Computational Genomics
The Computational Genomics Group comprises a dynamic team of ten computational biologists with the substantial technical and bioinformatics expertise required to oversee the multiple platforms that acquire, store and analyze large and complex data sets generated by the IGM Genomic Services, Clinical and Technology Development laboratories. Integration of this team within the IGM is critical to its success, ensuring that team members are able to learn new methodologies and develop novel analysis approaches in pace with the technological growth that has become a primary driving force for biological discovery.
The group provides bioinformatics services on a collaborative basis at subsidized hourly rates and serves as an interface between the research investigator and the multiple domains that are required to handle the size and complexity of genomic data. IGM has built a dedicated cloud-based computational resource through Amazon Web Services (AWS), allowing large HPC or Hadoop clusters to be provisioned on demand. AWS has granted us extensions to our account limits enabling us to launch up to 1,000 simultaneous instances, enabling us to support the analysis of both large- and small-scale sequencing projects. We are uniquely positioned to adapt and develop new computational tools in a manner that is driven by the demands of our research community as it utilizes new technologies.
The development of analytical pipelines for human exome and genome sequencing analysis, and the identification of disease-causing genetic variants, are key areas of focus for the Computational Genomics Group. The group also evaluates and supports multiple software products for genomics applications that are designed to make data analysis tools accessible to biologists.
Training and education in genomics and bioinformatics are an essential component of our mission. IGM provides internship opportunities in genomics and bioinformatics to undergraduate and graduate students. We also train and mentor our research faculty and junior scientists through one-on-one consultation and software training and relevant workshops.
The focus of the core is customer service and we work incessantly towards providing cutting edge data in a cost effective and timely manner, while balancing larger collaborations that require extensive intellectual and time commitments.
Translational Bioinformatics Team
The Translational Bioinformatics team develops and applies challenging and complex software solutions for the next-generation sequencing (NGS) data produced by the Institute and collaborators. The team supports the needs of all aspects of NGS analysis including data generation, analysis, and interpretation, preparing novel methods and technologies for research and clinical production. Members possess diverse computational and biological expertise, working closely with investigators within IGM, transcribing biological questions to code, and with the Clinical Informatics team, translating research pipelines to clinical applications.
Data Management Team
The Data Management team manages sequencing and laboratory processing data for the IGM Clinical and Service Laboratories. The team is responsible for supporting, customizing and further developing the Laboratory Information Management System (LIMS) to facilitate the flow of information to and from other equipment and systems used in the labs, improving lab efficiency, ensuring sample integrity, and promoting easy reporting. Members work closely with the IGM Production Informatics and Cloud Infrastructure teams to track analysis locations and support production systems for analysis.
Computational Solutions Team
The Computational Solutions team implements, operates and maintains the high-performance computer infrastructure that is tailor designed to address the substantial processing, networking and data moving challenges arising from genomic science. Utilizing the elasticity of the Cloud and innovative Big Data technologies, the team collaborates with IGM faculty and R&D teams to develop highly optimized state-of-the-art bioinformatics solutions.
Clinical Informatics Team
The Clinical Informatics team supports the production informatics needs of IGM’s Clinical and Service laboratories. Members work closely with IGM faculty and R&D teams to design and build efficient instrument-to-interpretation pipelines for next-generation sequencing workflows, optimizing outcomes for our genomic medicine initiatives. Manages validated pipelines, as well as any vendor-provided solutions, in compliance with CAP/CLIA and HIPAA.
Churchill
Advancing sequencing technologies make genomic medicine and population scale whole genome sequencing studies a possibility. However, current strategies for analysis of this data rely upon parallelization approaches that have limited scalability, lack reproducibility and are complex to implement, requiring substantial investment in specialized IT solutions.
To overcome these challenges we developed Churchill, a highly accurate and deterministic analysis solution, which fully automates the analytical process required to perform the complex and computationally intensive process of alignment, post-alignment processing, local realignment, recalibration and genotyping. Our balanced regional parallelization strategy enables division of each analysis step across multiple compute instances, enabling whole genome variant discovery and genotyping via local re-assembly of haplotypes to be completed in minutes. For whole genome sequencing, the entire analysis process from FASTQ to high confidence variant calls can be completed in as little as 90 minutes.