Technical Specialist (Genome Specialist)

The Hamilton Regional Laboratory Medicine Program (HRLMP) is seeking a Genome Specialist to manage, analyze, and interpret clinical genetic data. As a team member, you will assist in analyzing and interpreting clinical data derived from high throughput genotyping and sequencing platforms. You will work closely with members of the Hamilton Regional Genetics Program and as well as other key partners and collaborators.

Interpret and analyze genetic and genomic variants from next generation sequencing and SNP analyses, progressing from raw data to variant annotation and classification, including both somatic and germline testing using multiple molecular platforms and methodologies

Prepare draft clinical 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 comprehensive literature reviews, database searches, and bioinformatics analyses to evaluate the clinical significance and disease association of sequence, copy-number, structural, and epigenomic variants.

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 technical guidance and support for systems used by laboratory scientists for variant visualization, annotation, filtering, review, and interpretation.

Collaborate with informatics team to maintain data storage systems for NGS-related data in accordance with applicable clinical diagnostic laboratory requirements.

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 ,Ion Reporter, Alamut, Gene Marker, Affymetrix GeneChip Command Console (AGCC) and Chromosome Analysis Suite (ChAS)).

Contribute to new test development, validation and implementation of new technologies

Contribute to existing laboratory quality management system and accreditation requirements to ensure quality and safety metrics are followed

Collaborate with the Hospital’s HITS Department in the resolution of IT issues as required.

Participate in the education and training of CCMG Fellows, Michener Students and other learners in genomic analysis, variant interpretation, and related laboratory workflows.

Apply subject-matter expertise and laboratory experience to guide, mentor and support trainees and new staff.

Attend and contribute to staff meetings.

Essential:

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

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.

Experience with relevant public databases (e.g., Variant databases, Gene Ontology, UCSC Genome Browser)

Excellent written and communication skills

Preferred:

Experience working with SNP-microarray analysis

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 developing NGS bioinformatics pipelines