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Related Experiment Video

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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.

Hisashi Tanaka¹, Michael Murata¹, Fumie Igari²

¹Cedars-Sinai Medical Center.

Research Square

|January 23, 2024

Summary

This summary is machine-generated.

Detecting cancer using plasma cell-free DNA (cfDNA) is promising. A new method, GAPF-seq, analyzes structural variants (SVs) like DNA palindromes for cancer detection in liquid biopsies.

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Last Updated: Jun 28, 2026

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Area of Science:

Genomics
Molecular Biology
Cancer Research

Background:

Plasma cell-free DNA (cfDNA) analysis shows potential for cancer detection.
Current cfDNA tests do not comprehensively analyze genomic structural variants (SVs).
Structural variants, such as DNA palindromes, are linked to genomic amplification and cancer.

Approach:

Developed Genome-wide Analysis of Palindrome Formation sequencing (GAPF-seq), a method to enrich and analyze tumorigenic SVs.
Combined low-throughput next-generation sequencing with automated machine learning.
Utilized high-coverage 1-kb bins (HCBs) to identify skewed chromosomal distributions indicative of tumor DNA.

Key Points:

GAPF-seq successfully differentiated tumor DNA from normal DNA in breast cancer samples with high accuracy (AUC 0.9819).
A proof-of-concept liquid biopsy study demonstrated cfDNA from 0.5 mL plasma could detect prostate cancer (AUC 0.965).
Identified X chromosome HCBs as a key feature associated with AR amplification in prostate cancer.

Conclusions:

GAPF-seq offers a novel approach for cancer detection by analyzing SVs in cfDNA.
This method provides unique, cancer-specific SV profiles in an agnostic liquid biopsy setting.
GAPF-seq holds potential for non-invasive cancer screening and diagnosis.