Single molecule quantitation and sequencing of rare translocations using microfluidic nested digital PCR
dc.contributor.author | Shuga, Joe | |
dc.contributor.author | Zeng, Yong | |
dc.contributor.author | Novak, Richard | |
dc.contributor.author | Lan, Qing | |
dc.contributor.author | Tang, Xiaojiang | |
dc.contributor.author | Rothman, Nathaniel | |
dc.contributor.author | Vermeulen, Roel | |
dc.contributor.author | Li, Laiyu | |
dc.contributor.author | Hubbard, Alan | |
dc.contributor.author | Zhang, Luoping | |
dc.contributor.author | Mathies, Richard A. | |
dc.contributor.author | Smith, Martyn T. | |
dc.date.accessioned | 2014-04-11T19:50:33Z | |
dc.date.available | 2014-04-11T19:50:33Z | |
dc.date.issued | 2013-06-23 | |
dc.identifier.citation | Shuga, Joe, Yong Zeng, Richard Novak, Qing Lan, Xiaojiang Tang, Nathaniel Rothman, Roel Vermeulen, et al. 2013. “Single Molecule Quantitation and Sequencing of Rare Translocations Using Microfluidic Nested Digital PCR.” Nucleic Acids Research 41 (16). http://dx.doi.org/10.1093/nar/gkt613 | |
dc.identifier.uri | http://hdl.handle.net/1808/13460 | |
dc.description.abstract | Cancers are heterogeneous and genetically unstable. New methods are needed that provide the sensitivity and specificity to query single cells at the genetic loci that drive cancer progression, thereby enabling researchers to study the progression of individual tumors. Here, we report the development and application of a bead-based hemi-nested microfluidic droplet digital PCR (dPCR) technology to achieve ‘quantitative’ measurement and single-molecule sequencing of somatically acquired carcinogenic translocations at extremely low levels (<10−6) in healthy subjects. We use this technique in our healthy study population to determine the overall concentration of the t(14;18) translocation, which is strongly associated with follicular lymphoma. The nested dPCR approach improves the detection limit to 1 × 10−7 or lower while maintaining the analysis efficiency and specificity. Further, the bead-based dPCR enabled us to isolate and quantify the relative amounts of the various clonal forms of t(14;18) translocation in these subjects, and the single-molecule sensitivity and resolution of dPCR led to the discovery of new clonal forms of t(14;18) that were otherwise masked by the conventional quantitative PCR measurements. In this manner, we created a quantitative map for this carcinogenic mutation in this healthy population and identified the positions on chromosomes 14 and 18 where the vast majority of these t(14;18) events occur. | |
dc.description.sponsorship | Trans-National Institutes of Health Genes, Environment and Health Initiative, Biological Response Indicators of Environmental Systems Center Grant [U54 ES016115-01 to M.T.S. and R.A.M.] and National Institute of Environmental Health Sciences Superfund Basic Research Program Grant [P42 ES004705 to M.T.S.]; Canary Foundation and ACS Postdoctoral Fellowship Award in Early Detection [116373-PFTED-08-251-01-SIED to J.S.] from the American Cancer Society; New faculty start-up funds from the University of Kansas (in part to Y.Z.). National Science Foundation Graduate Research Fellowship (to R.N.). Funding for open access charge: National Institutes of Health [U54 ES016115-01]. | |
dc.publisher | Oxford University Press | |
dc.rights | This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/3.0/), which permits unrestricted reuse, distribution, and reproduction in any medium, provided the original work is properly cited. | |
dc.rights.uri | http://creativecommons.org/licenses/by/3.0/ | |
dc.title | Single molecule quantitation and sequencing of rare translocations using microfluidic nested digital PCR | |
dc.type | Article | |
kusw.kuauthor | Zeng, Yong | |
kusw.kudepartment | Chemistry | |
kusw.oastatus | fullparticipation | |
dc.identifier.doi | 10.1093/nar/gkt613 | |
kusw.oaversion | Scholarly/refereed, publisher version | |
kusw.oapolicy | This item meets KU Open Access policy criteria. | |
dc.rights.accessrights | openAccess |
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