Linked Life Data

15681474

Source:http://linkedlifedata.com/resource/pubmed/id/15681474

Statements in which the resource exists as a subject.
PredicateObject
rdf:type
lifeskim:mentions
pubmed:issue
1
pubmed:dateCreated
2005-1-31
pubmed:abstractText
Analysis of gene expression in clinical samples poses special challenges, including limited RNA availability and poor RNA quality. Quantitative information regarding reliability of RNA amplification methodologies applied to primary cells and representativeness of resulting gene expression profiles is limited. We evaluated four protocols for RNA amplification from peripheral blood mononuclear cells. Results obtained with 100 ng or 10 ng of RNA amplified using two rounds of cDNA synthesis and in vitro transcription were compared with control 2.5-microg RNA samples processed using a single round of in vitro transcription. Samples were hybridized to Affymetrix HG-U133A arrays. Considerable differences in results were obtained with different protocols. The optimal protocol resulted in highly reproducible gene expression profiles from amplified samples (r = 0.98) and good correlation between amplified and control samples (r = 0.94). Using the optimal protocol dissimilarities of gene expression between mononuclear cells from a normal individual and a patient with myelodysplastic syndrome were primarily maintained after amplification compared with controls. We conclude that small variations in methodology introduce considerable distortion of gene expression profiles obtained after RNA amplification from clinical samples and too strong a focus on a very small number of genes picked from an array analysis could be unduly influenced by seemingly acceptable methodologies. However, it is possible to obtain reproducible and representative results using optimized protocols.
pubmed:grant
pubmed:commentsCorrections
http://linkedlifedata.com/resource/pubmed/commentcorrection/15681474-10545926, http://linkedlifedata.com/resource/pubmed/commentcorrection/15681474-10748532, http://linkedlifedata.com/resource/pubmed/commentcorrection/15681474-11222780, http://linkedlifedata.com/resource/pubmed/commentcorrection/15681474-12411319, http://linkedlifedata.com/resource/pubmed/commentcorrection/15681474-12417757, http://linkedlifedata.com/resource/pubmed/commentcorrection/15681474-12623852, http://linkedlifedata.com/resource/pubmed/commentcorrection/15681474-12714683, http://linkedlifedata.com/resource/pubmed/commentcorrection/15681474-12738660, http://linkedlifedata.com/resource/pubmed/commentcorrection/15681474-12782787, http://linkedlifedata.com/resource/pubmed/commentcorrection/15681474-12893766, http://linkedlifedata.com/resource/pubmed/commentcorrection/15681474-14513049, http://linkedlifedata.com/resource/pubmed/commentcorrection/15681474-1689846, http://linkedlifedata.com/resource/pubmed/commentcorrection/15681474-9634850, http://linkedlifedata.com/resource/pubmed/commentcorrection/15681474-9883850
pubmed:keyword
pubmed:language
eng
pubmed:journal
pubmed:citationSubset
IM
pubmed:chemical
pubmed:status
MEDLINE
pubmed:month
Feb
pubmed:issn
1525-1578
pubmed:author
pubmed:issnType
Print
pubmed:volume
7
pubmed:owner
NLM
pubmed:authorsComplete
Y
pubmed:pagination
48-56
pubmed:dateRevised
2009-11-18
pubmed:meshHeading
pubmed:year
2005
pubmed:articleTitle
Reproducibility, fidelity, and discriminant validity of mRNA amplification for microarray analysis from primary hematopoietic cells.
pubmed:affiliation
Division of Hematology and Bone Marrow Transplantation, City of Hope National Medical Center, 1500 East Duarte Rd., Duarte, CA 91010, USA.
pubmed:publicationType
Journal Article, Research Support, U.S. Gov't, P.H.S., Research Support, U.S. Gov't, Non-P.H.S., Research Support, Non-U.S. Gov't, Research Support, N.I.H., Extramural, Validation Studies