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
2607 - Single cycle induction treatment with Cisplatin/Docetaxel plus Durvalumab/Tremelimumab in Stage III-IVB head and neck squamous cell cancer (CheckRad-CD8 trial)
Presenter: Markus Hecht
Session: Poster Display session 3
Resources:
Abstract
1388 - Radiotherapy plus cisplatin (CDDP) or cetuximab (C225) in human papilloma-virus (HPV)-associated oropharyngeal cancer (OPC)? A dillema finally resolved. An updated meta-analysis.
Presenter: Petar Suton
Session: Poster Display session 3
Resources:
Abstract
1478 - Treatment outcomes of head and neck cancer patients 70 years and older receiving different chemo-radiation combinations.
Presenter: Majd Issa
Session: Poster Display session 3
Resources:
Abstract
3985 - Brachytherapy and non-cancer mortality in patients with oral cavity and oropharynx SCCs
Presenter: Jovian Yu
Session: Poster Display session 3
Resources:
Abstract
4036 - Final results of a phase II study of induction chemotherapy (CT) with paclitaxel (PTX) and panitumumab (P) followed by radiotherapy (RT) and P in patients (pts) with locally advanced head and neck cancer (LAHNC) no candidates to platinum: study PANTERA
Presenter: Javier Martinez Trufero
Session: Poster Display session 3
Resources:
Abstract
4779 - Window of Opportunity for Durvalumab (MEDI4736) plus Metformin Trial in Squamous Cell Carcinoma of the Head and Neck (SCCHN): interim safety analysis
Presenter: Tony Richa
Session: Poster Display session 3
Resources:
Abstract
2757 - Severe Oral Mucositis (SOM) Mitigation by Genetically Modified Lactococcus Lactis Bacteria (LLB) Producing Human Trefoil Factor 1 (hTFF1; AG013) in Patients Being Treated With Concomitant Chemoradiation (CRT) for Oral and Oropharyngeal Cancers (OCOPC)
Presenter: Suraj Singh
Session: Poster Display session 3
Resources:
Abstract
5559 - Transcriptome signatures of treatment responses in a preoperative window of opportunity trial of nivolumab and tadalafil in resectable squamous cell carcinoma of the head and neck
Presenter: Sanket Shukla
Session: Poster Display session 3
Resources:
Abstract
3263 - Risk and Impact of Renal Impairment of Locally Advanced Head and Neck Squamous Cell Carcinoma Patients Who Received Chemoradiotherapy with Cisplatin
Presenter: Thana Patimarattananan
Session: Poster Display session 3
Resources:
Abstract
3128 - Systemic bevacizumab for the treatment of recurrent respiratory papillomatosis: A retrospective analysis from an academic tertiary care center
Presenter: Sumita Trivedi
Session: Poster Display session 3
Resources:
Abstract