Ocean Genomics Granted $235,000 in Funding from the Chan Zuckerberg Initiative

PITTSBURGH, Pa. — Ocean Genomics, a biotechnology software company spun out of Carnegie Mellon University, has received $235,000 in funding from the Chan Zuckerberg Initiative (CZI) to expand the reach of open-source tools for fast and accurate gene expression analysis. 

Gene expression analysis compares the RNA expression levels of multiple genes in samples under various conditions. Such analyses can provide insight into variations in gene expression between healthy and diseased samples, and enable the discovery and validation of multidimensional biomarkers for disease. 

The CZI award will allow Ocean Genomics to improve the open-source projects called Salmon (bulk RNA-seq) and Alevin (single-cell RNA-seq) by expanding the types of input that Salmon and Alevin can support and the types of data processing they can handle. Salmon and Alevin were originally created by two of Ocean Genomics’ co-founders.

“Salmon and Alevin are easy, fast, and accurate methods to extract transcript- and gene-level expression quantification from RNA-seq samples. This award will make these tools even easier to use by supporting additional input formats and additional single-cell protocols.” 

– Carl Kingsford, Ph.D., Co-founder, CEO at Ocean Genomics.

Specifically, the award will support directly reading genomically aligned BAM files and NIH SRA files, two formats in which RNA-seq data is often stored, while keeping Salmon and Alevin’s well-known speed. It will also add support for highly multiplexed single-cell protocols such as Sci-seq, support for the QIAseq UPX 3′ protocol, and protocols with variable-length barcodes and UMIs to the software’s single-cell analysis module, Alevin, which is among the fastest and most accurate ways to process many types of single-cell protocols to produce expression estimates. This work will make that speed and accuracy available to more types of single-cell experiments, and improve the tools available to researchers worldwide.

The award will also fund creation of additional tutorials and documentation so a broader population can use the advanced features of Salmon and Alevin and help to strengthen the community of users and code contributions around the projects.

“We’re very excited to be able to work with the Chan-Zuckerberg Initiative through their Essential Open-Source Software program. CZI has demonstrated a strong commitment to support open-source tools in science, and we at Ocean Genomics are proud to participate in this effort.”

– Rob Patro, Ph.D., Co-founder, CTO at Ocean Genomics.

Ocean Genomics is dedicated to expanding the reach of accurate gene expression analysis. This award will bolster their efforts to continue to support and improve the open-source tools available to researchers worldwide.

 

About Ocean Genomics

Ocean Genomics’s AI-driven transcriptome analysis platform and expert services empower discovery and translational research. The company was founded by authors and inventors of several leading new-generation transcriptome analysis applications used by tens of thousands of researchers world-wide with over 1,500 citations. Ocean Genomics works to democratize transcriptome analysis and expand the usefulness of gene expression analysis by offering additional software, support, integration, and services around these tools by leveraging their larger and more comprehensive transcriptomics analysis framework. 

 

About the Chan Zuckerberg Initiative

Founded by Dr. Priscilla Chan and Mark Zuckerberg in 2015, the Chan Zuckerberg Initiative (CZI) is a new kind of philanthropy that’s leveraging technology to help solve some of the world’s toughest challenges — from eradicating disease, to improving education, to reforming the criminal justice system. Across three core Initiative focus areas of Science, Education, and Justice & Opportunity, we’re pairing engineering with grant-making, impact investing, and policy and advocacy work to help build an inclusive, just and healthy future for everyone. For more information, please visit www.chanzuckerberg.com.

Ocean abstract with Samsung Medical Center accepted to ASCO 2020: Novel target discovery in pembrolizumab-resistant gastric cancer using a comprehensive RNA-seq analysis pipeline.

Ocean provided our platform and expert services required to define approach, review analysis results, and work with partner to revise endpoint.
Ocean’s platform produced complete feature extraction, classifier generation, QC and comprehensive reporting on 55 samples (FASTQ) and patient metadata in 19 hours, providing a 24-hour turn-around time with partner.

Novel target discovery in pembrolizumab-resistant gastric cancer using a comprehensive RNA-seq analysis pipeline.

 

https://meetinglibrary.asco.org/record/186530/abstract

DOI:10.1200/JCO.2020.38.15_suppl.e16541

Authors:

Jeeyun Lee, Seung Tae Kim, Kyoung-Mee Kim, Eric Schultz, Stan Skrzypczak, Rob Patro, Carl Kingsford; Division of Hematology-Oncology, Department of Medicine, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, South Korea; Department of Pathology, Samsung Medical Center, Sungkyunkwan University School of Medicine, Seoul, South Korea; Ocean Genomics, Inc., Pittsburgh, PAAbstract Disclosures

Research Funding:

None

Background: Immune checkpoint inhibition (ICI) has made significant breakthroughs in several tumor types including gastric cancer (GC) in recent years. We recently showed that single agent pembrolizumab demonstrated remarkable and durable response in MSI and EBV GC. However, the response to ICI remains low in MSS and most patients progress after initial response. We explore novel targets in ICI-resistant GC patients by analyzing pre- and post-resistant expression.Methods:Of the 61 patients who were enrolled onto our previously reported phase II pembrolizumab trial (NCT#02589496), whole transcriptome RNA-seq analysis of 10 paired freshly collected tissue samples (all from primary gastric tumors) was performed using TruSeq. All biopsies were performed at progression following stable disease (SD) or partial response (PR) to pembrolizumab. All patients had a MSI status of MSS and EBV negative. Molecular features were extracted using the validated Ocean Genomics, Inc. gene expression analysis pipeline, which trims reads, computes transcript- and gene-level expression, predicts structural variants, assembles novel isoforms, and computes per-sample quality control metrics, among other analyses. Samples that passed quality control, with mapping rates > 88%, were selected for analysis. Differentially expressed (DE) genes between resistant and pre-resistant samples were identified using a statistical test with a study design that accounted for the pairing of samples for each patient.Results:16 genes (GENCODE v31) had absolute log2-fold expression changes (L2FC) > 2, P-value < 10−5 and FDR-adjusted P-value < 0.05. Because sex was only partially controlled for, we excluded genes on the X and Y chromosomes. We also excluded non-protein encoding genes and pseudogenes. The 7 remaining genes are in the table. PDL-1 (CD274) was not identified as significantly DE (FDR-adjusted P-value > 0.9999).Conclusions:This is the first study to identify novel targets in pembrolizumab-resistant GC using RNA-seq algorithms beyond PDL-1.

Gene Log2 Fold Change P-value FDR-Adjusted
P-value
Description
PGA5 -4.19 8.78E-09 5.17E-05 Pepsinogen A5
MSMB -4.39 7.06E-08 3.47E-04 Microseminoprotein beta
AC104389.5 -5.08 7.06E-08 8.69E-04 Novel protein
TRIM29 2.76 1.18E-06 3.49E-03 Tripartite motif containing 29
GJB5 3.32 6.94E-06 1.57E-02 Gap junction protein beta 5
GABRP 2.56 8.13E-06 1.60E-02 Gamma-aminobutyric acid type A receptor pi subunit
SERPINB7 3.02 9.79E-06 1.80E-02 Serpin family B member 7

 

Ocean Genomics Names Five Prominent Oncology Researchers to Its Scientific Advisory Board

Pittsburgh, PA. March 2, 2020

Ocean Genomics is pleased to announce the following individuals have joined our scientific advisory board.  Each has significant experience in oncology and adoption of new technologies and techniques involving the study and treatment of cancer. 

Stanley M. Marks, MD
Chairman, UPMC Hillman Cancer Center
Director of Clinical Services and Chief Medical Officer, UPMC Hillman Cancer Center
Chief Division of Hematology Oncology, UPMC Shadyside
Clinical Professor of Medicine, University of Pittsburgh School of Medicine 

Edith Perez, MD
Professor of Medicine
Mayo Clinic
Jacksonville, FL   

David R. Gandara, MD
Professor of Medicine Emeritus
Director, Thoracic Oncology
Senior Advisor to the Director
UC Davis Comprehensive Cancer Center
Sacramento, CA 

Adrian Lee, PhD
Professor and Director, Institute for Precision Medicine
University of Pittsburgh
Pittsburgh, PA 

Justin Odegaard, MD, PhD
VP, Clinical Development 
Guardant Health
Redwood City, CA
Adjunct Clinical Assistant Professor of Medicine
Stanford University
Palo Alto, CA 

“We are delighted to have a scientific advisory board with such great leaders in the field of oncology”, said Carl Kingsford, Ph.D., Herbert A. Simon Professor of Computer Science in the Computational Biology Department in the School of Computer Science at Carnegie Mellon University and Co-founder and CEO of Ocean Genomics. 

About Ocean Genomics: Ocean Genomics, Inc. (oceangenomics.com) creates software to analyze gene expression and RNA sequencing data. Our mission is to provide the world’s most accurate, efficient, and comprehensive gene expression analyses by supporting and extending our current state-of-the-art gene expression and transcriptome analysis software and engaging with customers in programs of biomarker discovery and validation.  

For more information, see our website at oceangenomics.com, or contact us via email at contact@oceangenomics.com.

Ocean Genomics Announces Initial Financing to Expand Their Whole-Transcriptome Analysis Platform for Research and Clinical Applications in Oncology

Pittsburgh, PA. September 9, 2019

Ocean Genomics Inc., a privately held company, has closed initial financing, led by Ocean Investors, LLC, that will be used to advance its whole-transcriptome analysis platform. The company will expand and support its advanced open-source expression analysis software pipeline while creating commercial enhancements and extensions using artificial intelligence-driven algorithms to deliver client solutions in oncology, in both research and clinical applications.

Ocean Genomics’ analysis platform is based on validated, open-source applications developed by the co-founders over the last 7 years. The platform includes a gene expression quantifier (Salmon), a transcript assembler (Scallop), a structural variant predictor (Squid), an HLA assembler (Kourami), as well as other analysis components. These components support extraction of informative features from high-throughput sequencing data, which are key for expression-based biomarker discovery. Salmon and its previous versions have been cited in over 1200 publications.

Carl Kingsford, Ph.D., Professor of Computational Biology in the School of Computer Science at Carnegie Mellon University and co-founder stated, “RNA has been used in a variety of applications in research for years. Advances in bioinformatics-driven by A.I. coupled with the ability to store and analyze vast amounts of data for interpretation makes now the right time to accelerate our work.”

Rob Patro, Ph.D., Assistant Professor of Computer Science at University of Maryland and co-founder states, “We aim to expand the reach of advanced transcriptome analysis techniques by offering and supporting a robust and harmonized solution based on open source technologies, and our commercial extensions and enhancements for custom client applications and analytic challenges.”

Stan Marks, M.D., founder and CEO of Oncology Hematology Associates, stated, “Ocean Genomics has the team and the vision to bring new computational technology into the clinic to interpret both tissue- and blood-based assays. I am excited to be an early part of the company’s development”.

Ocean Genomics’ executive team carries deep scientific and commercial experience in biotechnology. Carl Kingsford, Ph.D., (CEO) Professor of Computational Biology at Carnegie Mellon University and Rob Patro, Ph.D., (CTO) Assistant Professor of Computer Science at University of Maryland, College Park, are the technical founders and developers of the analysis pipeline. Eric Schultz (co-founder) and Stan Skrzypczak lead commercial strategy, corporate and business development, and marketing.  Eric Schultz also serves as advisor to the Carnegie Mellon Center for Machine Learning and Health, and was co-founder and former CEO of COTA, and of QuantiaMD, and has held executive roles at Microsoft and Qualcomm. Stan Skrzypczak was formerly V.P. of Corporate Development and Reimbursement at both Guardant Health and Invitae, and a senior marketing executive at Genomic Health.

About Ocean Genomics:

Ocean Genomics, Inc. (http://oceangenomics.com) creates software to analyze gene expression and RNA sequencing data. Our mission is to provide the world’s most accurate, efficient, and comprehensive gene expression analyses by supporting and extending our current state-of-the-art gene expression and transcriptome analysis software, and engaging with customers in programs of biomarker discovery and validation.

For more information, see our website at www.oceangenomics.com, or email Eric Schultz, eric@oceangenomics.com.