On the analysis of glycomics mass spectrometry data via the regularized area under the ROC curve
<p>Abstract</p> <p>Background</p> <p>Novel molecular and statistical methods are in rising demand for disease diagnosis and prognosis with the help of recent advanced biotechnology. High-resolution mass spectrometry (MS) is one of those biotechnologies that are highly p...
| Main Authors: | , , , , |
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| Format: | Article |
| Language: | English |
| Published: |
BMC
2007-12-01
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| Series: | BMC Bioinformatics |
| Online Access: | http://www.biomedcentral.com/1471-2105/8/477 |
| _version_ | 1828552827879817216 |
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| author | Lebrilla Carlito B Kirmiz Crystal Liu Hao Ye Jingjing Rocke David M |
| author_facet | Lebrilla Carlito B Kirmiz Crystal Liu Hao Ye Jingjing Rocke David M |
| author_sort | Lebrilla Carlito B |
| collection | DOAJ |
| description | <p>Abstract</p> <p>Background</p> <p>Novel molecular and statistical methods are in rising demand for disease diagnosis and prognosis with the help of recent advanced biotechnology. High-resolution mass spectrometry (MS) is one of those biotechnologies that are highly promising to improve health outcome. Previous literatures have identified some proteomics biomarkers that can distinguish healthy patients from cancer patients using MS data. In this paper, an MS study is demonstrated which uses glycomics to identify ovarian cancer. Glycomics is the study of glycans and glycoproteins. The glycans on the proteins may deviate between a cancer cell and a normal cell and may be visible in the blood. High-resolution MS has been applied to measure relative abundances of potential glycan biomarkers in human serum. Multiple potential glycan biomarkers are measured in MS spectra. With the objection of maximizing the empirical area under the ROC curve (AUC), an analysis method was considered which combines potential glycan biomarkers for the diagnosis of cancer.</p> <p>Results</p> <p>Maximizing the empirical AUC of glycomics MS data is a large-dimensional optimization problem. The technical difficulty is that the empirical AUC function is not continuous. Instead, it is in fact an empirical 0–1 loss function with a large number of linear predictors. An approach was investigated that regularizes the area under the ROC curve while replacing the 0–1 loss function with a smooth surrogate function. The constrained threshold gradient descent regularization algorithm was applied, where the regularization parameters were chosen by the cross-validation method, and the confidence intervals of the regression parameters were estimated by the bootstrap method. The method is called TGDR-AUC algorithm. The properties of the approach were studied through a numerical simulation study, which incorporates the positive values of mass spectrometry data with the correlations between measurements within person. The simulation proved asymptotic properties that estimated AUC approaches the true AUC. Finally, mass spectrometry data of serum glycan for ovarian cancer diagnosis was analyzed. The optimal combination based on TGDR-AUC algorithm yields plausible result and the detected biomarkers are confirmed based on biological evidence.</p> <p>Conclusion</p> <p>The TGDR-AUC algorithm relaxes the normality and independence assumptions from previous literatures. In addition to its flexibility and easy interpretability, the algorithm yields good performance in combining potential biomarkers and is computationally feasible. Thus, the approach of TGDR-AUC is a plausible algorithm to classify disease status on the basis of multiple biomarkers.</p> |
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| format | Article |
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| institution | Directory Open Access Journal |
| issn | 1471-2105 |
| language | English |
| last_indexed | 2024-12-12T05:07:11Z |
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| spelling | doaj.art-d017ef46ca104c02a88185c67693a8fe2022-12-22T00:37:04ZengBMCBMC Bioinformatics1471-21052007-12-018147710.1186/1471-2105-8-477On the analysis of glycomics mass spectrometry data via the regularized area under the ROC curveLebrilla Carlito BKirmiz CrystalLiu HaoYe JingjingRocke David M<p>Abstract</p> <p>Background</p> <p>Novel molecular and statistical methods are in rising demand for disease diagnosis and prognosis with the help of recent advanced biotechnology. High-resolution mass spectrometry (MS) is one of those biotechnologies that are highly promising to improve health outcome. Previous literatures have identified some proteomics biomarkers that can distinguish healthy patients from cancer patients using MS data. In this paper, an MS study is demonstrated which uses glycomics to identify ovarian cancer. Glycomics is the study of glycans and glycoproteins. The glycans on the proteins may deviate between a cancer cell and a normal cell and may be visible in the blood. High-resolution MS has been applied to measure relative abundances of potential glycan biomarkers in human serum. Multiple potential glycan biomarkers are measured in MS spectra. With the objection of maximizing the empirical area under the ROC curve (AUC), an analysis method was considered which combines potential glycan biomarkers for the diagnosis of cancer.</p> <p>Results</p> <p>Maximizing the empirical AUC of glycomics MS data is a large-dimensional optimization problem. The technical difficulty is that the empirical AUC function is not continuous. Instead, it is in fact an empirical 0–1 loss function with a large number of linear predictors. An approach was investigated that regularizes the area under the ROC curve while replacing the 0–1 loss function with a smooth surrogate function. The constrained threshold gradient descent regularization algorithm was applied, where the regularization parameters were chosen by the cross-validation method, and the confidence intervals of the regression parameters were estimated by the bootstrap method. The method is called TGDR-AUC algorithm. The properties of the approach were studied through a numerical simulation study, which incorporates the positive values of mass spectrometry data with the correlations between measurements within person. The simulation proved asymptotic properties that estimated AUC approaches the true AUC. Finally, mass spectrometry data of serum glycan for ovarian cancer diagnosis was analyzed. The optimal combination based on TGDR-AUC algorithm yields plausible result and the detected biomarkers are confirmed based on biological evidence.</p> <p>Conclusion</p> <p>The TGDR-AUC algorithm relaxes the normality and independence assumptions from previous literatures. In addition to its flexibility and easy interpretability, the algorithm yields good performance in combining potential biomarkers and is computationally feasible. Thus, the approach of TGDR-AUC is a plausible algorithm to classify disease status on the basis of multiple biomarkers.</p>http://www.biomedcentral.com/1471-2105/8/477 |
| spellingShingle | Lebrilla Carlito B Kirmiz Crystal Liu Hao Ye Jingjing Rocke David M On the analysis of glycomics mass spectrometry data via the regularized area under the ROC curve BMC Bioinformatics |
| title | On the analysis of glycomics mass spectrometry data via the regularized area under the ROC curve |
| title_full | On the analysis of glycomics mass spectrometry data via the regularized area under the ROC curve |
| title_fullStr | On the analysis of glycomics mass spectrometry data via the regularized area under the ROC curve |
| title_full_unstemmed | On the analysis of glycomics mass spectrometry data via the regularized area under the ROC curve |
| title_short | On the analysis of glycomics mass spectrometry data via the regularized area under the ROC curve |
| title_sort | on the analysis of glycomics mass spectrometry data via the regularized area under the roc curve |
| url | http://www.biomedcentral.com/1471-2105/8/477 |
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