System for Informatics in the Molecular Pathology Laboratory: An Open-Source End-to-End Solution for Next-Generation Sequencing Clinical Data Management

Wenjun Kang, Sabah Kadri, Rutika Puranik, Michelle N. Wurst, Sushant A. Patil, Ibro Mujacic, Sonia Benhamed, Nifang Niu, Chao Jie Zhen, Bekim Ameti, Bradley C. Long, Filipo Galbo, David Montes, Crystal Iracheta, Venessa L. Gamboa, Daisy Lopez, Michael Yourshaw, Carolyn A. Lawrence, Dara L. Aisner, Carrie FitzpatrickMegan E. McNerney, Y. Lynn Wang, Jorge Andrade, Samuel L. Volchenboum, Larissa V. Furtado, Lauren L. Ritterhouse, Jeremy P. Segal*

*Corresponding author for this work

Research output: Contribution to journalArticlepeer-review

3 Scopus citations

Abstract

Next-generation sequencing (NGS) diagnostic assays increasingly are becoming the standard of care in oncology practice. As the scale of an NGS laboratory grows, management of these assays requires organizing large amounts of information, including patient data, laboratory processes, genomic data, as well as variant interpretation and reporting. Although several Laboratory Information Systems and/or Laboratory Information Management Systems are commercially available, they may not meet all of the needs of a given laboratory, in addition to being frequently cost-prohibitive. Herein, we present the System for Informatics in the Molecular Pathology Laboratory (SIMPL), a free and open-source Laboratory Information System/Laboratory Information Management System for academic and nonprofit molecular pathology NGS laboratories, developed at the Genomic and Molecular Pathology Division at the University of Chicago Medicine. SIMPL was designed as a modular end-to-end information system to handle all stages of the NGS laboratory workload from test order to reporting. We describe the features of SIMPL, its clinical validation at University of Chicago Medicine, and its installation and testing within a different academic center laboratory (University of Colorado), and we propose a platform for future community co-development and interlaboratory data sharing.

Original languageEnglish (US)
Pages (from-to)522-532
Number of pages11
JournalJournal of Molecular Diagnostics
Volume20
Issue number4
DOIs
StatePublished - Jul 2018

ASJC Scopus subject areas

  • Pathology and Forensic Medicine
  • Molecular Medicine

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