Tumor cell enrichment by tissue suspension improves sensitivity to copy number variation in diffuse gastric cancer...

Area of Science:

• Oncology
• Genetics
• Molecular Biology

Background:

• Accurate detection of somatic alterations like copy number variations (CNVs) is crucial for targeted cancer therapy selection.
• Low tumor cell content in certain cancers, particularly those with sporadic tumor cells, poses a significant challenge for reliable somatic alteration detection via targeted sequencing.
• Formalin-fixed paraffin-embedded (FFPE) tissues are valuable archival resources but often present difficulties in molecular analysis due to sample quality and low tumor cellularity.

Purpose of the Study:

• To develop and validate a method for efficient tumor cell enrichment from FFPE tissue sections with low tumor content.
• To improve the detection rate and accuracy of copy number variations (CNVs) using targeted sequencing in challenging cancer samples.
• To enable the characterization of CNV profiles in diffuse-type gastric cancer with low tumor cellularity.

Main Methods:

• Tumor cell enrichment was performed on FFPE tissue suspensions from intestinal and diffuse-type gastric cancers with low tumor cell content.
• Tissue suspensions were separated into tumor-enriched and residual fractions.
• Targeted sequencing was conducted on a panel of 225 cancer-related genes using both enriched and residual fractions.

Main Results:

• Sequencing of tumor-enriched fractions significantly increased the number of detectable CNVs and the copy number of amplified genes.
• Utilizing the normal cell-enriched residual fraction as a reference improved CNV scoring accuracy.
• The developed approach successfully detected CNV characteristics specific to diffuse-type gastric cancer even with low tumor content.

Conclusions:

• Tumor enrichment is an effective strategy to enhance CNV detection rates in targeted sequencing of FFPE samples with low tumor cellularity.
• This method improves the accuracy of CNV detection in archival samples, eliminating the need for paired normal blood samples.
• The approach provides a valuable tool for molecular profiling and personalized medicine in challenging cancer types.