Digital Pathology provides a great reliable source for cancer diagnosis; however, this relatively new technique lacks an appropriate method of regulation and standardization. As a result the information obtained from cancer imaging system might suffer from inconsistency of the results (repeatability and reproducibility issues). Working with the BC Cancer Research Center, Logipath Medical Inc. has developed a number of quantitative pathology systems some of which have been spun off to commercial entities.
Medulloblastoma is the most common form of pediatric brain cancer with a five-year survival rate of approximately 70%, yet for some children’s survival is as low as 40%. Many of the treatment options for these patients may be effective in extending the five-year survival rate, however, quality of life issues still persist for these young patients including learning and developmental deficits. These side effects arise from damage to normal tissue in the developing brain by surgery and/or drug and radiation therapy.
Metastatic tumors are a major concern in childhood cancer and the single most prominent cause of patient mortality. Metastasis is a complex process involving several cellular processes, each of which involves numerous extra and intracellular events. Therapeutic targeting strategies are hampered by a large degree of redundancy in the systems controlling metastatic behaviour and by the lack of specific markers associated with tumor dissemination.
The Sorensen laboratory-based Childhood Cancer Research Program is specifically focused on elucidating the genetic and biological determinants of the metastatic process in childhood cancer. Metastatic disease remains the single most dominant driver of adverse outcome in most childhood cancers, particularly in childhood sarcomas. Cancer stem cells, malignant cells that share many characteristics with normal stem cells, have been implicated to have a central role in the metastatic process.
There is a pressing need to apply genomics-based tools for rapidly evaluating the impact of industrial and municipal waste management practices and climate change. In order to do this, information about the genome from relevant North American species is needed, yet acquiring these complex genome sequences had been cost and resource prohibitive until recently.
Fast structural variation (deletion, insertion and inversion) detection between genome of different individuals is the main goal of this project. The internship team is planning in extending new algorithms to reduce the number of false positive calls (especially for deletions) and to parallelize it using Graphics Processing Unit (GPU). The standard approach implementation of the algorithms, as a result of high computational needs, is not fast enough for every day use by health science centers (such as hospitals).
The throughput of next-gen sequencers is about 20 to 90 million base pairs per hour and increasing. To map this huge volume of data to reference genome and reduce the computation time, current mapping tools are installed on the clusters. Although using a cluster reduces the computation time but the cost of having such a cluster is considerable. So, there is a trade-off between computation time and computation cost. This project’s goal is to reduce the computation time as well as to reduce the computation cost.
Human genetic variation has been traditionally studied at the single nucleotide polymorphism (SNP) level. It is clear that, human genetic variation extends beyond single nucleotide polymorphism. New projects aimed at identifying structural variation have been initiated through the use of high throughput sequencing technologies. Although the new sequencing technologies produce short reads with respect to Sanger sequencing experiments, the focus of search for differences between a sample and its reference is moving from single based differences to structural variations.
This internship will be developing tools and solving algorithmic problems related to short read technologies (the new technologies of sequencing the human genome). The problem being solved will help the biology and molecular biology researchers to use these new tools to find variations between different individuals. This will be very important step in realizing the personalized genomics dream.
Non-Hodgkins Lymphoma (NHL)is the 5th most common cancer in Canada and its incidence has been increasing steadily every year. Unfortunately, little is known about the causes of the increased incidence, although it is likely that some combinations of genetic and environmental factors are involved. This internship with the BC Cancer Agency will examine genes that may interact with ultraviolet radiation, organochlorines and other environmental and lifestyle factors. This project will provide an important step in understanding the etiology of NHL.