Copy number analysis by low coverage whole genome sequencing using ultra low-input DNA from formalin-fixed paraffin embedded tumor tissue

Unlocking clinically translatable genomic information, including copy number alterations (CNA), from formalin-fixed paraffin-embedded (FFPE) tissue is challenging due to low yields and degraded DNA. We describe a robust, cost-effective low-coverage whole genome sequencing (LC WGS) method for CNA det...

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Autores principales: Kader, Tanjina, Goode, David L., Wong, Stephen Q., Connaughton, Jacquie, Rowley, Simone M., Devereux, Lisa, Byrne, David, Fox, Stephen B., Mir Arnau, Gisela, Tothill, Richard W., Campbell, Ian G., Gorringe, Kylie L.
Formato: Online Artículo Texto
Lenguaje:English
Publicado: BioMed Central 2016
Materias:
Method
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5111221/
https://www.ncbi.nlm.nih.gov/pubmed/27846907
http://dx.doi.org/10.1186/s13073-016-0375-z
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author Kader, Tanjina
Goode, David L.
Wong, Stephen Q.
Connaughton, Jacquie
Rowley, Simone M.
Devereux, Lisa
Byrne, David
Fox, Stephen B.
Mir Arnau, Gisela
Tothill, Richard W.
Campbell, Ian G.
Gorringe, Kylie L.
author_facet Kader, Tanjina
Goode, David L.
Wong, Stephen Q.
Connaughton, Jacquie
Rowley, Simone M.
Devereux, Lisa
Byrne, David
Fox, Stephen B.
Mir Arnau, Gisela
Tothill, Richard W.
Campbell, Ian G.
Gorringe, Kylie L.
author_sort Kader, Tanjina
collection PubMed
description Unlocking clinically translatable genomic information, including copy number alterations (CNA), from formalin-fixed paraffin-embedded (FFPE) tissue is challenging due to low yields and degraded DNA. We describe a robust, cost-effective low-coverage whole genome sequencing (LC WGS) method for CNA detection using 5 ng of FFPE-derived DNA. CN profiles using 100 ng or 5 ng input DNA were highly concordant and comparable with molecular inversion probe (MIP) array profiles. LC WGS improved CN profiles of samples that performed poorly using MIP arrays. Our technique enables identification of driver and prognostic CNAs in archival patient samples previously deemed unsuitable for genomic analysis due to DNA limitations. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (doi:10.1186/s13073-016-0375-z) contains supplementary material, which is available to authorized users.
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spelling pubmed-51112212016-11-25 Copy number analysis by low coverage whole genome sequencing using ultra low-input DNA from formalin-fixed paraffin embedded tumor tissue Kader, Tanjina Goode, David L. Wong, Stephen Q. Connaughton, Jacquie Rowley, Simone M. Devereux, Lisa Byrne, David Fox, Stephen B. Mir Arnau, Gisela Tothill, Richard W. Campbell, Ian G. Gorringe, Kylie L. Genome Med Method Unlocking clinically translatable genomic information, including copy number alterations (CNA), from formalin-fixed paraffin-embedded (FFPE) tissue is challenging due to low yields and degraded DNA. We describe a robust, cost-effective low-coverage whole genome sequencing (LC WGS) method for CNA detection using 5 ng of FFPE-derived DNA. CN profiles using 100 ng or 5 ng input DNA were highly concordant and comparable with molecular inversion probe (MIP) array profiles. LC WGS improved CN profiles of samples that performed poorly using MIP arrays. Our technique enables identification of driver and prognostic CNAs in archival patient samples previously deemed unsuitable for genomic analysis due to DNA limitations. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (doi:10.1186/s13073-016-0375-z) contains supplementary material, which is available to authorized users. BioMed Central 2016-11-15 /pmc/articles/PMC5111221/ /pubmed/27846907 http://dx.doi.org/10.1186/s13073-016-0375-z Text en © The Author(s). 2016 Open AccessThis article is distributed under the terms of the Creative Commons Attribution 4.0 International License (http://creativecommons.org/licenses/by/4.0/), which permits unrestricted use, distribution, and reproduction in any medium, provided you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. The Creative Commons Public Domain Dedication waiver (http://creativecommons.org/publicdomain/zero/1.0/) applies to the data made available in this article, unless otherwise stated.
spellingShingle Method
Kader, Tanjina
Goode, David L.
Wong, Stephen Q.
Connaughton, Jacquie
Rowley, Simone M.
Devereux, Lisa
Byrne, David
Fox, Stephen B.
Mir Arnau, Gisela
Tothill, Richard W.
Campbell, Ian G.
Gorringe, Kylie L.
Copy number analysis by low coverage whole genome sequencing using ultra low-input DNA from formalin-fixed paraffin embedded tumor tissue
title Copy number analysis by low coverage whole genome sequencing using ultra low-input DNA from formalin-fixed paraffin embedded tumor tissue
title_full Copy number analysis by low coverage whole genome sequencing using ultra low-input DNA from formalin-fixed paraffin embedded tumor tissue
title_fullStr Copy number analysis by low coverage whole genome sequencing using ultra low-input DNA from formalin-fixed paraffin embedded tumor tissue
title_full_unstemmed Copy number analysis by low coverage whole genome sequencing using ultra low-input DNA from formalin-fixed paraffin embedded tumor tissue
title_short Copy number analysis by low coverage whole genome sequencing using ultra low-input DNA from formalin-fixed paraffin embedded tumor tissue
title_sort copy number analysis by low coverage whole genome sequencing using ultra low-input dna from formalin-fixed paraffin embedded tumor tissue
topic Method
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5111221/
https://www.ncbi.nlm.nih.gov/pubmed/27846907
http://dx.doi.org/10.1186/s13073-016-0375-z
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