Bioinformatician

Institution/Company:
CHEO
Location:
Ottawa, ON, Canada
Job Type:
  • MSc
Degree Level Required:
Masters
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Bioinformatician

The Genetics Diagnostic Laboratory is seeking a bioinformatician to manage, analyze and integrate large scale genome wide sequence data. As a team member, you will assist in analyzing and interpreting clinical and experimental data derived from high throughput genotyping and sequencing platforms, such as Illumina’s next-generation sequencing (NGS) platforms. You will be responsible for developing and implementing pipelines to analyze NGS data, and to integrate the data and results with internal and external applications and databases. You will work closely with Associate Laboratory Heads in the Genetics Diagnostic Laboratory as well as other members of the Regional Genetics Program, the CHEO Research Institute and other key partners and collaborators.

Responsibilities:

  1. Develop, optimize, validate and implement a computational pipeline that facilitates analysis, filtering and interpretation of DNA variants identified by NGS-based assays. • Conduct literature reviews and liaise with collaborative informatics groups to develop and implement a pipeline for analysis of next generation sequencing data, progressing from genome alignment to variant calling and annotation . • Develop and/or implement a system that facilitates variant visualization, filtering and analysis of DNA variants by laboratory and clinical geneticists, genomic specialists and laboratory genetic counsellors. • Keep abreast of new and emerging technologies and literature pertaining to NGS analysis, variant detection and variant interpretation • Provide advice to laboratory leadership and implement adaptive changes to the pipeline as needed to ensure continuous optimization of data processing and quality.
  2. Conduct bioinformatics analysis of NGS-based data to identify variants and provide genetic counsellors, genomic specialists and laboratory scientists with information necessary for downstream variant interpretation. • Process data through the established pipeline and provide data in an appropriate format to the genomic specialists, genetic counsellors, researchers and laboratory scientists. • Troubleshoot and resolve issues related to pipeline data processing.

  3. Establish and maintain a secure and effective server system set up that ensures effective utilization of established bioinformatics pipelines. • Identify hardware and software necessary to establish a server set up for data processing. • Collaborate with appropriate personnel within and outside of CHEO to establish appropriate server set up. • Continually reevaluate effectiveness and capacity of server system, propose and implement changes as required.

  4. Establish and maintain a data storage system that enables storage of NGS related data (e.g. VCF files, variant & coverage reports) in accordance with applicable clinical diagnostic laboratory requirements. Identify tools necessary to establish and maintain a long-term scalable solution for data storage. • Collaborate with appropriate personnel within and outside of CHEO to establish appropriate storage set up. • Design and/or implement secure storage systems for NGS patient data and identified variants. Continually reevaluate effectiveness and capacity of storage system, propose and implement changes as required.

  5. Information technology support • Troubleshoot and resolve issues related to software used to detect and interpret clinical significance of sequence and copy number variants (e.g. Mutation Surveyor, NextGene, Alamut, Gene Marker, Affymetrix GeneChip Command Console (AGCC) and Chromosome Analysis Suite (ChAS)). • Conduct horizon scan to determine future needs of the Regional Genetics Program with respect to software applications, hardware needs and data storage needs • Aid in the implementation and maintenance of the existing and future computer systems in the laboratory, including the creation of a software inventory. • Collaborate with CHEO’s IS Department in the resolution of IT issues as required.

  6. Other • Participate in training CCMG Fellows, Royal College Fellows, Genetic Counselling Students and other trainees. • Use knowledge base and experience to guide, mentor and support trainees and new staff. • Attend and contribute to staff meetings. • Participate in ongoing professional development and continuous quality improvement opportunities and present internally (e.g. education rounds) and externally (e.g. conferences) on CHEO-based work. • Participate in grant applications and ongoing research projects. • Conform to all laboratory safety regulations (as per the Occupational Health and Safety Act, CHEO corporate and/or departmental policies), and follow specific instructions of the designated safety officer. • Behave in accordance with all relevant policies, procedures, protocols and guidelines (e.g. CHEO (IS) policy, IQMH requirements, ACMG guidelines for variant interpretation and relevant scientific literature).

Qualifications:

• Criminal Record Check (Essential) • Minimum of a Masters Degree in a relevant field such as bioinformatics, computer science or mathematics (Essential) • Experience working with next-generation sequencing data: Illumina base calling, sequencing quality control, sequence alignment, variant calling and de novo assembly, variant annotation, the Genome Analysis Tool Kit (GATK), RNA-sequencing analysis, germline and somatic mutational events, copy number variants etc. (Essential) • Advanced understanding of bioinformatics and computer science (Essential) • Experience working in an HPC environment and managing scheduling software (Preferred) • Advanced programming skills in at least one programming language as well as extensive experience with running and modifying Python, Perl, R, C++, MySQL, UNIX shell, Java, Matlab programs (Essential) • Proficiency in Linux (Essential) • Experience with bcbio-nextgen pipelines (Preferred) • Familiarity with statistical genomics (Preferred) • Proven experience developing bioinformatics tools and pipelines (Essential) • Excellent written and communication skills (Essential) • Experience with relevant public databases (e.g., Variant databases, Gene Ontology, UCSC Genome Browser) (Essential) • Bilingual (French / English) (Preferred)