Topic for July: Utilizing the Seven Bridges platform for training of a new generation of Health Data Scientists

This July, the CGC Webinar Series features a talk by our colleagues at Georgetown University: Dr. Yuriy Gusev, Associate Professor, and Krithika Bhuvaneshwar M.S, Research Faculty Instructor.

Dr. Yuriy Gusev is an Associate Professor of Bioinformatics and a Bioinformatics Lead at the Georgetown University Innovation Center for Biomedical Informatics (ICBI). Dr. Gusev is the director of the graduate program in Health Informatics and Data Science and co-director of the Informatics Shared resource for the Lombardi Comprehensive Cancer Center at Georgetown University. He has over 20 years of experience in teaching and training in bioinformatics and computational biology at several academic centers in the US. He has developed several new curricula for graduate and undergraduate programs at Georgetown.

Ms. Krithika Bhuvaneshwar is a Research Instructor Faculty & Curriculum Coordinator for the Master’s in Health Informatics and Data Science program, and is also a Senior Bioinformatician at the Innovation Center for Biomedical Informatics (ICBI), Georgetown University. She has helped organize training workshops in Elsevier Pathway Studio, Globus Genomics, system biology, immuno-oncology, and most recently – imaging informatics for faculty and staff at Georgetown University Medical Center (GUMC).

In addition, both Dr. Gusev and Ms. Bhuvaneshwar developed a successful Massive Open Online Course (MOOC) on EdX titled “Demystifying Big Biomedical Data – a user’s guide,” which attracted over 8000 students from around the world. At this upcoming webinar, Yuriy and Krithika will share their approach, methodology, and examples of graduate-level courses where they utilize the CGC as a teaching platform for the graduate education program in Masters in Health Informatics and Data Science program at Georgetown University.

Topic for May: Towards best practices in cancer mutation detection with whole-genome and whole-exome sequencing 

This May, the CGC Webinar series features a presentation by Dr. Wenming Xiao, Lead Bioinformatics Scientist of the Office of New Drugs and the Office of Oncological Diseases, at the Center for Drug Evaluation and Research, of the Food and Drug Administration (FDA). First formed in 1906, the United States FDA’s mission is to promote and protect public health by ensuring the safety and efficacy of food products, drugs, vaccines, cosmetics, and medical devices, among many others.

Clinical applications of precision oncology require accurate tests that can distinguish true cancer-specific mutations from errors introduced at each step of NGS. To date, no bulk sequencing study has addressed the effects of cross-site reproducibility or the biological, technical, and computational factors that influence variant identification.

In this upcoming webinar, Dr. Xiao will discuss his research into the systematic interrogation of somatic mutations in paired tumor-normal cell lines to identify factors affecting detection reproducibility and accuracy. Using whole-genome sequencing (WGS) and whole-exome sequencing (WES), Dr. Xiao evaluated the reproducibility of different sample types with varying input amount and tumor purity, multiple library construction protocols, followed by processing with nine bioinformatics pipelines. As a result, he found that read coverage and callers affected both WGS and WES reproducibility, but WES performance was influenced by insert fragment size, GC content, and the Global Imbalance Value (GIV; G>T/C>A) score. Finally, taking into account library preparation protocol, tumor content, read coverage, and bioinformatics processes concomitantly, Dr. Xiao is able to recommend actionable practices to improve reproducibility and accuracy of NGS experiments for cancer mutation detection.

Topic for April: Exploring the landscape of breast cancer multi-omics analysis on the Cancer Genomics Cloud

During the first CGC Webinar in 2021, Dave Roberson and Sai Lakshmi Subramanian provided a high-level overview and demonstration of the Cancer Genomics Cloud and its features. This month, Seven Bridges bioinformaticians Dr. Vesna Pajic and Nevena Vukojicic will present a detailed account of how to use these CGC features for integrative analysis of data coming from different omics experiments, commonly referred to as multi-omics analysis.

In this April webinar, Vesna and Nevena will provide an overview of multi-omics analysis, and how data can be integrated and jointly analyzed on CGC. Various features of CGC that enable such integration will be presented on a Breast Cancer Multi-omics Analysis Use Case, by combining mRNA and miRNA profiles from TCGA (specifically the TCGA BRCA dataset) and proteomics data from CPTAC dataset, all of which are available publicly on CGC.

Meet The Team

For More Information

To learn more about the CGC and its resources, please see our documentation. For any additional inquiries, please contact support@sbgenomics.com

Topic for March: Uncovering novel roles of microRNAs in tumors using the Cancer Genomics Cloud

This March, the CGC Webinar series features a talk from Dr. Xavier Bofill-De Ros, a Research Fellow from the National Cancer Institute (NCI). The NCI is the largest and oldest institute of the National Institutes of Health (NIH), with a mission to conduct and support research for the prevention, understanding, and treatment of cancer. Dr. Bofill-De Ros’s research includes studies of how microRNA biogenesis affects tumor progression, and of mechanisms affecting microRNA stability. Dr. Bofill-De Ros also aided in the NCI’s development of QuagmiR, the first cloud-based tool for microRNA isoform analysis from NGS data.

In this upcoming talk, Dr. Bofill-De Ros will discuss the analysis of microRNA isoforms using the Cancer Genomics Cloud, the role of RNA structures on microRNA function, and also how to leverage “The Cancer Genome Atlas (TCGA)” and a multi-omics approach in mechanistic studies.

For More Information

To learn more about the CGC and its resources, please see our documentation. For any additional inquiries, please contact support@sbgenomics.com

Links to resources mentioned in this webinar:

• PDXNet Website

• PDXNet Portal

• PDX Workflows on the Cancer Genomics Cloud

FEBRUARY’S TOPIC: A MODEL FOR ADVANCING PRE-CLINICAL TRIALS ON THE CANCER GENOMICS CLOUD — THE PDXNET STORY

In February, the CGC Webinar Series will feature a talk by Seven Bridges’ own Dr. Dennis A. Dean, II, on the Patient-Derived Xenografts Development and Trial Centers Research Network (PDXNet). The NCI-funded PDXNet Consortium aims to accelerate the identification of new multi-agent cancer treatments that advance to human clinical trials by facilitating collaboration between six PDX Development and Trial Centers. The task of facilitating research collaborations and making sequencing data publicly available falls to the PDXNet Coordinating Center, led by Jackson Laboratory and Seven Bridges.

In this upcoming webinar, Dr. Dean will discuss his experience working across PDXNet teams to develop standardized procedures on the Cancer Genomics Cloud for collecting and processing sequencing data, collecting and validating model/sequencing metadata, and making PDXNet data available to the research community. Additionally, Dr. Dean will introduce novel tools developed to accelerate data collection and publishing of resources generated by the PDXNet Consortium.

Who We Are

Seven Bridges is the leading biomedical data company, specializing in software and data analytics to drive public and private healthcare research. We deliver end-to-end bioinformatics solutions, including access to datasets, analytic workflows and algorithms, cloud-computing infrastructure, and scientific support, which all speed the path from raw experimental data to new treatments and diagnostics.

For more information…

To learn more about the CGC and its resources, please see our documentation. For any additional inquiries, please contact support@sbgenomics.com

Announcing the CGC Monthly Webinar Series

The Seven Bridges Cancer Genomics Cloud is starting a new monthly webinar series to highlight the many uses of our platform. The webinars are scheduled for the 4th Wednesday of each month at 2:00pm ET, beginning Jan 27th, 2021. Our speaker series will include experts from within Seven Bridges, as well as project collaborators, users, and more. For those that cannot attend, recordings of these webinars will be made available on our website whenever possible. Additionally, we will also feature a series of informative articles accompanying these webinars.

Topic: The Cancer Genomics Cloud: a secure and scalable cloud-based platform to access, share and analyze multi-omics datasets

The Cancer Genomics Cloud (CGC), powered by Seven Bridges, is one of three systems funded by the National Cancer Institute to explore the paradigm of co-localizing massive public datasets, like The Cancer Genomics Atlas (TCGA), alongside secure and scalable computational resources to analyze them.

For cancer genomics research and beyond, the Cancer Genomics Cloud provides a user-friendly, web-based portal for collaborative analysis of petabytes of multi-omics data alongside private data. These above features of the Cancer Genomics Cloud will be discussed in our first webinar.

Our First Speakers for January 2021

The inaugural speakers of this webinar series will be Seven Bridges own Dave Roberson and Sai Lakshmi Subramanian. Dave is our Community Engagement Specialist at Seven Bridges. Sai is a Program Manager at Seven Bridges, currently overseeing the activities of the Cancer Genomics Cloud.

Who We Are

Seven Bridges is the leading biomedical data company, specializing in software and data analytics to drive public and private healthcare research. We deliver end-to-end bioinformatics solutions, including access to datasets, analytic workflows and algorithms, cloud-computing infrastructure, and scientific support, which all speed the path from raw experimental data to new treatments and diagnostics.

For more information…

To learn more about the CGC and its resources, please see our documentation. For any additional inquiries, please contact support@sbgenomics.com