- ShatterProof: operational detection and quantification of chromothripsis
Shaylan K Govind
Ontario Institute for Cancer Research, M5G 0A3, Toronto, Canada
BMC Bioinformatics 15:78. 2014
..As such, findings of chromothripsis are difficult to compare and many cases likely escape detection altogether...
- Isolation and genomic analysis of circulating tumor cells from castration resistant metastatic prostate cancer
Mark Jesus M Magbanua
Department of Medicine, Division of Hematology Oncology, University of California San Francisco, USA
BMC Cancer 12:78. 2012
..However, it is the molecular characterization of CTCs that offers insight into the biology of these tumor cells in the context of personalized treatment...
- Next generation sequencing of prostate cancer from a patient identifies a deficiency of methylthioadenosine phosphorylase, an exploitable tumor target
Colin C Collins
Vancouver Prostate Centre, University of British Columbia, Vancouver, British Columbia, Canada
Mol Cancer Ther 11:775-83. 2012
..The combination of genome sequencing and patient-derived xenografts can identify candidate therapeutic agents and evaluate them for personalized oncology...
- ZNF217 confers resistance to the pro-apoptotic signals of paclitaxel and aberrant expression of Aurora-A in breast cancer cells
Universite de Lyon, Lyon, France
Mol Cancer 9:291. 2010
..The precise mechanisms involved in ZNF217 pro-survival function are currently unknown, and utmost importance is given to deciphering the role of ZNF217 in cancer therapy response...
- Detection of recurrent rearrangement breakpoints from copy number data
Department of Computer Science, Brown University, Providence, RI, USA
BMC Bioinformatics 12:114. 2011
..Typically, the interior of a recurrent CNV is examined for genes or other loci associated with a phenotype. However, in some cases, such as gene truncations and fusion genes, the target of variant lies at the boundary of the variant...
- Patient-derived bladder cancer xenografts in the preclinical development of novel targeted therapies
The Vancouver Prostate Centre and Department of Urologic Sciences, University of British Columbia, Vancouver, BC, Canada
Oncotarget 6:21522-32. 2015
..Investigations related to tumor biology and drug testing in these models are therefore more likely to be relevant to the disease state in patients. They represent a valuable tool for developing precision therapy in MIBC. ..
- ORMAN: optimal resolution of ambiguous RNA-Seq multimappings in the presence of novel isoforms
School of Computing Science, Simon Fraser University, Burnaby, BC, Canada, Department of Genome Sciences, University of Washington, Seattle, WA, USA, Vancouver Prostate Centre and Department of Urologic Sciences, University of British Columbia, Vancouver, BC, Canada and Division of Computer Science, School of Informatics and Computing, Indiana University, Bloomington, IN, USA
Bioinformatics 30:644-51. 2014
..ORMAN achieves this objective through a combinatorial optimization formulation, which is solved through well-known approximation algorithms, integer linear programs and heuristics...
- The long non-coding RNA PCGEM1 is regulated by androgen receptor activity in vivo
Honours Biotechnology Program, Department of Microbiology and Immunology, University of British Columbia, Vancouver, BC, Canada
Mol Cancer 14:46. 2015
..Here, we further examine the relevance of PCGEM1 and PRNCR1 in PCa, and their relationship with AR signaling, using patient-derived xenograft models...
- nFuse: discovery of complex genomic rearrangements in cancer using high-throughput sequencing
School of Computing Science, Simon Fraser University, Vancouver, British Columbia V5A 1S6, Canada
Genome Res 22:2250-61. 2012
..Finally, we illustrate how CGRs may be used to infer the gene expression history of a tumor...