# Operationalizing Next-Generation Sequencing in a Community-Based Academic Cancer Center: Workflow, Integration, and Impact

## TL;DR

This study shows how a cancer center successfully implemented in-house genomic testing to improve personalized cancer care.

## Contribution

The paper demonstrates a real-world workflow for integrating NGS and pharmacogenomics into clinical practice at a community-based cancer center.

## Key findings

- In-house NGS was performed in 90% of 279 patients with advanced cancers, averaging 11 business days.
- 54.2% of patients were identified as candidates for NGS-guided therapies, and 99.6% had pharmacogenomic variants affecting treatment.
- A multidisciplinary tumor board was established to provide actionable precision therapy recommendations.

## Abstract

This prospective study, the Kellogg Cancer Genomic Initiative, sought to expand the implementation of in-house next-generation sequencing (NGS) and pharmacogenomics within a community-based academic cancer center. Among 279 enrolled patients with advanced cancers, in-house NGS was performed in 90%, with an average turnaround of 11 business days. Over half of patients who had NGS were identified as candidates for NGS-guided therapies, and the majority had pharmacogenomic variants relevant to treatment management. Additionally, by establishing an in-house bioinformatics pipeline and a multidisciplinary molecular tumor board, we enhanced institutional workflows, clinician engagement, and precision oncology care delivery. The KCGI culminated in the successful adoption and integration of personalized data within our community health system.

Background/Objectives: Prompt integration of molecular and clinical data into electronic medical records, with a sustainable workflow that supports clinicians in rendering genomics-guided care, is critical. We sought to expand the implementation of in-house NGS at our community-based academic cancer center to operationalize the utilization of molecular diagnostic studies to optimize cancer care for all patients, including those outside this study, through broader adoption and diffusion. Methods: In this prospective IRB-approved study, the Kellogg Cancer Genomic Initiative (KCGI), patients with advanced cancers underwent in-house NGS, including tumor mutational burden (TMB) and pharmacogenomics. In-house bioinformatics (Flype) was used for structured reporting and served as a molecular knowledgebase. A multidisciplinary molecular tumor board (MTB) was created to provide precision therapy recommendations. Results: In-house NGS, completed within 11 business days on average, was performed in 90% (251) of the 279 patients in the KCGI with advanced cancers. RNA and TMB analyses were successful in 89.2% and 86.5% of patients, respectively. A total of 54.2% of patients were identified as candidates for use of on- or off-label FDA-approved therapies, and 99.6% of patients who underwent pharmacogenomics testing had at least one gene alteration associated with medication dose adjustment/avoidance. An MTB was established to discuss these and other molecularly challenging cases continues to function as a consultative service that provides actionable recommendations. Conclusions: In this real-world trial, the utilization of in-house NGS with an adaptable bioinformatics pipeline and the establishment of an MTB enabled the refinement of institutional processes and created an environment that enhanced clinician interest in genomics and improved genomics-guided care for patients with advanced cancers.