Technical Specialist (Genomic Bioinformatician) – Hamilton Health Sciences

Title of the Job: Technical Specialist (Genomic Bioinformatician)

Location: Hamilton, ON

Job Description: The Hamilton Regional Laboratory Medicine Program (HRLMP) is seeking a Genomic Bioinformatician to manage, analyze and integrate large scale gene sequence data. As a team member you will assist in analyzing and interpreting clinical data derived from high throughput genotyping and sequencing platforms. You will also be responsible for developing and implementing pipelines to align, normalize, visualize, and analyze data, and to integrate the data and results with internal and external applications and databases. You will work closely with members of the Hamilton Regional Genetics Program, as well as other key partners and collaborators.
1. Keep abreast with new and emerging technologies and literature pertaining to high throughput (epi) genomic 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 literature reviews, develop and implement pipelines for processing next-generation sequencing, optical genome mapping, and microarray data, from raw data to variant annotation and classification. Conduct bioinformatics analyses, troubleshoot pipeline issues, and assess the disease-causing potential of variants. Generate reports following current nomenclature and variant review guidelines.
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, continually reevaluate effectiveness and capacity of server set up system, propose and implement changes as required.
4. Establish and maintain a data storage system that enables storage of NGS related data in accordance with applicable clinical diagnostic laboratory requirements. Identify tools necessary to establish and maintain a long-term scalable solution for data storage in consultation with information technology.
5. Liaise with laboratory scientists to submit variant classification data to appropriate databases (e.g. ClinVar and COGR).
6. Troubleshoot and resolve issues related to softwares used to detect and interpret the clinical significance of sequence and copy number variants (e.g. Mutation Surveyor, NextGene ,Ion Reporter, Alamut, Gene Marker, Affymetrix GeneChip Command Console (AGCC) and Chromosome Analysis Suite (ChAS)).
7. Aids the disciplines quality management program and strives for operational excellence.
8. Committed to patient care, applying bioinformatics practices with an understanding of the patient population’s needs to positively impact clinical outcomes.
9. Conduct horizon scan to determine future needs of the HRLMP with respect to software applications, hardware needs and data storage needs
10. Aid in the implementation and maintenance of the existing and future computer systems in the laboratory, including the creation of a software inventory.
11. Participate in knowledge sharing and training of fellows, students, staff, and other trainees. Attend and contribute to staff meetings and huddlesQualificationsEssential:
Master’s Degree or Ph.D. in bioinformatics or computer science; or molecular biology and genetics and relevant experience in the field such as:
o Understanding of how to create, structure, and maintain local databases (ex. SQL, Access, etc.)
o Experience with programming languages such as Python, R, C++, MySQL, UNIX shell, and Java, and familiarity with using such languages in relation to an API
o Experience working with next-generation sequencing data
o Proven experience developing NGS bioinformatics pipelines, including GATK-based pipelines, and optimizing ready-made, vendor-supplied pipelines (commercial bioinformatics softwares)
o Experience with full-stack development, databases, frameworks, and APIs
o Experience with relevant public databases (e.g., Variant databases (gnomAD, ClinVar, COSMIC, OncoKB, etc.), Gene Ontology, UCSC Genome Browser)
o Experience in the utilization of data cleaning, data normalization and data visualization methods and the development of open-source databases
o Demonstrated experience contributing to scientific research endeavors, and the preparation of presentations, publications, SOPs, and resources for improved learningPreferred (Assets):
– Experience working with SNP-microarray analysis
– Experience with epigenomic data analysis
– Familiarity with statistical genomics
– Familiarity with the ACMG/AMP/ASCO/CAP guidelines for variant annotation and classification

Company Name: Hamilton Health Sciences

Salary:

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