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BSD HGD - Molecular Diagnostics

About the Department

The Department of Human Genetics is the home within the Division of Biological Sciences for the study of basic principles of genetics and genomics as applied to human disease. We provide broad training in experimental genetics and genomics, statistical and population genetics, bioinformatics, and clinical genetics. A common theme throughout our research is the application of basic genetic principles and strategies to the study of disease mechanism, disease susceptibility, and the genetic architecture of complex traits. Our faculty bridge between basic and clinical research and train students for careers in academia, industry, and medicine.

Job Summary

The Genetic Services Laboratory at the University of Chicago is a CLIA and CAP certified and accredited laboratory that performs both clinical and research activities pertaining to the understanding of the molecular basis and diagnosis of rare orphan genetic diseases. The laboratory performs a variety of DNA-based techniques for mutation detection and is involved in the continuous development of new assays for mutation detection in new disease genes, as well as in the development and application of new technologies for the improvement of disease diagnostics.

We are seeking a bioinformatician, to work with our bioinformatics group, to maintain and develop essential lab applications and provide bioinformatics support for next generation sequencing-based clinical testing. This position can be on-site or remote.

The candidate will work largely on the support and maintenance of analysis pipelines for automated processing of data from next generation sequencing projects in the Genetic Services Laboratory, Department of Human Genetics. The candidate will be expected to maintain and upgrade our in-house developed LAMP stack based NGS data review system. The candidate will also work on new assay design, development and validation. The candidate will be expected to work with laboratory personnel to design, develop, test and execute custom applications for laboratory automation including interfaces to/from scientific instruments and the Laboratory Information System (LIS).

Responsibilities

• Supports and maintains automated analytic pipelines for next generation sequencing data analysis.
• Maintains and upgrades our in-house NGS data analysis and review system.
• Documents scripts and updates in a systematic and detailed manner.
• Maintains accurate records of all activities carried out in conjunction with different projects.
• Attends lab meetings/exome meetings and reading current journal articles pertaining to relevant projects.
• Applies basic application of computational tools and information technology to gather, analyze and visualize data in biology and biomedical research.
• Plans own resources to implement or modify existing web-based bioinformatics tools.
• Performs other related work as needed.

Minimum Qualifications

Education:

Minimum requirements include a college or university degree in related field.

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Work Experience:

Minimum requirements include knowledge and skills developed through 2-5 years of work experience in a related job discipline.

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Certifications:

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Preferred Qualifications

Education:

• Bachelor\'s degree in bioinformatics or a related field.
• Master\'s degree in bioinformatics or a related field.

Technical Skills or Knowledge:

• Prior experience related to the analysis of high-throughput sequencing data.
• Hands-on experience with mapping, variant calling (SNV, CNV) and annotation.
• Knowledge and demonstrated expe ience of the following languages: Perl/Python, PHP, MySQL, HTML, JavaScript, CSS, bash.
• Proficient in version control with Git.
• Proficient with modern workflow mangers (Nextflow).
• Strong ability to administer/navigate Linux/Unix and OSX environments.
• Creating and maintaining databases with MySQL.
• Knowledge of various next generation sequencing data analysis tools such as BWA, GATK, samtools, Picard, snpEff, Annovar etc.
• Familiarity with the following - NCBI databases, UCSC Genome Browser, HGMD, ClinVar, gnomAD, OMIM, HPO.
• Developing, deploying and managing NGS data analysis pipelines.
• HPC job submission, monitoring and debugging.
• Background in genetics.
• Skilled with CAP/CLIAprotocols/requirements.

Preferred Competencies

• Coordinate multiple projects in a demanding research and diagnostic environment.
• Strong communication and organizational skills.

Working Conditions

Office setting