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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...
Autores principales: | , , , , , , , , , , , , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
Elsevier
2021
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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). |
format | Online Article Text |
id | pubmed-8243513 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2021 |
publisher | Elsevier |
record_format | MEDLINE/PubMed |
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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