Decoding genetic and epigenetic information embedded in cell free DNA with adapted SALP-seq

Area of Science:

• Molecular Biology
• Genomics
• Cancer Research

Background:

• Cell-free DNA (cfDNA) in plasma is crucial for noninvasive prenatal testing and liquid biopsies.
• Next-generation sequencing (NGS) effectively decodes genetic and epigenetic information from cfDNA.
• Constructing NGS libraries from degraded cfDNA requires specialized, often complex, methods.

Purpose of the Study:

• To adapt a single-strand adaptor library preparation (SALP) method for cfDNA library construction.
• To develop a simpler and more efficient method for cfDNA NGS library preparation.
• To identify genetic and epigenetic differences in cfDNA between esophageal cancer patients and healthy individuals.

Main Methods:

• Adapted SALP method involving cfDNA denaturation and single-strand adaptor ligation.
• Taq polymerase used for dsDNA conversion and A-tailing.
• Barcode T adaptor (BTA) ligation and amplification with Illumina-compatible primers.
• Sequencing of 20 cfDNA samples (16 esophageal cancer patients, 4 healthy controls).

Main Results:

• Successfully constructed NGS libraries from cfDNA using the adapted SALP method.
• Bioinformatics analysis revealed genetic and epigenetic differences between patients and controls.
• Identified 23 epigenetic and 28 genetic altered esophageal cancer-specific genes.

Conclusions:

• The adapted SALP method provides a simple and effective approach for cfDNA library preparation for NGS.
• This method facilitates the discovery of cfDNA-based biomarkers for esophageal cancer.
• The identified genes offer potential targets for understanding esophageal cancer pathogenesis and developing diagnostics.