Jones lab

Dr. Jones' team uses bioinformatics to investigate the landscape of mutations present in cancer genomes and the early genomic events that give rise to and promote the progression of cancer. To achieve these goals, his laboratory analyzes Next Generation Sequencing data and develops novel computational approaches and methodologies. A significant aim of Dr. Jones’ research program is to find innovative ways to exploit specific genomic profiles within an individual cancer for therapeutic purposes. For example, his team has identified a number of epigenetic modifications that may potentially be targeted to reverse the effects of cancer initiating mutations. His lab is using computational approaches, such as molecular docking and molecular dynamics, to identify and refine compounds that can modify the cancer epigenome. 

Location

echelon

The Jones Lab is located at Canada's Michael Smith Genome Sciences Centre, Echelon Technology Platform.
 
570 West 7th Avenue 
Vancouver, British Columbia 
V5Z 4S6 

Projects

Selected Publications

The pink salmon genome: Uncovering the genomic consequences of a two-year life cycle

PLoS One
Kris A Christensen, Eric B Rondeau, Dionne Sakhrani, Carlo A Biagi, Hollie Johnson, Jay Joshi, Anne-Marie Flores, Sreeja Leelakumari, Richard Moore, Pawan K Pandoh, Ruth E Withler, Terry D Beacham, Rosalind A Leggatt, Carolyn M Tarpey, Lisa W Seeb, James E Seeb, Steven JM Jones, Robert H Devlin, Ben F Koop

Pink salmon (Oncorhynchus gorbuscha) adults are the smallest of the five Pacific salmon native to the western Pacific Ocean. Pink salmon are also the most abundant of these species and account for a large proportion of the commercial value of the salmon fishery worldwide. A two-year life history of pink salmon generates temporally isolated populations that spawn either in even-years or odd-years. To uncover the influence of this genetic isolation, reference genome assemblies were generated for each year-class and whole genome re-sequencing data was collected from salmon of both year-classes. The salmon were sampled from six Canadian rivers and one Japanese river. At multiple centromeres we identified peaks of Fst between year-classes that were millions of base-pairs long. The largest Fst peak was also associated with a million base-pair chromosomal polymorphism found in the odd-year genome near a centromere. These Fst peaks may be the result of a centromere drive or a combination of reduced recombination and genetic drift, and they could influence speciation. Other regions of the genome influenced by odd-year and even-year temporal isolation and tentatively under selection were mostly associated with genes related to immune function, organ development/maintenance, and behaviour.

Early-stage economic analysis of research-based comprehensive genomic sequencing for advanced cancer care

Journal of Community Genetics
Deirdre Weymann, Janessa Laskin, Steven JM Jones, Robyn Roscoe, Howard J Lim, Daniel J Renouf, Kasmintan A Schrader, Sophie Sun, Stephen Yip, Marco A Marra, Dean A Regier

Genomic research is driving discovery for future population beneft. Limited evidence exists on immediate patient and health system impacts of research participation. This study uses real-world data and quasi-experimental matching to examine early-stage cost and health impacts of research-based genomic sequencing. British Columbia’s Personalized OncoGenomics (POG) single-arm program applies whole genome and transcriptome analysis (WGTA) to characterize genomic landscapes in advanced cancers. Our cohort includes POG patients enrolled between 2014 and 2015 and 1:1 genetic algorithm–matched usual care controls. We undertake a cost consequence analysis and estimate 1-year efects of WGTA on patient management, patient survival, and health system costs reported in 2015 Canadian dollars. WGTA costs are imputed and forecast using system of equations modeling. We use Kaplan-Meier survival analysis to explore survival diferences and inverse probability of censoring weighted linear regression to estimate mean 1-year survival times and costs. Non-parametric bootstrapping simulates sampling distributions and enables scenario analysis, revealing drivers of incremental costs, survival, and net monetary beneft for assumed willingness to pay thresholds. We identifed 230 POG patients and 230 matched controls for cohort inclusion. The mean period cost of research-funded WGTA was $26,211 (SD: $14,191). Sequencing costs declined rapidly, with WGTA forecasts hitting $13,741 in 2021. The incremental healthcare system efect (non-research expenditures) was $5203 (95% CI: 75, 10,424) compared to usual care. No overall survival diferences were observed, but outcome heterogeneity was present. POG patients receiving WGTA-informed treatment experienced incremental survival gains of 2.49 months (95% CI: 1.32, 3.64). Future cost consequences became favorable as WGTA cost drivers declined and WGTAinformed treatment rates improved to 60%. Our study demonstrates the ability of real-world data to support evaluations of only-in-research health technologies. We identify situations where precision oncology research initiatives may produce survival beneft at a cost that is within healthcare systems’ willingness to pay. This economic evidence informs the early-stage healthcare impacts of precision oncology research.

An infant with congenital respiratory insufficiency and diaphragmatic paralysis: A novel BICD2 phenotype?

American Journal of Medical Genetics Part A
Hui-Lin Chin, Stephanie Huynh, Jahanshah Ashkani, Michael Castaldo, Katherine Dixon, Kathryn Selby, Yaoqing Shen, Marie Wright, Cornelius F Boerkoel, Glenda Hendson, Steven JM Jones

Monoallelic pathogenic variants in BICD2 are associated with autosomal dominant Spinal Muscular Atrophy Lower Extremity Predominant 2A and 2B (SMALED2A, SMALED2B). As part of the cellular vesicular transport, complex BICD2 facilitates the flow of constitutive secretory cargoes from the trans-Golgi network, and its dysfunction results in motor neuron loss. The reported phenotypes among patients with SMALED2A and SMALED2B range from a congenital onset disorder of respiratory insufficiency, arthrogryposis, and proximal or distal limb weakness to an adult-onset disorder of limb weakness and contractures. We report an infant with congenital respiratory insufficiency requiring mechanical ventilation, congenital diaphragmatic paralysis, decreased lung volume, and single finger camptodactyly. The infant displayed appropriate antigravity limb movements but had radiological, electrophysiological, and histopathological evidence of myopathy. Exome sequencing and long-read whole-genome sequencing detected a novel de novo BICD2 variant (NM_001003800.1:c.[1543G>A];[=]). This is predicted to encode p.(Glu515Lys); p.Glu515 is located in the coiled-coil 2 mutation hotspot. We hypothesize that this novel phenotype of diaphragmatic paralysis without clear appendicular muscle weakness and contractures of large joints is a presentation of BICD2-related disease.

Draft genome sequence of the lichenized fungus Bacidia gigantensis

Microbiology Resource Announcements
Jessica L Allen, Steven JM Jones, R Troy McMullin

The draft genome sequence of Bacidia gigantensis, a lichenized fungus in the order Lecanorales, was sequenced directly from a herbarium specimen collected from the type locality at Sleeping Giant Provincial Park in Ontario, Canada. Using long-read sequencing on the Oxford Nanopore PromethION platform, we assembled a nearly complete genome sequence.

Optimization of magnetic bead-based nucleic acid extraction for SARS-CoV-2 testing using readily available reagents

Journal of Virological Methods
Simon Haile, Aidan M Nikiforuk, Pawan K Pandoh, David D W Twa, Duane E Smailus, Jason Nguyen, Stephen Pleasance, Angus Wong, Yongjun Zhao, Diane Eisler, Michelle Moksa, Qi Cao, Marcus Wong, Edmund Su, Martin Krzywinski, Jessica Nelson, Andrew J Mungall, Frankie Tsang, Leah M Prentice, Agatha Jassem, Amee R Manges, Steven J M Jones, Robin J Coope, Natalie Prystajecky, Marco A Marra, Mel Krajden, Martin Hirst

The COVID-19 pandemic has highlighted the need for generic reagents and flexible systems in diagnostic testing. Magnetic bead-based nucleic acid extraction protocols using 96-well plates on open liquid handlers are readily amenable to meet this need. Here, one such approach is rigorously optimized to minimize cross-well contamination while maintaining sensitivity.

Contribution of Multiple Inherited Variants to Autism Spectrum Disorder (ASD) in a Family with 3 Affected Siblings

Genes
Jasleen Dhaliwal, Ying Qiao, Kristina Calli, Sally Martell, Simone Race, Chieko Chijiwa, Armansa Glodjo, Steven Jones, Evica Rajcan-Separovic, Stephen W Scherer, Suzanne Lewis

Autism Spectrum Disorder (ASD) is the most common neurodevelopmental disorder in children and shows high heritability. However, how inherited variants contribute to ASD in multiplex families remains unclear. Using whole-genome sequencing (WGS) in a family with three affected children, we identified multiple inherited DNA variants in ASD-associated genes and pathways (RELN, SHANK2, DLG1, SCN10A, KMT2C and ASH1L). All are shared among the three children, except ASH1L, which is only present in the most severely affected child. The compound heterozygous variants in RELN, and the maternally inherited variant in SHANK2, are considered to be major risk factors for ASD in this family. Both genes are involved in neuron activities, including synaptic functions and the GABAergic neurotransmission system, which are highly associated with ASD pathogenesis. DLG1 is also involved in synapse functions, and KMT2C and ASH1L are involved in chromatin organization. Our data suggest that multiple inherited rare variants, each with a subthreshold and/or variable effect, may converge to certain pathways and contribute quantitatively and additively, or alternatively act via a 2nd-hit or multiple-hits to render pathogenicity of ASD in this family. Additionally, this multiple-hits model further supports the quantitative trait hypothesis of a complex genetic, multifactorial etiology for the development of ASDs.

An approach to rapid characterization of DMD copy number variants for prenatal risk assessment

American Journal of Medical Genetics, 2021
Hui-Lin Chin, Kieran O'Neill, Kristal Louie, Lindsay Brown, Kamilla Schlade-Bartusiak, Patrice Eydoux, Rosemarie Rupps, Ali Farahani, Cornelius F Boerkoel, Steven J M Jones

Prenatal detection of structural variants of uncertain significance, including copy number variants (CNV), challenges genetic counseling, and creates ambiguity for expectant parents. In Duchenne muscular dystrophy, variant classification and phenotypic severity of CNVs are currently assessed by familial segregation, prediction of the effect on the reading frame, and precedent data. Delineation of pathogenicity by familial segregation is limited by time and suitable family members, whereas analytical tools can rapidly delineate potential consequences of variants. We identified a duplication of uncertain significance encompassing a portion of the dystrophin gene (DMD) in an unaffected mother and her male fetus. Using long-read whole genome sequencing and alignment of short reads, we rapidly defined the precise breakpoints of this variant in DMD and could provide timely counseling. The benign nature of the variant was substantiated, more slowly, by familial segregation to a healthy maternal uncle. We find long-read whole genome sequencing of clinical utility in a prenatal setting for accurate and rapid characterization of structural variants, specifically a duplication involving DMD.

Rare loss-of-function variants in type I IFN immunity genes are not associated with severe COVID-19

The Journal of Clinical Investigation
Gundula Povysil, Guillaume Butler-Laporte, Ning Shang, Chen Wang, Atlas Khan, Manal Alaamery, Tomoko Nakanishi, Sirui Zhou, Vincenzo Forgetta, Robert JM Eveleigh, Mathieu Bourgey, Naveed Aziz, Steven JM Jones, Bartha Knoppers, Stephen W Scherer, Lisa J Strug, Pierre Lepage, Jiannis Ragoussis, Guillaume Bourque, Jahad Alghamdi, Nora Aljawini, Nour Albes, Hani M Al-Afghani, Bader Alghamdi, Mansour S Almutairi, Ebrahim Sabri Mahmoud, Leen Abu-Safieh, Hadeel El Bardisy, Fawz S Al Harthi, Abdulraheem Alshareef, Bandar Ali Suliman, Saleh A Alqahtani, Abdulaziz Almalik, May M Alrashed, Salam Massadeh, Vincent Mooser, Mark Lathrop, Mohamed Fawzy, Yaseen M Arabi, Hamdi Mbarek, Chadi Saad, Wadha Al-Muftah, Junghyun Jung, Serghei Mangul, Radja Badji, Asma Al Thani, Said I Ismail, Ali G Gharavi, Malak S Abedalthagafi, J Brent Richards, David B Goldstein, Krzysztof Kiryluk

A recent report found that rare predicted loss-of-function (pLOF) variants across 13 candidate genes in TLR3- and IRF7-dependent type I IFN pathways explain up to 3.5% of severe COVID-19 cases. We performed whole-exome or whole-genome sequencing of 1,864 COVID-19 cases (713 with severe and 1,151 with mild disease) and 15,033 ancestry-matched population controls across 4 independent COVID-19 biobanks. We tested whether rare pLOF variants in these 13 genes were associated with severe COVID-19. We identified only 1 rare pLOF mutation across these genes among 713 cases with severe COVID-19 and observed no enrichment of pLOFs in severe cases compared to population controls or mild COVID-19 cases. We found no evidence of association of rare LOF variants in the 13 candidate genes with severe COVID-19 outcomes.

In vitro modeling of glioblastoma initiation using PDGF-AA and p53-null neural progenitors

Neuro-Oncology
Alexandra K Bohm, Jessica DePetro, Carmen E Binding, Amanda Gerber, Nicholas Chahley, N Dan Berger, Mathaeus Ware, Kaitlin Thomas, U Senapathi, Shazreh Bukhari, Cindy Chen, Erin Chahley, Cameron Grisdale, Sam Lawn, Yaping Yu, Raymond Wong, Yaoqing Shen, Hiba Omairi, Reza Mirzaei, Nourah Alshatti, Haley Pedersen, Wee Yong, Samuel Weiss, Jennifer Chan, P J Cimino, John Kelly, Steve Jones, Eric Holland, Michael Blough, Gregory Cairncross

Background

Imagining ways to prevent or treat glioblastoma (GBM) has been hindered by a lack of understanding of its pathogenesis. Although overexpression of platelet derived growth factor with two A-chains (PDGF-AA) may be an early event, critical details of the core biology of GBM are lacking. For example, existing PDGF-driven models replicate its microscopic appearance, but not its genomic architecture. Here we report a model that overcomes this barrier to authenticity.

Methods

Using a method developed to establish neural stem cell cultures, we investigated the effects of PDGF-AA on subventricular zone (SVZ) cells, one of the putative cells of origin of GBM. We microdissected SVZ tissue from p53-null and wild-type adult mice, cultured cells in media supplemented with PDGF-AA, and assessed cell viability, proliferation, genome stability, and tumorigenicity.

Results

Counterintuitive to its canonical role as a growth factor, we observed abrupt and massive cell death in PDGF-AA: wild-type cells did not survive, whereas a small fraction of null cells evaded apoptosis. Surviving null cells displayed attenuated proliferation accompanied by whole chromosome gains and losses. After approximately 100 days in PDGF-AA, cells suddenly proliferated rapidly, acquired growth factor independence, and became tumorigenic in immune-competent mice. Transformed cells had an oligodendrocyte precursor-like lineage marker profile, were resistant to platelet derived growth factor receptor alpha inhibition, and harbored highly abnormal karyotypes similar to human GBM.

Conclusion

This model associates genome instability in neural progenitor cells with chronic exposure to PDGF-AA and is the first to approximate the genomic landscape of human GBM and the first in which the earliest phases of the disease can be studied directly.

Gene Fusions Are Recurrent, Clinically Actionable Gene Rearrangements in Wild-Type Pancreatic Ductal Adenocarcinoma.

Clinical cancer research : an official journal of the American Association for Cancer Research, 2019
Jones, Martin R, Williamson, Laura M, Topham, James T, Lee, Michael K C, Goytain, Angela, Ho, Julie, Denroche, Robert E, Jang, GunHo, Pleasance, Erin, Shen, Yaoquing, Karasinska, Joanna M, McGhie, John P, Gill, Sharlene, Lim, Howard J, Moore, Malcolm J, Wong, Hui-Li, Ng, Tony, Yip, Stephen, Zhang, Wei, Sadeghi, Sara, Reisle, Carolyn, Mungall, Andrew J, Mungall, Karen L, Moore, Richard A, Ma, Yussanne, Knox, Jennifer J, Gallinger, Steven, Laskin, Janessa, Marra, Marco A, Schaeffer, David F, Jones, Steven J M, Renouf, Daniel J
Gene fusions involving neuregulin 1 () have been noted in multiple cancer types and have potential therapeutic implications. Although varying results have been reported in other cancer types, the efficacy of the HER-family kinase inhibitor afatinib in the treatment of fusion-positive pancreatic ductal adenocarcinoma is not fully understood.

Genomic characterization of a well-differentiated grade 3 pancreatic neuroendocrine tumor.

Cold Spring Harbor molecular case studies, 2019
Williamson, Laura M, Steel, Michael, Grewal, Jasleen K, Thibodeau, My Lihn, Zhao, Eric Y, Loree, Jonathan M, Yang, Kevin C, Gorski, Sharon M, Mungall, Andrew J, Mungall, Karen L, Moore, Richard A, Marra, Marco A, Laskin, Janessa, Renouf, Daniel J, Schaeffer, David F, Jones, Steven J M
Pancreatic neuroendocrine neoplasms (PanNENs) represent a minority of pancreatic neoplasms that exhibit variability in prognosis. Ongoing mutational analyses of PanNENs have found recurrent abnormalities in chromatin remodeling genes (e.g., and ), and mTOR pathway genes (e.g., , , and ), some of which have relevance to patients with related familial syndromes. Most recently, grade 3 PanNENs have been divided into two groups based on differentiation, creating a new group of well-differentiated grade 3 neuroendocrine tumors (PanNETs) that have had a limited whole-genome level characterization to date. In a patient with a metastatic well-differentiated grade 3 PanNET, our study utilized whole-genome sequencing of liver metastases for the comparative analysis and detection of single-nucleotide variants, insertions and deletions, structural variants, and copy-number variants, with their biologic relevance confirmed by RNA sequencing. We found that this tumor most notably exhibited a -disrupting fusion, showed a novel fusion, and lacked any somatic variants in , , and .

Application of a Neural Network Whole Transcriptome-Based Pan-Cancer Method for Diagnosis of Primary and Metastatic Cancers.

JAMA network open, 2019
Grewal, Jasleen K, Tessier-Cloutier, Basile, Jones, Martin, Gakkhar, Sitanshu, Ma, Yussanne, Moore, Richard, Mungall, Andrew J, Zhao, Yongjun, Taylor, Michael D, Gelmon, Karen, Lim, Howard, Renouf, Daniel, Laskin, Janessa, Marra, Marco, Yip, Stephen, Jones, Steven J M
A molecular diagnostic method that incorporates information about the transcriptional status of all genes across multiple tissue types can strengthen confidence in cancer diagnosis.

Sources of erroneous sequences and artifact chimeric reads in next generation sequencing of genomic DNA from formalin-fixed paraffin-embedded samples.

Nucleic acids research, 2019
Haile, Simon, Corbett, Richard D, Bilobram, Steve, Bye, Morgan H, Kirk, Heather, Pandoh, Pawan, Trinh, Eva, MacLeod, Tina, McDonald, Helen, Bala, Miruna, Miller, Diane, Novik, Karen, Coope, Robin J, Moore, Richard A, Zhao, Yongjun, Mungall, Andrew J, Ma, Yussanne, Holt, Rob A, Jones, Steven J, Marra, Marco A
Tissues used in pathology laboratories are typically stored in the form of formalin-fixed, paraffin-embedded (FFPE) samples. One important consideration in repurposing FFPE material for next generation sequencing (NGS) analysis is the sequencing artifacts that can arise from the significant damage to nucleic acids due to treatment with formalin, storage at room temperature and extraction. One such class of artifacts consists of chimeric reads that appear to be derived from non-contiguous portions of the genome. Here, we show that a major proportion of such chimeric reads align to both the 'Watson' and 'Crick' strands of the reference genome. We refer to these as strand-split artifact reads (SSARs). This study provides a conceptual framework for the mechanistic basis of the genesis of SSARs and other chimeric artifacts along with supporting experimental evidence, which have led to approaches to reduce the levels of such artifacts. We demonstrate that one of these approaches, involving S1 nuclease-mediated removal of single-stranded fragments and overhangs, also reduces sequence bias, base error rates, and false positive detection of copy number and single nucleotide variants. Finally, we describe an analytical approach for quantifying SSARs from NGS data.

The Genome of the Beluga Whale (Delphinapterus leucas).

Genes, 2017
Jones, Steven J M, Taylor, Gregory A, Chan, Simon, Warren, René L, Hammond, S Austin, Bilobram, Steven, Mordecai, Gideon, Suttle, Curtis A, Miller, Kristina M, Schulze, Angela, Chan, Amy M, Jones, Samantha J, Tse, Kane, Li, Irene, Cheung, Dorothy, Mungall, Karen L, Choo, Caleb, Ally, Adrian, Dhalla, Noreen, Tam, Angela K Y, Troussard, Armelle, Kirk, Heather, Pandoh, Pawan, Paulino, Daniel, Coope, Robin J N, Mungall, Andrew J, Moore, Richard, Zhao, Yongjun, Birol, Inanc, Ma, Yussanne, Marra, Marco, Haulena, Martin
The beluga whale is a cetacean that inhabits arctic and subarctic regions, and is the only living member of the genus . The genome of the beluga whale was determined using DNA sequencing approaches that employed both microfluidic partitioning library and non-partitioned library construction. The former allowed for the construction of a highly contiguous assembly with a scaffold N50 length of over 19 Mbp and total reconstruction of 2.32 Gbp. To aid our understanding of the functional elements, transcriptome data was also derived from brain, duodenum, heart, lung, spleen, and liver tissue. Assembled sequence and all of the underlying sequence data are available at the National Center for Biotechnology Information (NCBI) under the Bioproject accession number PRJNA360851A.

Assembling the 20 Gb white spruce (Picea glauca) genome from whole-genome shotgun sequencing data.

Bioinformatics (Oxford, England), 2013
Birol, Inanc, Raymond, Anthony, Jackman, Shaun D, Pleasance, Stephen, Coope, Robin, Taylor, Greg A, Yuen, Macaire Man Saint, Keeling, Christopher I, Brand, Dana, Vandervalk, Benjamin P, Kirk, Heather, Pandoh, Pawan, Moore, Richard A, Zhao, Yongjun, Mungall, Andrew J, Jaquish, Barry, Yanchuk, Alvin, Ritland, Carol, Boyle, Brian, Bousquet, Jean, Ritland, Kermit, Mackay, John, Bohlmann, Jörg, Jones, Steven J M
White spruce (Picea glauca) is a dominant conifer of the boreal forests of North America, and providing genomics resources for this commercially valuable tree will help improve forest management and conservation efforts. Sequencing and assembling the large and highly repetitive spruce genome though pushes the boundaries of the current technology. Here, we describe a whole-genome shotgun sequencing strategy using two Illumina sequencing platforms and an assembly approach using the ABySS software. We report a 20.8 giga base pairs draft genome in 4.9 million scaffolds, with a scaffold N50 of 20,356 bp. We demonstrate how recent improvements in the sequencing technology, especially increasing read lengths and paired end reads from longer fragments have a major impact on the assembly contiguity. We also note that scalable bioinformatics tools are instrumental in providing rapid draft assemblies.

Circos: an information aesthetic for comparative genomics.

Genome research, 2009
Krzywinski, Martin, Schein, Jacqueline, Birol, Inanç, Connors, Joseph, Gascoyne, Randy, Horsman, Doug, Jones, Steven J, Marra, Marco A
We created a visualization tool called Circos to facilitate the identification and analysis of similarities and differences arising from comparisons of genomes. Our tool is effective in displaying variation in genome structure and, generally, any other kind of positional relationships between genomic intervals. Such data are routinely produced by sequence alignments, hybridization arrays, genome mapping, and genotyping studies. Circos uses a circular ideogram layout to facilitate the display of relationships between pairs of positions by the use of ribbons, which encode the position, size, and orientation of related genomic elements. Circos is capable of displaying data as scatter, line, and histogram plots, heat maps, tiles, connectors, and text. Bitmap or vector images can be created from GFF-style data inputs and hierarchical configuration files, which can be easily generated by automated tools, making Circos suitable for rapid deployment in data analysis and reporting pipelines.

Staff

Dr. Erin Pleasance

Staff Scientist

Dr. Jianhong An

Staff Scientist

Dr. Mikhail (Misha) Bilenky

Staff Scientist

Dr. Gordon Robertson

Staff Scientist

Dr. Veronika Csizmok

Research Associate

Dr. Chandra Lebovitz

Research Associate

Dr. Kathleen Wee

Research Associate

Dr. Rohan Abraham

Research Associate

Dr. Jahanshah Ashkani

Research Associate

Dr. Jean-Michel Garant

Research Associate

Dr. Sreeja Leelakumari

Research Associate

Dr. Cameron Grisdale

Research Associate

Dr. Cathy Zhang

Research Associate

Dr. Kieran O'Neill

Process Development Coordinator

Sitanshu Gakkhar

Computational Biologist

Melika Bonakdar

Computational Biologist

Greg Taylor

Computational Biologist

Emma Titmuss

Research Programmer

Courtney Gosselin

Research Programmer

Jimmy Li

Research Programmer

Postdoctoral Fellows

Dr. Katherine Dixon

Postdoctoral Fellow

Dr. Jasleen Grewal

Postdoctoral Fellow

Trainees

Vahid Akbari

Graduate Student

Sarah Dada

Graduate Student

Luka Culibrk

Graduate Student

Faeze Keshavarz

Graduate Student

Tyler Kolisnik

Graduate Student

Caralyn Reisle

Graduate Student

Sina Hossein Zadeh

Student Researcher - M.D. Flex Program

Daniel Shirvani

Student Volunteer

Open Positions

Postdoctoral Fellow–Bioinformatics

Canada’s Michael Smith Genome Sciences Centre (GSC)

Today’s Research. Tomorrow’s Medicine.

The GSC is a department of the BC Cancer Research Institute and a high-throughput genome sequencing facility. We are leaders in genomics, proteomics and bioinformatics in pursuit of novel treatment strategies for cancers and other diseases.

Among the world’s first genome centres to be established within a cancer clinic, for more than two decades our scientists and innovators have been designing and deploying cutting-edge technologies to benefit health and advance clinical research.

Among the GSC’s most significant accomplishments are the first publication to demonstrate the use of whole-genome sequencing to inform cancer treatment planning, the first published sequence of the SARS coronavirus genome and major contributions to the first physical map of the human genome as part of the Human Genome Project.

By joining the GSC you will become part of an exceptional and diverse team of scientists, clinicians, experts and professionals operating at the leading edge of clinical research. We look for people who share our core values—science, timeliness, respect—to join us on our mission to use genome science for the betterment of health and society.

Summary

Job Reference No: PDF_01553_Jones Lab_2021_10_01

The GSC is currently looking for a Post-Doctoral Fellow to work on the Genome Canada funded LSARP, “Canada’s Earth BioGenome project”. 

The successful incumbent will work with the project team to lead the activities on the development, application and validation of novel approaches and workflows in the area of integrated de novo genome assembly over multiple sequencing technologies. They will develop automated bioinformatics workflow as well as assembly submission. They will also work closely together with Earth BioGenome Project (EBP) consortium on the sequencing and assembly standards. The successful incumbent will work with project leaders to ensure all scientific milestones are achieved and contribute to progress reporting as required. There will be expectations to represent the project within the global EBP consortium and the development of outreach materials and website information. Opportunities will exist for further research on the genomic information developed and for scholarly publication.​

Duties

  • Work with multidisciplinary scientists at the GSC and collaborators to analyze whole genome and transcriptome sequence data, and set up collaborative working plans.
  • Develop and maintain bioinformatics pipelines for genome assembly and data analysis.
  • Produce written documentation of algorithms, validations, SOPs, and other processes related to pipeline updates and procedures as required.
  • Present results of bioinformatics software testing internally and externally.
  • Perform literature searches, testing and validation of new data analysis software related to bioinformatics pipelines.
  • Perform other related duties as required.

Eligibility

Skills and Abilities

  • Knowledge of genomics, genome assembly, and genome analysis software.
  • Fluency in one or more programming languages, such as Python, Javascript and SQL.
  • Experience working in a UNIX/Linus environment and writing shell scripts.
  • Previous API development projects using Open API or Rest API is a plus.
  • Excellent communication and organization skills and ability to efficiently manage time and workflow, including skillfully prioritizing both long-term projects and day-to-day responsibilities.
  • Ability for critical thinking and independent learning.

Apply

Please submit a detailed cover letter and resume to bcgscjobs@bcgsc.ca, using PDF_01553_Jones Lab_2021_10_01 in the subject line of your email.

This posting will remain online until filled.

Due to current COVID-19 restrictions, the position would require working remotely within British Columbia on a temporary basis with an ability to come to the normal workplace within reasonable notice. This restriction would be re-evaluated after finalization of reopening plans.

As per the current Public Health Order, full vaccination against COVID-19 is a condition of employment with PHSA as of October 26, 2021.

We believe that equity, diversity and inclusivity are essential for the advancement of human knowledge and science.

We welcome all applicants and provide all employees with equal opportunity for advancement, regardless of race, colour, ancestry, place of origin, political belief, religion, marital status, family status, physical or mental disability, sex, sexual orientation, gender identity or expression, age, conviction of a criminal or summary conviction offence unrelated to their employment.

All qualified candidates are encouraged to apply; however, Canadian citizens and permanent residents will be given priority.

Research Associate–Bioinformatics

Canada’s Michael Smith Genome Sciences Centre (GSC)

Today’s Research. Tomorrow’s Medicine.

The GSC is a department of the BC Cancer Research Institute and a high-throughput genome sequencing facility. We are leaders in genomics, proteomics and bioinformatics in pursuit of novel treatment strategies for cancers and other diseases.

Among the world’s first genome centres to be established within a cancer clinic, for more than two decades our scientists and innovators have been designing and deploying cutting-edge technologies to benefit health and advance clinical research.

Among the GSC’s most significant accomplishments are the first publication to demonstrate the use of whole-genome sequencing to inform cancer treatment planning, the first published sequence of the SARS coronavirus genome and major contributions to the first physical map of the human genome as part of the Human Genome Project.

By joining the GSC you will become part of an exceptional and diverse team of scientists, clinicians, experts and professionals operating at the leading edge of clinical research. We look for people who share our core values — science, timeliness, respect — to join us on our mission to use genome science for the betterment of health and society.

Job Reference No.; RA_R00006_Jones Lab_2021_09_28

Summary

The GSC is currently looking for a Research Associate to work on the Genome Canada funded LSARP, “Canada’s Earth BioGenome project”. 

The successful incumbent will work with the project team to lead the activities on the development, application and validation of novel approaches and workflows in the area of integrated de novo genome assembly over multiple sequencing technologies. They will develop automated bioinformatics workflow as well as assembly submission. They will also work closely together with Earth BioGenome Project (EBP) consortium on the sequencing and assembly standards. They will work with Project Leaders to ensure all scientific milestones are achieved and contribute to progress reporting as required. There will be expectations to represent the project within the global EBP consortium and the development of outreach materials and website information. Opportunities will exist for further research on the genomic information developed and for scholarly publication.​

Duties

  • Work with multidisciplinary scientists at the GSC and collaborators to analyze whole genome and transcriptome sequence data, and set up collaborative working plans.
  • Develop and maintain bioinformatic pipelines for genome assembly and data analysis.
  • Produces written documentation of algorithms, validations, SOPs, and other processes related to pipeline updates and procedures as required.
  • Presents results of bioinformatics software testing internally and externally.
  • Performs literature searches, testing and validation of new data analysis software related to bioinformatics pipelines.
  • Performs other related duties as required.

Skills and Abilities

  • Expertise in bioinformatics, emphasizing genome sequence analysis and gene annotation.
  • Knowledge and experience using scientific tools, technologies and online resources as pertaining to de novo genome assembly.
  • Fluency in multiple programming languages, including Python, Javascript and SQL.
  • Expertise developing and operating in a UNIX/Linus environment and writing shell scripts.
  • Experience developing custom scripts and pipelines using high performance computing and other available tools. Pipelines may include de novo assembly, annotation, database query, pan-genome construction and visualization tools, RNA-seq, phylogenetic tree reconstruction.
  • Previous API development projects using Open API or Rest API is a plus.
  • Excellent communication and organization skills, and ability to efficiently manage time and workflow, including skillfully prioritizing both long-term projects and day-to-day responsibilities.
  • Ability for critical thinking and independent learning.
  • Experience in a supervisory role is an asset.  

Apply

Please submit a detailed cover letter and resume to bcgscjobs@bcgsc.ca, using RA_R00006_Jones Lab_2021_09_28 in the subject line of your email.

This position will remain online until filled.

Due to current COVID-19 restrictions, the position would require working remotely within British Columbia on a temporary basis with an ability to come to the normal workplace within reasonable notice. This restriction would be re-evaluated after finalization of reopening plans.

As per the current Public Health Order, full vaccination against COVID-19 is a condition of employment with PHSA as of October 26, 2021.

We believe that equity, diversity and inclusivity are essential for the advancement of human knowledge and science.

We welcome all applicants and provide all employees with equal opportunity for advancement, regardless of race, colour, ancestry, place of origin, political belief, religion, marital status, family status, physical or mental disability, sex, sexual orientation, gender identity or expression, age, conviction of a criminal or summary conviction offence unrelated to their employment.

All qualified candidates are encouraged to apply; however, Canadian citizens and permanent residents will be given priority.

Research Programmer - Jones Lab

Canada’s Michael Smith Genome Sciences Centre (GSC)

Today’s Research. Tomorrow’s Medicine.

The GSC is a department of the BC Cancer Research Institute and a high-throughput genome sequencing facility. We are leaders in genomics, proteomics and bioinformatics in pursuit of novel treatment strategies for cancers and other diseases.

Among the world’s first genome centres to be established within a cancer clinic, for more than two decades our scientists and innovators have been designing and deploying cutting-edge technologies to benefit health and advance clinical research.

Among the GSC’s most significant accomplishments are the first publication to demonstrate the use of whole-genome sequencing to inform cancer treatment planning, the first published sequence of the SARS coronavirus genome and major contributions to the first physical map of the human genome as part of the Human Genome Project.

By joining the GSC you will become part of an exceptional and diverse team of scientists, clinicians, experts and professionals operating at the leading edge of clinical research. We look for people who share our core values—science, timeliness, respect—to join us on our mission to use genome science for the betterment of health and society.

Summary

Job Reference No: RP_R00008_Jones Lab_2021_07_30

The GSC is looking for an enthusiastic and self-motivated Research Programmer to work on the next generation of federated genome and health data sharing platform, CanDIG—a Canadian data-sharing platform contributing to the development of an international effort to facilitate information exchange as part of the Global Alliance for Genomics & Health (GA4GH). CanDIG also supports large-scale provincial and national data sharing projects, including BC Cancer’s Personalized OncoGenomics program, the Terry Fox Research Institute's (TFRI) PROFYLE project and the TFRI-led Marathon of Hope Cancer Centres Network—a major federal initiative to accelerate the adoption of precision medicine for cancer in Canada. This role requires a combination of interest in DNA technology and a strong background in software development.

Key Responsibilities

  • Designs, plans and implements computer modeling of research data.
  • Works with other project team members to develop and test code, and implements software.
  • Develops graphical user interfaces.
  • Prepares programming documentation in accordance with prescribed standards.
  • Conducts literature reviews and provides input and recommendations to the Department Head or Principal Investigator regarding new computer applications or statistical techniques.
  • Participates in the lab meetings and presents work for review by others.
  • May provide day to day work direction to others.
  • Provides contributions to the preparation and/or presentation of research papers.

Qualifications

The successful candidate will have an undergraduate degree in computer science, bioinformatics or a related subject.

Abilities

  • 2+ years of experience in Python programming.
  • Previous experience or exposure in the bioinformatics settings.
  • Full stack web development experience with web frameworks such as Flask or Django.
  • Previous experience in designing, implementing and testing REST APIs.
  • General understanding or previous experience in microservice architecture and development.
  • General knowledge in Unix environment, Version Control (Git), and Agile methodologies. 
  • The position requires working with a wide variety of researchers, software developers and clinicians, thus excellent communication skills are essential.

Assets

  • Experience or knowledge in handling genomics data files.
  • Prior experience in developing front-end applications using React.js.
  • Experience building rich queries using GraphQL or other data query language.
  • Experience working with distributed systems.
  • Basic understanding of DNA technology or previous work experience with genetic data is a plus, but not required for the position.

Apply

Please submit a detailed cover letter and resume to bcgscjobs@bcgsc.ca, using Job Reference No: RP_R00008_Jones Lab_2021_07_30 in the subject line of your email.

This posting will remain online until filled.

Important

Due to current COVID-19 restrictions, the position would require working remotely within British Columbia on a temporary basis with an ability to come to the normal workplace within reasonable notice. This restriction would be re-evaluated after finalization of reopening plans.

As per the current Public Health Order, full vaccination against COVID-19 is a condition of employment with PHSA as of October 26, 2021.

We believe that diversity and inclusivity are essential for the advancement of human knowledge and science.

We welcome all applicants and provide all employees with equal opportunity for advancement, regardless of race, colour, ancestry, place of origin, political belief, religion, marital status, family status, physical or mental disability, sex, sexual orientation, gender identity or expression, age, conviction of a criminal or summary conviction offence unrelated to their employment.

All qualified candidates are encouraged to apply; however, Canadian citizens and permanent residents will be given priority.

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