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Título : Copy number and loss of heterozygosity detected by SNP array of formalin-fixed tissues using whole-genome amplification
Autor : Stokes, Angela
Drozdov, Ignat
Silva, Eliete Neves da
Ouzounis, Christos A.
Warnakulasuriya, Saman
Gleeson, Michael J.
McGurk, Mark
Tavassoli, Mahvash
Odell, Edward W.
Assunto:: Genes
Genética
Fecha de publicación : sep-2011
Editorial : Hassan Ashktorab, Howard University, United States of America
Citación : STOKES, Angela et al. Copy number and loss of heterozygosity detected by SNP array of formalin-fixed tissues using whole-genome amplification. Plos One, v. 6, n. 9, set. 2011. Disponível em: <http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0024503>. Acesso em: 9 set. 2013. DOI: 10.1371/journal.pone.0024503.
Resumen : The requirement for large amounts of good quality DNA for whole-genome applications prohibits their use for small, laser capture micro-dissected (LCM), and/or rare clinical samples, which are also often formalin-fixed and paraffin-embedded (FFPE). Whole-genome amplification of DNA from these samples could, potentially, overcome these limitations. However, little is known about the artefacts introduced by amplification of FFPE-derived DNA with regard to genotyping, and subsequent copy number and loss of heterozygosity (LOH) analyses. Using a ligation adaptor amplification method, we present data from a total of 22 Affymetrix SNP 6.0 experiments, using matched paired amplified and non-amplified DNA from 10 LCM FFPE normal and dysplastic oral epithelial tissues, and an internal method control. An average of 76.5% of SNPs were called in both matched amplified and non-amplified DNA samples, and concordance was a promising 82.4%. Paired analysis for copy number, LOH, and both combined, showed that copy number changes were reduced in amplified DNA, but were 99.5% concordant when detected, amplifications were the changes most likely to be ‘missed’, only 30% of nonamplified LOH changes were identified in amplified pairs, and when copy number and LOH are combined ,50% of gene changes detected in the unamplified DNA were also detected in the amplified DNA and within these changes, 86.5% were concordant for both copy number and LOH status. However, there are also changes introduced as ,20% of changes in the amplified DNA are not detected in the non-amplified DNA. An integrative network biology approach revealed that changes in amplified DNA of dysplastic oral epithelium localize to topologically critical regions of the human protein-protein interaction network, suggesting their functional implication in the pathobiology of this disease. Taken together, our results support the use of amplification of FFPE-derived DNA, provided sufficient samples are used to increase power and compensate for increased error rates.
Licença:: © 2011 Stokes et al. This is an open-access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited. Fonte: http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0024503. Acesso em: 9 set. 2013.
DOI: https://dx.doi.org/10.1371/journal.pone.0024503
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