Canada is credited with its fair share of historic breakthroughs in medicine, and the modern fields of genetics and genomics are no exception. Whether it is the discovery of the gene responsible for cystic fibrosis or contributing to world-renowned research in autism, Canadian researchers make a global impact. Today an impressive group of organizations are leading the genomic movement within Canada, including Genome Canada, CEPMED and the The Centre for Applied Genomics (TGAC), to name a few.
Motivation: The sequencing of personal genomes enabled analysis of variation in transcription factor (TF) binding, chromatin structure and gene expression and indicated how they contribute to phenotypic variation. It is hypothesized that using the reference genome for mapping ChIP-seq or RNA-seq reads may introduce errors, especially at polymorphic genomic regions.
A pilot trial reported in Science Translational Medicine further underlines the potential benefit of genomic tumour sequencing to inform clinical management.
Samples from a small number of patients with different forms of advanced cancer were examined using whole genome, exome and RNA transcriptome sequencing, in each case revealing abnormalities that suggested specific treatments.
Individual cancers harbor a set of genetic aberrations that can be informative for identifying rational therapies currently available or in clinical trials. We implemented a pilot study to explore the practical challenges of applying high-throughput sequencing in clinical oncology. We enrolled patients with advanced or refractory cancer who were eligible for clinical trials. For each patient, we performed whole-genome sequencing of the tumor, targeted whole-exome sequencing of tumor and normal DNA, and transcriptome sequencing (RNA-Seq) of the tumor to identify potentially informative mutations in a clinically relevant time frame of 3 to 4 weeks. With this approach, we detected several classes of cancer mutations including structural rearrangements, copy number alterations, point mutations, and gene expression alterations. A multidisciplinary Sequencing Tumor Board (STB) deliberated on the clinical interpretation of the sequencing results obtained. We tested our sequencing strategy on human prostate cancer xenografts. Next, we enrolled two patients into the clinical protocol and were able to review the results at our STB within 24 days of biopsy. The first patient had metastatic colorectal cancer in which we identified somatic point mutations in NRAS, TP53, AURKA, FAS, and MYH11, plus amplification and overexpression of cyclin-dependent kinase 8 (CDK8). The second patient had malignant melanoma, in which we identified a somatic point mutation in HRAS and a structural rearrangement affecting CDKN2C. The STB identified the CDK8 amplification and Ras mutation as providing a rationale for clinical trials with CDK inhibitors or MEK (mitogen-activated or extracellular signal–regulated protein kinase kinase) and PI3K (phosphatidylinositol 3-kinase) inhibitors, respectively. Integrative high-throughput sequencing of patients with advanced cancer generates a comprehensive, individual mutational landscape to facilitate biomarker-driven clinical trials in oncology.
Where are the jobs going to come from in the new economy? Some areas are roaring ahead, and those associated with “big” data” are leading the pack. Bioinformatics—using information technology to support medical and genetic research—is a boom area, with important lessons for job seekers.
Slowly, slowly, synthetic biology has been inching toward clinical applications. Those closest to this decade-old field say the time has come to test it against some of the most pressing global clinical challenges.
The goal of synthetic biology is the manipulation of biological cells in a predictable and rational fashion at the molecular level to carry out a given task efficiently and reliably at a cost of mere pennies. James J. Collins, a Howard Hughes Medical Institute investigator at Boston University, explains that over time, the community has become more efficient and savvy in manipulating biomolecules “to reprogram organisms and endow them with novel functions.”
Dr. Stephen Scherer is the Director of the McLaughlin Centre and The Centre for Applied Genomics, affiliated with both the Hospital for Sick Children and University of Toronto. Dr. Scherer leads one of Canada’s busiest laboratories. His group has discovered numerous disease susceptibility genes and most recently has defined CNV and other genetic factors underlying autism. He collaborated with Craig Venter’s team to decode human chromosome 7 and to generate the first genome sequence of an individual
Motivation: BioPAX is a standard language for representing and exchanging models of biological processes at the molecular and cellular levels. It is widely used by different pathway databases and genomics data analysis software. Currently, the primary source of BioPAX data is direct exports from the curated pathway databases. It is still uncommon for wet-lab biologists to share and exchange pathway knowledge using BioPAX. Instead, pathways are usually represented as informal diagrams in the literature. In order to encourage formal representation of pathways, we describe a software package that allows users to create pathway diagrams using CellDesigner, a user-friendly graphical pathway-editing tool and save the pathway data in BioPAX Level 3 format.
The notion of "personal genomics" has generated a great deal of buzz over the last several years but according to one researcher, many of the promises that lie at the "plateau of productivity" for this technology are tied to some significant...
The Office of Public Health Genomics (OPHG) of the US Centers for Disease Control and Prevention (CDC) has released a new report outlining priorities for public health genomics over the next five years to 2017.
Death, taxes and January prediction columns: these things are inevitable. So what? A new year offers a convenient—if arbitrary—time to review the year that was and contemplate what lies ahead. Without further ado, here are five of the questions the Genomics Law Report is asking as we kick off 2010.
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