Genetics, Genomics & Proteomics
From the identification of genetic mutations underlying disease to the development of prognostic technologies that impact health care delivery, this area of research is critical to the pursuit of personalized and translational medicine. Our researchers uncover how relationships between genes and/or proteins are set and integrated within large molecular networks. These networks ultimately determine the fate of cells and organisms. Our laboratories encompass a wide array of biological and clinical settings related to the understanding of diverse health and disease states.
These laboratories investigate:
- molecular evolution
- chromatin structure and function
- structural analysis of nucleic acids and proteins
- repetitive DNA
- genome stability
- copy number variation
Faculty Involved in Genetics, Genomics & Proteomics Research
Current research interest is in molecular biology and cytogentics of skin malignancies particularly melanoma and the implementation of molecular testing for diagnostic and targeted therapeutic purposes as part of personalized medicine.
Other areas of research include evaluation and implementation of whole slide imaging (WSI) as a tool for teledermatopathology
Dr. Aldape is a neuropathologist with a research interest in primary brain tumors. He has experience with identification of biomarkers in gliomas, including microarray studies. He has identified a mesenchymal subgroup of glioma, which may be related to microenvironmental factors. His work characterizes glioma subtypes as well as identifies clinically relevant molecular alterations in these tumors.
My laboratory conducts multi-disciplinary studies to identify genetic alterations that play a role in breast cancer and sarcoma and to determine their clinical importance. Our goals are to explore the biology of these genetic alterations, to aid in diagnosis and treatment, and to discover novel targets for therapeutics.
Main fields in which I collaborate with researchers, clinicians, biotech or Pharmaceutical companies: Evaluation of biomarkers and clinical validation all the way to regulatory submissions (FDA, Health Canada), development and optimization of biomarkers/assays, handling clinical trials (development of assays, project management,…), validation of medical devices, and any process or assays towards personalized medicine.
Dr. Baltzer is a hand surgeon with a strong interest in hand and wrist arthritis. Specifically she focuses on translational proteomics to investigate systemic and joint-specific biomarkers related to the development and progression of symptomatic osteoarthritis in the hand and wrist.This information has the potential application of understanding disease progression and predicting response to OA treatment based on patient reported outcomes.
My research program is focused on translational genomics - specifically discovery and functional characterization of cancer biomarkers and their applications to clinical setting. A major area of current research is investigation of epigenetic markers of genitor-urinary and gastro-intestinal neoplasms using genome-wide interrogation strategies.
Dr. Bartlett is Director of OICR’s Transformative Pathology Platform. He is developing new diagnostic approaches to improve patient diagnosis and treatment. By gaining an understanding of the molecular complexity of cancer, accurate diagnostic approaches can be developed to ensure that patients receive the most appropriate treatment.
We study the process by which a mutation in a single cell eventually leads to malignant cancer. We utilize a variety of techniques that incorporate cutting edge genetics, genomics, and proteomics strategies.
I am interested in projects that aim to discover biomarkers of disease or biomarkers that are informative about the patients’ response to therapy. As part of this effort, the aim is also to develop new methods for possible clinical laboratory applications, such as immuno-mass spectrometry or improved immunoassays, capable of detecting proteins with specific post-translational modifications, isoforms, or activity.
Initiates and implements research studies in molecular epidemiology of Clostridium difficile, investigates biomarkers associated with strains causing outbreaks in hospitals, develops methods for detection and typing of this pathogen, supervises implementation of these methods for routine testing at the Public Health Ontario Laboratories.
Dr. Chandran’s research expertise is in the area of translational research involving the identification of soluble biomarkers. His bench research aims to identify mechanisms underlying inflammation and joint damage. His program aims to address the current gaps in disease assessment such as early diagnosis and prognostication to prevent joint damage and development of tools to facilitate efficient management of psoriatic arthritis.
Dr. Charames' research interests are in the development of genomic and proteomic strategies for improved clinical diagnostics, with a special focus in breast, ovarian and colorectal cancers. His translational research approach aims to use high-throughput genomic sequencing, in addition to proteomics and biomarker discovery technologies, to improve individualized medicine.
Dr. Chaudhry's research interests include detailed delineation of phenotype of rare genetic disorders. She is also interested in research aimed at finding genetic etiology of craniofacial disorders, autism and intellectual disability.
Current genetic evaluation of stillbirths is based on clinical grounds (autopsy, examination of tissues) and laboratory testing (karyotype, microarray analysis). For 25-65% of stillbirths the etiology cannot be determined by current standard investigations. Our current research is aimed towards finding single gene disorders assocaited with fetal abnormalities by using whole exome sequencing (WES) and in the future whole exome sequencing.
My laboratory interests include the role of the human microbiome in infectious diseases pathogenesis, it's potential as a clinical biomarker in infectious and non-infectious diseases and the interactions of the human microbiome, host and antibiotics during treatment for infection.
Our research interests include a wide range of genetic conditions, but our laboratory has a specific focus on genetic and non-genetic contributions to disordered bone and mineral metabolism.
Research and education focus on transfusion medicine and benign hematology (ie- adverse reactions to blood products; immunologic hematopathologies in autoimmune disease, transfusion, or transplantation; and adaptive/evolutionary blood group biology).
From the point-of-view of human disease research, our major interest is cancer, but other diseases including neurodegeneration, inflammation and skin disorders are also of interest. Our laboratory integrates basic, cell biology and translational research under one roof.
Breast cancer has to invade the breast to be able to spread. It is the two steps of invasion and spread beyond the breast (metastasis) that result in breast cancer deaths. I believe that the study of these changes will lead to the identification of potential diagnostic, prognostic and predictive markers and also valuable therapeutic targets.
My research interests include: developing new panels of immunohistochemical markers for the differentiation of high grade tumours and exploring radiology- pathology correlation particularly in the area of prostate cancer and MRI. I am also interested in studies utilizing histomorphological features and biomarkers to predict disease progression and outcome especially in urothelial carcinoma.
My current research interests include proteomics, mass spectrometry and biomarker discovery. My basic research program is focused on the development of proteomic methods to analyze proteins in biological samples and study protein function. My clinical research program is aimed at improving diagnostics of male infertility and prostate cancer.
Kidney and prostate cancer. Molecular pathogenesis, biomarkers for predicting disease progression, clinical behaviour in relation to histopathological and molecular characteristics of kidney and prosatte cancers, pathologic evaluation of tumour tissue following new innovations in treatment (ablative and targeted molecular therapies).
Translational cancer genomics primarily in the areas of gastrointestinal cancers
I study the pathobiology of Osteoarthritis (OA) and OA pain. I am interested in identifying novel therapeutic targets; studying the particular differences in disease across gender and ethnicity. Further, we are investigating the role of Mesenchymal stem cells in OA; particularly their paracrine and anti-inflammatory effects within the synovial joint. My expertise includes proteomics, genomics, molecular biology, and epidemiology.
To understand how changes in structure and organization of chromosomes and the genome contribute to genomic disease. To gain insight into genomic alterations and their predisposing underlying mechanisms using both classical and more advanced cytogenomic technologies as investigative tools.
Primary research interests include: (1) the application of molecular techniques to assist in the diagnosis and prognosis of solid and hematologic tumours; (2) understanding the genetic and epigenetic landscape of leukemias and lymphomas to determine its impact on disease pathogenesis.
My research interests include the study of respiratory viruses and emerging viral pathogens, with a focus on laboratory detecion, molecular epidemiology, antiviral resistance and clinical significance of viral loads.
The Hawkins laboratory focuses on genetic and proteomic markers for prognostication and therapy guidance in paediatric brain tumours including astrocytoma, diffuse intrinsic pontine glioma and ependymoma.
Dr. Jim Hu's major research goal is to develop novel gene delivery strategies in order to translate the genetic discoveries into clinical applications. His team developed novel viral vectors that can protect CF mice from acute lung bacterial infection and established methods for efficient airway gene delivery to large animals. His current endeavour is to achieve permanent airway gene correction by targeting the airway stem cells.
Our laboratory is studying the impact of the microbial communities (i.e. the microbiome) in the lungs of patients with cystic fibrosis and other chronic lung diseases. We also participate in collaborative research investigating various aspects of lung injury, repair, and transplantation.
Our research interests are in the origin and evolution of new gene function focusing on genes that are involved in Diabetes.
My research is focused on the molecular epidemiology and genomics, and determinants of resistance and virulence in M. tuberculosis strains and non-tuberculosis mycobacteria (NTM). Research initiatives have been undertaken using comparative genomics and strain characterization (e.g. LSPs and SNPs) to recognize and identify virulence factors associated with local, circulating strains of M. tuberculosis.
Work in my laboratory focuses on the development of new testing that can be utilized in the clinical setting. We are using next generation sequencing and multiplex mutation testing to genotype blood and tissue samples from patients with diseases such as melanoma and lung cancer to better understand their underlying biology.
Dr. Kapoor's research program is directed towards understanding the complex pathophysiology of osteoarthritis (OA) and identifying new therapeutic strategies to counteract the destruction of the articular cartilage during OA.
As a perinatal pathologist my research focuses on the placenta and on improving clincopatholgic correlation in diseases of pregnancy. Current and recent studies include correlation of neuropathologic findings with placental pathology in stillbirth, the effect of heparin on the development of the high risk placenta and the clinical and pathologic correlates of distal villous hypoplasia.
My research is focussed on basic, translational and clinical aspects of the placental complications of pregnancy, with a focus on severe pre-eclampsia and intra-uterine growth restriction (IUGR).
The major focus of my research is the development and application of genomic technologies to the understanding of the causes of reproductive failure. Identification and characterization of copy number variation in infertile males, preimplantation embryos and perinatal samples provide insight into the mechanisms that cause infertility and abnormal embryonic development.
My current research interests include novel tumor biomarker discovery for ovarian cancer and application of proteomics to clinical practice.
My research focuses on genetic metabolic disorders. Currently, the emphasis is on understanding the pathobiology of Congenital Disorders of Glycosylation as well as developing new methods for the diagnosis of this group of diseases.
Dr Lerner-Ellis is a molecular geneticist who serves as Head and Director of the Advanced Molecular Diagnostics Laboratory at Mount Sinai Hospital and an Associate at the Ontario Institute for Cancer Research. In addition to his core interests in molecular diagnostics, as applied to breast and colon cancer, a major aim of his research is to integrate genome sequencing into the general practice of medicine.
Complement-based kidney diseases and the translational aspects involved through clinical and basic reseach
My research is focused on using high throughput genomic technologies, including microarrays and sequencing, for gene discovery and diagnostics in neurodevelopmental disorders.
I’m focused on discovering and understanding the function of genes and abnormalities in genes (“mutations”) that cause disease in children and adults. My pathology lab studies tissue changes associated with mutations. My molecular biology lab focuses on R&D in design and production of mutant mouse models, particularly Cas9 RNA-guided nucleases, germ cell cryopreservation, and in vitro fertilization.
My lab is involved in the detection and characterization of resistance mechanisms to different antibiotic families in both Gram-negative and -positive pathogens. Elucidation of genetic platforms and enzymatic activity are part of that molecular characterization. Development of genetic and phenotypic tests is also part of our work through new technologies applied to diagnosis.
Dr. Mete’s research focusses on the translation of basic findings to clinical tests that provide diagnostic, prognostic, and predictive biomarkers for endocrine tumors. His other interests involve development of practice guidelines, digital pathology, and innovative teaching designs.
Dr. Morgen's research focuses on pathologic and laboratory precitors of fetal, obstetrical, and neonatal complications, and as such he collaborates extensively with obstetricians and neonatologists.
I am interested in pathology phenotyping of genetically engineered mice. Our lab performs analysis of all organs systems using gross pathology techniques, histopathology interpretation, special and immunihistochemical stains, image analysis from digital images (static and whole slide scans), laser capture microdissection, and specialized mouse embryo collection and pathological analyses.
My research focuses on identification of genomic copy number variants associated with developmental disorders and development of new tests to improve diagnosis of the genetic disorders. I am also interested in implementing new genomic technologies in the clinical setting. In our laboratory, we use high density microarray and other cytogenomic and molecular tests for prenatal and perinatal diagnosis.
Microbiology, epidemiology - My clinical and research interests include identification and diagnosis of pathogens including rare or emerging pathogens. In addition, I am involved in detection and characterization of antibiotic resistant organisms.
Primary research is in cancer biomarkers, particularly the application of mismatch repair (MMR) gene expression immunohistochemistry and biomarkers in colorectal carcinoma.
Secondary research is in pathology informatics and the application of information tools to support and enhance pathology reporting.
The major focus of research in my lab is to define mechanisms by which secreted growth factors and their cognate receptors control branching morphogenesis, formation of a contractile ureter, and generation of nephrons. We study these mechanisms using primary kidney cell cultures, tissue explants, transgenic mice and 'knock-out' mice.
My research has focused on exploring markers and diagnostic tools in clinical practice as well as development of an integrated morphological and molecular approach in cytopathology, especially for effusions and fine needle aspirates of lung and lymph nodes. Current projects are oriented to applying advanced molecular techniques for genomic profiling of different tumors using cytological samples and exploring new strategies for bio-banking.
Research interests focus primarily on the study of genomic disease and pediatric leukemias using molecular cytogenetic techniques, and the application of genomic microarray technology to the study of genomic disease.
My research uses the tools of modern sequence-based genomics to discover the mutations that are present in the genomes of paediatric cancer patients, and to understand how these mutations alter the somatic transcriptome. I have a strong interest in sarcoma biology. I'm directly involved with the introduction of cutting-edge genomics, such as whole genome sequencing, into clinical practice.
Clinical and translational studies investigating the role of genes in cutaneous lymphomas, melanoma and merkel cell carcinoma through immunohistochemical and molecular characterization.
Our lab is primarily interested in chromosomal changes occuring in cancer. We provide clinical analysis for primarily adult cancer patients with a focus on hematological malignancies. Primary techniques include karyotyping and FISH but research and translational studies are also being developed using SNP arrays and next-generation sequencing.
Research is focused on the identification and characterization of genetic conditions in psychiatric patients, particularly those with dual diagnosis (psychiatric disorder + intellectual disability). In collaboration with psychiatrists, the goal is to develop protocols and tools for psychiatrists and primary care physicians to optimize the diagnosis, management and treatment of psychiatric patients with underlying genetic disorders.
Clinical applications of new technologies in genetic diagnoses and treatments.
We use advanced genomic technologies to identify novel genetic variants responsible for neurodevelopmental disorders, with the ultimate goal of understanding the downstream biological pathways.
Dr. Stockley’s research interests include development of genomic tests for molecular diagnostics, application of new technologies such as Next-Generation Sequencing to clinical care for acquired and inherited disease, and quality management for high-complexity clinical laboratory testing.
Researcj interests encompass the standardization of HLA laboratory testing, clinical programs to increase transplant in highly sensitized patients, the contribution of HLA antibodies to antibody mediated rejection pathways and outcomes and the management of HLA related alloimmune injury.
Transplantation remains to be one of the ultimate life-saving treatments for patients suffering from end stage organ/tissue failures. HLA lab is playing a major role in identifying suitable donors for allo transplantation. My interest is to develop more clinical applicable assays to improvise, enhance and supplement the current assays and to look into the clinical outcomes based on the interpretation of various HLA lab testing data.
My research interests are clinically oriented and centered around head and neck/thyroid pathology.
My laboratory is focusing on understanding the pathogenesis of urologic tumors including renal cell carcinoma and prostate cancer using an integrated genomic, quantitative proteomic, transcriptomic and miRNA approach with extensive bioinformatics analysis, for the purpose of biomarker discovery, understanding mechanisms of drug resistance, and the development of new targeted therapy.
Current research interest in genetics and pharmacogenetics of neuropsychiatric disorders and suicidal behaviour. Secondary interests include rodent behavioural models and whole-genome study methods.