Clinical Bioinformatician (Competition #: 42-19-764025245)

CancerCare Manitoba; Research Institute of Oncology and Hematology
Winnipeg, MB, Canada
Job Type:
  • Programmer/Developer (1 year Term (may expire with two weeks’ notice) – Grant funded)
Degree Level Required:
Masters, PhD
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Clinical Bioinformatician (Competition #: 42-19-764025245)

CancerCare Manitoba is working with the Genomics discipline at Shared Health Diagnostics to adopt Next Generation Sequencing (NGS) and microarray technology using the Illumina platform for routine clinical diagnostics. The discipline will require its own start-to-end bioinformatics pipeline to integrate with the clinical workflow. This is a part-time (0.6 EFT) one-year term position with strong potential for extension and expansion to a full-time EFT.


Tasks include (but not limited to):

  1. Review and optimize the primary analysis pipeline from raw data to annotated variants to assure clinical standards are achieved.
  2. Determine that variant filtering (including SNV, indels, and CNV) is appropriately optimized. Assess the feasibility of quality flags in the pipeline to appropriately alert the interpreting professional to perform additional review (i.e. vertically or horizontally complex variants).
  3. Assess the need for a second independent analysis pipeline from raw data to annotated variants and if needed, help implement a cost-effective alternate solution that conforms to local IT requirements.
  4. Assess quality metrics used during the bioinformatic process. Provide possible improvements and/or streamline ongoing quality control processes.
  5. Ensure vendor solutions (e.g. NextGENe, Geneticist Assistant, BlueFuse Multi) are optimally and appropriately utilized.
  6. Write and/or review the documentation process to ensure it is sufficient in tracking the bioinformatics pipelines. Provide advice as to how to implement upgrades to vendor-supplied software and support the lab staff in determining the amount and extent of revalidation required when a change is made to a component of the bioinformatics pipeline.
  7. Verify that the bioinformatics pipelines used to meet PHIA and FIPPA standards.
  8. Assess if the file naming systems used across the bioinformatics pipelines maintain sample identity, is compatible in an HL7 environment and meets current best practice.
  9. Develop and implement data transfer and storage processes that ensure data integrity and alerts or prevents the use of data files that were altered in an unintentional or unauthorized manner.
  10. Establish a protocol allowing the laboratory to share variant data with relevant databases (i.e. NCBI’s ClinVar) at timely intervals.


Ph.D. or Master’s degree in bioinformatics, computational biology, computer science or related discipline

Two years of experience developing and validating a bioinformatics pipeline for a clinical genomics laboratory.

Experience managing and working with NGS data is required

Extensive knowledge and experience in the use of existing bioinformatics tools such as NextGENe®, Geneticist Assistant®, ANNOVAR, as well as biological databases

Experience with the Illumina sequencing platforms

Familiar with a version control system

Able to legally work in Canada


Knowledge of Manitoba eHealth environment

Understanding SQL database development

Ability to speak French

Will be assessed During the Interview Process:

Excellent interpersonal, communication, organizational and problem-solving skills

Ability to work both independently and as a member of a multi-disciplinary team

Demonstrated effective verbal and written communication skills

  • How to Apply

    Please submit a detailed cover letter outlining how you meet the requirements for this position along with a current resume which references the Competition Number

Additional Information

This position is subject to a Criminal Record Check, including Vulnerable Sector Search, an Adult Abuse Registry Check and a Child Abuse Registry Check. The successful candidate will be responsible for any service charges incurred.

CancerCare Manitoba is committed to developing inclusive, barrier-free recruitment processes and work environment. If you are contacted by CancerCare Manitoba regarding a job opportunity or testing, please advise if accommodation measures must be taken to enable you to apply and be assessed in a fair and equitable manner.

We thank all that apply and advise that only those applicants selected for further consideration will be contacted.