原创力文档analyses and interpretation of whole-genome gene expression from formalin-fixed paraffin-embedded tissue an illustration with breast cancer tissues分析的全基因组基因表达和解释formalin-fixed石蜡包埋组织说明与乳腺癌组织.pdfVIP
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analyses and interpretation of whole-genome gene expression from formalin-fixed paraffin-embedded tissue an illustration with breast cancer tissues分析的全基因组基因表达和解释formalin-fixed石蜡包埋组织说明与乳腺癌组织
Kibriya et al. BMC Genomics 2010, 11:622
/1471-2164/11/622
RESEARCH ARTICLE Open Access
Analyses and interpretation of whole-genome
gene expression from formalin-fixed
paraffin-embedded tissue: an illustration with
breast cancer tissues
1 1 1 1 1
Muhammad G Kibriya , Farzana Jasmine , Shantanu Roy , Rachelle M Paul-Brutus , Maria Argos ,
Habibul Ahsan1,2,3,4*
Abstract
Background: We evaluated (a) the feasibility of whole genome cDNA-mediated Annealing, Selection, extension
and Ligation (DASL) assay on formalin-fixed paraffin-embedded (FFPE) tissue and (b) whether similar conclusions
can be drawn by examining FFPE samples as proxies for fresh frozen (FF) tissues. We used a whole genome DASL
assay (addressing 18,391 genes) on a total of 72 samples from paired breast tumor and surrounding healthy tissues
from both FF and FFPE samples.
Results: Gene detection was very good with comparable success between the FFPE and FF samples.
Reproducibility was also high (r2 = 0.98); however, concordance between the two types of samples was low. Only
one-third of the differentially expressed genes in tumor tissues (compared to corresponding normal) from FF
samples could be detected in FFPE samples and conversely only one-fourth of the differentially expressed genes
from FFPE samples could be detected in FF samples. GO-enrichment analysis, gene set enrichment analysis (GSEA)
and GO-ANOVA analyses also suggested small overlap between the lead functional groups that were differentially
expressed in tumor detectable by examining FFPE and FF samples. In other words, FFPE samples may not be ideal
for picking individual target gene(s), but may be used to identify some of the lead functional group(s) of genes
that are differentially
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