Technical Specialist (Genome Specialist)

The Hamilton Regional Laboratory Medicine Program (HRLMP) is seeking a Bioinformatician and Genome Specialist

to manage, analyze and integrate large scale gene sequence data. As a team member you will assist in analyzing and

interpreting clinical experimental 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 and as well as other key partners and collaborators.

• Develop, implement and optimize computational pipelines that facilitates analysis, filtering and interpretation of DNA

variants identified by high throughput genomics platforms including NGS- and microarray (SNP, methylation) platforms

within the laboratory, as required.

• Conduct literature reviews and liaise with collaborative informatics groups to develop and implement a pipeline for

analysis of next generation sequencing/microarray data, progressing from raw data processing to variant annotation

and classification. This may include detection and classification of single nucleotide variants, insertions/deletions, copy

number variants, structural chromosome rearrangements and/or epigenetic modifications in either the constitutional or

somatic setting.

• Keep abreast of 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.

• Provide guidance and support for maintenance of a system that facilitates variant visualization, filtering and analysis of

DNA variants by laboratory scientists.

• Conduct bioinformatics analysis of NGS-based and microarray data to identify variants and provide laboratory scientists

with information necessary for downstream variant interpretation.

• Process data through the established pipeline and provide data in an appropriate format to the technical specialist and

laboratory scientists.

• Troubleshoot and resolve issues related to pipeline data processing.
• Summarize current state of knowledge for specific variants and generate draft reports in accordance with current

nomenclature and guidelines for variant interpretation (e.g. ACMG, HGVS, ISCN) for review and reporting by Clinical

Laboratory Scientists.

• Conduct literature reviews, database searches and bioinformatics analyses to assess the disease-causing potential of

specific sequence/copy number/epigenomic variants.

• 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.
• Liaise with appropriate personnel within and outside of the HRLMP to establish appropriate server set up.
• Establish and maintain a data storage system that enables storage of NGS related data (e.g. variant & coverage

reports, variant classifications) in accordance with applicable clinical diagnostic laboratory requirements. Identify tools

necessary to establish and maintain a long-term scalable solution for data storage.

• Liaise with appropriate personnel within and outside of the HRLMP to establish appropriate storage set up.
• Design and/or implement secure storage systems for NGS patient data and identified variants and associated

classifications.

• Troubleshoot and resolve issues related to software used to detect and interpret clinical significance of sequence and
• Continually reevaluate effectiveness and capacity of storage system, propose and implement changes as required.
• Liaise with laboratory scientists to submit variant classification data to appropriate databases (e.g. ClinVar and COGR).
• Information technology support

copy number variants (e.g. Mutation Surveyor, NextGene ,Ion Reporter, Alamut, Gene Marker, Affymetrix GeneChip

Command Console (AGCC) and Chromosome Analysis Suite (ChAS)).

• Conduct horizon scan to determine future needs of the HRLMP 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 the Hospital’s IS Department in the resolution of IT issues as required.
• Use knowledge base and experience to guide, mentor and support trainees and new staff.
• Participate in training CCMG Fellows, Mitchener Students and other trainees.
• Attend and contribute to staff meetings.
• Other

Essential

Master’s Degree or Ph.D. in molecular biology, genetics or a relevant field such as bioinformatics, computer science or mathematics

• Excellent written and communication skills
• Experience working with next-generation sequencing data: ThermoFisher and Illumina base calling, sequencing quality control, sequence alignment, variant calling and annotation, RNA-sequencing analysis, germline and somatic mutational events, copy number variants etc.
• Proven experience developing NGS bioinformatics pipelines
• Experience with relevant public databases (e.g., Variant databases, Gene Ontology, UCSC Genome Browser)

Preferred

• Experience with epigenomic data analysis
• Programming skills in at least one programming language such as Python, Perl, R, C++, MySQL, UNIX shell, Java, Matlab programs
• Experience working with SNP-microarray analysis
• Familiarity with statistical genomics

Job

Administrative/Service

Primary Location

Ontario-Hamilton

This position will be located at

McMaster University Medical Centre

Organization

GENETICS MUMC

Status

Regular

Hours per week

37.5

Number of Openings

1

Union Code

Non Union Employees

Minimum Salary

43.8200

Maximum Salary

56.1800

Post Date

Jul 12, 2023, 4:00:00 AM

Jul 19, 2023, 3:59:00 AM

Unit Summary

The Hamilton Regional Laboratory Medicine Program (HRLMP) is a collaborative program funded and operated jointly by Hamilton Health Sciences and St. Joseph's Hospital. The Program is committed to change and innovation through education, service and research; to bring the highest quality science into health care for the benefit of the community, and to participate in the clinical application, delivery and interpretation of that science.

Schedule Work Hours

Monday to Friday, days

Guidelines

Hamilton Health Sciences fosters a culture of patient and staff safety, whereby all employees are guided by our Mission, Vision, Values, and Values Based Code of Conduct. Hamilton Health Sciences is a teaching hospital and all staff and physicians are expected to support students and other learners.

To be considered for this opportunity applicants must apply during the posting period. All internal and external applicants may ONLY apply via the Careers website.

Hamilton Health Sciences is an equal opportunity employer and we will accommodate any needs under the Canadian Charter of Rights and Freedom, Accessibility for Ontarians with Disabilities Act and the Ontario Human Rights Code. Hiring processes will be modified to remove barriers to accommodate those with disabilities, if requested. Should any applicant require accommodation through the application processes, please contact HR Operations at 905-521-2100, Ext. 46947 for assistance. If the applicant requires a specific accommodation because of a disability during an interview, the applicant will need to advise the hiring manager when scheduling the interview and the appropriate accommodations can be made.

This competition is open to all qualified applicants, however, qualified internal applicants will be considered first. Past performance will be considered as part of the selection process. If you are a previous employee of Hamilton Health Sciences, please note: the circumstances around an employee's exit will be considered prior to an offer of employment

Proficiency in both Official Languages, French and English, is considered an asset

If this position is temporary, selection for this position will be as per the outlined Collective Agreements:

Article 30 (k), CUPE Collective Agreement

Article 10.7 (d), ONA Collective Agreement

Article 13.01 (b) (ii), OPSEU 273 Collective Agreement

Article 14.04, OPSEU 209 Collective Agreement

Article 2.07 and Article 13, PIPSC RT Collective Agreement