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Ontario Cancer Institute

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Patent
Ontario Cancer Institute | Date: 2017-05-24

The invention features methods, devices, and kits for predicting the responsiveness of a cancer patient (e.g., a breast cancer patient, such as a grade 1, 2, or 3 breast cancer patient) to anthracycline treatment by determining the expression levels of four chromosomal instability (CIN) genes including HDGF, KIAA0286, RFC4, and MSH6, collectively referred to as CIN4. Patients that have a low CIN4 score benefit from anthracycline treatment compared patients with a high CIN4 score.


Patent
Ontario Cancer Institute | Date: 2015-07-23

Methods, systems, devices and computer implemented methods of prognosing or classifying patients using a biomarker comprising a plurality of subnetwork modules are disclosed. In some embodiments, the method comprises determining an activity of a plurality of genes in a test sample of a patient, wherein the plurality of genes are associated with the plurality of subnetwork modules. An expression profile is constructed using the activity of the plurality of genes. The dysregulation of each of the plurality of subnetwork modules is determined by calculating a score proportional to a degree of dysregulation in each of the plurality of subnetwork modules from the expression profile. The patient is prognosed or classified by inputting each dysregulation score into a model for predicting patient outcomes for patients having a disease, and inputting a clinical indicator of the patient into the model, to obtain a risk associated with the disease.


Patent
Ontario Cancer Institute | Date: 2015-07-27

Systems, methods and computer-readable media are provided for determining the amount of sequencing required to achieve a target sequencing quality of a genetic sample to be sequenced. The method comprises receiving a genetic sample and sequencing a portion of the genetic sample. A sequencing quality metric belonging to a category of sequencing quality metrics is generated from the sequencing. The amount of sequencing of the genetic sample required to achieve the target sequencing quality is determined by inputting the sequencing quality metric into a trained model. A system is also disclosed for genetic sequencing. Corresponding methods and computer-readable media are also provided.


Patent
Ontario Cancer Institute | Date: 2017-05-31

Methods, systems, devices and computer impemented methods of prognosing or classifying patients using a biomarker comprising a plurality of subnetwork modules are disclosed. In some embodiments, the method comprises determining an activity of a plurality of genes in a test sample of a patient, wherein the plurality of genes are associated with the plurality of subnetwork modules. An expression profile is constructed using the activity of the plurality of genes. The dysregulation of each of the plurality of subnetwork modules is determined by calculating a score proportional to a degree of dysregulation in each of the plurality of subnetwork modules from the expression profile. The patient is prognosed or classified by inputting each dysregulation score into a model for predicting patient outcomes for patients having a disease, and inputting a clinical indicator of the patient into the model, to obtain a risk associated with the disease.


Patent
Ontario Cancer Institute | Date: 2015-07-15

The invention features methods, devices, and kits for predicting the responsiveness of a cancer patient (e.g., a breast cancer patient, such as a grade 1, 2, or 3 breast cancer patient) to anthracycline treatment by determining the expression levels of four chromosomal instability (CIN) genes including HDGF, KIAA0286, RFC4, and MSH6, collectively referred to as CIN4. Patients that have a low CIN4 score benefit from anthracycline treatment compared patients with a high CIN4 score.


Simpson J.T.,Ontario Cancer Institute
Bioinformatics | Year: 2014

Motivation: The de novo assembly of large, complex genomes is a significant challenge with currently available DNA sequencing technology. While many de novo assembly software packages are available, comparatively little attention has been paid to assisting the user with the assembly. Results: This article addresses the practical aspects of de novo assembly by introducing new ways to perform quality assessment on a collection of sequence reads. The software implementation calculates per-base error rates, paired-end fragment-size distributions and coverage metrics in the absence of a reference genome. Additionally, the software will estimate characteristics of the sequenced genome, such as repeat content and heterozygosity that are key determinants of assembly difficulty. © The Author 2013. Published by Oxford University Press.


Khokha R.,Ontario Cancer Institute
Cold Spring Harbor perspectives in biology | Year: 2011

The adult mammary structure provides for the rapid growth, development, and immunological protection of the live-born young of mammals through its production of milk. The dynamic remodeling of the branched epithelial structure of the mammary gland in response to physiological stimuli that allow its programmed branching morphogenesis at puberty, cyclical turnover during the reproductive cycle, differentiation into a secretory organ at parturition, postlactational involution, and ultimately, regression with age is critical for these processes. Extracellular metalloproteinases are essential for the remodeling programs that operate in the tissue microenvironment at the interface of the epithelium and the stroma, coupling form with function. Deregulated proteolytic activity drives the transition of a physiological mammary microenvironment into a tumor microenvironment, facilitating malignant transformation.


Stein L.D.,Ontario Cancer Institute
Genome Biology | Year: 2010

With DNA sequencing now getting cheaper more quickly than data storage, the time may have come to use cloud computing for genome informatics. © 2010 BioMed Central Ltd.


Integrin α11β1 is a stromal cell-specific receptor for fibrillar collagens and is overexpressed in carcinoma-associated fibroblasts (CAFs). We have investigated its direct role in cancer progression by generating severe combined immune deficient (SCID) mice deficient in integrin α11 (α11) expression. The growth of A549 lung adenocarcinoma cells and two patient-derived non-small cell lung carcinoma (NSCLC) xenografts in these α11 knockout (α11-/-) mice was significantly impeded, as compared with wild-type (α11+/+) SCID mice. Orthotopic implantation of a spontaneously metastatic NCI-H460SM cell line into the lungs of α11-/- and α11+/+ mice showed significant reduction in the metastatic potential of these cells in the α11-/- mice. We identified that collagen cross-linking is associated with stromal α11 expression, and the loss of tumor stromal α11 expression was correlated with decreased collagen reorganization and stiffness. This study shows the role of integrin α11β1, a receptor for fibrillar collagen in differentiation of fibroblasts into CAFs. Furthermore, our data support an important role for α11 signaling pathway in CAFs, promoting tumor growth and metastatic potential of NSCLC cells and being closely associated with collagen cross-linking and the organization and stiffness of fibrillar collagen matrices.Oncogene advance online publication, 6 July 2015; doi:10.1038/onc.2015.254. © 2015 Macmillan Publishers Limited


Dancey J.,Ontario Cancer Institute
Nature Reviews Clinical Oncology | Year: 2010

Mammalian target of rapamycin (mTOR) is a protein kinase of the PI3K/Akt signaling pathway. Activation of mTOR in response to growth, nutrient and energy signals leads to an increase in protein synthesis, which is required for tumor development. This feature makes mTOR an attractive target for cancer therapy. First-generation mTOR inhibitors are sirolimus derivatives (rapalogs), which have been evaluated extensively in cancer patients. Everolimus and temsirolimus are already approved for the treatment of renal-cell carcinoma. Temsirolimus is also approved for the treatment of mantle-cell lymphoma. These drugs, in addition to ridaforolimus (formerly deforolimus) and sirolimus, are currently being evaluated in clinical trials of various cancers. Second-generation mTOR inhibitors are small molecules that target the kinase domain, and have also entered clinical development. Clinical trials are underway to identify additional malignancies that respond to mTOR inhibitors, either alone or in combination with other therapies. Future research should evaluate the optimal drug regimens, schedules, patient populations, and combination strategies for this novel class of agents. © 2010 Macmillan Publishers Limited. All rights reserved.

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