Abstract 5744
Background
The advent of high-throughput next-generation sequencing (NGS) technologies has resulted in a deluge of data for a wide variety of clinical uses, with millions of samples sequenced to date. Data generated at an “-omics” level (genomics, transcriptomics, epigenomics, proteomics, etc) in cancer research and for clinical decision making is ushering in a new era of personalized cancer care. However this requires fast, accurate, and easily automatable bioinformatics pipelines capable of large scale analytics on big datasets without sacrificing accuracy. Here we present OncOS, a cloud-based auto-scaling architecture capable of performing highly accurate molecular profiling for personalized clinical insights.
Methods
A flexible cloud architecture implements bioinformatics pipelines dynamically depending on the input data, including a range of possible sample types (FFPE, fresh frozen, plasma/cfDNA), and clinical insights (clinical trial matching, drug matching, and genomic insights such as mutation calls, copy number variant calls, and MSI/TMB). This is powered by a pipeline scheduler and an elastic container service cluster that is capable of initializing a large number of elastic compute cloud instances for scalable and parallelized processing. Data is stored on HIPAA compliant and securely encrypted databases and simple storage services, with key information relayed to a web app for use in a clinical setting.
Results
OncOS has also been optimized for Positive Predictive Value (PPV), with testing on samples from the Multi-Center Mutation Calling in Multiple Cancers (MC3) project, a collaborative effort to provide a high confidence set of variants for patients in The Cancer Genome Atlas (TCGA). Benchmarking shows OncOS performs with a PPV of 87.4%, outperforming similar variant calling pipelines (BROAD institute 75.4%; MD Anderson 80.1%).
Conclusions
OncOS is a precision oncology platform with a cloud architecture capable of processing a variety of sample types at scale, optimized for variant calling PPV and drawing of key clinical insights.
Clinical trial identification
Editorial acknowledgement
Legal entity responsible for the study
The authors.
Funding
Cambridge Cancer Genomics.
Disclosure
J.S. Thompson: Shareholder / Stockholder / Stock options, Full / Part-time employment: Cambridge Cancer Genomics. J.H.R. Farmery: Shareholder / Stockholder / Stock options: Cambridge Cancer Genomics. H. Dobson: Shareholder / Stockholder / Stock options, Full / Part-time employment: Cambridge Cancer Genomics. S. Frost: Shareholder / Stockholder / Stock options, Full / Part-time employment: Cambridge Cancer Genomics. J.W. Cassidy: Leadership role, Shareholder / Stockholder / Stock options, Full / Part-time employment, Officer / Board of Directors: Cambridge Cancer Genomics. N. Patel: Leadership role, Shareholder / Stockholder / Stock options, Full / Part-time employment: Cambridge Cancer Genomics. H. Thompson: Leadership role, Shareholder / Stockholder / Stock options, Full / Part-time employment: Cambridge Cancer Genomics. H.W. Clifford: Leadership role, Shareholder / Stockholder / Stock options, Full / Part-time employment: Cambridge Cancer Genomics.
Resources from the same session
5056 - Phase 2 study of 2 dosing regimens of cemiplimab, a human monoclonal anti–PD-1, in metastatic cutaneous squamous cell carcinoma (mCSCC)
Presenter: Danny Rischin
Session: Poster Display session 3
Resources:
Abstract
5710 - Avelumab for advanced Merkel cell carcinoma in the Netherlands; a nationwide survey
Presenter: Sonja Levy
Session: Poster Display session 3
Resources:
Abstract
3152 - Health-related quality of life in patients with metastatic Merkel cell carcinoma receiving second-line or later avelumab treatment: 36-month follow-up data
Presenter: Sandra D'Angelo
Session: Poster Display session 3
Resources:
Abstract
5715 - A Phase 2, Randomized Study of Nivolumab (NIVO) and Ipilimumab (IPI) versus NIVO, IPI and Stereotactic Body Radiation Therapy (SBRT) for Metastatic Merkel Cell Carcinoma (MCC, NCT03071406) – a preliminary report.
Presenter: Sungjune Kim
Session: Poster Display session 3
Resources:
Abstract
2854 - Real-world impact of immune checkpoint inhibitors in metastatic uveal melanoma
Presenter: Kalijn Bol
Session: Poster Display session 3
Resources:
Abstract
2928 - Immune checkpoint inhibitors in a cohort of 206 metastatic uveal melanomas patients
Presenter: Mathilde Saint-Ghislain
Session: Poster Display session 3
Resources:
Abstract
1235 - Incidence and survival of Uveal Melanoma occurring as single cancer versus its occurrence as a first or second primary neoplasm
Presenter: Ahmad Alfaar
Session: Poster Display session 3
Resources:
Abstract
3615 - Validation of a Clinicopathological and Gene Expression Profile (CP-GEP) Model for Sentinel Lymph Node Metastasis in Primary Cutaneous Melanoma
Presenter: Evalyn Mulder
Session: Poster Display session 3
Resources:
Abstract
1793 - External validation of the 8th Edition Melanoma Staging System of the American Joint Committee on Cancer (AJCC) using the Surveillance, Epidemiology and End Results (SEER) Program
Presenter: Angelina Tjokrowidjaja
Session: Poster Display session 3
Resources:
Abstract
4278 - Clinical factors and overall survival (OS) associated with patterns of metastases (mets) in melanoma patients (pts).
Presenter: Ines Pires da Silva
Session: Poster Display session 3
Resources:
Abstract