Genomic Alterations in Extraskeletal Myxoid Chondrosarcoma

The CGC webinar series is back in March, featuring a talk by Ms. Trudy Zou from the University of Pittsburgh School of Medicine, in Pittsburgh, PA, USA. Trudy conducts research primarily studying chondrosarcoma with Drs. Rebecca Watters and Kurt Weiss at the Musculoskeletal Oncology Laboratory (MOL). 

The Musculoskeletal Oncology Laboratory aims to better understand the biology of various primary and metastatic musculoskeletal tumors and translate discoveries into clinical solutions. Trudy’s project looks at extraskeletal myxoid chondrosarcoma (EMC), a rare musculoskeletal tumor with an indolent course and right rates of recurrence and metastasis to the lungs. In 70% of cases, it is characterized by the translocation of the NR4A3 gene on chromosome 9 to the EWSR1 N-terminal transactivation domain on chromosome 22.

In this webinar, Trudy will present an extremely rare primary EMC sample collected from a patient with matching lung metastasis, pelvic metastasis, normal lung, and blood available at the MOL lab. They used whole genome sequencing to identify structural variants that contribute to metastasis to the lungs and progression to pelvic metastases and that can be targeted for therapy. Trudy started using the Cancer Genomics Cloud in November 2021, and will be presenting the results of her and the lab’s work.

Trudy Zou is a medical student in the Physician Scientist Training Program at the University of Pittsburgh School of Medicine. She is primarily studying chondrosarcoma with Drs. Rebecca Watters and Kurt Weiss at the Musculoskeletal Oncology Laboratory (MOL). She earned her Bachelor of Science in cellular and molecular biology at Duke University, where she also studied drivers of metastasis and therapeutics for chondrosarcoma under Dr. Julia Visgauss. 

More about us and the CGC

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 bioinformatic solutions — including access to datasets, analytic workflows and algorithms, cloud-computing infrastructure, and scientific support — that speed the path from raw experimental data to new treatments and diagnostics.

The Cancer Genomics Cloud (CGC), powered by Seven Bridges and funded by the National Cancer Institute, is a flexible cloud resource platform that enables storage, analysis, and computation of large cancer datasets in the cloud. Since its launch in 2016, the platform has been continuously iterated with new applications and features to address the exponential growth and diversity of complex datasets. With the CGC, any user with an account can easily access petabytes of data, share it, analyze and use the computational power of the cloud without having to learn how to program and get familiar with several different data portals.

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