Copy Number and Loss of Heterozygosity Detected by SNP Array of Formalin-Fixed Tissues Using Whole-Genome Amplification

被引：10

作者：

Stokes, Angela ^{[1
]}

Drozdov, Ignat ^{[2
,3
]}

Guerra, Eliete ^{[1
,4
]}

Ouzounis, Christos A. ^{[3
]}

Warnakulasuriya, Saman ^{[5
]}

Gleeson, Michael J. ^{[6
]}

McGurk, Mark ^{[7
]}

Tavassoli, Mahvash ^{[1
]}

Odell, Edward W. ^{[1
]}

机构：

[1] Kings Coll London, Inst Dent, Dept Oral Pathol, London WC2R 2LS, England

[2] Kings Coll London, British Heart Fdn Ctr Res Excellence, Div Cardiovasc, London WC2R 2LS, England

[3] Kings Coll London, Ctr Bioinformat, Dept Informat, Sch Nat & Math Sci, London WC2R 2LS, England

[4] Univ Brasilia, Fac Hlth Sci, Dept Dent, Brasilia, DF, Brazil

[5] Kings Coll London, Inst Dent, Dept Oral Med, London WC2R 2LS, England

[6] Guys Hosp, Dept Otolaryngol, London SE1 9RT, England

[7] Kings Coll London, Inst Dent, Dept Oral & Maxillofacial Surg, London WC2R 2LS, England

来源：

PLOS ONE | 2011年 / 6卷 / 09期

关键词：

DNA; CANCER; SAMPLES; WIDE;

D O I：

10.1371/journal.pone.0024503

中图分类号：

O [数理科学和化学]; P [天文学、地球科学]; Q [生物科学]; N [自然科学总论];

学科分类号：

07 ; 0710 ; 09 ;

摘要：

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 non-amplified LOH changes were identified in amplified pairs, and when copy number and LOH are combined similar to 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 similar to 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.

引用

页数：8