Document Detail


Purity for clarity: the need for purification of tumor cells in DNA microarray studies.
MedLine Citation:
PMID:  15744349     Owner:  NLM     Status:  MEDLINE    
Abstract/OtherAbstract:
It is now well established that gene expression profiling using DNA microarrays can provide novel information about various types of hematological malignancies, which may lead to identification of novel diagnostic markers. However, to successfully use microarrays for this purpose, the quality and reproducibility of the procedure need to be guaranteed. The quality of microarray analyses may be severely reduced, if variable frequencies of nontarget cells are present in the starting material. To systematically investigate the influence of different types of impurity, we determined gene expression profiles of leukemic samples containing different percentages of nonleukemic leukocytes. Furthermore, we used computer simulations to study the effect of different kinds of impurity as an alternative to conducting hundreds of microarray experiments on samples with various levels of purity. As expected, the percentage of erroneously identified genes rose with the increase of contaminating nontarget cells in the samples. The simulations demonstrated that a tumor load of less than 75% can lead to up to 25% erroneously identified genes. A tumor load of at least 90% leads to identification of at most 5% false-positive genes. We therefore propose that in order to draw well-founded conclusions, the percentage of target cells in microarray experiment samples should be at least 90%.
Authors:
D de Ridder; C E van der Linden; T Schonewille; W A Dik; M J T Reinders; J J M van Dongen; F J T Staal
Related Documents :
15177569 - Are data from different gene expression microarray platforms comparable?
20421339 - Monitoring developmental toxicity in the embryonic stem cell test using differential ge...
11935369 - Study of thyroid gene expression and regulation by dna array technology: pitfalls and n...
14744289 - Gene microarray analysis of human brain arteriovenous malformations.
19524659 - Construction and evaluation of an orfeome-based brucella whole-genome dna microarray.
17322329 - Comparative high-density microarray analysis of gene expression during growth of lactob...
15509699 - Molecular cloning of porcine growth differentiation factor 9 (gdf-9) cdna and its role ...
9738029 - Restriction fragment length polymorphism analysis of some flagellin genes of salmonella...
12589679 - Role of the two type ii myosins, myo2 and myp2, in cytokinetic actomyosin ring formatio...
Publication Detail:
Type:  Journal Article    
Journal Detail:
Title:  Leukemia     Volume:  19     ISSN:  0887-6924     ISO Abbreviation:  Leukemia     Publication Date:  2005 Apr 
Date Detail:
Created Date:  2005-04-29     Completed Date:  2005-05-26     Revised Date:  2013-03-04    
Medline Journal Info:
Nlm Unique ID:  8704895     Medline TA:  Leukemia     Country:  England    
Other Details:
Languages:  eng     Pagination:  618-27     Citation Subset:  IM    
Affiliation:
Department of Immunology, Erasmus MC, University Medical Center Rotterdam, Rotterdam, The Netherlands.
Export Citation:
APA/MLA Format     Download EndNote     Download BibTex
MeSH Terms
Descriptor/Qualifier:
Cell Separation / methods*
Computer Simulation
DNA, Neoplasm / isolation & purification*
Gene Expression Regulation, Leukemic
Guidelines as Topic
Humans
Leukemia, Myelogenous, Chronic, BCR-ABL Positive / genetics*
Leukemia-Lymphoma, Adult T-Cell / genetics*
Leukocytes, Mononuclear / cytology
Oligonucleotide Array Sequence Analysis / methods*,  standards
Reproducibility of Results
Chemical
Reg. No./Substance:
0/DNA, Neoplasm

From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine


Previous Document:  Value of intravenous 6-mercaptopurine during continuation treatment in childhood acute lymphoblastic...
Next Document:  Cloning and functional characterization of MEF2D/DAZAP1 and DAZAP1/MEF2D fusion proteins created by ...