Methanol-based fixation is superior to buffered formalin for next-generation sequencing of DNA from clinical cancer samples

High-quality tumour DNA is essential for any personalised treatment strategy based on NGS. Here we show that methanol fixation is superior to formalin, greater DNA yield, longer fragment size and more accurate copy-number calling using sWGS. We also show provide a new approach to understand fixation...

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Main Authors:	Piskorz, A. M., Ennis, D., Macintyre, G., Goranova, T. E., Eldridge, M., Segui-Gracia, N., Valganon, M., Hoyle, A., Orange, C., Moore, L., Jimenez-Linan, M., Millan, D., McNeish, I. A., Brenton, J. D.
Format:	Online
Language:	English
Published:	Oxford University Press 2016
Online Access:	https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4769995/

id	pubmed-4769995
recordtype	oai_dc
spelling	pubmed-47699952016-02-29 Methanol-based fixation is superior to buffered formalin for next-generation sequencing of DNA from clinical cancer samples Piskorz, A. M. Ennis, D. Macintyre, G. Goranova, T. E. Eldridge, M. Segui-Gracia, N. Valganon, M. Hoyle, A. Orange, C. Moore, L. Jimenez-Linan, M. Millan, D. McNeish, I. A. Brenton, J. D. Original Articles High-quality tumour DNA is essential for any personalised treatment strategy based on NGS. Here we show that methanol fixation is superior to formalin, greater DNA yield, longer fragment size and more accurate copy-number calling using sWGS. We also show provide a new approach to understand fixation artefacts using non-negative matrix factorization. Oxford University Press 2016-03 2015-12-17 /pmc/articles/PMC4769995/ /pubmed/26681675 http://dx.doi.org/10.1093/annonc/mdv613 Text en © The Author 2015. Published by Oxford University Press on behalf of the European Society for Medical Oncology. http://creativecommons.org/licenses/by/4.0/ This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/4.0/), which permits unrestricted reuse, distribution, and reproduction in any medium, provided the original work is properly cited
repository_type	Open Access Journal
institution_category	Foreign Institution
institution	US National Center for Biotechnology Information
building	NCBI PubMed
collection	Online Access
language	English
format	Online
author	Piskorz, A. M. Ennis, D. Macintyre, G. Goranova, T. E. Eldridge, M. Segui-Gracia, N. Valganon, M. Hoyle, A. Orange, C. Moore, L. Jimenez-Linan, M. Millan, D. McNeish, I. A. Brenton, J. D.
spellingShingle	Piskorz, A. M. Ennis, D. Macintyre, G. Goranova, T. E. Eldridge, M. Segui-Gracia, N. Valganon, M. Hoyle, A. Orange, C. Moore, L. Jimenez-Linan, M. Millan, D. McNeish, I. A. Brenton, J. D. Methanol-based fixation is superior to buffered formalin for next-generation sequencing of DNA from clinical cancer samples
author_facet	Piskorz, A. M. Ennis, D. Macintyre, G. Goranova, T. E. Eldridge, M. Segui-Gracia, N. Valganon, M. Hoyle, A. Orange, C. Moore, L. Jimenez-Linan, M. Millan, D. McNeish, I. A. Brenton, J. D.
author_sort	Piskorz, A. M.
title	Methanol-based fixation is superior to buffered formalin for next-generation sequencing of DNA from clinical cancer samples
title_short	Methanol-based fixation is superior to buffered formalin for next-generation sequencing of DNA from clinical cancer samples
title_full	Methanol-based fixation is superior to buffered formalin for next-generation sequencing of DNA from clinical cancer samples
title_fullStr	Methanol-based fixation is superior to buffered formalin for next-generation sequencing of DNA from clinical cancer samples
title_full_unstemmed	Methanol-based fixation is superior to buffered formalin for next-generation sequencing of DNA from clinical cancer samples
title_sort	methanol-based fixation is superior to buffered formalin for next-generation sequencing of dna from clinical cancer samples
description	High-quality tumour DNA is essential for any personalised treatment strategy based on NGS. Here we show that methanol fixation is superior to formalin, greater DNA yield, longer fragment size and more accurate copy-number calling using sWGS. We also show provide a new approach to understand fixation artefacts using non-negative matrix factorization.
publisher	Oxford University Press
publishDate	2016
url	https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4769995/
_version_	1613544284162621440

Methanol-based fixation is superior to buffered formalin for next-generation sequencing of DNA from clinical cancer samples

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