Optimizing clinical cytology touch preparations for next generation sequencing

Stephen J. Murphy, Faye R. Harris, James B. Smadbeck, Vishnu Serla, Giannoula Karagouga, Sarah H. Johnson, Farhad Kosari, Karlyn E. Pierson, Aaron O. Bungum, Eric S. Edell, Aaron S. Mansfield, Dennis A. Wigle, Benjamin R. Kipp, George Vasmatzis, Marie Christine Aubry

Research output: Contribution to journalArticlepeer-review

Abstract

Intraoperative diagnosis is routinely performed on cytology touch preparations (TPs) from core needle biopsies (CNBs). Current interest promotes their utility as an important source of patient tissue for clinical genomic testing. Herein we present whole genome structural variant analysis (SVA) from mate-pair sequencing (MPseq) and whole exome sequencing (WES) mutation calling in DNA directly whole genome amplified (WGA) from TPs. Chromosomal copy changes and somatic DNA junction detection from MPseq of TPs were highly consistent with associated CNBs and bulk resected tissues in all cases. While increased frequency coverage noise from limitations of amplification of limited sample input was significant, this was effectively compensated by natural tumor enrichment during the TP process, which also enhanced variant detection and loss of heterozygosity evaluations from WES. This novel TP methodology enables expanded utility of frequently limited CNB for both clinical and research genomic testing.

Original languageEnglish (US)
Pages (from-to)5313-5323
Number of pages11
JournalGenomics
Volume112
Issue number6
DOIs
StatePublished - Nov 2020

Keywords

  • Cytology
  • Mate pair sequencing
  • Structural variance analysis
  • Touch preparations
  • Whole exome sequencing
  • Whole genome sequencing

ASJC Scopus subject areas

  • Genetics

Fingerprint Dive into the research topics of 'Optimizing clinical cytology touch preparations for next generation sequencing'. Together they form a unique fingerprint.

Cite this