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Measurement error correction in the least absolute shrinkage and selection operator model when validation data are available.

ABSTRACT: Measurement of serum biomarkers by multiplex assays may be more variable as compared to single biomarker assays. Measurement error in these data may bias parameter estimates in regression analysis, which could mask true associations of serum biomarkers with an outcome. The Least Absolute Shrinkage and Selection Operator (LASSO) can be used for variable selection in these high-dimensional data. Furthermore, when the distribution of measurement error is assumed to be known or estimated with replication data, a simple measurement error correction method can be applied to the LASSO method. However, in practice the distribution of the measurement error is unknown and is expensive to estimate through replication both in monetary cost and need for greater amount of sample which is often limited in quantity. We adapt an existing bias correction approach by estimating the measurement error using validation data in which a subset of serum biomarkers are re-measured on a random subset of the study sample. We evaluate this method using simulated data and data from the Tucson Epidemiological Study of Airway Obstructive Disease (TESAOD). We show that the bias in parameter estimation is reduced and variable selection is improved.

SUBMITTER: Vasquez MM

PROVIDER: S-EPMC7449511 | biostudies-literature | 2019 Mar

REPOSITORIES: biostudies-literature

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Measurement error correction in the least absolute shrinkage and selection operator model when validation data are available.

Vasquez Monica M MM Hu Chengcheng C Roe Denise J DJ Halonen Marilyn M Guerra Stefano S

Statistical methods in medical research 20171123 3

Measurement of serum biomarkers by multiplex assays may be more variable as compared to single biomarker assays. Measurement error in these data may bias parameter estimates in regression analysis, which could mask true associations of serum biomarkers with an outcome. The Least Absolute Shrinkage and Selection Operator (LASSO) can be used for variable selection in these high-dimensional data. Furthermore, when the distribution of measurement error is assumed to be known or estimated with replic ...[more]

PMID: 29166842

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Project description:Objective: Dilated cardiomyopathy (DCM) is a heart disease with high mortality characterized by progressive cardiac dilation and myocardial contractility reduction. The molecular signature of dilated cardiomyopathy remains to be defined. Hence, seeking potential biomarkers and therapeutic of DCM is urgent and necessary. Methods: In this study, we utilized the Robust Rank Aggregation (RRA) method to integrate four eligible DCM microarray datasets from the GEO and identified a set of significant differentially expressed genes (DEGs) between dilated cardiomyopathy and non-heart failure. Moreover, LASSO analysis was carried out to clarify the diagnostic and DCM clinical features of these genes and identify dilated cardiomyopathy derived diagnostic signatures (DCMDDS). Results: A total of 117 DEGs were identified across the four microarrays. Furthermore, GO analysis demonstrated that these DEGs were mainly enriched in the regulation of inflammatory response, the humoral immune response, the regulation of blood pressure and collagen-containing extracellular matrix. In addition, KEGG analysis revealed that DEGs were mainly enriched in diverse infected signaling pathways. Moreover, Gene set enrichment analysis revealed that immune and inflammatory biological processes such as adaptive immune response, cellular response to interferon and cardiac muscle contraction, dilated cardiomyopathy are significantly enriched in DCM. Moreover, Least absolute shrinkage and selection operator (LASSO) analyses of the 18 DCM-related genes developed a 7-gene signature predictive of DCM. This signature included ANKRD1, COL1A1, MYH6, PERELP, PRKACA, CDKN1A, and OMD. Interestingly, five of these seven genes have a correlation with left ventricular ejection fraction (LVEF) in DCM patients. Conclusion: Our present study demonstrated that the signatures could be robust tools for predicting DCM in clinical practice. And may also be potential treatment targets for clinical implication in the future.

Project description:BackgroundHyperuricemia is a common complication of type 2 diabetes mellitus and can lead to serious consequences such as gout and kidney disease.MethodsPatients with type 2 diabetes mellitus from six different communities in Fuzhou were recruited from June to December 2022. Questionnaires, physical examinations, and laboratory tests were conducted to collect data on various variables. Variable screening steps were performed using univariate and multivariate stepwise regression, least absolute shrinkage and selection operator (LASSO) regression, and Boruta feature selection. The dataset was divided into a training-testing set (80%) and an independent validation set (20%). Six machine learning models were built and validated.ResultsA total of 8243 patients with type 2 diabetes mellitus were included in this study. According to Occam's razor method, the LASSO regression algorithm was determined to be the optimal risk factors selection method, and nine variables were identified as parameters for the risk assessment model. The absence of diabetes medication and elevated fasting blood glucose levels exhibited a negative correlation with the risk of hyperuricemia. Conversely, seven other variables demonstrated a positive association with the risk of hyperuricemia among patients diagnosed with type 2 diabetes mellitus. Among the six machine learning models, the artificial neural network (ANN) model demonstrated the highest performance. It achieved an areas under curve of 0.736, accuracy of 68.3%, sensitivity of 65.0%, specificity of 72.2%, precision of 73.6% and F1-score of 69.0%.ConclusionsWe developed an ANN model to better evaluate the risk of hyperuricemia in the type 2 diabetes population. In the type 2 diabetes population, women should pay particular attention to their uric acid levels, and type 2 diabetics should not neglect their obesity level, blood pressure, kidney function and lipid profile during their regular medical check-ups, in order to do their best to avoid the risks associated with the combination of type 2 diabetes and hyperuricemia.

Dataset Information

Measurement error correction in the least absolute shrinkage and selection operator model when validation data are available.

Publications

Measurement error correction in the least absolute shrinkage and selection operator model when validation data are available.

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