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Related Experiment Video

Updated: Dec 2, 2025

Simple and Rapid Method to Obtain High-quality Tumor DNA from Clinical-pathological Specimens Using Touch Imprint Cytology
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Optimizing clinical cytology touch preparations for next generation sequencing.

Stephen J Murphy1, Faye R Harris1, James B Smadbeck1

  • 1Center for Individualized Medicine, Bio-marker Discovery Program, Mayo Clinic, Rochester, MN, United States.

Genomics
|November 4, 2020
PubMed
Summary

This study shows that whole genome amplified DNA from cytology touch preparations (TPs) can accurately detect genomic alterations. This novel method expands the use of limited core needle biopsy (CNB) samples for genomic testing.

Keywords:
CytologyMate pair sequencingStructural variance analysisTouch preparationsWhole exome sequencingWhole genome sequencing

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Area of Science:

  • Genomic Medicine
  • Oncology
  • Molecular Pathology

Background:

  • Cytology touch preparations (TPs) from core needle biopsies (CNBs) are vital for intraoperative diagnosis.
  • There is growing interest in utilizing TPs for clinical genomic testing due to limited tissue availability.
  • Standard genomic analysis often requires larger tissue samples than typically obtained from CNBs.

Purpose of the Study:

  • To evaluate the feasibility of whole genome amplification (WGA) from TPs for genomic analysis.
  • To assess the accuracy of structural variant analysis (SVA) and mutation calling using DNA from TPs.
  • To determine if TP-derived DNA can reliably supplement or replace CNB or bulk tissue for genomic testing.

Main Methods:

  • DNA extracted from TPs underwent whole genome amplification (WGA).
  • Mate-pair sequencing (MPseq) was performed for structural variant analysis (SVA).
  • Whole exome sequencing (WES) was used for mutation calling.

Main Results:

  • MPseq of WGA-amplified TP DNA showed high concordance with associated CNBs and bulk tissues for chromosomal copy changes and somatic DNA junctions.
  • Despite amplification noise, tumor enrichment in TPs enhanced variant detection and loss of heterozygosity evaluations in WES.
  • The novel TP methodology proved effective for genomic analyses.

Conclusions:

  • Genomic analysis of WGA-amplified DNA from TPs is feasible and accurate.
  • This technique expands the utility of limited CNB samples for both clinical and research genomic testing.
  • TPs can serve as a valuable source of patient tissue for comprehensive genomic profiling.