Wood, HM, Belvedere, O, Conway, C et al. (16 more authors) (2010) Using next-generation sequencing for high resolution multiplex analysis of copy number variation from nanogram quantities of DNA from formalin-fixed paraffin-embedded specimens. Nucleic Acids Research, 38 (14). e151. ISSN 0305-1048
Abstract
The use of next-generation sequencing technologies to produce genomic copy number data has recently been described. Most approaches, however, reply on optimal starting DNA, and are therefore unsuitable for the analysis of formalinfixed paraffin-embedded (FFPE) samples, which largely precludes the analysis of many tumour series. We have sought to challenge the limits of this technique with regards to quality and quantity of starting material and the depth of sequencing required. We confirm that the technique can be used to interrogate DNA from cell lines, fresh frozen material and FFPE samples to assess copy number variation. We show that as little as 5 ng of DNA is needed to generate a copy number karyogram, and follow this up with data from a series of FFPE biopsies and surgical samples. We have used various levels of sample multiplexing to demonstrate the adjustable resolution of the methodology, depending on the number of samples and available resources. We also demonstrate reproducibility by use of replicate samples and comparison with microarray-based comparative genomic hybridization (aCGH) and digital PCR. This technique can be valuable in both the analysis of routine diagnostic samples and in examining large repositories of fixed archival material.
Metadata
Item Type: | Article |
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Authors/Creators: |
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Copyright, Publisher and Additional Information: | © The Author(s) 2010. Published by Oxford University Press. This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/2.5), which permits unrestricted non-commercial use, distribution, and reproduction in any medium, provided the original work is properly cited. |
Keywords: | Squamous-cell carcinoma; Lung-cancer; Array CGH; Genome browser; Allelic loss; Variants; Identification; Lines; UCSC; MCC |
Dates: |
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Institution: | The University of Leeds |
Academic Units: | The University of Leeds > Faculty of Medicine and Health (Leeds) > Institute of Molecular Medicine (LIMM) (Leeds) > Section of Experimental Therapeutics (Leeds) |
Depositing User: | Symplectic Publications |
Date Deposited: | 29 Sep 2015 14:15 |
Last Modified: | 22 Oct 2019 15:14 |
Published Version: | http://dx.doi.org/10.1093/nar/gkq510 |
Status: | Published |
Publisher: | Oxford University Press |
Identification Number: | 10.1093/nar/gkq510 |
Open Archives Initiative ID (OAI ID): | oai:eprints.whiterose.ac.uk:81490 |