Karsan lab

The Karsan Lab focuses on two major areas: 

  1. Understanding the molecular basis of myeloid malignancies, in particular the preleukemic bone marrow failure conditions called myelodysplastic syndromes (MDS); and 
  2. Determining the role of the endothelium in the development of the hematopoietic system. With respect to both areas we have been studying the role of two pathways: innate immune signaling as represented by the Toll-like receptor (TLR) pathways, and the Notch signaling pathway.



BC Cancer Research Centre
675 West 10th Avenue 
Vancouver, British Columbia 
V5Z 1L3 


Automation of the Clinical Bioinformatics Pipeline at the Centre for Clinical Genomics (Genome BC)

The aim of this project is to streamline the clinical bioinformatics pipeline by creating an automated and modular framework that will reduce training time, reduce reporting turnaround time, facilitate adaptation to new tools and changes to wet lab processes and reduce errors through tracking of information from the entire pipeline.

Development of an automated end-to-end next generation sequencing assay to detect all classes of genetic variant in a single diagnostic test

The aim of this project is to create a single genetic assay that will provide a comprehensive panel of cancer mutations required for both standard therapy and for patients to participate in cancer research.

The Terry Fox New Frontiers Program Project Grant in Exploiting Pathogenic Mechanisms in Acute Leukemia for Clinical Translation

The long term goal of this project is to better understand the difference between normal blood forming cells and leukemic cells. The lab aims to identify and exploit vulnerable disease causing pathways that may be shared across different types of acute leukemias.

Selected Publications

Loss of lenalidomide-induced megakaryocytic differentiation leads to therapy resistance in del(5q) myelodysplastic syndrome.

Nature cell biology, 2020
Martinez-Høyer, Sergio, Deng, Yu, Parker, Jeremy, Jiang, Jihong, Mo, Angela, Docking, T Roderick, Gharaee, Nadia, Li, Jenny, Umlandt, Patricia, Fuller, Megan, Jädersten, Martin, Kulasekararaj, Austin, Malcovati, Luca, List, Alan F, Hellström-Lindberg, Eva, Platzbecker, Uwe, Karsan, Aly
Interstitial deletion of the long arm of chromosome 5 (del(5q)) is the most common structural genomic variant in myelodysplastic syndromes (MDS){{sup}}1{{/sup}}. Lenalidomide (LEN) is the treatment of choice for patients with del(5q) MDS, but half of the responding patients become resistant{{sup}}2{{/sup}} within 2 years. TP53 mutations are detected in ~20% of LEN-resistant patients{{sup}}3{{/sup}}. Here we show that patients who become resistant to LEN harbour recurrent variants of TP53 or RUNX1. LEN upregulated RUNX1 protein and function in a CRBN- and TP53-dependent manner in del(5q) cells, and mutation or downregulation of RUNX1 rendered cells resistant to LEN. LEN induced megakaryocytic differentiation of del(5q) cells followed by cell death that was dependent on calpain activation and CSNK1A1 degradation{{sup}}4,5{{/sup}}. We also identified GATA2 as a LEN-responsive gene that is required for LEN-induced megakaryocyte differentiation. Megakaryocytic gene-promoter analyses suggested that LEN-induced degradation of IKZF1 enables a RUNX1-GATA2 complex to drive megakaryocytic differentiation. Overexpression of GATA2 restored LEN sensitivity in the context of RUNX1 or TP53 mutations by enhancing LEN-induced megakaryocytic differentiation. Screening for mutations that block LEN-induced megakaryocytic differentiation should identify patients who are resistant to LEN.

Sample Tracking Using Unique Sequence Controls.

The Journal of molecular diagnostics : JMD, 2020
Moore, Richard A, Zeng, Thomas, Docking, T Roderick, Bosdet, Ian, Butterfield, Yaron S, Munro, Sarah, Li, Irene, Swanson, Lucas, Starks, Elizabeth R, Tse, Kane, Mungall, Andrew J, Holt, Robert A, Karsan, Aly
Sample tracking and identity are essential when processing multiple samples in parallel. Sequencing applications often involve high sample numbers, and the data are frequently used in a clinical setting. As such, a simple and accurate intrinsic sample tracking process through a sequencing pipeline is essential. Various solutions have been implemented to verify sample identity, including variant detection at the start and end of the pipeline using arrays or genotyping, bioinformatic comparisons, and optical barcoding of samples. None of these approaches are optimal. To establish a more effective approach using genetic barcoding, we developed a panel of unique DNA sequences cloned into a common vector. A unique DNA sequence is added to the sample when it is first received and can be detected by PCR and/or sequencing at any stage of the process. The control sequences are approximately 200 bases long with low identity to any sequence in the National Center for Biotechnology Information nonredundant database (<30 bases) and contain no long homopolymer (>7) stretches. When a spiked next-generation sequencing library is sequenced, sequence reads derived from this control sequence are generated along with the standard sequencing run and are used to confirm sample identity and determine cross-contamination levels. This approach is used in our targeted clinical diagnostic whole-genome and RNA-sequencing pipelines and is an inexpensive, flexible, and platform-agnostic solution.

Fixation Effects on Variant Calling in a Clinical Resequencing Panel.

The Journal of molecular diagnostics : JMD, 2019
Parker, Jeremy D K, Yap, Shyong Quin, Starks, Elizabeth, Slind, Jillian, Swanson, Lucas, Docking, T Roderick, Fuller, Megan, Zhou, Chen, Walker, Blair, Filipenko, Douglas, Xiong, Wei, Karimuddin, Ahmer A, Phang, P Terry, Raval, Manoj, Brown, Carl J, Karsan, Aly
Formalin fixation is the standard method for the preservation of tissue for diagnostic purposes, including pathologic review and molecular assays. However, this method is known to cause artifacts that can affect the accuracy of molecular genetic test results. We assessed the applicability of alternative fixatives to determine whether these perform significantly better on next-generation sequencing assays, and whether adequate morphology is retained for primary diagnosis, in a prospective study using a clinical-grade, laboratory-developed targeted resequencing assay. Several parameters relating to sequencing quality and variant calling were examined and quantified in tumor and normal colon epithelial tissues. We identified an alternative fixative that suppresses many formalin-related artifacts while retaining adequate morphology for pathologic review.

Endothelial Sash1 Is Required for Lung Maturation through Nitric Oxide Signaling.

Cell reports, 2019
Coulombe, Patrick, Paliouras, Grigorios N, Clayton, Ashley, Hussainkhel, Angela, Fuller, Megan, Jovanovic, Vida, Dauphinee, Shauna, Umlandt, Patricia, Xiang, Ping, Kyle, Alistair H, Minchinton, Andrew I, Humphries, R Keith, Hoodless, Pamela A, Parker, Jeremy D K, Wright, Joanne L, Karsan, Aly
The sterile alpha motif (SAM) and SRC homology 3 (SH3) domain containing protein 1 (Sash1) acts as a scaffold in TLR4 signaling. We generated Sash1{{sup}}-/-{{/sup}} mice, which die in the perinatal period due to respiratory distress. Constitutive or endothelial-restricted Sash1 loss leads to a delay in maturation of alveolar epithelial cells causing reduced surfactant-associated protein synthesis. We show that Sash1 interacts with β-arrestin 1 downstream of the TLR4 pathway to activate Akt and endothelial nitric oxide synthase (eNOS) in microvascular endothelial cells. Generation of nitric oxide downstream of Sash1 in endothelial cells affects alveolar epithelial cells in a cGMP-dependent manner, inducing maturation of alveolar type 1 and 2 cells. Thus, we identify a critical cell nonautonomous function for Sash1 in embryonic development in which endothelial Sash1 regulates alveolar epithelial cell maturation and promotes pulmonary surfactant production through nitric oxide signaling. Lung immaturity is a major cause of respiratory distress and mortality in preterm infants, and these findings identify the endothelium as a potential target for therapy.

Genomic testing in myeloid malignancy.

International journal of laboratory hematology, 2019
Docking, T Roderick, Karsan, Aly
Clinical genetic testing in the myeloid malignancies is undergoing a rapid transition from the era of cytogenetics and single-gene testing to an era dominated by next-generation sequencing (NGS). This transition promises to better reveal the genetic alterations underlying disease, but there are distinct risks and benefits associated with different NGS testing platforms. NGS offers the potential benefit of being able to survey alterations across a wider set of genes, but analytic and clinical challenges associated with incidental findings, germ line variation, turnaround time, and limits of detection must be addressed. Additionally, transcriptome-based testing may offer several distinct benefits beyond traditional DNA-based methods. In addition to testing at disease diagnosis, research indicates potential benefits of genetic testing both prior to disease onset and at remission. In this review, we discuss the transition from the era of cytogenetics and single-gene tests to the era of NGS panels and genome-wide sequencing-highlighting both the potential and drawbacks of these novel technologies.

miR-143/145 differentially regulate hematopoietic stem and progenitor activity through suppression of canonical TGFβ signaling.

Nature communications, 2018
Lam, Jeffrey, van den Bosch, Marion, Wegrzyn, Joanna, Parker, Jeremy, Ibrahim, Rawa, Slowski, Kate, Chang, Linda, Martinez-Høyer, Sergio, Condorelli, Gianluigi, Boldin, Mark, Deng, Yu, Umlandt, Patricia, Fuller, Megan, Karsan, Aly
Expression of miR-143 and miR-145 is reduced in hematopoietic stem/progenitor cells (HSPCs) of myelodysplastic syndrome patients with a deletion in the long arm of chromosome 5. Here we show that mice lacking miR-143/145 have impaired HSPC activity with depletion of functional hematopoietic stem cells (HSCs), but activation of progenitor cells (HPCs). We identify components of the transforming growth factor β (TGFβ) pathway as key targets of miR-143/145. Enforced expression of the TGFβ adaptor protein and miR-145 target, Disabled-2 (DAB2), recapitulates the HSC defect seen in miR-143/145{{sup}}-/-{{/sup}} mice. Despite reduced HSC activity, older miR-143/145{{sup}}-/-{{/sup}} and DAB2-expressing mice show elevated leukocyte counts associated with increased HPC activity. A subset of mice develop a serially transplantable myeloid malignancy, associated with expansion of HPC. Thus, miR-143/145 play a cell context-dependent role in HSPC function through regulation of TGFβ/DAB2 activation, and loss of these miRNAs creates a preleukemic state.

Applications of Bayesian network models in predicting types of hematological malignancies.

Scientific reports, 2018
Agrahari, Rupesh, Foroushani, Amir, Docking, T Roderick, Chang, Linda, Duns, Gerben, Hudoba, Monika, Karsan, Aly, Zare, Habil
Network analysis is the preferred approach for the detection of subtle but coordinated changes in expression of an interacting and related set of genes. We introduce a novel method based on the analyses of coexpression networks and Bayesian networks, and we use this new method to classify two types of hematological malignancies; namely, acute myeloid leukemia (AML) and myelodysplastic syndrome (MDS). Our classifier has an accuracy of 93%, a precision of 98%, and a recall of 90% on the training dataset (n = 366); which outperforms the results reported by other scholars on the same dataset. Although our training dataset consists of microarray data, our model has a remarkable performance on the RNA-Seq test dataset (n = 74, accuracy = 89%, precision = 88%, recall = 98%), which confirms that eigengenes are robust with respect to expression profiling technology. These signatures are useful in classification and correctly predicting the diagnosis. They might also provide valuable information about the underlying biology of diseases. Our network analysis approach is generalizable and can be useful for classifying other diseases based on gene expression profiles. Our previously published Pigengene package is publicly available through Bioconductor, which can be used to conveniently fit a Bayesian network to gene expression data.

Identification of miR-145 and miR-146a as mediators of the 5q- syndrome phenotype.

Nature medicine, 2010
Starczynowski, Daniel T, Kuchenbauer, Florian, Argiropoulos, Bob, Sung, Sandy, Morin, Ryan, Muranyi, Andrew, Hirst, Martin, Hogge, Donna, Marra, Marco, Wells, Richard A, Buckstein, Rena, Lam, Wan, Humphries, R Keith, Karsan, Aly
5q- syndrome is a subtype of myelodysplastic syndrome characterized by severe anemia and variable neutropenia but normal or high platelet counts with dysplastic megakaryocytes. We examined expression of microRNAs (miRNAs) encoded on chromosome 5q as a possible cause of haploinsufficiency. We show that deletion of chromosome 5q correlates with loss of two miRNAs that are abundant in hematopoietic stem/progenitor cells (HSPCs), miR-145 and miR-146a, and we identify Toll-interleukin-1 receptor domain-containing adaptor protein (TIRAP) and tumor necrosis factor receptor-associated factor-6 (TRAF6) as respective targets of these miRNAs. TIRAP is known to lie upstream of TRAF6 in innate immune signaling. Knockdown of miR-145 and miR-146a together or enforced expression of TRAF6 in mouse HSPCs resulted in thrombocytosis, mild neutropenia and megakaryocytic dysplasia. A subset of mice transplanted with TRAF6-expressing marrow progressed either to marrow failure or acute myeloid leukemia. Thus, inappropriate activation of innate immune signals in HSPCs phenocopies several clinical features of 5q- syndrome.

Jagged1-mediated Notch activation induces epithelial-to-mesenchymal transition through Slug-induced repression of E-cadherin.

The Journal of experimental medicine, 2007
Leong, Kevin G, Niessen, Kyle, Kulic, Iva, Raouf, Afshin, Eaves, Connie, Pollet, Ingrid, Karsan, Aly
Aberrant expression of Jagged1 and Notch1 are associated with poor outcome in breast cancer. However, the reason that Jagged1 and/or Notch overexpression portends a poor prognosis is unknown. We identify Slug, a transcriptional repressor, as a novel Notch target and show that elevated levels of Slug correlate with increased expression of Jagged1 in various human cancers. Slug was essential for Notch-mediated repression of E-cadherin, which resulted in beta-catenin activation and resistance to anoikis. Inhibition of ligand-induced Notch signaling in xenografted Slug-positive/E-cadherin-negative breast tumors promoted apoptosis and inhibited tumor growth and metastasis. This response was associated with down-regulated Slug expression, reexpression of E-cadherin, and suppression of active beta-catenin. Our findings suggest that ligand-induced Notch activation, through the induction of Slug, promotes tumor growth and metastasis characterized by epithelial-to-mesenchymal transition and inhibition of anoikis.

Recent insights into the role of Notch signaling in tumorigenesis.

Blood, 2006
Leong, Kevin G, Karsan, Aly
Members of the Notch family of transmembrane receptors play an important role in cell fate determination. Over the past decade, a role for Notch in the pathogenesis of hematologic and solid malignancies has become apparent. Numerous cellular functions and microenvironmental cues associated with tumorigenesis are modulated by Notch signaling, including proliferation, apoptosis, adhesion, epithelial-to-mesenchymal transition, and angiogenesis. It is becoming increasingly evident that Notch signaling can be both oncogenic and tumor suppressive. This review highlights recent findings regarding the molecular and functional aspects of Notch-mediated neoplastic transformation. In addition, cellular mechanisms that potentially explain the complex role of Notch in tumorigenesis are discussed.




Kenyon Alexander

Research Programmer

Joshua Bridgers

Staff Scientist

Grace Cole

Research Assistant

Deborah Deng

Research Assistant

Anita Fang

Projects Manager

Chad Fibke

Research Programmer

Maria Ho

Administrative Assistant

Jihong Jiang

Research Assistant

Christina May

Research Associate

Jeremy Parker

Staff Scientist

Zahra Jalali Sefid Dashti

Research Programmer

Derek Tam

Computational Biologist


Vijay Suresh Akhade

Post-Doctoral Fellow

Nadia Gharaee

Graduate Student

Aparna Gopal

Graduate Student

Jennifer Grants

Post-Doctoral Fellow

Patrick Lac

Graduate Student

Angela Mo

Graduate Student

Xuan Wang

Graduate Student


Patrick Coulombe

Graduate Student

Rod Docking

Graduate Student

Arshvir Kaur

Co-op Student

Jessica Tran

Research Assistant

Open Positions

Research Programmer

About us
Canada's Michael Smith Genome Sciences Centre (GSC) at BC Cancer is an international leader in genomics, proteomics, and bioinformatics for precision medicine. By developing and deploying genome sequencing, computational and analytical technology, we are creating novel strategies to prevent and diagnose cancers and other diseases, uncovering new therapeutic targets, and helping the world realize the social and economic benefits of genome science

Learn more about how the GSC is Bringing Genomics to Life.

Why work at the GSC
As the first genome centre to be established within a cancer clinic, our story began by thinking outside of the box. From being the first in the world to sequence the SARS coronavirus during the 2003 global outbreak to publishing the first study demonstrating the use of whole-genome sequencing to influence personalized cancer treatment planning in 2010, our passion for pushing scientific frontiers continues to this day.

Our technology platforms enable the transformative science being done at the GSC, but it is our world-class team of scientists and innovators that make it happen. By joining the GSC you will become part of a diverse and dedicated group of biologists, bioinformaticians, computer scientists, computational biologists, biochemists, engineers, and clinicians. We look for people who share our core values—science, timeliness, and respect—to join us in our mission to provide genomics, bioinformatics, and proteomics technology and expertise for the benefit of human health and society.

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.

*Due to COVID-19 restrictions, the position would require working remotely.  This restriction would be re-evaluated upon re-contracting*

Role Summary

The Karsan lab team at Canada’s Michael Smith Genome Sciences Centre (GSC) is seeking a research programmer to join a Genome British Columbia software automation project. The team will be working with the Karsan lab, which is responsible for developing high-throughput, clinically accredited pipelines to analyse sequenced data from genomic assays for individualized patient management of cancer. We seek candidates with strong Python software and programming skills to automate and improve existing pipelines and potentially incorporate third-party software into the system.

The role is ideally suited for a creative individual with a strong interest in software development and testing, data analysis, and automation within a high throughput academic setting.

Key responsibilities

  • Design, plan, and implement automated bioinformatics pipelines to meet the objectives of the project
  • Work with other project team members to develop and test code, and implement software
  • Evaluate third-party software and incorporate new systems into legacy systems
  • Produce thorough but concise written documentation of algorithms, validations, SOPs, and other processes and procedures as required


Education, training and experience

  • Graduation from a recognized Bachelor of Science Program in Computer Science. A Master’s degree in a relevant field would be a strong asset. 
  • Two (2) years of recent related experience or an equivalent combination of education, training, and experience acceptable to the project lead.

Core Skills and Abilities 

  • Expertise with Python 3.X and able to provide links to code samples via GitHub or another open repository
  • Comfortable working in a Unix environment, including experience with shell scripting and common command-line tools
  • Familiarity with molecular and cellular biology
  • Excellent verbal and written communication skills.
  • Demonstrated ability to efficiently organize work assignments and establish priorities.
  • Demonstrated interpersonal skills including the ability to work effectively with others in a team environment.

Additional Assets

  • Familiarity in statistical analysis using modern computational tools.  Experience with any relevant tools will be considered, but R and Python are preferred
  • Familiarity with the development, testing, and maintenance of relational databases
  • Familiarity in next-generation sequencing
  • Experience with software testing
  • Experience with Agile software practices
  • Functional knowledge of distributed version control systems, such as SVN or GIT

To Apply

Please email your cover letter and resume to bcgscjobs@bcgsc.ca

Please note that this position will remain posted until filled.

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