@article{e9b490a27546403ab31eb16fd4f1e411,
title = "Optimizing clinical cytology touch preparations for next generation sequencing",
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 = "Funding Information: This study was performed under full approval of our institutional review board (IRB #15-007961). This work was supported by Oncospire Genomics and the Mayo Clinic Centre for Individualized Medicine (CIM) Biomarker Discovery (BMD) Program and Department of Laboratory Medicine and Pathology. We would like to also acknowledge the expert library preparation and next generation sequencing services provided by Bruce Eckloff, Robert Sikkink and Yean (Kit) K Lee of the Mayo Clinic genomics sequencing core. Funding Information: This study was performed under full approval of our institutional review board (IRB #15-007961). This work was supported by Oncospire Genomics and the Mayo Clinic Centre for Individualized Medicine (CIM) Biomarker Discovery (BMD) Program and Department of Laboratory Medicine and Pathology. We would like to also acknowledge the expert library preparation and next generation sequencing services provided by Bruce Eckloff, Robert Sikkink and Yean (Kit) K Lee of the Mayo Clinic genomics sequencing core. Publisher Copyright: {\textcopyright} 2020 The Authors",
year = "2020",
month = nov,
doi = "10.1016/j.ygeno.2020.10.031",
language = "English (US)",
volume = "112",
pages = "5313--5323",
journal = "Genomics",
issn = "0888-7543",
publisher = "Academic Press Inc.",
number = "6",
}