Post Doctoral Fellow - Jones Lab 

BC Cancer 

Vancouver, BC

 

 

 

The post-doctoral fellow will lead the development of an integrated analysis pipeline for detecting minimal residual disease in head and neck cancer patients by analyzing longitudinal plasma ctDNA. Using whole-genome sequencing from both Illumina and Oxford Nanopore platforms, the fellow will combine genomic mutations, copy-number alterations, methylation signatures, fragmentomics and viral integration data to sensitively track tumour burden over time. They will adapt and create bioinformatics methods, apply tumour-informed analyses using matched tumour and normal WGS, and analyze baseline and follow-up blood samples to identify early ctDNA signals before clinical standard of care recurrence. The fellow will collaborate within the GSC and PATH project to produce reports and manuscripts, and help scale the pipeline for future studies to impact cancer patient care.

 

 

 

About the GSC

 

Advancing Genomics Technologies for Health and Life Sciences.

 

 

The Michael Smith Genome Sciences Centre (GSC), a provincial program within the Provincial Health Services Authority (PHSA), is a recognized international leader in genomics, bioinformatics, and genome technology innovation. By developing and deploying cutting-edge sequencing and computational platforms, the GSC supports breakthrough research across cancer, rare and infectious diseases, and the broader life sciences. Our work enables earlier diagnosis, novel therapeutic approaches, and transformative applications of genomics to improve human health and environmental resilience—delivering both social and economic impact through science.

 

 

 

Background

 

The Personalized Approaches in the Treatment of Head and Neck Cancer (PATH) study aims to use longitudinal plasma cell-free DNA sequencing to develop a minimally invasive method for detecting minimal residual disease (MRD) and recurrence in head and neck squamous cell carcinoma (HNSCC). Approximately 35 % of patients with HNSCC recur and die despite aggressive treatment. There are currently no validated biomarkers to monitor treatment response or detect residual disease. The proposed pilot will collect serial blood draws from 30–50 patients per year and perform whole-genome sequencing (WGS) on Illumina and Oxford Nanopore Technology (ONT) platforms. It will integrate genomic, epigenomic and fragmentomic features (SNVs, copy-number variants, methylation marks, fragment size, end-motifs, nucleosomal positioning, viral integration) to sensitively detect low tumour fractions. The project’s third aim is to explore bioinformatics tools to develop a genome-wide multimodal MRD analysis pipeline, analyze baseline plasma samples, and retrospectively analyze longitudinal samples to detect tumour burden. This position will be central to achieving those aims.

 

Key Responsibilities

 

• Explore, design, and implement an analysis pipeline to sensitively detect low tumour fractions from plasma ctDNA using data from Illumina short-read and ONT long-read WGS. This includes integrating whole genomic alterations (SNVs, indels, copy-number variants), epigenetic marks, fragmentomics (fragment length, end-motifs, nucleosome positioning) and viral integration patterns.
• Adapt and evaluate existing tools and develop novel algorithms as required to improve MRD sensitivity and specificity.
• Perform longitudinal analyses of serial plasma samples from patients with and without recurrence, tracking ctDNA tumour fraction over time and correlating ctDNA trends with clinical events and imaging.
• Incorporate tumour-informed analysis by leveraging matched tumour and normal WGS data from the PATH study; build HNSCC-specific methylation classification models.
• Identify and characterize genomic features of HPV/EBV-positive cancers, including viral integration and methylation patterns.
• Generate comprehensive reports, visualizations and manuscripts for internal review, conference presentations and peer-reviewed publications.

 

 

Core Competencies

 

• Brings an understanding of the Indigenous specific racism and the broader systemic racism that exists in the colonial health care structure, and has demonstrated initiatives in breaking down barriers and ensuring a safe environment ensuring a sense of belonging to all and informed by Indigenous Cultural Safety.
• Awareness of social, economic, political and historical realities of settler colonialism on Indigenous Peoples and familiarity with addressing Indigenous-specific anti-racism, anti-racism and Indigenous Cultural Safety and foundational documents and legislative commitments (the Declaration Act, the Declaration Action Plan, TRC, IPS, Remembering Keegan, etc.).

 

 

Qualifications:

 

• Ph.D. in Bioinformatics, Computational Biology, Genomics, Computer Science or a related discipline.
• Expertise in next-generation sequencing data analysis; familiarity with both short-read (Illumina) and long-read (ONT) platforms; experience with variant calling, copy-number analysis, methylation analysis, fragmentomics and viral integration analysis.
• Strong programming skills (Python, R, C/C++ or similar), proficiency with workflow management (Snakemake, Nextflow, CWL), version control (Git), and high-performance computing.
• Knowledge of cancer genomics, liquid biopsy technologies, epigenetics and MRD; experience with tumour-informed analysis or minimal residual disease detection is highly desirable.
• Experience developing or customizing bioinformatics tools and demonstrated ability to analyze complex genomic datasets.
• Excellent communication and interpersonal skills to collaborate with a multidisciplinary team.
• Proven publication record in cancer genomics or related fields and commitment to open-science principles.

 

 

You have:

 

• Demonstrated knowledge of the historic and ongoing impacts of settler colonialism on Indigenous Peoples in social and health contexts, including supported by significant knowledge of Indigenous-specific mandates, including clear understanding of and commitment to eradicate Indigenous-specific racism and discrimination and embed Indigenous Cultural Safety and Humility.
• Demonstrate comprehensive knowledge of the historic and ongoing impacts of settler colonialism and systemic racism on Indigenous Peoples within social and health contexts. This includes understanding how these factors contribute to current health disparities and barriers to care. Show a clear commitment to identifying, challenging, and eradicating Indigenous-specific racism and all forms of discrimination impacting equity-deserving groups within health care settings. This involves familiarity and understanding Indigenous Cultural Safety and Humility recognizing personal biases, institutional barriers, engaging in anti-racism education and training and advocating for systemic change.
• Demonstrated knowledge and understanding of legislative obligations and provincial commitments within [insert name of Program Area] contexts found in the foundational documents including Truth & Reconciliation Commission’s Calls to Action (2015), In Plain Sight (2020), BC's Declaration on the Rights of Indigenous Peoples Act (2019), United Nations Declaration on the Rights of Indigenous Peoples (UNDRIP), Reclaiming Power and Place Missing and Murdered Indigenous Women & Girls Calls for Justice (2019), the Declaration Act Action Plan and Remembering Keegan: A First Nations Case Study - BC Human Rights Code, BC Anti-racism Act and how they intersect across the health care system.
• Demonstrates a commitment to beginning and/or continuing their personal learning journey related to Indigenous-specific racism and dismantling systems of oppression, as well as addressing racism more broadly. Shows willingness to articulate and share their learning experiences to contribute to a culture of motivation and inspiration among peers.
• Demonstrates foundational knowledge of the social, economic, and political realities of settler-colonialism and its impacts on Indigenous peoples and equity-deserving groups within social and health contexts. Understands the impact of social determinants of health-on-health outcomes. Shows a commitment to learning about and upholding legislative obligations and provincial commitments outlined in foundational documents such as the Truth & Reconciliation Commission’s Calls to Action (2015), In Plain Sight (2020), BC's Declaration on the Rights of Indigenous Peoples Act (2019), United Nations Declaration on the Rights of Indigenous Peoples (UNDRIP), Reclaiming Power and Place: Missing and Murdered Indigenous Women & Girls Calls for Justice (2019), the Declaration Act Action Plan, Remembering Keegan: A First Nations Case Study, the BC Human Rights Code, Anti-Racism Data Act, and the Distinctions Based Approach.

 

 

What we bring

 

 

Every PHSA employee enables the best possible patient care for our patients and their families. Whether you are providing direct care, conducting research, or making it possible for others to do their work, you impact the lives of British Columbians today and in the future. That’s why we’re focused on your care too – offering health, wellness, development programs to support you – at work and at home.

• Join one of BC’s largest employers with province-wide programs, services and operations – offering vast opportunities for growth and development.
• Access to professional development opportunities through our 2,000+ in-house courses including a range of experience level, profession-specific, or other essential training on Indigenous Cultural Safety; Indigenous-specific anti-racism; Diversity, Equity, Inclusion and accessibility, mental health and well-being, and more.
• Enjoy a comprehensive benefits package, including municipal pension plan, and psychological health & safety programs and holistic wellness resources.
• Annual statutory holidays (13) with generous vacation entitlement and accruement.
• PHSA is a remote work friendly employer, welcoming flexible work options to support our people (eligibility may vary, depending on position).
• Perks include access to fitness classes and discounts to 350 BC-wide recreational programs, travel, technology, car and bike sharing, and more.

 

 

Job Type: Temporary, Full-Time (Until March 1, 2027)
Salary: $50,000 - $70,000. The starting salary for this position would be determined with consideration of the successful candidate’s relevant education and experience, and would be in alignment with the provincial compensation reference plan and grant fund availability.
Location: 675 West 10th Avenue, Vancouver  BC V5Z 1G1    
Hours of work: Monday - Friday; 0930-1630
Applications will be accepted until the positions are filled. 
Requisition Number: 194496E

 

 

 

What we do

 

 

 

BC Cancer provides comprehensive cancer control for the people of British Columbia. 

 

 

 

BC Cancer is part of the Provincial Health Services Authority (PHSA). 

 

 

 

The Provincial Health Services Authority (PHSA) plans, manages and evaluates specialized health services with the BC health authorities to provide equitable and cost-effective health care for people throughout the province. Our values reflect our commitment to excellence and include: Respect people – Be compassionate – Dare to innovate – Create equity – Be courageous.

 

 

 

Learn more about PHSA and our programs: jobs.phsa.ca/programs-and-services

 

 

 

PHSA is committed to anti-racism and equity in our hiring and employment practices. With learning and compassion, we are addressing existing inequities and barriers throughout our systems. PHSA is seeking to create a diverse workforce and to establish an inclusive and culturally safe environment. We invite applications and enquiries from all people, particularly those belonging to the historically, systemically, and/or persistently excluded groups identified under the B.C. Human Rights Code.

 

 

 

One of PHSA’s North Star priorities is to eradicate Indigenous-specific racism, which includes ongoing commitments to Indigenous recruitment and employee experience as well as dismantling barriers to health care employment at every level. We welcome Indigenous individuals to apply and/or contact the Sanya’k̓ula Team (Indigenous Recruitment & Employee Experience) for support at indigenous.employment@phsa.ca.

 

 

 

Indigenous-specific anti-racism initiatives are rooted in addressing the unique forms of discrimination, historical and ongoing injustices, and exclusion faced by Indigenous peoples. These initiatives align with an Indigenous rights-based approach, recognizing the inherent rights and title of BC First Nations and self-determination of all First Nations, Inuit and Métis communities. PHSA is mandated to uphold legislative obligations and provincial commitments found in the foundational documents including the Truth & Reconciliation Commission’s Calls to Action (2015), In Plain Sight (2020), BC's Declaration on the Rights of Indigenous Peoples Act (2019), United Nations Declaration on the Rights of Indigenous Peoples (UNDRIP), Reclaiming Power and Place Missing and Murdered Indigenous Women & Girls Calls for Justice (2019), the Declaration Act Action Plan and Remembering Keegan: A First Nations Case Study.

 

 

 

 

Attention current employees of PHSA:

 

 

You must apply via your internal profile at http://internaljobs.phsa.ca.

 

 

 

The internal job posting expires on February 9, 2026, and will no longer be accessible. If the internal job posting has expired, please e-mail internaljobshelpu@phsa.ca with the six-digit job requisition number and your PHSA employee ID number to be considered as a late internal applicant. Please do not apply for the external job posting.

 

 

 

If you have not yet set up an internal profile, please e-mail internaljobshelpu@phsa.ca with your PHSA employee ID number to obtain your temporary password. Our business hours are Monday-Friday 8:30am-4:30pm, excluding Statutory Holidays and a Help Desk Representative will respond to you with 1-2 business days.

 

 

 

If you are not a current employee of PHSA and require assistance with your application, please contact the External Careers team at careers@phsa.ca.