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Related Experiment Video

Updated: Jan 12, 2026

Integration of Wet and Dry Bench Processes Optimizes Targeted Next-generation Sequencing of Low-quality and Low-quantity Tumor Biopsies

Integration of Wet and Dry Bench Processes Optimizes Targeted Next-generation Sequencing of Low-quality and Low-quantity Tumor Biopsies

Published on: April 11, 2016

Brain tumor classification from FFPE samples using nanopore methylation sequencing.

Galina Feinberg-Gorenshtein¹, Assaf Grunwald², Carlo Vermeulen³

¹The Rina Zaizov Division of Pediatric Hematology-Oncology, Schneider Children's Medical Center of Israel, P.O. Box 559, Petach Tikva, Israel.

|November 3, 2025

Summary

This summary is machine-generated.

Oxford Nanopore Technology (ONT) methylation sequencing can now classify brain tumors using formalin-fixed paraffin-embedded (FFPE) tissue. This new protocol works even with small DNA samples from stained slides, improving cancer diagnostics.

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Last Updated: Jan 12, 2026

Integration of Wet and Dry Bench Processes Optimizes Targeted Next-generation Sequencing of Low-quality and Low-quantity Tumor Biopsies

Integration of Wet and Dry Bench Processes Optimizes Targeted Next-generation Sequencing of Low-quality and Low-quantity Tumor Biopsies

Published on: April 11, 2016

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Published on: October 31, 2016

Detecting Somatic Genetic Alterations in Tumor Specimens by Exon Capture and Massively Parallel Sequencing

Detecting Somatic Genetic Alterations in Tumor Specimens by Exon Capture and Massively Parallel Sequencing

Published on: October 18, 2013

Area of Science:

Molecular Oncology
Genomics
Pathology

Background:

Oxford Nanopore Technology (ONT)-based methylation sequencing offers rapid brain tumor classification for precision oncology.
Clinical adoption is hindered by the need for fresh-frozen (FF) tissue, unlike the common formalin-fixed paraffin-embedded (FFPE) specimens.

Purpose of the Study:

To evaluate FFPE processing effects on DNA methylation profiles.
To develop and validate a protocol for ONT-based brain tumor classification using DNA from FFPE slides.

Main Methods:

DNA extraction from pathology-marked regions on stained FFPE slides.
Targeted selection of tumor-rich areas post-histological assessment.
ONT-based methylation sequencing for classification.

Main Results:

Successful classification of brain tumors from low-input DNA (≥25 ng) extracted from FFPE tissue.
High concordance between ONT classification and neuropathological diagnoses.
Modest methylation loss due to formalin fixation, but robust classification performance.
Correlation between methylation degradation and formalin fixation time (≤3-4 days recommended).

Conclusions:

A validated protocol enables accurate methylation-based tumor classification from routine FFPE tissue.
This expands accessibility of ONT diagnostics into standard clinical workflows.
Facilitates timely treatment decisions, even with limited or urgent tissue samples.