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Related Experiment Video

Updated: Apr 23, 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

Filter Paper-based Nucleic Acid Storage in High-throughput Solid Tumor Genotyping.

Matthew Stachler¹, Yonghui Jia, Nematullah Sharaf

¹*Brigham and Women's Hospital and Harvard Medical School †Dana Farber Cancer Institute, Boston, MA ‡Case Western Reserve School of Medicine, Cleveland, OH §University of Vermont College of Medicine, Burlington, VT ∥Mount Sinai Medical Center, New York, NY.

Applied Immunohistochemistry & Molecular Morphology : AIMM

|September 16, 2014

Summary

Filter paper collection of tumor DNA offers a practical alternative to formalin-fixed paraffin-embedded (FFPE) tissue for solid tumor genotyping. This method preserves high-quality nucleic acid, simplifying molecular testing workflows.

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Last Updated: Apr 23, 2026

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Published on: April 11, 2016

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Published on: October 18, 2013

Area of Science:

Oncology
Molecular Diagnostics
Biotechnology

Background:

Molecular testing of tumors from formalin-fixed paraffin-embedded (FFPE) tissue is crucial but requires histology support and increases turnaround time.
Fresh frozen tissue collection is logistically challenging, requiring special handling, storage, and may not be suitable for small specimens.

Purpose of the Study:

To evaluate the performance of tumor smears on filter paper for solid tumor genotyping compared to paired FFPE samples.
To assess the feasibility of filter paper-based DNA preservation for automated, high-throughput genotyping.

Main Methods:

Tumor DNA was collected using Whatman FTA Micro Card (FTA preps) from 21 fresh tumor samples.
DNA was isolated from FTA preps and FFPE core samples using automated methods.
Genotyping was performed for 471 mutations on a mass spectrophotometry-based platform.

Main Results:

DNA quality from FTA preps was higher with less fragmentation compared to FFPE.
76% of FTA preps and 86% of FFPE samples yielded adequate DNA for genotyping.
15 out of 16 paired DNA samples (94%) showed concordant genotyping results.

Conclusions:

Filter paper-based sample preservation is a viable alternative to FFPE for molecular testing.
This method reduces the need for histology support and simplifies storage requirements.
Filter paper is suitable for automated, high-throughput genotyping, particularly for carcinomas.