Tissue sampling for genomic testing in a community-based center.

Abstract

e18000 Background: Genomic testing requires greater quality than routine clinical diagnostic tests. As genomic testing proliferates and becomes more widespread, adjustments in processes may be needed by community-based pathology, radiology, and surgery groups. Both tissue quality and quantity parameters are essential for successful completion of next-generation sequencing (NGS) panels. Methods: A NGS genomic platform ( > 600 genes) was implemented in a hybrid academic community-based cancer institute, with success/failure rates recorded.. Data were collected from the electronic medical records and biorepository data system. Descriptive statistics assessed success or failure rates by tissue quality or quantity with subgroup analyses by disease sites (primary/metastases), collection procedure, and specimen age. Results: From 6/2015-2/2017, 809 NGS tests yielded 143 (17%) failures [specimen quality (34%) and specimen quantity (66%)]. Of the failed tests, specimens were collected from 26 primary disease sites [lung (21%)] and 18 metastatic sites [liver (29%), lymph node (19%), and lung, omentum, brain, and peritoneal specimens (all < 10%)]. Of the failed tests, all bronchoscopy, EBUS, and peritoneal fluid specimens and the majority of FNAs (78%) were due to insufficient tissue quantity, whereas surgical resection or excision had more issues with quality of the specimen (60%). Of note, surgical specimens ranged from 2005-2016; NGS quality initiatives were implemented system-wide in 2015, leading to substantially fewer failed tests. Cores biopsies had fewer quantity (24%) or quality (18%) issues. The number of tests failing due to insufficient quantity also declined due to education and communication processes implemented. Conclusions: The majority of NGS tests provided valuable information. Implementation of systematic tissue collection (core biopsies) and processing, for primary lung and lung and liver metastases using core biopsies consistently provided the fewest failures and implementing NGS-specific processes improved NGS success rates.