Computational Genomics

The “big data” nature of genome-based clinical tests and research studies requires advanced high-performance computing and bioinformatics platforms to rapidly analyze and interpret information. Leveraging the flexibility of the cloud, the group continues to develop highly optimized solutions to address the substantial processing, networking and big data challenges arising from genomic science.

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.

http://churchill.nchri.org/