Roderick Docking
A5006812104- Acute Myeloid Leukemia Research
- Histone Deacetylase Inhibitors Research
- Forest Insect Ecology and Management
- Cancer Genomics and Diagnostics
- Multiple Myeloma Research and Treatments
- Genomics and Phylogenetic Studies
- Chronic Lymphocytic Leukemia Research
- Insect-Plant Interactions and Control
- Epigenetics and DNA Methylation
- Genomics and Rare Diseases
- Entomopathogenic Microorganisms in Pest Control
- Bioinformatics and Genomic Networks
- Protein Degradation and Inhibitors
- Molecular Biology Techniques and Applications
- BRCA gene mutations in cancer
- Chromosomal and Genetic Variations
- CRISPR and Genetic Engineering
- RNA modifications and cancer
- Gene expression and cancer classification
- Chronic Myeloid Leukemia Treatments
- Forest Ecology and Biodiversity Studies
- Plant and Fungal Interactions Research
- Insect and Pesticide Research
- Mycobacterium research and diagnosis
- Gene Regulatory Network Analysis
Canada's Michael Smith Genome Sciences Centre
2011-2023
University of British Columbia
2019-2021
BC Cancer Agency
2009-2019
Open Group
2017
McGill University
2006
The process of generating raw genome sequence data continues to become cheaper, faster, and more accurate. However, assembly such into high-quality, finished sequences remains challenging. Many tools are available, but they differ greatly in terms their performance (speed, scalability, hardware requirements, acceptance newer read technologies) final output (composition assembled sequence). More importantly, it largely unclear how best assess the quality sequences. Assemblathon competitions...
Low-cost short read sequencing technology has revolutionized genomics, though it is only just becoming practical for the high-quality de novo assembly of a novel large genome. We describe Assemblathon 1 competition, which aimed to comprehensively assess state art in methods when applied current technologies. In collaborative effort, teams were asked assemble simulated Illumina HiSeq data set an unknown, diploid A total 41 assemblies from 17 different groups received. Novel haplotype aware...
The mountain pine beetle, Dendroctonus ponderosae Hopkins, is the most serious insect pest of western North American forests. A recent outbreak destroyed more than 15 million hectares forests, with major environmental effects on forest health, and economic industry. has in part been driven by climate change, will contribute to increased carbon emissions through decaying We developed a genome sequence resource for beetle better understand unique aspects this insect's biology. draft de novo...
Oligodendroglioma is characterized by unique clinical, pathological, and genetic features. Recurrent losses of chromosomes 1p 19q are strongly associated with this brain cancer but knowledge the identity function genes affected these alterations limited. We performed exome sequencing on a discovery set 16 oligodendrogliomas 1p/19q co-deletion to identify new molecular features at base-pair resolution. As anticipated, there was high rate IDH mutations: all cases had mutations in either IDH1...
In western North America, the current outbreak of mountain pine beetle (MPB) and its microbial associates has destroyed wide areas lodgepole forest, including more than 16 million hectares in British Columbia. Grosmannia clavigera (Gc), a critical component outbreak, is symbiont MPB pathogen trees. To better understand interactions between Gc, MPB, hosts, we sequenced ∼30-Mb Gc genome assembled it into 18 supercontigs. We predict 8,314 protein-coding genes, support gene models with proteome,...
Sequencing-by-synthesis technologies can reduce the cost of generating de novo genome assemblies. We report a method for assembling draft sequences eukaryotic organisms that integrates sequence information from different sources, and demonstrate its effectiveness by an approximately 32.5 Mb forest pathogen Grosmannia clavigera, ascomycete fungus. also developed assessing assemblies using Illumina paired end read data how we are it to guide future finishing. Our results be accurately...
As more clinically-relevant genomic features of myeloid malignancies are revealed, it has become clear that targeted clinical genetic testing is inadequate for risk stratification. Here, we develop and validate a transcriptome-based assay stratification acute leukemia (AML). Comparison ribonucleic acid sequencing (RNA-Seq) to whole genome exome reveals standalone RNA-Seq offers the greatest diagnostic return, enabling identification expressed gene fusions, single nucleotide short...
Network analysis is the preferred approach for detection of subtle but coordinated changes in expression an interacting and related set genes. We introduce a novel method based on analyses coexpression networks Bayesian networks, we use this new to classify two types hematological malignancies; namely, acute myeloid leukemia (AML) myelodysplastic syndrome (MDS). Our classifier has accuracy 93%, precision 98%, recall 90% training dataset (n = 366); which outperforms results reported by other...
Abstract Background Ophiostoma piceae is a wood-staining fungus that grows in the sapwood of conifer logs and lumber. We sequenced its genome analyzed transcriptomes under range growth conditions. A comparison with mountain pine beetle-associated pathogen Grosmannia clavigera highlights differences between colonizes kills living trees saprophyte wood inner bark dead trees. Results assembled 33 Mbp 45 scaffolds, predicted approximately 8,884 genes. The size gene content were similar to those...
The Pleiades Promoter Project integrates genomewide bioinformatics with large-scale knockin mouse production and histological examination of expression patterns to develop MiniPromoters related tools designed study treat the brain by directed gene expression. Genes interest are subjected bioinformatic analysis delineate candidate regulatory regions, which then incorporated into a panel compact human drive regions cell types interest. Using single-copy, homologous-recombination “knockins” in...
Abstract Background The mountain pine beetle (MPB, Dendroctonus ponderosae ) epidemic has affected lodgepole ( Pinus contorta across an area of more than 18 million hectares forests in western Canada, and is a threat to the boreal jack banksiana forest. Defence pines against MPB associated fungal pathogens, as well other pests, involves oleoresin monoterpenes, which are biosynthesized by families terpene synthases (TPSs). Volatile monoterpenes also serve host recognition cues for precursors...
The distinct types of hematological malignancies have different biological mechanisms and prognoses. For instance, myelodysplastic syndrome (MDS) is generally indolent low risk; however, it may transform into acute myeloid leukemia (AML), which much more aggressive. We develop a novel network analysis approach that uses expression eigengenes to delineate the differences between these two diseases. find specific genes in extracellular matrix pathway are underexpressed AML. validate this...
Abstract Background As scientists continue to pursue various 'omics-based research, there is a need for high quality data the most fundamental 'omics of all: genomics. The bacterium Paenibacillus larvae causative agent honey bee disease American foulbrood. If untreated, it can lead demise an entire hive; highly social nature bees also leads easy spread, between both individuals and colonies. Biologists have studied this organism since early 1900s, century later, molecular mechanism infection...
Grosmannia clavigera is a bark beetle-vectored fungal pathogen of pines that causes wood discoloration and may kill trees by disrupting nutrient water transport. Trees respond to attacks from beetles associated fungi releasing terpenoid phenolic defense compounds. It unclear which genes are important for G. clavigera's ability overcome antifungal pine terpenoids phenolics.We constructed seven cDNA libraries eight isolates grown under various culture conditions, Sanger sequenced the 5' 3'...
Meningioma 1 (MN1) is an independent prognostic marker for normal karyotype acute myeloid leukemia (AML), with high expression linked to all-trans retinoic acid resistance and poor survival. MN1 also a potent sufficient oncogene in murine models, strongly dependent on the MEIS1/AbdB-like HOX protein complex transform common progenitors, block differentiation, promote leukemic stem cell self-renewal. To identify key genes pathways underlying activity, we functionally assessed phenotypic...
Chimeric transcripts, including partial and internal tandem duplications (PTDs, ITDs) gene fusions, are important in the detection, prognosis, treatment of human cancers.We describe Barnacle, a production-grade analysis tool that detects such chimeras de novo assemblies RNA-seq data, supports prioritizing them for review validation by reporting relative coverage co-occurring chimeric wild-type transcripts. We demonstrate applications large-scale disease studies, identifying PTDs MLL, ITDs...
Abstract Integration of orthogonal data could provide new opportunities to pinpoint the underlying molecular mechanisms hematologic disorders. Using a novel gene network approach, we integrated DNA methylation from The Cancer Genome Atlas ( n = 194 cases) with corresponding expression profile. Our analysis classified AML patients into low‐, intermediate‐, and high‐risk groups. identified group had significantly shorter overall survival compared low‐risk p ‐value ≤). Specifically, our...