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Related Experiment Video

Updated: Mar 9, 2026

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

Generating Exome Enriched Sequencing Libraries from Formalin-Fixed, Paraffin-Embedded Tissue DNA for Next-Generation

Beth A Marosy¹, Brian D Craig¹, Kurt N Hetrick¹

¹Center for Inherited Disease Research, McKusick-Nathans Institute of Genetic Medicine, Johns Hopkins University, Baltimore, Maryland.

Current Protocols in Human Genetics

|January 12, 2017

Summary

This study details a method for creating exome sequencing libraries from formalin-fixed paraffin-embedded (FFPE) DNA. The workflow efficiently repairs FFPE-induced damage, enhancing sequence quality for next-generation sequencing.

Keywords:

DNA library preparation DNA repair FFPE next-generation sequencing whole exome sequencing

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

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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

Area of Science:

Molecular Biology
Genomics
Biotechnology

Background:

Formalin-fixed paraffin-embedded (FFPE) tissues are a valuable source of clinical samples.
DNA extracted from FFPE samples often suffers from degradation and chemical modifications.
Generating high-quality sequencing libraries from FFPE DNA can be challenging.

Purpose of the Study:

To describe a robust method for exome-enriched sequencing library preparation from FFPE DNA.
To optimize a low-input workflow suitable for limited FFPE sample quantities.
To improve the quality and reliability of sequencing data derived from FFPE samples.

Main Methods:

Utilized commercially available kits for library preparation.
Implemented a DNA repair step to mitigate FFPE-induced damage.
Performed in-solution targeted exonic selection.
Sequenced libraries using the Illumina next-generation short-read platform.

Main Results:

Successfully generated exome-enriched sequencing libraries from FFPE DNA.
The low-input workflow requires only 50 ng of DNA.
The DNA repair step significantly improved sequence quality.
The method is compatible with standard short-read sequencing technologies.

Conclusions:

This protocol provides an effective approach for exome sequencing of FFPE samples.
The described technique enhances the utility of FFPE archives for genomic studies.
The improved library preparation method facilitates reliable genetic analysis from challenging FFPE specimens.