title: GeneMed: An Informatics Hub for the Coordination of Next-Generation Sequencing Studies that Support Precision Oncology Clinical Trials.
abstract: We have developed an informatics system, GeneMed, for the National Cancer Institute (NCI) molecular profiling-based assignment of cancer therapy (MPACT) clinical trial (NCT01827384) being conducted in the National Institutes of Health (NIH) Clinical Center. This trial is one of the first to use a randomized design to examine whether assigning treatment based on genomic tumor screening can improve the rate and duration of response in patients with advanced solid tumors. An analytically validated next-generation sequencing (NGS) assay is applied to DNA from patients' tumors to identify mutations in a panel of genes that are thought likely to affect the utility of targeted therapies available for use in the clinical trial. The patients are randomized to a treatment selected to target a somatic mutation in the tumor or with a control treatment. The GeneMed system streamlines the workflow of the clinical trial and serves as a communications hub among the sequencing lab, the treatment selection team, and clinical personnel. It automates the annotation of the genomic variants identified by sequencing, predicts the functional impact of mutations, identifies the actionable mutations, and facilitates quality control by the molecular characterization lab in the review of variants. The GeneMed system collects baseline information about the patients from the clinic team to determine eligibility for the panel of drugs available. The system performs randomized treatment assignments under the oversight of a supervising treatment selection team and generates a patient report containing detected genomic alterations. NCI is planning to expand the MPACT trial to multiple cancer centers soon. In summary, the GeneMed system has been proven to be an efficient and successful informatics hub for coordinating the reliable application of NGS to precision medicine studies.
authors: Biometric Research Branch, Division of Cancer Treatment and Diagnosis, National Cancer Institute, Rockville, MD, USA.
authors: Yingdong
authors: Y
authors: Zhao
authors: Biometric Research Branch, Division of Cancer Treatment and Diagnosis, National Cancer Institute, Rockville, MD, USA.
authors: Eric C
authors: EC
authors: Polley
authors: Biometric Research Branch, Division of Cancer Treatment and Diagnosis, National Cancer Institute, Rockville, MD, USA.
authors: Ming-Chung
authors: MC
authors: Li
authors: Molecular Characterization and Clinical Assay Development Laboratory, Leidos Biomedical Research Inc., Frederick National Laboratory for Cancer Research, Frederick, MD, USA.
authors: Chih-Jian
authors: CJ
authors: Lih
authors: Biometric Research Branch, Division of Cancer Treatment and Diagnosis, National Cancer Institute, Rockville, MD, USA.
authors: Alida
authors: A
authors: Palmisano
authors: Molecular Characterization and Clinical Assay Development Laboratory, Leidos Biomedical Research Inc., Frederick National Laboratory for Cancer Research, Frederick, MD, USA.
authors: David J
authors: DJ
authors: Sims
authors: Biometric Research Branch, Division of Cancer Treatment and Diagnosis, National Cancer Institute, Rockville, MD, USA.
authors: Lawrence V
authors: LV
authors: Rubinstein
authors: Cancer Diagnosis Program, Division of Cancer Treatment and Diagnosis, National Cancer Institute, Rockville, MD, USA.
authors: Barbara A
authors: BA
authors: Conley
authors: Division of Cancer Treatment and Diagnosis, National Cancer Institute, Bethesda, MD, USA.
authors: Alice P
authors: AP
authors: Chen
authors: Molecular Characterization and Clinical Assay Development Laboratory, Leidos Biomedical Research Inc., Frederick National Laboratory for Cancer Research, Frederick, MD, USA.
authors: P Mickey
authors: PM
authors: Williams
authors: Division of Cancer Treatment and Diagnosis, National Cancer Institute, Bethesda, MD, USA.
authors: Shivaani
authors: S
authors: Kummar
authors: Division of Cancer Treatment and Diagnosis, National Cancer Institute, Bethesda, MD, USA.
authors: James H
authors: JH
authors: Doroshow
authors: Biometric Research Branch, Division of Cancer Treatment and Diagnosis, National Cancer Institute, Rockville, MD, USA.
authors: Richard M
authors: RM
authors: Simon
keywords: GeneMed; MPACT; clinical trial; informatics system; next-generation sequencing; precision medicine