Thermodynamic framework to assess low abundance DNA mutation detection by hybridization.
The knowledge of genomic DNA variations in patient samples has a high and increasing value for human diagnostics in its broadest sense. Although many methods and sensors to detect or quantify these variations are available or under development, the number of underlying physico-chemical detection pri...
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doaj-d84d78285c094713916cbfa5c2ec178b2020-11-24T20:45:29ZengPublic Library of Science (PLoS)PLoS ONE1932-62032017-01-01125e017738410.1371/journal.pone.0177384Thermodynamic framework to assess low abundance DNA mutation detection by hybridization.Hanny WillemsAn JacobsWahyu Wijaya HadiwikartaTom VenkenDirk ValkenborgNadine Van RoyJo VandesompeleJef HooyberghsThe knowledge of genomic DNA variations in patient samples has a high and increasing value for human diagnostics in its broadest sense. Although many methods and sensors to detect or quantify these variations are available or under development, the number of underlying physico-chemical detection principles is limited. One of these principles is the hybridization of sample target DNA versus nucleic acid probes. We introduce a novel thermodynamics approach and develop a framework to exploit the specific detection capabilities of nucleic acid hybridization, using generic principles applicable to any platform. As a case study, we detect point mutations in the KRAS oncogene on a microarray platform. For the given platform and hybridization conditions, we demonstrate the multiplex detection capability of hybridization and assess the detection limit using thermodynamic considerations; DNA containing point mutations in a background of wild type sequences can be identified down to at least 1% relative concentration. In order to show the clinical relevance, the detection capabilities are confirmed on challenging formalin-fixed paraffin-embedded clinical tumor samples. This enzyme-free detection framework contains the accuracy and efficiency to screen for hundreds of mutations in a single run with many potential applications in molecular diagnostics and the field of personalised medicine.http://europepmc.org/articles/PMC5444680?pdf=render |
collection |
DOAJ |
language |
English |
format |
Article |
sources |
DOAJ |
author |
Hanny Willems An Jacobs Wahyu Wijaya Hadiwikarta Tom Venken Dirk Valkenborg Nadine Van Roy Jo Vandesompele Jef Hooyberghs |
spellingShingle |
Hanny Willems An Jacobs Wahyu Wijaya Hadiwikarta Tom Venken Dirk Valkenborg Nadine Van Roy Jo Vandesompele Jef Hooyberghs Thermodynamic framework to assess low abundance DNA mutation detection by hybridization. PLoS ONE |
author_facet |
Hanny Willems An Jacobs Wahyu Wijaya Hadiwikarta Tom Venken Dirk Valkenborg Nadine Van Roy Jo Vandesompele Jef Hooyberghs |
author_sort |
Hanny Willems |
title |
Thermodynamic framework to assess low abundance DNA mutation detection by hybridization. |
title_short |
Thermodynamic framework to assess low abundance DNA mutation detection by hybridization. |
title_full |
Thermodynamic framework to assess low abundance DNA mutation detection by hybridization. |
title_fullStr |
Thermodynamic framework to assess low abundance DNA mutation detection by hybridization. |
title_full_unstemmed |
Thermodynamic framework to assess low abundance DNA mutation detection by hybridization. |
title_sort |
thermodynamic framework to assess low abundance dna mutation detection by hybridization. |
publisher |
Public Library of Science (PLoS) |
series |
PLoS ONE |
issn |
1932-6203 |
publishDate |
2017-01-01 |
description |
The knowledge of genomic DNA variations in patient samples has a high and increasing value for human diagnostics in its broadest sense. Although many methods and sensors to detect or quantify these variations are available or under development, the number of underlying physico-chemical detection principles is limited. One of these principles is the hybridization of sample target DNA versus nucleic acid probes. We introduce a novel thermodynamics approach and develop a framework to exploit the specific detection capabilities of nucleic acid hybridization, using generic principles applicable to any platform. As a case study, we detect point mutations in the KRAS oncogene on a microarray platform. For the given platform and hybridization conditions, we demonstrate the multiplex detection capability of hybridization and assess the detection limit using thermodynamic considerations; DNA containing point mutations in a background of wild type sequences can be identified down to at least 1% relative concentration. In order to show the clinical relevance, the detection capabilities are confirmed on challenging formalin-fixed paraffin-embedded clinical tumor samples. This enzyme-free detection framework contains the accuracy and efficiency to screen for hundreds of mutations in a single run with many potential applications in molecular diagnostics and the field of personalised medicine. |
url |
http://europepmc.org/articles/PMC5444680?pdf=render |
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