Identification and validation of suitable endogenous reference genes for gene expression studies in human peripheral blood
Identifieur interne : 000261 ( Pmc/Curation ); précédent : 000260; suivant : 000262Identification and validation of suitable endogenous reference genes for gene expression studies in human peripheral blood
Auteurs : Boryana S. Stamova [États-Unis] ; Michelle Apperson [États-Unis] ; Wynn L. Walker [États-Unis] ; Yingfang Tian [États-Unis] ; Huichun Xu [États-Unis] ; Peter Adamczy [États-Unis] ; Xinhua Zhan [États-Unis] ; Da-Zhi Liu ; Bradley P. Ander [États-Unis] ; Isaac H. Liao [États-Unis] ; Jeffrey P. Gregg [États-Unis] ; Renee J. Turner [États-Unis] ; Glen Jickling [États-Unis] ; Lisa Lit [États-Unis] ; Frank R. Sharp [États-Unis]Source :
- BMC Medical Genomics [ 1755-8794 ] ; 2009.
Abstract
Gene expression studies require appropriate normalization methods. One such method uses stably expressed reference genes. Since suitable reference genes appear to be unique for each tissue, we have identified an optimal set of the most stably expressed genes in human blood that can be used for normalization.
Whole-genome Affymetrix Human 2.0 Plus arrays were examined from 526 samples of males and females ages 2 to 78, including control subjects and patients with Tourette syndrome, stroke, migraine, muscular dystrophy, and autism. The top 100 most stably expressed genes with a broad range of expression levels were identified. To validate the best candidate genes, we performed quantitative RT-PCR on a subset of 10 genes (TRAP1, DECR1, FPGS, FARP1, MAPRE2, PEX16, GINS2, CRY2, CSNK1G2 and A4GALT), 4 commonly employed reference genes (GAPDH, ACTB, B2M and HMBS) and PPIB, previously reported to be stably expressed in blood. Expression stability and ranking analysis were performed using GeNorm and NormFinder algorithms.
Reference genes were ranked based on their expression stability and the minimum number of genes needed for nomalization as calculated using GeNorm showed that the fewest, most stably expressed genes needed for acurate normalization in RNA expression studies of human whole blood is a combination of TRAP1, FPGS, DECR1 and PPIB. We confirmed the ranking of the best candidate control genes by using an alternative algorithm (NormFinder).
The reference genes identified in this study are stably expressed in whole blood of humans of both genders with multiple disease conditions and ages 2 to 78. Importantly, they also have different functions within cells and thus should be expressed independently of each other. These genes should be useful as normalization genes for microarray and RT-PCR whole blood studies of human physiology, metabolism and disease.
Url:
DOI: 10.1186/1755-8794-2-49
PubMed: 19656400
PubMed Central: 2736983
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<author><name sortKey="Lit, Lisa" sort="Lit, Lisa" uniqKey="Lit L" first="Lisa" last="Lit">Lisa Lit</name>
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<front><div type="abstract" xml:lang="en"><sec><title>Background</title>
<p>Gene expression studies require appropriate normalization methods. One such method uses stably expressed reference genes. Since suitable reference genes appear to be unique for each tissue, we have identified an optimal set of the most stably expressed genes in human blood that can be used for normalization.</p>
</sec>
<sec sec-type="methods"><title>Methods</title>
<p>Whole-genome Affymetrix Human 2.0 Plus arrays were examined from 526 samples of males and females ages 2 to 78, including control subjects and patients with Tourette syndrome, stroke, migraine, muscular dystrophy, and autism. The top 100 most stably expressed genes with a broad range of expression levels were identified. To validate the best candidate genes, we performed quantitative RT-PCR on a subset of 10 genes (TRAP1, DECR1, FPGS, FARP1, MAPRE2, PEX16, GINS2, CRY2, CSNK1G2 and A4GALT), 4 commonly employed reference genes (GAPDH, ACTB, B2M and HMBS) and PPIB, previously reported to be stably expressed in blood. Expression stability and ranking analysis were performed using GeNorm and NormFinder algorithms.</p>
</sec>
<sec><title>Results</title>
<p>Reference genes were ranked based on their expression stability and the minimum number of genes needed for nomalization as calculated using GeNorm showed that the fewest, most stably expressed genes needed for acurate normalization in RNA expression studies of human whole blood is a combination of TRAP1, FPGS, DECR1 and PPIB. We confirmed the ranking of the best candidate control genes by using an alternative algorithm (NormFinder).</p>
</sec>
<sec><title>Conclusion</title>
<p>The reference genes identified in this study are stably expressed in whole blood of humans of both genders with multiple disease conditions and ages 2 to 78. Importantly, they also have different functions within cells and thus should be expressed independently of each other. These genes should be useful as normalization genes for microarray and RT-PCR whole blood studies of human physiology, metabolism and disease.</p>
</sec>
</div>
</front>
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<front><journal-meta><journal-id journal-id-type="nlm-ta">BMC Med Genomics</journal-id>
<journal-title>BMC Medical Genomics</journal-title>
<issn pub-type="epub">1755-8794</issn>
<publisher><publisher-name>BioMed Central</publisher-name>
</publisher>
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<article-id pub-id-type="doi">10.1186/1755-8794-2-49</article-id>
<article-categories><subj-group subj-group-type="heading"><subject>Research Article</subject>
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<title-group><article-title>Identification and validation of suitable endogenous reference genes for gene expression studies in human peripheral blood</article-title>
</title-group>
<contrib-group><contrib id="A1" corresp="yes" contrib-type="author"><name><surname>Stamova</surname>
<given-names>Boryana S</given-names>
</name>
<xref ref-type="aff" rid="I1">1</xref>
<email>boryana.stamova@ucdmc.ucdavis.edu</email>
</contrib>
<contrib id="A2" contrib-type="author"><name><surname>Apperson</surname>
<given-names>Michelle</given-names>
</name>
<xref ref-type="aff" rid="I1">1</xref>
<email>michelle.apperson@ucdmc.ucdavis.edu</email>
</contrib>
<contrib id="A3" contrib-type="author"><name><surname>Walker</surname>
<given-names>Wynn L</given-names>
</name>
<xref ref-type="aff" rid="I1">1</xref>
<email>wlwalker326@gmail.com</email>
</contrib>
<contrib id="A4" contrib-type="author"><name><surname>Tian</surname>
<given-names>Yingfang</given-names>
</name>
<xref ref-type="aff" rid="I1">1</xref>
<email>yftian@ucdavis.edu</email>
</contrib>
<contrib id="A5" contrib-type="author"><name><surname>Xu</surname>
<given-names>Huichun</given-names>
</name>
<xref ref-type="aff" rid="I1">1</xref>
<email>huixu@ucdavis.edu</email>
</contrib>
<contrib id="A6" contrib-type="author"><name><surname>Adamczy</surname>
<given-names>Peter</given-names>
</name>
<xref ref-type="aff" rid="I1">1</xref>
<email>peter.adamczyk@ucdmc.ucdavis.edu</email>
</contrib>
<contrib id="A7" contrib-type="author"><name><surname>Zhan</surname>
<given-names>Xinhua</given-names>
</name>
<xref ref-type="aff" rid="I1">1</xref>
<email>xzhan@ucdavis.edu</email>
</contrib>
<contrib id="A8" contrib-type="author"><name><surname>Liu</surname>
<given-names>Da-Zhi</given-names>
</name>
<email>dzliu@ucdavis.edu</email>
</contrib>
<contrib id="A9" contrib-type="author"><name><surname>Ander</surname>
<given-names>Bradley P</given-names>
</name>
<xref ref-type="aff" rid="I1">1</xref>
<email>bander@ucdavis.edu</email>
</contrib>
<contrib id="A10" contrib-type="author"><name><surname>Liao</surname>
<given-names>Isaac H</given-names>
</name>
<xref ref-type="aff" rid="I1">1</xref>
<email>isaacliao@gmail.com</email>
</contrib>
<contrib id="A11" contrib-type="author"><name><surname>Gregg</surname>
<given-names>Jeffrey P</given-names>
</name>
<xref ref-type="aff" rid="I2">2</xref>
<email>jpgregg@ucdavis.edu</email>
</contrib>
<contrib id="A12" contrib-type="author"><name><surname>Turner</surname>
<given-names>Renee J</given-names>
</name>
<xref ref-type="aff" rid="I1">1</xref>
<email>renee.turner@ucdmc.ucdavis.edu</email>
</contrib>
<contrib id="A13" contrib-type="author"><name><surname>Jickling</surname>
<given-names>Glen</given-names>
</name>
<xref ref-type="aff" rid="I1">1</xref>
<email>glen.jickling@ucdmc.ucdavis.edu</email>
</contrib>
<contrib id="A14" contrib-type="author"><name><surname>Lit</surname>
<given-names>Lisa</given-names>
</name>
<xref ref-type="aff" rid="I1">1</xref>
<email>LLit@ucdavis.edu</email>
</contrib>
<contrib id="A15" contrib-type="author"><name><surname>Sharp</surname>
<given-names>Frank R</given-names>
</name>
<xref ref-type="aff" rid="I1">1</xref>
<email>frank.sharp@ucdmc.ucdavis.edu</email>
</contrib>
</contrib-group>
<aff id="I1"><label>1</label>
Department of Neurology and M.I.N.D. Institute, University of California at Davis Medical Center, Sacramento, CA 95817, USA</aff>
<aff id="I2"><label>2</label>
Department of Pathology, and M.I.N.D. Institute, University of California at Davis Medical Center, Sacramento, CA 95817, USA</aff>
<pub-date pub-type="collection"><year>2009</year>
</pub-date>
<pub-date pub-type="epub"><day>5</day>
<month>8</month>
<year>2009</year>
</pub-date>
<volume>2</volume>
<fpage>49</fpage>
<lpage>49</lpage>
<ext-link ext-link-type="uri" xlink:href="http://www.biomedcentral.com/1755-8794/2/49"></ext-link>
<history><date date-type="received"><day>12</day>
<month>1</month>
<year>2009</year>
</date>
<date date-type="accepted"><day>5</day>
<month>8</month>
<year>2009</year>
</date>
</history>
<permissions><copyright-statement>Copyright © 2009 Stamova et al; licensee BioMed Central Ltd.</copyright-statement>
<copyright-year>2009</copyright-year>
<copyright-holder>Stamova et al; licensee BioMed Central Ltd.</copyright-holder>
<license license-type="open-access" xlink:href="http://creativecommons.org/licenses/by/2.0"><p>This is an Open Access article distributed under the terms of the Creative Commons Attribution License (<ext-link ext-link-type="uri" xlink:href="http://creativecommons.org/licenses/by/2.0"></ext-link>
), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.</p>
<pmc-comment>
Stamova
S
Boryana
boryana.stamova@ucdmc.ucdavis.edu
Identification and validation of suitable endogenous reference genes for gene expression studies in human peripheral blood
2009 BMC Medical Genomics 2(1): 49-. (2009) 1755-8794(2009)2:1<49> urn:ISSN:1755-8794 </pmc-comment>
</license>
</permissions>
<abstract><sec><title>Background</title>
<p>Gene expression studies require appropriate normalization methods. One such method uses stably expressed reference genes. Since suitable reference genes appear to be unique for each tissue, we have identified an optimal set of the most stably expressed genes in human blood that can be used for normalization.</p>
</sec>
<sec sec-type="methods"><title>Methods</title>
<p>Whole-genome Affymetrix Human 2.0 Plus arrays were examined from 526 samples of males and females ages 2 to 78, including control subjects and patients with Tourette syndrome, stroke, migraine, muscular dystrophy, and autism. The top 100 most stably expressed genes with a broad range of expression levels were identified. To validate the best candidate genes, we performed quantitative RT-PCR on a subset of 10 genes (TRAP1, DECR1, FPGS, FARP1, MAPRE2, PEX16, GINS2, CRY2, CSNK1G2 and A4GALT), 4 commonly employed reference genes (GAPDH, ACTB, B2M and HMBS) and PPIB, previously reported to be stably expressed in blood. Expression stability and ranking analysis were performed using GeNorm and NormFinder algorithms.</p>
</sec>
<sec><title>Results</title>
<p>Reference genes were ranked based on their expression stability and the minimum number of genes needed for nomalization as calculated using GeNorm showed that the fewest, most stably expressed genes needed for acurate normalization in RNA expression studies of human whole blood is a combination of TRAP1, FPGS, DECR1 and PPIB. We confirmed the ranking of the best candidate control genes by using an alternative algorithm (NormFinder).</p>
</sec>
<sec><title>Conclusion</title>
<p>The reference genes identified in this study are stably expressed in whole blood of humans of both genders with multiple disease conditions and ages 2 to 78. Importantly, they also have different functions within cells and thus should be expressed independently of each other. These genes should be useful as normalization genes for microarray and RT-PCR whole blood studies of human physiology, metabolism and disease.</p>
</sec>
</abstract>
</article-meta>
</front>
</pmc>
</record>
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