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

doi:10.1016/j.ygeno.2020.10.031

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 journal › Article › peer-review

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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 language	English (US)
Pages (from-to)	5313-5323
Number of pages	11
Journal	Genomics
Volume	112
Issue number	6
DOIs	https://doi.org/10.1016/j.ygeno.2020.10.031
State	Published - Nov 2020

Keywords

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

ASJC Scopus subject areas

Genetics

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10.1016/j.ygeno.2020.10.031

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Murphy, S. J., Harris, F. R., Smadbeck, J. B., Serla, V., Karagouga, G., Johnson, S. H., Kosari, F., Pierson, K. E., Bungum, A. O., Edell, E. S., Mansfield, A. S., Wigle, D. A., Kipp, B. R., Vasmatzis, G., & Aubry, M. C. (2020). Optimizing clinical cytology touch preparations for next generation sequencing. Genomics, 112(6), 5313-5323. https://doi.org/10.1016/j.ygeno.2020.10.031

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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.",

keywords = "Cytology, Mate pair sequencing, Structural variance analysis, Touch preparations, Whole exome sequencing, Whole genome sequencing",

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

note = "Publisher Copyright: {\textcopyright} 2020 The Authors",

year = "2020",

month = nov,

doi = "10.1016/j.ygeno.2020.10.031",

language = "English (US)",

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AU - Johnson, Sarah H.

AU - Kosari, Farhad

AU - Pierson, Karlyn E.

AU - Bungum, Aaron O.

AU - Edell, Eric S.

AU - Mansfield, Aaron S.

AU - Wigle, Dennis A.

AU - Kipp, Benjamin R.

AU - Vasmatzis, George

AU - Aubry, Marie Christine

PY - 2020/11

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AB - 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.

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KW - Whole exome sequencing

KW - Whole genome sequencing

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Optimizing clinical cytology touch preparations for next generation sequencing

Abstract

Keywords

ASJC Scopus subject areas

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