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
4822 - Efficiacy of different nutritional intervention on nutritional status and quality of life for local advanced nasopharyngeal carcinoma patients: a prospective clinical trial
Presenter: Yuan-yuan Chen
Session: Poster Display session 3
Resources:
Abstract
2628 - Apatinib in treating patients with platinum-resistant or platinum-refractory recurrent or metastatic nasopharyngeal carcinoma
Presenter: Changjuan Tao
Session: Poster Display session 3
Resources:
Abstract
4887 - Impact of tumor site and adjuvant radiotherapy on survival of adenoid cystic carcinoma: a SEER database analysis
Presenter: Jason Tasoulas
Session: Poster Display session 3
Resources:
Abstract
2634 - Efficacy and safety of anlotinib for patients with recurrent and/or metastatic salivary gland carcinomas
Presenter: Wen Jiang
Session: Poster Display session 3
Resources:
Abstract
3568 - ACCURACY a phase (P) 2 trial of AL101, a pan-Notch inhibitor, in recurrent/metastatic (R/M) adenoid cystic carcinoma (ACC) patients (pts) with Notch activating mutations (Notch act mut): preliminary safety and efficacy data.
Presenter: Renata Ferrarotto
Session: Poster Display session 3
Resources:
Abstract
683 - Pathologic Staging Changes in Oral Cavity Squamous Cell Carcinoma—Stage Migration and Implications for Adjuvant Treatment
Presenter: Zain Husain
Session: Poster Display session 3
Resources:
Abstract
563 - Expression of immune response biomarkers in head and neck squamous cell carcinoma (HNSCC) in irradiated area
Presenter: Carole Pflumio
Session: Poster Display session 3
Resources:
Abstract
4030 - HLA-Ligandome analysis reveals target antigens of oropharyngeal squamous cell carcinoma
Presenter: Simon Laban
Session: Poster Display session 3
Resources:
Abstract
2979 - Topographical distribution of sentinel lymph nodes in early tongue squamous cell carcinomas
Presenter: Hiroyuki Goda
Session: Poster Display session 3
Resources:
Abstract
3517 - Role of follow-up (FU) FDG-PET/CT (FU-FDG-PET/CT) in patients with locoregionally advanced squamous cell carcinoma of the head and neck (LA-HNSCC) treated with chemotherapy and radiotherapy (RT), either concurrent (CRT) or sequential (ST).
Presenter: Bert Van Den Heuvel
Session: Poster Display session 3
Resources:
Abstract