Summary of project PR001279
This data is available at the NIH Common Fund's National Metabolomics Data Repository (NMDR) website, the Metabolomics Workbench, https://www.metabolomicsworkbench.org, where it has been assigned Project ID PR001279. The data can be accessed directly via it's Project DOI: 10.21228/M8CX10 This work is supported by NIH grant, U2C- DK119886.
See: https://www.metabolomicsworkbench.org/about/howtocite.php
| Project ID: | PR001279 |
| Project DOI: | doi: 10.21228/M8CX10 |
| Project Title: | Dysregulated Alanine as a Potential Predictive Marker of Glioma—An Insight from Untargeted HRMAS-NMR and Machine Learning Data |
| Project Type: | Untargeted HRMAS NMR, Glioma |
| Project Summary: | Metabolic alterations play a crucial role in glioma development and progression and can be detected even before the appearance of the fatal phenotype. We have compared the circulating metabolic fingerprints of glioma patients versus healthy controls, for the first time, in a quest to identify a panel of small, dysregulated metabolites with potential to serve as a predictive and/or diagnostic marker in the clinical settings. High-resolution magic angle spinning nuclear magnetic resonance spectroscopy (HRMAS-NMR) was used for untargeted metabolomics and data acquisition followed by a machine learning (ML) approach for the analyses of large metabolic datasets. Cross-validation of ML predicted NMR spectral features was done by statistical methods (Wilcoxon-test) using JMP-pro16 software. Alanine was identified as the most critical metabolite with potential to detect glioma with precision of 1.0, recall of 0.96, and F1 measure of 0.98. The top 10 metabolites identified for glioma detection included alanine, glutamine, valine, methionine, N-acetylaspartate (NAA), γ-aminobutyric acid (GABA), serine, α-glucose, lactate, and arginine. We achieved 100% accuracy for the detection of glioma using ML algorithms, extra tree classifier, and random forest, and 98% accuracy with logistic regression. Classification of glioma in low and high grades was done with 86% accuracy using logistic regression model, and with 83% and 79% accuracy using extra tree classifier and random forest, respectively. The predictive accuracy of our ML model is superior to any of the previously reported algorithms, used in tissue- or liquid biopsy-based metabolic studies. The identified top metabolites can be targeted to develop early diagnostic methods as well as to plan personalized treatment strategies. |
| Institute: | University of the Punjab |
| Department: | School of Biochemistry and Biotechnology |
| Laboratory: | Biopharmaceuticals and Biomarkers Discovery Lab |
| Last Name: | Firdous |
| First Name: | Safia |
| Address: | Quaid e Azam Campus, University of the Punjab, Lahore. |
| Email: | saima.ibb@pu.edu.pk |
| Phone: | +924299231098 |
| Funding Source: | HEC-IRSIP, USA NIH grants: S10OD023406 and R21CA243255 |
| Publications: | Dysregulated Alanine as a Potential Predictive Marker of Glioma—An Insight from Untargeted HRMAS-NMR and Machine Learning Data |
| Contributors: | Safia Firdous, Rizwan Abid, Zubair Nawaz, Faisal Bukhari, Ammar Anwer, Leo L Cheng, Saima Sadaf |
Summary of all studies in project PR001279
| Study ID | Study Title | Species | Institute | Analysis(* : Contains Untargted data) | Release Date | Version | Samples | Download(* : Contains raw data) |
|---|---|---|---|---|---|---|---|---|
| ST002015 | Dysregulated Alanine as a Potential Predictive Marker of Glioma—An Insight from Untargeted HRMAS-NMR and Machine Learning Data | Homo sapiens | University of the Punjab | NMR* | 2022-06-01 | 1 | 42 | Uploaded data (67.7K) |
