Selection of DNA aptamers for ovarian cancer biomarker HE4 using CE-SELEX and high-throughput sequencing

Title:
Selection of DNA aptamers for ovarian cancer biomarker HE4 using CE-SELEX and high-throughput sequencing
Authors:
Eaton, Rachel M.; Shallcross, Jamie A.; Mael, Liora E.; Mears, Kepler S.; Minkoff, Lisa; Scoville, Delia J.; Whelan, Rebecca J. ( 0000-0002-9293-1528 )
Abstract:
The development of novel affinity probes for cancer biomarkers may enable powerful improvements in analytical methods for detecting and treating cancer. In this report, we describe our use of capillary electrophoresis (CE) as the separation mechanism in the process of selecting DNA aptamers with affinity for the ovarian cancer biomarker HE4. Rather than the conventional use of cloning and sequencing as the last step in the aptamer selection process, we used high-throughput sequencing on an Illumina platform. This data-rich approach, combined with a bioinformatics pipeline based on freely available computational tools, enabled the entirety of the selection process-and not only its endpoint-to be characterized. Affinity probe CE and fluorescence anisotropy assays demonstrate the binding affinity of a set of aptamer candidates identified through this bioinformatics approach. Graphical Abstract A population of candidate aptamers is sequenced on an Illumina platform, enabling the process by which aptamers are selected over multiple SELEX rounds to be characterized. Bioinformatics tools are used to identify enrichment of selected aptamers and groupings into clusters based on sequence and structural similarity. A subset of sequenced aptamers may be intelligently chosen for in vitro testing.
Citation:
Eaton, R.M., J.A. Shallcross, L.E. Mael, K.S. Mears, L. Minkoff, D.J. Scoville, and R. Whelan. 2015. "Selection of DNA aptamers for ovarian cancer biomarker HE4 using CE-SELEX and high-throughput sequencing." Analytical and Bioanalytical Chemistry 407(23): 6965-73.
Publisher:
Springer Verlag
DATE ISSUED:
2015-09
Department:
Chemistry and Biochemistry
Type:
Article
PUBLISHED VERSION:
10.1007/s00216-015-8665-7
PERMANENT LINK:
http://hdl.handle.net/11282/582316

Full metadata record

DC FieldValue Language
dc.contributor.authorEaton, Rachel M.en
dc.contributor.authorShallcross, Jamie A.en
dc.contributor.authorMael, Liora E.en
dc.contributor.authorMears, Kepler S.en
dc.contributor.authorMinkoff, Lisaen
dc.contributor.authorScoville, Delia J.en
dc.contributor.authorWhelan, Rebecca J.en
dc.date.accessioned2015-11-17T16:30:22Zen
dc.date.available2015-11-17T16:30:22Zen
dc.date.issued2015-09en
dc.identifier.citationEaton, R.M., J.A. Shallcross, L.E. Mael, K.S. Mears, L. Minkoff, D.J. Scoville, and R. Whelan. 2015. "Selection of DNA aptamers for ovarian cancer biomarker HE4 using CE-SELEX and high-throughput sequencing." Analytical and Bioanalytical Chemistry 407(23): 6965-73.en
dc.identifier.issn1618-2642en
dc.identifier.urihttp://hdl.handle.net/11282/582316en
dc.description.abstractThe development of novel affinity probes for cancer biomarkers may enable powerful improvements in analytical methods for detecting and treating cancer. In this report, we describe our use of capillary electrophoresis (CE) as the separation mechanism in the process of selecting DNA aptamers with affinity for the ovarian cancer biomarker HE4. Rather than the conventional use of cloning and sequencing as the last step in the aptamer selection process, we used high-throughput sequencing on an Illumina platform. This data-rich approach, combined with a bioinformatics pipeline based on freely available computational tools, enabled the entirety of the selection process-and not only its endpoint-to be characterized. Affinity probe CE and fluorescence anisotropy assays demonstrate the binding affinity of a set of aptamer candidates identified through this bioinformatics approach. Graphical Abstract A population of candidate aptamers is sequenced on an Illumina platform, enabling the process by which aptamers are selected over multiple SELEX rounds to be characterized. Bioinformatics tools are used to identify enrichment of selected aptamers and groupings into clusters based on sequence and structural similarity. A subset of sequenced aptamers may be intelligently chosen for in vitro testing.en
dc.language.isoen_USen
dc.publisherSpringer Verlagen
dc.identifier.doi10.1007/s00216-015-8665-7en
dc.subject.departmentChemistry and Biochemistryen_US
dc.titleSelection of DNA aptamers for ovarian cancer biomarker HE4 using CE-SELEX and high-throughput sequencingen_US
dc.typeArticleen
dc.identifier.journalAnalytical and Bioanalytical Chemistryen
dc.subject.keywordAptameren_US
dc.subject.keywordCE-SELEXen_US
dc.subject.keywordHE4en_US
dc.subject.keywordOvarian canceren_US
dc.subject.keywordBiomarkeren_US
dc.subject.keywordHigh-throughput sequencingen_US
dc.identifier.volume407en_US
dc.identifier.issue23en_US
dc.identifier.startpage6965en_US
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