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A protocol for representative sampling of solid tumors to improve the accuracy of sequencing results

Owing to spatial segregation of tumor subclones, solid tumor sampling using formalin-fixed, paraffin-embedded blocks is often inadequate to represent the genomic heterogeneity of solid tumors. We present an approach, representative sampling, to dissect and homogenize leftover residual surgical tissu...

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Autores principales: Gallegos, Lisa L., Gilchrist, Ashley, Spain, Lavinia, Stanislaw, Stacey, Hill, Samantha M., Primus, Vanessa, Jones, Carol, Agrawal, Somya, Tippu, Zayd, Barhoumi, Aoune, Noel-Storr, Glenn, Alexander, Nelson R., Turajlic, Samra
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Elsevier 2021
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8243513/
https://www.ncbi.nlm.nih.gov/pubmed/34223198
http://dx.doi.org/10.1016/j.xpro.2021.100624
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author Gallegos, Lisa L.
Gilchrist, Ashley
Spain, Lavinia
Stanislaw, Stacey
Hill, Samantha M.
Primus, Vanessa
Jones, Carol
Agrawal, Somya
Tippu, Zayd
Barhoumi, Aoune
Noel-Storr, Glenn
Alexander, Nelson R.
Turajlic, Samra
author_facet Gallegos, Lisa L.
Gilchrist, Ashley
Spain, Lavinia
Stanislaw, Stacey
Hill, Samantha M.
Primus, Vanessa
Jones, Carol
Agrawal, Somya
Tippu, Zayd
Barhoumi, Aoune
Noel-Storr, Glenn
Alexander, Nelson R.
Turajlic, Samra
author_sort Gallegos, Lisa L.
collection PubMed
description Owing to spatial segregation of tumor subclones, solid tumor sampling using formalin-fixed, paraffin-embedded blocks is often inadequate to represent the genomic heterogeneity of solid tumors. We present an approach, representative sampling, to dissect and homogenize leftover residual surgical tissue prior to sequencing. We also detail optional tumor cell enrichment and DNA preparation. This method, applicable only to surgically removed tumors with leftover tissue, facilitates robust sampling to avoid missing or over-representing actionable variants. For complete details on the use and execution of this protocol, please refer to Litchfield et al. (2020).
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spelling pubmed-82435132021-07-02 A protocol for representative sampling of solid tumors to improve the accuracy of sequencing results Gallegos, Lisa L. Gilchrist, Ashley Spain, Lavinia Stanislaw, Stacey Hill, Samantha M. Primus, Vanessa Jones, Carol Agrawal, Somya Tippu, Zayd Barhoumi, Aoune Noel-Storr, Glenn Alexander, Nelson R. Turajlic, Samra STAR Protoc Protocol Owing to spatial segregation of tumor subclones, solid tumor sampling using formalin-fixed, paraffin-embedded blocks is often inadequate to represent the genomic heterogeneity of solid tumors. We present an approach, representative sampling, to dissect and homogenize leftover residual surgical tissue prior to sequencing. We also detail optional tumor cell enrichment and DNA preparation. This method, applicable only to surgically removed tumors with leftover tissue, facilitates robust sampling to avoid missing or over-representing actionable variants. For complete details on the use and execution of this protocol, please refer to Litchfield et al. (2020). Elsevier 2021-06-26 /pmc/articles/PMC8243513/ /pubmed/34223198 http://dx.doi.org/10.1016/j.xpro.2021.100624 Text en © 2021 The Authors https://creativecommons.org/licenses/by-nc-nd/4.0/This is an open access article under the CC BY-NC-ND license (http://creativecommons.org/licenses/by-nc-nd/4.0/).
spellingShingle Protocol
Gallegos, Lisa L.
Gilchrist, Ashley
Spain, Lavinia
Stanislaw, Stacey
Hill, Samantha M.
Primus, Vanessa
Jones, Carol
Agrawal, Somya
Tippu, Zayd
Barhoumi, Aoune
Noel-Storr, Glenn
Alexander, Nelson R.
Turajlic, Samra
A protocol for representative sampling of solid tumors to improve the accuracy of sequencing results
title A protocol for representative sampling of solid tumors to improve the accuracy of sequencing results
title_full A protocol for representative sampling of solid tumors to improve the accuracy of sequencing results
title_fullStr A protocol for representative sampling of solid tumors to improve the accuracy of sequencing results
title_full_unstemmed A protocol for representative sampling of solid tumors to improve the accuracy of sequencing results
title_short A protocol for representative sampling of solid tumors to improve the accuracy of sequencing results
title_sort protocol for representative sampling of solid tumors to improve the accuracy of sequencing results
topic Protocol
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8243513/
https://www.ncbi.nlm.nih.gov/pubmed/34223198
http://dx.doi.org/10.1016/j.xpro.2021.100624
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