Department of Breast and Molecular Oncology

Title: Statistical Analyst (posting #3008)

Term: 1 year (renewable)

POSITION SUMMARY

The Molecular Oncology Laboratory at the British Columbia Cancer Research Centre is a leading edge facility with a fast paced environment.  Research areas involve the latest laboratory and statistical methods and equipment applicable to basic cell biology in the quest to understand cancer mechanisms and develop treatments to continue reducing the impact of this disease. The Statistical Analyst will perform statistical analysis of these laboratory experiment results.

WORKING RELATIONSHIPS

• The Statistical Analyst reports to the Senior Statistician in the Molecular Oncology Research Laboratory
• Works with laboratory scientists, staff, trainees and other statisticians.

WORK PERFORMED

• Works with laboratory personnel to acquire and clean data
• Develops initial review graphs and tables
• Collaborates with laboratory scientists and statisticians to implement analysis plans.
• Carries out statistical analysis and develops appropriate reports
• Displays and presents results
• Develops and maintains statistical analysis software
• Assists with automated data entry to database and database maintenance
• Assists with maintenance and development of web-based statistical analysis applications

SUPERVISION RECEIVED

The Statistical Analyst works independently with a minimum of direction from the Senior Analyst and Head of the Research Laboratory.

SUPERVISION GIVEN

The Statistical Analyst may be responsible for supervising other trainees.

WORKING CONDITIONS

The environment is within a laboratory facility located within the British Columbia Research Centre.

MINIMUM QUALIFICATIONS & SKILLS

• Education
  • Master’s Degree in Statistics, or Bachelor’s Degree with strong emphasis in Statistics
• Experience/Knowledge:
  • Two or more years of experience in a biomedical research environment
  • Understanding of and ability to carry out:
    • Basic data acquisition, cleaning and warehousing
    • Basic data plotting
    • Exploratory analysis; basic tables, box plots and other graphs
    • Contingency table analysis (Chi-square tests, Fisher’s exact)
    • Regression analysis (linear models, binomial models)
    • Survival analysis (Cox models, competing risks)
    • Demonstrated knowledge of R, Matlab, SPSS and similar programs
    • Knowledge of and experience with software version control systems
    • Knowledge of C, Java, HTML/XML a plus
    • Ability to design and maintain databases
    • Ability to learn biological concepts for research performed
    • Excellent verbal and written communication, interpersonal and organizational skills
    • Ability to exercise confidentiality, initiative, be able to meet deadlines and to work both independently and within a team environment

Please send a CV and cover letter to cennis [at] bccrc [dot] ca, quoting job posting #3008

Position/Business Title:

Bioinformatician (job posting #9393)

Position Summary:

This individual will analyse diverse sets of high throughput genomic data derived from clinical breast and ovarian tumours.  Focused on next-generation sequencing of tumours, the individual will execute routine analyses of data as they emerge and collate results into reportable databases to investigators.  The position will focus on characterizing mutations in different cancer subtypes and determining molecular heterogeneity of large cohorts of patients to enable subtype-specific therapies for cancer patients.  In addition, project and data management will be a component of this position.

Organizational Status:

Working independently and reporting to the Principal Investigator in Molecular Oncology or designate, and in conjunction with investigators within the BCCA, UBC and internationally.

Work Performed:

1. Provides expertise in the planning and development and application of novel algorithms and statistical models
2. Performs algorithmic and statistical analyses on next generation sequencing data, Affymetrix, SNP 6.0 array data
3. Contributes interpretive analysis on large data sets in the context of affected genes and pathways
4. Contributes to writing scientific manuscripts
5. Performs other duties as related to the position such as data and project management to ensure data is being processed in an efficient and timely manner

Supervision Received:

Supervision from Principal Investigator or designate.  Results reviewed for achievement of overall objectives.

Supervision Given:

May manage undergraduate, research and bioinformatician trainees.

Education/Work Experience:

• Post-graduate degree in one of the following:
  • bioinformatics, biostatistics, computer science (with some complementary background in molecular biology/genetics), statistics or genetics (with significant computational expertise)
• Minimum of 5 years related experience working in a research or corporate environment or the equivalent combination of education and experience.
• Strong knowledge of Unix/Linux operating system
• Programming/scripting skills in at least two of the following:
  • C/C++, Java, Perl
• Expertise with at least one of the following:
  • Matlab, R
• Working knowledge of SQL/relational databases
• Familiarity with human genome databases such as Ensembl, UCSC genome browser, NCBI
• Familiarity with parallel computing environments (Linux clusters, SunGridEngine, OpenPBS, etc…)
• Experience with bioinformatics tools such as Bioconductor, BioPerl/BioJava, BLAST considered an asset
• Experience in development of algorithms/machine learning/statistical models for bioinformatics considered an asset
• Ability to work in different locations as required.

Please send a CV and cover letter to cennis [at] bccrc [dot] ca, quoting job posting #9393

The world is facing a shortage of the key medical isotope Technetium-99m (Tc-99m). More  than 80% of the estimated 1.5 million nuclear medicine procedures performed annually in Canada use radiopharmaceuticals based on this isotope, which is currently produced using nuclear reactors.

Together with TRIUMF and other partners, the BC Cancer Agency (BCCA) has received a $1.3-million grant from the Canadian Institutes of Health Research (CIHR) and the Natural Sciences and Engineering Research Council of Canada (NSERC) to develop an alternative source of medical isotopes. The grant is part of a $5.4-million research program called Alternative Radiopharmaceuticals for Medical Imaging. The project will be led by co-principal investigators Dr. François Bénard, Scientific Director of the Centre of Excellence for Functional Cancer Imaging at the BC Cancer Agency, and Dr. Thomas J. Ruth, Senior Research Scientist at TRIUMF and Senior Scientist at the BC Cancer Agency.  Dr. Bénard holds the BC Leadership Chair in Functional Cancer Imaging and is a professor of radiology at the University of British Columbia, as well as a principal investigator in the BCCA’s Molecular Oncology Department.

BCCA, TRIUMF, and collaborators in Edmonton, Sherbrooke, and London, Ontario will collaborate on the two-year research project. The aim is to develop methods to produce technetium using cyclotrons instead of nuclear reactors. Conventional medical cyclotron machines are already being used to produce radioisotopes for many diagnostic procedures, and a cyclotron is currently under construction at the BC Cancer Agency, an initiative made possible through funding provided by the British Columbia Ministry of Health Services and the BC Cancer Foundation. The research team expects to initiate clinical studies to validate new production methods within two years.

“Finding alternatives to reactor produced medical isotopes is vital to staying ahead of the supply curve and meeting the health needs of patients,” said Dr. Bénard. “Producing technetium radioisotopes from cyclotrons could be a safe, reliable and cost-effective alternative to using material produced in nuclear reactors.”

Dr. Nigel Lockyer, TRIUMF Director, added, “we’re thrilled to be working with the leading cancer agency in Canada and some of the best minds in Canada on this research program. We each bring something unique to the table.  Together, we will find solutions to this problem that will work for Canadians and even the world. ”

We have released a C implementation of the software used in Shah et al (2009) Nature: “Mutational evolution in a lobular breast tumour profiled at single nucleotide resolution.”   Please click here for more information.

Dr. Sam Aparicio of the Molecular Oncology Department, in partnership with Dr. Marco Marra of the Genome Sciences Centre, has published the first complete genome sequence of a breast cancer. The article is featured on the front cover of this weeks issue of Nature, one of the world’s most prestigious science journals.

The study describes the use of next-generation DNA sequencing technology to identify all of the 32 gene mutations present in a metastatic breast cancer. The team then searched for the same mutations in the original breast tumour from nine years earlier; only five were present at high enough levels for them to have been present in every cell of the original tumour. Six other mutations were present in small subsets of the original tumour cells, confirming for the first time that there is considerable genetic heterogeneity even at the earliest stages of breast cancer. This finding highlights the need to target all breast tumour cells at an early stage of treatment, rather than treating the tumour as a single uniform mass.

Further details can be found in today’s press release from the BC Cancer Foundation. To date, the story has also been covered by the CBC, CTV, Global, Canada.com, Vancouver Sun, The Province, and MIT’s Technology Review.

Dr. Sam Aparicio will be taking part in the Canadian Breast Cancer Foundation’s “Ask an Expert” live chat on Thursday. Tune in to the Vancouver Sun website at noon PST on Thursday October 8th, and ask Sam your questions about breast cancer research!

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This site is still under development, and your feedback is welcome! Please direct all comments and questions to cennis [at] bccrc [dot] ca.