Bioinformatics Specialist, Genetics, Hamilton, Ontario
Sylva Donaldson Ilchyna
Bioinformatics Specialist, Genetics
Hamilton Regional Laboratory Medicine Program and McMaster University
Hamilton, Ontario, Canada
The Hamilton Regional Laboratory Medicine Program (HRLMP) is inviting applications from bioinformatics specialists with experience in human genome analysis who are interested in providing expertise for a large clinical academic laboratory program serving the Central South region of Ontario. The Laboratory is located at the McMaster University campus, and has a catchment of approximately 2.5 million people. The current workload comes from a referral base that includes tertiary genetic, pediatric, hematology, pathology, oncology and obstetrical services that are provided in a multi-site hospital environment.
The Laboratory is seeking a Bioinformatics Specialist to manage, analyze and integrate large scale genetic and genomic data. The successful candidate will work closely with members of the Hamilton Regional Genetics Program and other key partners and collaborators. Responsibilities and requirements for the Bioinformatics Specialist role are provided below.
If interested in application, please submit a cover letter and CV to:
Teresa DiFrancesco
HRLMP Genetics Operations Manager
Responsibilities:
1. 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.
2. 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.
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.
• Liaise with appropriate personnel within and outside of the HRLMP to establish appropriate server set up.
• 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 (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.
• Liaise with laboratory scientists to submit variant classification data to appropriate databases (e.g. ClinVar and COGR).
• 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 ,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.
6. Other
• Participate in training CCMG Fellows, Mitchener Students and other trainees.
• Use knowledge base and experience to guide, mentor and support trainees and new staff.
• Attend and contribute to staff meetings.
Requirements
Minimum of a Masters Degree in a relevant field such as bioinformatics, computer
science or mathematics (Essential)
• Advanced understanding of bioinformatics and computer science (Essential)
• Advanced programming skills in at least one programming language such as Python, Perl, R, C++, MySQL, UNIX shell, Java, Matlab programs (Essential)
• Proficiency in Linux (Essential)
• Experience working with next-generation sequencing data: ThermoFisher and
• Illumina base calling, sequencing quality control, sequence alignment, variant calling
• and de novo assembly, variant annotation., RNA-sequencing analysis, germline
• and somatic mutational events, copy number variants etc. (Essential)
• Experience working with SNP-,microarray analysis (Preferred)
• Experience with epigenomic data analysis (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)