ma, Michael K C, Lee, Jean-Michel, Lavoie, Shehara, Mendis, Joanna M, Karasinska, Balvir, Deol, Ana, Fisic, David F, Schaeffer, Stephen, Yip, Kasmintan, Schrader, Dean A, Regier, Deirdre, Weymann, Stephen, Chia, Karen, Gelmon, Anna, Tinker, Sophie, Sun, Howard, Lim, Daniel J, Renouf, Janessa, Laskin, Steven J M, Jones, and Marco A, Marra
- Subjects
Neoplasms ,Humans - Abstract
Advanced and metastatic tumors with complex treatment histories drive cancer mortality. Here we describe the POG570 cohort, a comprehensive whole-genome, transcriptome and clinical dataset, amenable for exploration of the impacts of therapies on genomic landscapes. Previous exposure to DNA-damaging chemotherapies and mutations affecting DNA repair genes, including POLQ and genes encoding Polζ, were associated with genome-wide, therapy-induced mutagenesis. Exposure to platinum therapies coincided with signatures SBS31 and DSB5 and, when combined with DNA synthesis inhibitors, signature SBS17b. Alterations in ESR1, EGFR, CTNNB1, FGFR1, VEGFA and DPYD were consistent with drug resistance and sensitivity. Recurrent noncoding events were found in regulatory region hotspots of genes including TERT, PLEKHS1, AP2A1 and ADGRG6. Mutation burden and immune signatures corresponded with overall survival and response to immunotherapy. Our data offer a rich resource for investigation of advanced cancers and interpretation of whole-genome and transcriptome sequencing in the context of a cancer clinic.
- Published
- 2019
11. The Genome of the Beluga Whale (Delphinapterus leucas)
- Author
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Kristina M. Miller, Armelle Troussard, Steven Bilobram, Amy M. Chan, Inanc Birol, Yussanne Ma, René L. Warren, Pawan Pandoh, Kane Tse, Caleb Choo, Irene Li, Adrian Ally, Daniel Paulino, Gideon J. Mordecai, Curtis A. Suttle, Steven J.M. Jones, Andrew J. Mungall, Heather Kirk, Richard A. Moore, Yongjun Zhao, Noreen Dhalla, Martin Haulena, S. Austin Hammond, Samantha J. Jones, Dorothy Cheung, Gregory A. Taylor, Karen Mungall, Simon K. Chan, Marco A. Marra, Angela D. Schulze, Angela K Y Tam, and Robin Coope
- Subjects
0301 basic medicine ,genome ,genome assembly ,beluga whale ,Delphinapterus leucas ,Cetacea ,lcsh:QH426-470 ,Sequence assembly ,Genome ,DNA sequencing ,Article ,Transcriptome ,03 medical and health sciences ,0302 clinical medicine ,Genetics ,Genetics (clinical) ,Leucas ,biology ,Accession number (bioinformatics) ,biology.organism_classification ,lcsh:Genetics ,030104 developmental biology ,Evolutionary biology ,Beluga Whale ,030217 neurology & neurosurgery - Abstract
The beluga whale is a cetacean that inhabits arctic and subarctic regions, and is the only living member of the genus Delphinapterus. The genome of the beluga whale was determined using DNA sequencing approaches that employed both microfluidic partitioning library and non-partitioned library construction. The former allowed for the construction of a highly contiguous assembly with a scaffold N50 length of over 19 Mbp and total reconstruction of 2.32 Gbp. To aid our understanding of the functional elements, transcriptome data was also derived from brain, duodenum, heart, lung, spleen, and liver tissue. Assembled sequence and all of the underlying sequence data are available at the National Center for Biotechnology Information (NCBI) under the Bioproject accession number PRJNA360851A.
- Published
- 2019
- Full Text
- View/download PDF
12. The Genome of the Northern Sea Otter (Enhydra lutris kenyoni)
- Author
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Yongjun Zhao, Richard A. Moore, Angela K Y Tam, Martin Haulena, Simon K. Chan, René L. Warren, Yussanne Ma, S. Austin Hammond, Marco A. Marra, Gregory A. Taylor, Noreen Dhalla, Inanc Birol, Armelle Troussard, Robin Coope, Heather Kirk, Samantha J. Jones, Andrew J. Mungall, Steven Bilobram, Steven J.M. Jones, Adrian Ally, Daniel Paulino, Karen Mungall, Pawan Pandoh, and Caleb Choo
- Subjects
0106 biological sciences ,0301 basic medicine ,lcsh:QH426-470 ,Mustelidae ,Sequence assembly ,010603 evolutionary biology ,01 natural sciences ,Genome ,Article ,Otter ,DNA sequencing ,03 medical and health sciences ,genome ,genome assembly ,northern sea otter ,Enhyrda lutris kenyoni ,biology.animal ,parasitic diseases ,Genetics ,Genetics (clinical) ,Whole genome sequencing ,biology ,Enhydra lutris ,Accession number (bioinformatics) ,biology.organism_classification ,lcsh:Genetics ,030104 developmental biology ,Evolutionary biology - Abstract
The northern sea otter inhabits coastal waters of the northern Pacific Ocean and is the largest member of the Mustelidae family. DNA sequencing methods that utilize microfluidic partitioned and non-partitioned library construction were used to establish the sea otter genome. The final assembly provided 2.426 Gbp of highly contiguous assembled genomic sequences with a scaffold N50 length of over 38 Mbp. We generated transcriptome data derived from a lymphoma to aid in the determination of functional elements. The assembled genome sequence and underlying sequence data are available at the National Center for Biotechnology Information (NCBI) under the BioProject accession number PRJNA388419.
- Published
- 2017
- Full Text
- View/download PDF
13. Comprehensive molecular characterization of muscle invasive bladder cancer
- Author
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A. Gordon Robertson, Jaegil Kim, Hikmat Al-Ahmadie, Joaquim Bellmunt, Guangwu Guo, Andrew D. Cherniack, Toshinori Hinoue, Peter W. Laird, Katherine A. Hoadley, Rehan Akbani, Mauro A.A. Castro, Ewan A. Gibb, Rupa S. Kanchi, Dmitry A. Gordenin, Sachet A. Shukla, Francisco Sanchez-Vega, Donna E. Hansel, Bogdan A. Czerniak, Victor E. Reuter, Xiaoping Su, Benilton de Sa Carvalho, Vinicius S. Chagas, Karen L. Mungall, Sara Sadeghi, Chandra Sekhar Pedamallu, Yiling Lu, Leszek J. Klimczak, Jiexin Zhang, Caleb Choo, Akinyemi I. Ojesina, Susan Bullman, Kristen M. Leraas, Tara M. Lichtenberg, Catherine J. Wu, Nicholaus Schultz, Gad Getz, Matthew Meyerson, Gordon B. Mills, David J. McConkey, John N. Weinstein, David J. Kwiatkowski, Seth P. Lerner, Monique Albert, Iakovina Alexopoulou, Adrian Ally, Tatjana Antic, Manju Aron, Miruna Balasundaram, John Bartlett, Stephen B. Baylin, Allison Beaver, Inanc Birol, Lori Boice, Moiz S. Bootwalla, Jay Bowen, Reanne Bowlby, Denise Brooks, Bradley M. Broom, Wiam Bshara, Eric Burks, Flavio M. Cárcano, Rebecca Carlsen, Benilton S. Carvalho, Andre L. Carvalho, Eric P. Castle, Patricia Castro, James W. Catto, David W. Chesla, Eric Chuah, Sudha Chudamani, Victoria K. Cortessis, Sandra L. Cottingham, Daniel Crain, Erin Curley, Siamak Daneshmand, John A. Demchok, Noreen Dhalla, Hooman Djaladat, John Eckman, Sophie C. Egea, Jay Engel, Ina Felau, Martin L. Ferguson, Johanna Gardner, Julie M. Gastier-Foster, Mark Gerken, Carmen R. Gomez-Fernandez, Jodi Harr, Arndt Hartmann, Lynn M. Herbert, Thai H. Ho, Robert A. Holt, Carolyn M. Hutter, Steven J.M. Jones, Merce Jorda, Richard J. Kahnoski, Katayoon Kasaian, Phillip H. Lai, Brian R. Lane, Jia Liu, Laxmi Lolla, Yair Lotan, Fabiano R. Lucchesi, Yussanne Ma, Roberto D. Machado, Dennis T. Maglinte, David Mallery, Marco A. Marra, Sue E. Martin, Michael Mayo, Anoop Meraney, Alireza Moinzadeh, Richard A. Moore, Edna M. Mora Pinero, Scott Morris, Carl Morrison, Andrew J. Mungall, Jerome B. Myers, Rashi Naresh, Peter H. O'Donnell, Dipen J. Parekh, Jeremy Parfitt, Joseph D. Paulauskis, Robert J. Penny, Todd Pihl, Sima Porten, Mario E. Quintero-Aguilo, Nilsa C. Ramirez, W. Kimryn Rathmell, Kimberly Rieger-Christ, Charles Saller, Andrew Salner, George Sandusky, Cristovam Scapulatempo-Neto, Jacqueline E. Schein, Anne K. Schuckman, Nikolaus Schultz, Candace Shelton, Troy Shelton, Jeff Simko, Parminder Singh, Payal Sipahimalani, Norm D. Smith, Heidi J. Sofia, Andrea Sorcini, Melissa L. Stanton, Gary D. Steinberg, Robert Stoehr, Travis Sullivan, Qiang Sun, Angela Tam, Roy Tarnuzzer, Katherine Tarvin, Helge Taubert, Nina Thiessen, Leigh Thorne, Kane Tse, Kelinda Tucker, David J. Van Den Berg, Kim E. van Kessel, Sven Wach, Yunhu Wan, Zhining Wang, Daniel J. Weisenberger, Lisa Wise, Tina Wong, Ye Wu, Liming Yang, Leigh Anne Zach, Jean C. Zenklusen, Jiashan (Julia) Zhang, Erik Zmuda, and Ellen C. Zwarthoff
- Subjects
0301 basic medicine ,Urinary Bladder ,Biology ,medicine.disease_cause ,General Biochemistry, Genetics and Molecular Biology ,Article ,03 medical and health sciences ,0302 clinical medicine ,microRNA ,medicine ,Carcinoma ,Cluster Analysis ,Humans ,Neoplasm Invasiveness ,Gene ,Survival analysis ,Aged ,Mutation ,Bladder cancer ,Urinary bladder ,Muscle, Smooth ,DNA Methylation ,Middle Aged ,medicine.disease ,Survival Analysis ,MicroRNAs ,030104 developmental biology ,medicine.anatomical_structure ,Urinary Bladder Neoplasms ,030220 oncology & carcinogenesis ,DNA methylation ,Cancer research ,RNA, Long Noncoding - Abstract
We report a comprehensive analysis of 412 muscle-invasive bladder cancers characterized by multiple TCGA analytical platforms. Fifty-eight genes were significantly mutated, and the overall mutational load was associated with APOBEC-signature mutagenesis. Clustering by mutation signature identified a high-mutation subset with 75% 5-year survival. mRNA expression clustering refined prior clustering analyses and identified a poor-survival "neuronal" subtype in which the majority of tumors lacked small cell or neuroendocrine histology. Clustering by mRNA, long non-coding RNA (lncRNA), and miRNA expression converged to identify subsets with differential epithelial-mesenchymal transition status, carcinoma in situ scores, histologic features, and survival. Our analyses identified 5 expression subtypes that may stratify response to different treatments.
- Published
- 2017
14. The Genome of the Northern Sea Otter (Enhydra lutris kenyoni).
- Author
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Jones, Samantha J., Haulena, Martin, Taylor, Gregory A., Simon Chan, Bilobram, Steven, Warren, René L., Austin Hammond, S., Mungall, Karen L., Caleb Choo, Kirk, Heather, Pandoh, Pawan, Ally, Adrian, Dhalla, Noreen, Tam, Angela K. Y., Troussard, Armelle, Paulino, Daniel, Coope, Robin J. N., Mungall, Andrew J., Moore, Richard, and Yongjun Zhao
- Subjects
GENOMES ,SEA otter ,NUCLEOTIDE sequencing ,LYMPHOMAS ,DATA analysis - Abstract
The northern sea otter inhabits coastal waters of the northern Pacific Ocean and is the largest member of the Mustelidae family. DNA sequencing methods that utilize microfluidic partitioned and non-partitioned library construction were used to establish the sea otter genome. The final assembly provided 2.426 Gbp of highly contiguous assembled genomic sequences with a scaffold N50 length of over 38 Mbp. We generated transcriptome data derived from a lymphoma to aid in the determination of functional elements. The assembled genome sequence and underlying sequence data are available at the National Center for Biotechnology Information (NCBI) under the BioProject accession number PRJNA388419. [ABSTRACT FROM AUTHOR]
- Published
- 2017
- Full Text
- View/download PDF
15. FeatureStack: Perl module for comparative visualization of gene features
- Author
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Caleb Choo, Nansheng Chen, and Christian Frech
- Subjects
Statistics and Probability ,Computer science ,Scalable Vector Graphics ,Portable Network Graphics ,computer.software_genre ,Biochemistry ,Glyph (data visualization) ,Computer graphics ,Exon ,Software ,Computer Graphics ,Gene family ,Protein Interaction Domains and Motifs ,Regulatory Elements, Transcriptional ,Molecular Biology ,Gene ,computer.programming_language ,Programming language ,business.industry ,Intron ,Proteins ,computer.file_format ,Exons ,Introns ,Computer Science Applications ,Visualization ,Computational Mathematics ,Computational Theory and Mathematics ,Genes ,Data mining ,Perl ,business ,computer - Abstract
Summary FeatureStack is a Perl module for the automatic generation of multi-gene images. FeatureStack takes BioPerl-compliant gene or transcript features as input and renders them side by side using a user-defined BioPerl glyph. Output images can be generated in SVG or PNG format. FeatureStack comes with a new BioPerl glyph, decorated_gene, which can highlight protein features on top of gene models. Used in combination, FeatureStack and decorated_gene enable rapid and automated generation of annotation-rich images of stacked gene models that greatly facilitate evolutionary studies of related gene structures and gene families. Availability and implementation Bio-Draw-FeatureStack and Bio-Graphics-glyph-decorated_gene are freely available at the Comprehensive Perl Archive Network (CPAN) and GitHub. Contact chenn@sfu.ca Supplementary information Supplementary data are available at Bioinformatics online.
- Published
- 2012
16. Genome of Acanthamoeba castellanii highlights extensive lateral gene transfer and early evolution of tyrosine kinase signaling
- Author
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Christian Frech, Gregory Gimenez, Pauline Schaap, Piers Nash, Bernard A. Liu, Ivan A. Paponov, Gilbert Greub, John M. Synnott, Matthias Horn, Lis Caler, Amanda J. Lohan, Daniel J. Rigden, Michael L. Ginger, Christina Schilde, David A. Fitzpatrick, Cheng-Hsun Chiu, Alex Bateman, Didier Raoult, Thomas Rattei, Jeffery Sc Chu, Brendan J. Loftus, Manuel Irimia, Claire Bertelli, Thomas Weinmeier, Diego Miranda-Saavedra, Bernard Turcotte, Nansheng Chen, Arash Kianianmomeni, Aliza Finkler, Peter Hegemann, Petrus Tang, Klaus O. Kopec, Jacob Lorenzo-Morales, Mike Clarke, Scott William Roy, Caleb Choo, Andrew P. Hutchins, Chris Soon Heng Tan, Nikhat Zafar, Ilias Lagkouvardos, Thomas R. Bürglin, and Hillel Fromm
- Subjects
Gene Transfer, Horizontal ,ved/biology.organism_classification_rank.species ,Protozoan Proteins ,Biology ,Genome ,Amoebozoa ,Evolution, Molecular ,03 medical and health sciences ,Model organism ,Gene ,030304 developmental biology ,Genetics ,0303 health sciences ,Acanthamoeba castellanii ,030306 microbiology ,ved/biology ,Research ,Protein-Tyrosine Kinases ,Unikont ,biology.organism_classification ,Introns ,Multicellular organism ,Horizontal gene transfer ,Genome, Protozoan ,Signal Transduction - Abstract
Background The Amoebozoa constitute one of the primary divisio ns of eukaryotes encompassing taxa of both biomedic al and evolutionary importance, yet its genomic divers ity remains largely unsampled. Here we present an analysis of a whole genome assembly of Acanthamoeba castellanii ( Ac ) the first representative from a solitary free-living amoebozoan. Results Ac encodes 15,455 compact intron rich genes a signifi cant number of which are predicted to have arisen through interkingdom lateral gene transfer (LGT). A majority of the LGT candidates have undergone a substantial degree of intronization and Ac appears to have incorporated them into established transcriptional programs. Ac manifests a complex signaling and cell communicati on repertoire including a complete tyrosine kinase signaling toolkit and a comparable diversity of predicted extracellular receptors to that found in the facultatively multicellular dictyostelids. An impor tant environmental host of a diverse range of bacte ria and viruses, Ac utilizes a diverse repertoire of predicted pattern recognition receptors many with predicted orthologous functions in the innate immune systems of higher organisms. Conclusions Our analysis highlights the important role of LGT i n the biology of Ac and in the diversification of microbial eukaryotes. The early evolution of a key signaling facility implicated in the evolution of metazoan multicellularity strongly argues for its emergence early in the Unikont lineage. Overall the availabil ity of an Ac genome should aid in deciphering the biology of th e Amoebozoa and facilitate functional genomic studi es in this important model organism and environmental host.
- Published
- 2012
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