A comparison of RNA amplification techniques at sub-nanogram input concentration

Persistent Link:
http://hdl.handle.net/10150/610005
Title:
A comparison of RNA amplification techniques at sub-nanogram input concentration
Author:
Lang, Julie; Magbanua, Mark; Scott, Janet; Makrigiorgos, G. M.; Wang, Gang; Federman, Scot; Esserman, Laura; Park, John; Haqq, Christopher
Affiliation:
Department of Surgery, UCSF Comprehensive Cancer Center, 1500 Divisadero Street, San Francisco, CA 94143, USA; Department of Medical Oncology, UCSF Comprehensive Cancer Center, San Francisco, CA 94143, USA; Department of Urology, UCSF Comprehensive Cancer Center, San Francisco, CA 94143, USA; Dana Farber Cancer Institute, Harvard Medical School, 44 Binney Street, Boston, MA 02115, USA; Department of Surgery, Arizona Cancer Center, University of Arizona, 1515 N, Campbell Ave #1968, PO Box 245024, Tucson, AZ 85724, USA
Issue Date:
2009
Publisher:
BioMed Central
Citation:
BMC Genomics 2009, 10:326 doi:10.1186/1471-2164-10-326
Journal:
BMC Genomics
Rights:
© 2009 Lang et al; licensee BioMed Central Ltd. This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/2.0)
Collection Information:
This item is part of the UA Faculty Publications collection. For more information this item or other items in the UA Campus Repository, contact the University of Arizona Libraries at repository@u.library.arizona.edu.
Abstract:
BACKGROUND:Gene expression profiling of small numbers of cells requires high-fidelity amplification of sub-nanogram amounts of RNA. Several methods for RNA amplification are available; however, there has been little consideration of the accuracy of these methods when working with very low-input quantities of RNA as is often required with rare clinical samples. Starting with 250 picograms-3.3 nanograms of total RNA, we compared two linear amplification methods 1) modified T7 and 2) Arcturus RiboAmp HS and a logarithmic amplification, 3) Balanced PCR. Microarray data from each amplification method were validated against quantitative real-time PCR (QPCR) for 37 genes.RESULTS:For high intensity spots, mean Pearson correlations were quite acceptable for both total RNA and low-input quantities amplified with each of the 3 methods. Microarray filtering and data processing has an important effect on the correlation coefficient results generated by each method. Arrays derived from total RNA had higher Pearson's correlations than did arrays derived from amplified RNA when considering the entire unprocessed dataset, however, when considering a gene set of high signal intensity, the amplified arrays had superior correlation coefficients than did the total RNA arrays.CONCLUSION:Gene expression arrays can be obtained with sub-nanogram input of total RNA. High intensity spots showed better correlation on array-array analysis than did unfiltered data, however, QPCR validated the accuracy of gene expression array profiling from low-input quantities of RNA with all 3 amplification techniques. RNA amplification and expression analysis at the sub-nanogram input level is both feasible and accurate if data processing is used to focus attention to high intensity genes for microarrays or if QPCR is used as a gold standard for validation.
EISSN:
1471-2164
DOI:
10.1186/1471-2164-10-326
Version:
Final published version
Additional Links:
http://www.biomedcentral.com/1471-2164/10/326

Full metadata record

DC FieldValue Language
dc.contributor.authorLang, Julieen
dc.contributor.authorMagbanua, Marken
dc.contributor.authorScott, Janeten
dc.contributor.authorMakrigiorgos, G. M.en
dc.contributor.authorWang, Gangen
dc.contributor.authorFederman, Scoten
dc.contributor.authorEsserman, Lauraen
dc.contributor.authorPark, Johnen
dc.contributor.authorHaqq, Christopheren
dc.date.accessioned2016-05-20T08:56:14Z-
dc.date.available2016-05-20T08:56:14Z-
dc.date.issued2009en
dc.identifier.citationBMC Genomics 2009, 10:326 doi:10.1186/1471-2164-10-326en
dc.identifier.doi10.1186/1471-2164-10-326en
dc.identifier.urihttp://hdl.handle.net/10150/610005-
dc.description.abstractBACKGROUND:Gene expression profiling of small numbers of cells requires high-fidelity amplification of sub-nanogram amounts of RNA. Several methods for RNA amplification are availableen
dc.description.abstracthowever, there has been little consideration of the accuracy of these methods when working with very low-input quantities of RNA as is often required with rare clinical samples. Starting with 250 picograms-3.3 nanograms of total RNA, we compared two linear amplification methods 1) modified T7 and 2) Arcturus RiboAmp HS and a logarithmic amplification, 3) Balanced PCR. Microarray data from each amplification method were validated against quantitative real-time PCR (QPCR) for 37 genes.RESULTS:For high intensity spots, mean Pearson correlations were quite acceptable for both total RNA and low-input quantities amplified with each of the 3 methods. Microarray filtering and data processing has an important effect on the correlation coefficient results generated by each method. Arrays derived from total RNA had higher Pearson's correlations than did arrays derived from amplified RNA when considering the entire unprocessed dataset, however, when considering a gene set of high signal intensity, the amplified arrays had superior correlation coefficients than did the total RNA arrays.CONCLUSION:Gene expression arrays can be obtained with sub-nanogram input of total RNA. High intensity spots showed better correlation on array-array analysis than did unfiltered data, however, QPCR validated the accuracy of gene expression array profiling from low-input quantities of RNA with all 3 amplification techniques. RNA amplification and expression analysis at the sub-nanogram input level is both feasible and accurate if data processing is used to focus attention to high intensity genes for microarrays or if QPCR is used as a gold standard for validation.en
dc.language.isoenen
dc.publisherBioMed Centralen
dc.relation.urlhttp://www.biomedcentral.com/1471-2164/10/326en
dc.rights© 2009 Lang et al; licensee BioMed Central Ltd. This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/2.0)en
dc.titleA comparison of RNA amplification techniques at sub-nanogram input concentrationen
dc.typeArticleen
dc.identifier.eissn1471-2164en
dc.contributor.departmentDepartment of Surgery, UCSF Comprehensive Cancer Center, 1500 Divisadero Street, San Francisco, CA 94143, USAen
dc.contributor.departmentDepartment of Medical Oncology, UCSF Comprehensive Cancer Center, San Francisco, CA 94143, USAen
dc.contributor.departmentDepartment of Urology, UCSF Comprehensive Cancer Center, San Francisco, CA 94143, USAen
dc.contributor.departmentDana Farber Cancer Institute, Harvard Medical School, 44 Binney Street, Boston, MA 02115, USAen
dc.contributor.departmentDepartment of Surgery, Arizona Cancer Center, University of Arizona, 1515 N, Campbell Ave #1968, PO Box 245024, Tucson, AZ 85724, USAen
dc.identifier.journalBMC Genomicsen
dc.description.collectioninformationThis item is part of the UA Faculty Publications collection. For more information this item or other items in the UA Campus Repository, contact the University of Arizona Libraries at repository@u.library.arizona.edu.en
dc.eprint.versionFinal published versionen
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