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Shallow whole genome sequencing for robust copy number profiling of formalin-fixed paraffin-embedded breast cancers
Pathology archives with linked clinical data are an invaluable resource for translational research, with the limitation that most cancer samples are formalin-fixed paraffin-embedded (FFPE) tissues. Therefore, FFPE tissues are an important resource for genomic profiling studies but are under-utilised...
Autores principales: | , , , , , , , , , , , , , , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
Elsevier
2018
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Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5993858/ https://www.ncbi.nlm.nih.gov/pubmed/29608913 http://dx.doi.org/10.1016/j.yexmp.2018.03.006 |
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author | Chin, Suet-Feung Santonja, Angela Grzelak, Marta Ahn, Soomin Sammut, Stephen-John Clifford, Harry Rueda, Oscar M. Pugh, Michelle Goldgraben, Mae A. Bardwell, Helen A. Cho, Eun Yoon Provenzano, Elena Rojo, Federico Alba, Emilio Caldas, Carlos |
author_facet | Chin, Suet-Feung Santonja, Angela Grzelak, Marta Ahn, Soomin Sammut, Stephen-John Clifford, Harry Rueda, Oscar M. Pugh, Michelle Goldgraben, Mae A. Bardwell, Helen A. Cho, Eun Yoon Provenzano, Elena Rojo, Federico Alba, Emilio Caldas, Carlos |
author_sort | Chin, Suet-Feung |
collection | PubMed |
description | Pathology archives with linked clinical data are an invaluable resource for translational research, with the limitation that most cancer samples are formalin-fixed paraffin-embedded (FFPE) tissues. Therefore, FFPE tissues are an important resource for genomic profiling studies but are under-utilised due to the low amount and quality of extracted nucleic acids. We profiled the copy number landscape of 356 breast cancer patients using DNA extracted FFPE tissues by shallow whole genome sequencing. We generated a total of 491 sequencing libraries from 2 kits and obtained data from 98.4% of libraries with 86.4% being of good quality. We generated libraries from as low as 3.8 ng of input DNA and found that the success was independent of input DNA amount and quality, processing site and age of the fixed tissues. Since copy number alterations (CNA) play a major role in breast cancer, it is imperative that we are able to use FFPE archives and we have shown in this study that sWGS is a robust method to do such profiling. |
format | Online Article Text |
id | pubmed-5993858 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2018 |
publisher | Elsevier |
record_format | MEDLINE/PubMed |
spelling | pubmed-59938582018-06-11 Shallow whole genome sequencing for robust copy number profiling of formalin-fixed paraffin-embedded breast cancers Chin, Suet-Feung Santonja, Angela Grzelak, Marta Ahn, Soomin Sammut, Stephen-John Clifford, Harry Rueda, Oscar M. Pugh, Michelle Goldgraben, Mae A. Bardwell, Helen A. Cho, Eun Yoon Provenzano, Elena Rojo, Federico Alba, Emilio Caldas, Carlos Exp Mol Pathol Article Pathology archives with linked clinical data are an invaluable resource for translational research, with the limitation that most cancer samples are formalin-fixed paraffin-embedded (FFPE) tissues. Therefore, FFPE tissues are an important resource for genomic profiling studies but are under-utilised due to the low amount and quality of extracted nucleic acids. We profiled the copy number landscape of 356 breast cancer patients using DNA extracted FFPE tissues by shallow whole genome sequencing. We generated a total of 491 sequencing libraries from 2 kits and obtained data from 98.4% of libraries with 86.4% being of good quality. We generated libraries from as low as 3.8 ng of input DNA and found that the success was independent of input DNA amount and quality, processing site and age of the fixed tissues. Since copy number alterations (CNA) play a major role in breast cancer, it is imperative that we are able to use FFPE archives and we have shown in this study that sWGS is a robust method to do such profiling. Elsevier 2018-06 /pmc/articles/PMC5993858/ /pubmed/29608913 http://dx.doi.org/10.1016/j.yexmp.2018.03.006 Text en © 2018 The Authors http://creativecommons.org/licenses/by/4.0/ This is an open access article under the CC BY license (http://creativecommons.org/licenses/by/4.0/). |
spellingShingle | Article Chin, Suet-Feung Santonja, Angela Grzelak, Marta Ahn, Soomin Sammut, Stephen-John Clifford, Harry Rueda, Oscar M. Pugh, Michelle Goldgraben, Mae A. Bardwell, Helen A. Cho, Eun Yoon Provenzano, Elena Rojo, Federico Alba, Emilio Caldas, Carlos Shallow whole genome sequencing for robust copy number profiling of formalin-fixed paraffin-embedded breast cancers |
title | Shallow whole genome sequencing for robust copy number profiling of formalin-fixed paraffin-embedded breast cancers |
title_full | Shallow whole genome sequencing for robust copy number profiling of formalin-fixed paraffin-embedded breast cancers |
title_fullStr | Shallow whole genome sequencing for robust copy number profiling of formalin-fixed paraffin-embedded breast cancers |
title_full_unstemmed | Shallow whole genome sequencing for robust copy number profiling of formalin-fixed paraffin-embedded breast cancers |
title_short | Shallow whole genome sequencing for robust copy number profiling of formalin-fixed paraffin-embedded breast cancers |
title_sort | shallow whole genome sequencing for robust copy number profiling of formalin-fixed paraffin-embedded breast cancers |
topic | Article |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5993858/ https://www.ncbi.nlm.nih.gov/pubmed/29608913 http://dx.doi.org/10.1016/j.yexmp.2018.03.006 |
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