dorsal/arxiv
View SchemaHybridization Isotherms of DNA Microarrays and the Quantification of Mutation Studies
| Authors | Avraham Halperin, Arnaud Buhot, Ekaterina B. Zhulina |
|---|---|
| Categories | |
| ArXiv ID | q-bio/0411014 |
| URL | https://arxiv.org/abs/q-bio/0411014 |
| Journal | Clin. Chem. 50, 2254-2262, (2004). |
Abstract
Background: Diagnostic DNA arrays for detection of point mutations as markers for cancer usually function in the presence of a large excess of wild type DNA. This excess can give rise to false positives due to competitive hybridization of the wild type target at the mutation spot. The analysis of the DNA array data is typically qualitative aiming to establish the presence or absence of a particular point mutation. Our theoretical approach yields methods for quantifying the analysis so as to obtain the ratio of concentrations of mutated and wild type DNA. Method: The theory is formulated in terms of the hybridization isotherms relating the hybridization fraction at the spot to the composition of the sample solutions at thermodynamic equilibrium. It focuses on samples containing an excess of single stranded DNA and on DNA arrays with low surface density of probes. The hybridization equilibrium constants can be obtained by the nearest neighbor method. Results: Two approaches allow us to obtain quantitative results from the DNA array data. In one the signal of the mutation spot is compared with that of the wild type spot. The implementation requires knowledge of the saturation intensity of the two spots. The second approach requires comparison of the intensity of the mutation spot at two different temperatures. In this case knowledge of the saturation signal is not always necessary. Conclusions: DNA arrays can be used to obtain quantitative results on the concentration ratio of mutated DNA to wild type DNA in studies of somatic point mutations.
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"abstract": "Background: Diagnostic DNA arrays for detection of point mutations as markers\nfor cancer usually function in the presence of a large excess of wild type DNA.\nThis excess can give rise to false positives due to competitive hybridization\nof the wild type target at the mutation spot. The analysis of the DNA array\ndata is typically qualitative aiming to establish the presence or absence of a\nparticular point mutation. Our theoretical approach yields methods for\nquantifying the analysis so as to obtain the ratio of concentrations of mutated\nand wild type DNA. Method: The theory is formulated in terms of the\nhybridization isotherms relating the hybridization fraction at the spot to the\ncomposition of the sample solutions at thermodynamic equilibrium. It focuses on\nsamples containing an excess of single stranded DNA and on DNA arrays with low\nsurface density of probes. The hybridization equilibrium constants can be\nobtained by the nearest neighbor method. Results: Two approaches allow us to\nobtain quantitative results from the DNA array data. In one the signal of the\nmutation spot is compared with that of the wild type spot. The implementation\nrequires knowledge of the saturation intensity of the two spots. The second\napproach requires comparison of the intensity of the mutation spot at two\ndifferent temperatures. In this case knowledge of the saturation signal is not\nalways necessary. Conclusions: DNA arrays can be used to obtain quantitative\nresults on the concentration ratio of mutated DNA to wild type DNA in studies\nof somatic point mutations.",
"arxiv_id": "q-bio/0411014",
"authors": [
"Avraham Halperin",
"Arnaud Buhot",
"Ekaterina B. Zhulina"
],
"categories": [
"q-bio.BM",
"cond-mat.soft",
"q-bio.GN"
],
"journal_ref": "Clin. Chem. 50, 2254-2262, (2004).",
"title": "Hybridization Isotherms of DNA Microarrays and the Quantification of Mutation Studies",
"url": "https://arxiv.org/abs/q-bio/0411014"
},
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