Tumor cell enrichment by tissue suspension improves sensitivity to copy number variation in diffuse gastric cancer with low tumor content

Sep 21, 2026

Uploaded by Violet

Accurate detection of copy number variations (CNVs) and somatic mutations is critical for selecting targeted cancer drugs, yet low tumor content in sporadic tumors can hinder reliable detection in targeted sequencing. This study enriches tumor cells from FFPE tissue sections using tissue suspension to separate tumor-enriched and residual fractions. Targeted sequencing of 225 cancer-related genes shows that tumor-enriched fractions increase detectable CNVs and amplified gene copies. Using the normal-equivalent residual fraction for CNV scoring further enables CNV characterization in diffuse-type gastric cancer samples without paired blood.

LanguageEnglish

CategoryResearch & Report

FormatPDF

Pages8

Reading Time20 min

AccessFree to download

Abstract

Tumor cell enrichment

Targeted sequencing and CNV detection

[www. nature.com/scientificreports](www. nature.com/scientificreports) OPEN Tumor cell enrichment by tissue suspension improves sensitivity to copy number variation in diffuse gastric cancer with low tumor content Keiichi Hatakeyama1*, Koji Muramatsu2, Takeshi Nagashima 3,4, Hiroyuki Ichida 5, Yuichi Kawanishi 5, Ryutaro Fukumura 5, Keiichi Ohshima6, Yuji Shimoda3, Sumiko Ohnami3, Shumpei Ohnami3, Koji Maruyama7, Akane Naruoka8, Hirotsugu Kenmotsu9, Kenichi Urakami 3, YasutoAkiyama10, Takashi Sugino2 & Ken Yamaguchi11 The detection of copy number variations (CNVs) and somatic mutations in cancer is important for the selection of specific drugs for patients with cancer. In cancers with sporadic tumor cells, low tumor content prevents the accurate detection of somatic alterations using targeted sequencing. To efficiently identify CNVs, we performed tumor cell enrichment using tissue suspensions of formalinfixed paraffin-embedded (FFPE) tissue sections with low tumor cell content. Tumor-enriched and residual fractions were separated from FFPE tissue suspensions of intestinal and diffuse-type gastric cancers containing sporadic tumor cells, and targeted sequencing was performed on 225 cancerrelated genes. Sequencing of a targeted panel of cancer-related genes using tumor-enriched fractions increased the number of detectable CNVs and the copy number of amplified genes. Furthermore, CNV analysis using the normal cell-enriched residual fraction as a reference for CNV scoring allowed targeted sequencing to detect CNV characteristics of diffuse-type gastric cancer with low tumor content. Our approach improves the CNV detection rate in targeted sequencing with tumor enrichment and the accuracy ofCNV detection in archival samples without paired blood. Cancer-related gene testing panel using next-generation sequencing (NGS) has expanded opportunities for drugselection in cancer treatment1. Several drugs have been developed for solid tumors with copy number variations (CNV) in cancer-related genes (e.g., ERBB2, FGFR1/2, MET, MDM2), and panel testing is being increasingly used to recruit patients for clinical trials. In addition, understanding CNVs in cancer-related genes is expected to lead to the discovery of candidate genes that may serve as new drug targets2,3. Recently, a relationship between therapeutic resistance, drug sensitivity, and copy number alterations has also been revealed4–6. Therefore, accurate evaluation of CNVs in targeted sequencing, where the number of genes is limited, has become important for therapeutic selection. NGS is influenced by tumor content and often underestimates somatic alterations, especially in tumors with low tumor content7. Furthermore, large-scale analyses have revealed that focal copy number alterations are more 1Cancer Multiomics Division, Shizuoka Cancer Center Research Institute, Sunto-gun, Shizuoka 411-8777, Japan. 2Division of Pathology, Shizuoka Cancer Center, Sunto-gun, Shizuoka 411-8777, Japan. 3Cancer Diagnostics Research Division, Shizuoka Cancer Center Research Institute, Sunto-gun, Shizuoka 411-8777, Japan. 4SRL Inc., Shinjuku-ku, Tokyo 163-0409, Japan. 5SRL and Shizuoka Cancer Center Collaborative Laboratories Inc., Sunto-gun, Shizuoka 411-8777, Japan. 6Medical Genetics Division, Shizuoka Cancer Center Research Institute, Sunto-gun, Shizuoka 411-8777, Japan. 7Experimental Animal Facility, Shizuoka Cancer Center Research Institute, Sunto-gun, Shizuoka 411-8777, Japan. 8Drug Discovery and Development Division, Shizuoka Cancer Center Research Institute, Sunto-gun, Shizuoka 411-8777, Japan. 9Division of Thoracic Oncology, Shizuoka Cancer Center, Sunto-gun, Shizuoka 411-8777, Japan. 10Immunotheraphy Division, Shizuoka Cancer Center Research Institute, Sunto-gun, Shizuoka 411-8777, Japan. 11Shizuoka Cancer Center, Sunto-gun, Shizuoka 411-8777, Japan. *email: [k.hatakeyama@scchr.jp](k.hatakeyama@scchr.jp) [www. nature.com/scientificreports/](www. nature.com/scientificreport

FAQs

Why does low tumor content affect CNV detection in targeted sequencing?

Low tumor content in sporadic cancers reduces sequencing sensitivity and can cause underestimation of somatic alterations, limiting accurate CNV evaluation.

What enrichment strategy was used to improve CNV detection?

Tumor cell enrichment was performed using tissue suspensions of FFPE sections, separating a tumor-enriched fraction from a residual fraction containing mainly non-tumor cells.

How was CNV scoring enhanced without paired blood samples?

CNV analysis used the normal cell-enriched residual fraction as a reference for CNV scoring, improving CNV detection accuracy in archival samples lacking paired blood.

Sep 21, 2026

Uploaded by Violet