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Functional quality control for human blood-based gene expression products
Descriptive
TitleInfo
Title
Functional quality control for human blood-based gene expression products
Name
(type = personal)
NamePart
(type = family)
Frahm
NamePart
(type = given)
Stephanie A.
NamePart
(type = date)
1983-
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Stephanie Frahm
Role
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(authority = RULIB)
author
Name
(type = personal)
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(type = family)
Brooks
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(type = given)
Andrew I
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Andrew I Brooks
Affiliation
Advisory Committee
Role
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(authority = RULIB)
chair
Name
(type = personal)
NamePart
(type = family)
Tischfield
NamePart
(type = given)
Jay A
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Jay A Tischfield
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Advisory Committee
Role
RoleTerm
(authority = RULIB)
internal member
Name
(type = personal)
NamePart
(type = family)
Matise
NamePart
(type = given)
Tara C
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Tara C Matise
Affiliation
Advisory Committee
Role
RoleTerm
(authority = RULIB)
internal member
Name
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NamePart
Rutgers University
Role
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(authority = RULIB)
degree grantor
Name
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NamePart
Graduate School - New Brunswick
Role
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(authority = RULIB)
school
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Text
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theses
OriginInfo
DateCreated
(qualifier = exact)
2012
DateOther
(qualifier = exact);
(type = degree)
2012-01
CopyrightDate
(qualifier = exact)
2012
Place
PlaceTerm
(type = code)
xx
Language
LanguageTerm
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(type = code)
eng
Abstract
(type = abstract)
Reliable and robust gene expression data generated by microarrays or quantitative real-time polymerase chain reaction (qPCR) is directly dependent upon use of high-quality input material, namely high caliber cDNA generated from intact, non-degraded RNA. Due to its labile nature, the integrity of RNA can be jeopardized at multiple points during sample collection, extraction, and storage, adversely affecting downstream gene expression data interpretation and discovery. Accurately assessing RNA and cDNA quality prior to gene expression analysis proves to be a critical step requiring a highly sensitive and specific quality control method. Existing industry-standard RNA quality control techniques rely on microcapillary electrophoresis, which provides an analytical assessment of ribosomal RNA (rRNA) integrity. While providing a gross evaluation of total RNA quality using rRNA as a surrogate, these methods fail to adequately predict the downstream functional performance of messenger RNA (mRNA), the class of RNA used to study gene expression. Conversely, real-time qPCR offers a sensitive functional quality control tool for evaluating mRNA integrity and predicting future performance on gene expression platforms by directly evaluating cDNA functionality. Design of tissue-specific assay panels targeting a select set of genes provides a focused and versatile solution, which is lacking in broad-spectrum microcapillary electrophoresis analysis methods. Furthermore, qPCR assays offer high-throughput laboratories and biorepositories an efficient and automatable quality control screening method. By taking advantage of regional degradation patterns of RNA, class prediction algorithms can be developed for individual assays to measure RNA quality as a function of the magnitude of deviation from an expected gene expression value, or CT value. By determining the degree of shift from an expected CT value for each assay in the panel, individual algorithm outputs can be collectively evaluated to determine an overall RNA quality score, allowing researchers to properly weight or exclude subpar samples from analysis. The following work describes the ongoing development of a novel functional quality control method for RNA samples extracted from human whole blood, consisting of a custom gene expression assay panel and complementary class prediction algorithms.
Subject
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Topic
Microbiology and Molecular Genetics
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Title
Rutgers University Electronic Theses and Dissertations
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ETD_3740
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electronic resource
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application/pdf
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Extent
vii, 129 p. : ill.
Note
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M.S.
Note
(type = bibliography)
Includes bibliographical references
Note
(type = statement of responsibility)
by Stephanie A. Frahm
Subject
(authority = ETD-LCSH)
Topic
RNA
Subject
(authority = ETD-LCSH)
Topic
Reverse transcriptase
Subject
(authority = ETD-LCSH)
Topic
Gene expression
Identifier
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http://hdl.rutgers.edu/1782.1/rucore10001600001.ETD.000064089
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TitleInfo
Title
Graduate School - New Brunswick Electronic Theses and Dissertations
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rucore19991600001
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(displayLabel = Rutgers, The State University of New Jersey)
NjNbRU
Identifier
(type = doi)
doi:10.7282/T3DN442F
Genre
(authority = ExL-Esploro)
ETD graduate
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Rights
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The author owns the copyright to this work.
RightsHolder
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Name
FamilyName
Frahm
GivenName
Stephanie
Role
Copyright Holder
RightsEvent
Type
Permission or license
DateTime
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(qualifier = exact);
(point = start)
2011-12-22 14:06:48
AssociatedEntity
Name
Stephanie Frahm
Role
Copyright holder
Affiliation
Rutgers University. Graduate School - New Brunswick
AssociatedObject
Type
License
Name
Author Agreement License
Detail
I hereby grant to the Rutgers University Libraries and to my school the non-exclusive right to archive, reproduce and distribute my thesis or dissertation, in whole or in part, and/or my abstract, in whole or in part, in and from an electronic format, subject to the release date subsequently stipulated in this submittal form and approved by my school. I represent and stipulate that the thesis or dissertation and its abstract are my original work, that they do not infringe or violate any rights of others, and that I make these grants as the sole owner of the rights to my thesis or dissertation and its abstract. I represent that I have obtained written permissions, when necessary, from the owner(s) of each third party copyrighted matter to be included in my thesis or dissertation and will supply copies of such upon request by my school. I acknowledge that RU ETD and my school will not distribute my thesis or dissertation or its abstract if, in their reasonable judgment, they believe all such rights have not been secured. I acknowledge that I retain ownership rights to the copyright of my work. I also retain the right to use all or part of this thesis or dissertation in future works, such as articles or books.
RightsEvent
DateTime
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(qualifier = exact);
(point = start)
2012-01-31
DateTime
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2014-01-30
Type
Embargo
Detail
Access to this PDF has been restricted at the author's request. It will be publicly available after January 30th, 2014.
Copyright
Status
Copyright protected
Availability
Status
Open
Reason
Permission or license
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