How Bridge Informatics Enabled a Biotech Company to Accelerate Research with a Tailored Bioinformatics Pipeline and Cloud Infrastructure
Situation
The Director of Translational Biology and Pharmacology at a biotechnology company focused on developing innovative therapies for metabolic syndrome-related diseases sought to establish a robust bioinformatics pipeline for processing and analyzing low coverage whole genome sequencing (WGS) data from patient samples. The company’s Head of Information Technology (IT) was tasked with ensuring the availability of a cloud infrastructure to deploy the pipeline and secure data backup using low-cost storage options, however, they did not have the bandwidth or capability to do so.
Recognizing the dual challenge of pipeline development and cloud infrastructure setup, the company sought a partner who could provide an integrated team of data scientists and cloud engineers to address both sides of the problem efficiently.
Strategy
The Company selected Bridge Informatics (BI) as the best fit to comprehensively, quickly, and cost effectively address their needs. Our data scientists leveraged their expertise in pipeline development using workflow management systems, variant calling, and imputation of low-coverage WGS data to create a Statement of Work that included:
Data Acquisition: We accessed our Client’s low-coverage WGS data generated from patient samples using the Illumina platform.
Quality Control: We implemented rigorous quality control measures to ensure the integrity and accuracy of the raw sequencing data. As a component in the pipeline, a MultiQC report was generated integrating various quality control measures on the input WGS files.
BAM File Processing and WGS Genotype Imputation: We prepared the data for analysis and imputed phased genotypes in the WGS data using the high coverage (30X) 1000 Genomes Project NYGC reference panel set.
Variant Calling, Filtering, and Annotation: We utilized industry-standard tools and best practices, such as the GATK workflow and GLIMPSE2, to identify high quality genetic variants. Then, functional annotation.was added to the variant calls to provide actionable insight to the client.
Pipeline Implementation: We integrated all the analysis steps into a streamlined and reproducible pipeline using a workflow management system.
Concordance Analysis: We performed concordance analysis to validate the accuracy and precision of the variant calls using the down-sampled NA12878 WGS data from the Genome In A Bottle (GIAB) consortium hosted by NIST.
Output Specification: We ensured that the pipeline’s output files were in a format that the Company’s Director of Translational Biology and Pharmacology could readily use for further analysis and interpretation.
In conjunction with pipeline development, our cloud engineers worked closely with the company’s head of IT to understand the company’s broader IT environment needs and goals. We then designed and implemented a secure and scalable Amazon Web Services (AWS) cloud architecture that met the specific storage, security, and computational requirements of the bioinformatics pipeline and data.
Results
Within the project timeframe, we equipped our Client with a powerful and efficient bioinformatics pipeline for processing and analyzing their genomic data, stored on a secure and scalable AWS cloud infrastructure. The pipeline enabled them to:
- Efficiently process low coverage WGS datasets
- Accurately identify and impute genetic variants
- Streamline their research into metabolic syndrome-related diseases
At the request of the head of IT, we continue to provide ad-hoc cloud management and bioinformatics support, allowing them to concentrate on the organization’s core IT needs while we expertly manage, maintain, and optimize their R&D team’s cloud infrastructure.
Contact us to learn more about how our team of experienced bioinformaticians and cloud engineers can help you achieve your research goals through expert data analysis, interpretation, and infrastructure support. We tailor our solutions to each client’s specific needs and constraints, ensuring a successful and impactful collaboration.
Jessica Corrado, Head of Business Development & Commercial Operations, Bridge Informatics
As the Head of Business Development & Commercial Operations, Jessica is responsible for driving strategic growth initiatives and overseeing the company’s commercial activities. She has both a keen understanding of the life sciences industry and a strong track record in building successful partnerships.
Prior to joining Bridge, Jessica held a number of leadership roles across sales, marketing, and communications. Outside of work, Jessica is responsible for the majority of marketing and event planning for Shore Saves, a non-profit animal rescue. She enjoys reading and is often reading at least two books of various genres at a time. If you’re interested in reaching out, please email [email protected] or [email protected]
