Acquire: an open-source comprehensive cancer biobanking system.

Heidi Dowst,Apollo Mcowiti,Chris Watkins,Benjamin Pew,Lauren B Becnel,Shijing Qu,Jonathan Barney

doi:10.1093/bioinformatics/btv012

Heidi Dowst, Apollo Mcowiti + Show 5 more

Open Access

https://doi.org/10.1093/bioinformatics/btv012

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Abstract

Motivation: The probability of effective treatment of cancer with a targeted therapeutic can be improved for patients with defined genotypes containing actionable mutations. To this end, many human cancer biobanks are integrating more tightly with genomic sequencing facilities and with those creating and maintaining patient-derived xenografts (PDX) and cell lines to provide renewable resources for translational research.Results: To support the complex data management needs and workflows of several such biobanks, we developed Acquire. It is a robust, secure, web-based, database-backed open-source system that supports all major needs of a modern cancer biobank. Its modules allow for i) up-to-the-minute ‘scoreboard’ and graphical reporting of collections; ii) end user roles and permissions; iii) specimen inventory through caTissue Suite; iv) shipping forms for distribution of specimens to pathology, genomic analysis and PDX/cell line creation facilities; v) robust ad hoc querying; vi) molecular and cellular quality control metrics to track specimens’ progress and quality; vii) public researcher request; viii) resource allocation committee distribution request review and oversight and ix) linkage to available derivatives of specimen.Availability and Implementation: Acquire implements standard controlled vocabularies, ontologies and objects from the NCI, CDISC and others. Here we describe the functionality of the system, its technological stack and the processes it supports. A test version Acquire is available at https://tcrbacquire-stg.research.bcm.edu; software is available in https://github.com/BCM-DLDCC/Acquire; and UML models, data and workflow diagrams, behavioral specifications and other documents are available at https://github.com/BCM-DLDCC/Acquire/tree/master/supplementaryMaterials.Contact: becnel@bcm.edu

Highlights

Access to high quality human cancer and matched normal tissues for ‘omics experimentation is critical for developing a better understanding of these diseases to design improved diagnostics and therapeutics
We developed Acquire to manage the full lifecycle of a specimen and its derivatives, distributions in different contexts and requests
Acquire is a modular system; caTissue Suite 1.2 was adopted as the biobank inventory module, whereas all other modules were constructed by the authors. caTissue technical specifications are described within its online deployment guide

Summary

Introduction

Access to high quality human cancer and matched normal tissues for ‘omics experimentation is critical for developing a better understanding of these diseases to design improved diagnostics and therapeutics. Biobanking standards provide guidance and best practices on how to collect, store and manage tissues to better assure high-quality DNA, RNA, protein or other derivatives such as cell lines and patient-derived xenografts (PDX) for research (e.g. International Society for Biological and Environmental Biorepositories [ISBER] 2012 Best Practices, http://bit.ly/1znXuEU). As such many commercial and some open-source software solutions exist to manage daily.

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