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Establishment of four head and neck squamous cell carcinoma cell lines: importance of reference DNA for accurate genomic characterisation
OBJECTIVE: There is significant interest in developing early passage cell lines with matched normal reference DNA to facilitate a precision medicine approach in assessing drug response. This study aimed to establish early passage cell lines, and perform whole exome sequencing and short tandem repeat...
Autores principales: | , , , , , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
Cambridge University Press
2023
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Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9975763/ https://www.ncbi.nlm.nih.gov/pubmed/35317874 http://dx.doi.org/10.1017/S0022215122000846 |
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author | Patel, K B Prokopec, S Barrett, J W Mymryk, J S Boutros, P C Nichols, A C |
author_facet | Patel, K B Prokopec, S Barrett, J W Mymryk, J S Boutros, P C Nichols, A C |
author_sort | Patel, K B |
collection | PubMed |
description | OBJECTIVE: There is significant interest in developing early passage cell lines with matched normal reference DNA to facilitate a precision medicine approach in assessing drug response. This study aimed to establish early passage cell lines, and perform whole exome sequencing and short tandem repeat profiling on matched normal reference DNA, primary tumour and corresponding cell lines. METHODS: A cell culture based, in vitro study was conducted of patients with primary human papillomavirus positive and human papillomavirus negative tumours. RESULTS: Four early passage cell lines were established. Two cell lines were human papillomavirus positive, confirmed by sequencing and p16 immunoblotting. Short tandem repeat profiling confirmed that all cell lines were established from their index tumours. Whole exome sequencing revealed that the matched normal reference DNA was critical for accurate mutational analysis: a high rate of false positive mutation calls were excluded (87.6 per cent). CONCLUSION: Early passage cell lines were successfully established. Patient-matched reference DNA is important for accurate cell line mutational calls. |
format | Online Article Text |
id | pubmed-9975763 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2023 |
publisher | Cambridge University Press |
record_format | MEDLINE/PubMed |
spelling | pubmed-99757632023-03-02 Establishment of four head and neck squamous cell carcinoma cell lines: importance of reference DNA for accurate genomic characterisation Patel, K B Prokopec, S Barrett, J W Mymryk, J S Boutros, P C Nichols, A C J Laryngol Otol Main Article OBJECTIVE: There is significant interest in developing early passage cell lines with matched normal reference DNA to facilitate a precision medicine approach in assessing drug response. This study aimed to establish early passage cell lines, and perform whole exome sequencing and short tandem repeat profiling on matched normal reference DNA, primary tumour and corresponding cell lines. METHODS: A cell culture based, in vitro study was conducted of patients with primary human papillomavirus positive and human papillomavirus negative tumours. RESULTS: Four early passage cell lines were established. Two cell lines were human papillomavirus positive, confirmed by sequencing and p16 immunoblotting. Short tandem repeat profiling confirmed that all cell lines were established from their index tumours. Whole exome sequencing revealed that the matched normal reference DNA was critical for accurate mutational analysis: a high rate of false positive mutation calls were excluded (87.6 per cent). CONCLUSION: Early passage cell lines were successfully established. Patient-matched reference DNA is important for accurate cell line mutational calls. Cambridge University Press 2023-03 2022-03-23 /pmc/articles/PMC9975763/ /pubmed/35317874 http://dx.doi.org/10.1017/S0022215122000846 Text en © The Author(s) 2022 https://creativecommons.org/licenses/by/4.0/This is an Open Access article, distributed under the terms of the Creative Commons Attribution licence (http://creativecommons.org/licenses/by/4.0/), which permits unrestricted re-use, distribution and reproduction, provided the original article is properly cited. |
spellingShingle | Main Article Patel, K B Prokopec, S Barrett, J W Mymryk, J S Boutros, P C Nichols, A C Establishment of four head and neck squamous cell carcinoma cell lines: importance of reference DNA for accurate genomic characterisation |
title | Establishment of four head and neck squamous cell carcinoma cell lines: importance of reference DNA for accurate genomic characterisation |
title_full | Establishment of four head and neck squamous cell carcinoma cell lines: importance of reference DNA for accurate genomic characterisation |
title_fullStr | Establishment of four head and neck squamous cell carcinoma cell lines: importance of reference DNA for accurate genomic characterisation |
title_full_unstemmed | Establishment of four head and neck squamous cell carcinoma cell lines: importance of reference DNA for accurate genomic characterisation |
title_short | Establishment of four head and neck squamous cell carcinoma cell lines: importance of reference DNA for accurate genomic characterisation |
title_sort | establishment of four head and neck squamous cell carcinoma cell lines: importance of reference dna for accurate genomic characterisation |
topic | Main Article |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9975763/ https://www.ncbi.nlm.nih.gov/pubmed/35317874 http://dx.doi.org/10.1017/S0022215122000846 |
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