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Register a new userMulticlass Disease Predictions Based on Integrated Clinical and Genomics Datasets
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Clinical predictions using clinical data by computational methods are common in bioinformatics. However, clinical predictions using information from genomics datasets as well is not a frequently observed phenomenon in research. Precision medicine research requires information from all available datasets to provide intelligent clinical solutions. In this paper, we have attempted to create a prediction model which uses information from both clinical and genomics datasets. We have demonstrated multiclass disease predictions based on combined clinical and genomics datasets using machine learning methods. We have created an integrated dataset, using a clinical (ClinVar) and a genomics (gene expression) dataset, and trained it using instance-based learner to predict clinical diseases. We have used an innovative but simple way for multiclass classification, where the number of output classes is as high as 75. We have used Principal Component Analysis for feature selection. The classifier predicted diseases with 73% accuracy on the integrated dataset. The results were consistent and competent when compared with other classification models. The results show that genomics information can be reliably included in datasets for clinical predictions and it can prove to be valuable in clinical diagnostics and precision medicine.
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In recent years, functional genomics approaches combining genetic information with bulk RNA-sequencing data have identified the downstream expression effects of disease-associated genetic risk factors through so-called expression quantitative trait locus (eQTL) analysis. Single-cell RNA-sequencing creates enormous opportunities for mapping eQTLs across different cell types and in dynamic processes, many of which are obscured when using bulk methods. The enormous increase in throughput and reduction in cost per cell now allow this technology to be applied to large-scale population genetics studies. Therefore, we have founded the single-cell eQTLGen consortium (sc-eQTLGen), aimed at pinpointing disease-causing genetic variants and identifying the cellular contexts in which they affect gene expression. Ultimately, this information can enable development of personalized medicine. Here, we outline the goals, approach, potential utility and early proofs-of-concept of the sc-eQTLGen consortium. We also provide a set of study design considerations for future single-cell eQTL studies.
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