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Screening for Functional Non-coding Genetic Variants Using Electrophoretic Mobility Shift Assay EMSA and DNA-affinity Precipitation Assay DAPA

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A Practical Approach for Targeting Structural Variants Genome-wide in Plasma Cell-free DNA.

Michael M Murata, Fumie Igari, Ryan Urbanowicz

Biorxiv : the Preprint Server for Biology

|November 14, 2023

Summary

This summary is machine-generated.

Genome-wide Analysis of Palindrome Formation (GAPF-seq) detects cancer by analyzing DNA structural variants (SVs) in plasma. This novel liquid biopsy method shows high accuracy in differentiating tumors from normal DNA, offering a new tool for cancer detection.

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Area of Science:

Genomics
Molecular Biology
Cancer Research

Background:

Plasma cell-free DNA (cfDNA) is a valuable resource for cancer detection via liquid biopsy, primarily focusing on gene mutations.
Current liquid biopsy methods do not comprehensively analyze chromosomal structural variants (SVs) genome-wide.

Approach:

Developed Genome-wide Analysis of Palindrome Formation (GAPF-seq), a workflow to detect DNA palindromes, a type of SV linked to gene amplification.
Utilized low-throughput next-generation sequencing and machine learning to analyze high-coverage 1-kb bins (HCBs) in tumor DNA.
Applied GAPF-seq to cfDNA from prostate cancer patients and healthy individuals for liquid biopsy analysis.

Key Points:

GAPF-seq identified skewed chromosomal distributions of HCBs, effectively distinguishing 39 breast tumors from matched normal DNA (AUC of 0.9819).
A liquid biopsy study demonstrated GAPF-seq's efficacy in prostate cancer detection, achieving an average AUC of 0.965.
HCBs on the X chromosome were identified as a key feature, correlating with androgen receptor gene amplification.

Conclusions:

GAPF-seq represents a novel, agnostic liquid biopsy approach for interrogating genome-wide SVs.
This method addresses a technological gap, providing unique, cancer-specific SV profiles.
GAPF-seq has the potential to significantly advance cancer detection and characterization through liquid biopsies.