正常多甲醛固定、石蜡包埋（FFPE）样本保获充分的情况下，能够忠实地保留肿瘤特征。内镜活检组织代表着一个有吸引力的资源，可用于鉴定预测生物标记物，以评估晚期胃癌患者治疗前的反应。然而，使用活检样本通过下一代测序（NGS）获得的基因组文件与那些从手术获取的FFPE样本获得的文件是否匹配，仍然是一个问题。 我们从参加第III期临床试验JCOG1509的GC患者中收集了50个FFPE样本（26个活检和24个手术样本）。对于使用NGS进行深度测序，FFPE样本的质量和数量进行了确定。我们查询了一个435基因面板CANCERPLEX-JP，以生成包括肿瘤突变负荷（TMB）在内的全面基因组分析数据。 与手术样本相比，活检样本的中位DNA产量和NGS成功率分别为879ng和80.8％，8523ng和100％。在活检样本中检测到了9.5％的EB病毒和微卫星不稳定性高。我们比较了18对配对样本的基因组文件，发现配对活检和手术样本中的同种体细胞突变是相同的（kappa系数为0.8692）。TMB在配对的活检和手术样本之间呈正相关（相关系数为0.6911）。 使用NGS可以分析由内镜活检获取的GC的FFPE样本，数据与相同患者的手术标本中获取的数据高度一致。 © 2022年。本作者在国际胃癌协会和日本胃癌协会的独家许可下发表。

Formalin-fixed, paraffin-embedded (FFPE) samples acquired and preserved adequately are expected to faithfully maintain tumor characteristics. Endoscopic biopsy tissues represent an attractive resource for identifying predictive biomarkers to evaluate pretreatment responses of patients with advanced gastric cancer (GC). However, whether genomic profiles obtained through next-generation sequencing (NGS) using biopsy samples match well with those gained from surgical FFPE samples remains a concern.We collected 50 FFPE samples (26 biopsies and 24 surgical samples) from patients with GC who participated in phase III clinical trial JCOG1509. The quality and quantity of FFPE samples were determined for deep sequencing using NGS. We queried a 435-gene panel CANCERPLEX-JP to generate comprehensive genomic profiling data including the tumor mutation burden (TMB).The median DNA yields and NGS success rates of biopsy samples compared with surgical samples were 879 ng and 80.8% vs 8523 ng and 100%, respectively. Epstein-Barr virus and microsatellite instability-high were detected in 9.5% of biopsy samples. Comparing the genomic profiles of 18 paired samples for which NGS data were available, we detected identical somatic mutations in paired biopsy and surgical samples (kappa coefficient, 0.8692). TMB positively correlated between paired biopsy and surgical samples (correlation coefficient, 0.6911).NGS is applicable to the analysis of FFPE samples of GC acquired by the endoscopic biopsy, and the data were highly concordant with those obtained from surgical specimens of the same patients.© 2022. The Author(s) under exclusive licence to The International Gastric Cancer Association and The Japanese Gastric Cancer Association.