Harnessing Qatar Biobank to understand type 2 diabetes and obesity in adult Qataris from the First Qatar Biobank Project

A Survey on the Role of Artificial Intelligence in Biobanking Studies: A Systematic Review

Introduction: In biobanks, participants' biological samples are stored for future research. The application of artificial intelligence (AI) involves the analysis of data and the prediction of any pathological outcomes. In AI, models are used to diagnose diseases as well as classify and predict disease risks. Our research analyzed AI's role in the development of biobanks in the healthcare industry, systematically. Methods: The literature search was conducted using three digital reference databases, namely PubMed, CINAHL, and WoS. Guidelines for preferred reporting elements for systematic reviews and meta-analyses (PRISMA)-2020 in conducting the systematic review were followed. The search terms included "biobanks", "AI", "machine learning", and "deep learning", as well as combinations such as "biobanks with AI", "deep learning in the biobanking field", and "recent advances in biobanking". Only English-language papers were included in the study, and to assess the quality of selected works, the Newcastle-Ottawa scale (NOS) was used. The good quality range (NOS ≥ 7) is only considered for further review. Results: A literature analysis of the above entries resulted in 239 studies. Based on their relevance to the study's goal, research characteristics, and NOS criteria, we included 18 articles for reviewing. In the last decade, biobanks and artificial intelligence have had a relatively large impact on the medical system. Interestingly, UK biobanks account for the highest percentage of high-quality works, followed by Qatar, South Korea, Singapore, Japan, and Denmark. Conclusions: Translational bioinformatics probably represent a future leader in precision medicine. AI and machine learning applications to biobanking research may contribute to the development of biobanks for the utility of health services and citizens.

Prevalence of asymptomatic hyperuricemia and its association with prediabetes, dyslipidemia and subclinical inflammation markers among young healthy adults in Qatar

AIM

The aim of this study is to investigate the prevalence of asymptomatic hyperuricemia in Qatar and to examine its association with changes in markers of dyslipidemia, prediabetes and subclinical inflammation.

METHODS

A cross-sectional study of young adult participants aged 18 - 40 years old devoid of comorbidities collected between 2012 and 2017. Exposure was defined as uric acid level, and outcomes were defined as levels of different blood markers. De-identified data were collected from Qatar Biobank. T-tests, correlation tests and multiple linear regression were all used to investigate the effects of hyperuricemia on blood markers. Statistical analyses were conducted using STATA 16.

RESULTS

The prevalence of asymptomatic hyperuricemia is 21.2% among young adults in Qatar. Differences between hyperuricemic and normouricemic groups were observed using multiple linear regression analysis and found to be statistically and clinically significant after adjusting for age, gender, BMI, smoking and exercise. Significant associations were found between uric acid level and HDL-c p = 0.019 (correlation coefficient -0.07 (95% CI [-0.14, -0.01]); c-peptide p = 0.018 (correlation coefficient 0.38 (95% CI [0.06, 0.69]) and monocyte to HDL ratio (MHR) p = 0.026 (correlation coefficient 0.47 (95% CI [0.06, 0.89]).

CONCLUSIONS

Asymptomatic hyperuricemia is prevalent among young adults and associated with markers of prediabetes, dyslipidemia, and subclinical inflammation.

Systems biology analysis of human genomes points to key pathways conferring spina bifida risk

Genetic investigations of most structural birth defects, including spina bifida (SB), congenital heart disease, and craniofacial anomalies, have been underpowered for genome-wide association studies because of their rarity, genetic heterogeneity, incomplete penetrance, and environmental influences. Our systems biology strategy to investigate SB predisposition controls for population stratification and avoids much of the bias inherent in candidate gene searches that are pervasive in the field. We examine both protein coding and noncoding regions of whole genomes to analyze sequence variants, collapsed by gene or regulatory region, and apply machine learning, gene enrichment, and pathway analyses to elucidate molecular pathways and genes contributing to human SB.

Spina bifida (SB) is a debilitating birth defect caused by multiple gene and environment interactions. Though SB shows non-Mendelian inheritance, genetic factors contribute to an estimated 70% of cases. Nevertheless, identifying human mutations conferring SB risk is challenging due to its relative rarity, genetic heterogeneity, incomplete penetrance, and environmental influences that hamper genome-wide association studies approaches to untargeted discovery. Thus, SB genetic studies may suffer from population substructure and/or selection bias introduced by typical candidate gene searches. We report a population based, ancestry-matched whole-genome sequence analysis of SB genetic predisposition using a systems biology strategy to interrogate 298 case-control subject genomes (149 pairs). Genes that were enriched in likely gene disrupting (LGD), rare protein-coding variants were subjected to machine learning analysis to identify genes in which LGD variants occur with a different frequency in cases versus controls and so discriminate between these groups. Those genes with high discriminatory potential for SB significantly enriched pathways pertaining to carbon metabolism, inflammation, innate immunity, cytoskeletal regulation, and essential transcriptional regulation consistent with their having impact on the pathogenesis of human SB. Additionally, an interrogation of conserved noncoding sequences identified robust variant enrichment in regulatory regions of several transcription factors critical to embryonic development. This genome-wide perspective offers an effective approach to the interrogation of coding and noncoding sequence variant contributions to rare complex genetic disorders.

A Modelling Framework for Embedding-based Predictions for Compound-Viral Protein Activity

Motivation

A global effort is underway to identify compounds for the treatment of COVID-19. Since de novo compound design is an extremely long, time-consuming, and expensive process, efforts are underway to discover existing compounds that can be repurposed for COVID-19 and new viral diseases.

Model

We propose a machine learning representation framework that uses deep learning induced vector embeddings of compounds and viral proteins as features to predict compound-viral protein activity. The prediction model in-turn uses a consensus framework to rank approved compounds against viral proteins of interest.

Results

Our consensus framework achieves a highmean Pearson correlation of 0.916, mean R2 of 0.840 and a low mean squared error of 0.313 for the task of compound-viral protein activity prediction on an independent test set. As a use case, we identify a ranked list of 47 compounds common to three main proteins of SARS-COV-2 virus (PL-PRO, 3CL-PRO and Spike protein) as potential targets including 21 antivirals, 15 anticancer, 5 antibiotics and 6 other investigationalhuman compounds.We performadditional molecular docking simulations to demonstrate thatmajority of these compounds have low binding energies and thus high binding affinity with the potential to be effective against the SARS-COV-2 virus.

Availability

All the source code and data is available at: https://github.com/raghvendra5688/Drug-Repurposing and https://dx.doi.org/10.17632/8rrwnbcgmx.3. We also implemented a web-server at: https://machinelearning-protein.qcri.org/index.html.

Supplementary information

Supplementary data are available at Bioinformatics online.

Artificial Intelligence (AI) based machine learning models predict glucose variability and hypoglycaemia risk in patients with type 2 diabetes on a multiple drug regimen who fast during ramadan (The PROFAST - IT Ramadan study)

OBJECTIVE

To develop a machine-based algorithm from clinical and demographic data, physical activity and glucose variability to predict hyperglycaemic and hypoglycaemic excursions in patients with type 2 diabetes on multiple glucose lowering therapies who fast during Ramadan.

PATIENTS AND METHODS

Thirteen patients (10 males and three females) with type 2 diabetes on 3 or more anti-diabetic medications were studied with a Fitbit-2 pedometer device and Freestyle Libre (Abbott Diagnostics) 2 weeks before and 2 weeks during Ramadan. Several machine learning techniques were trained to predict blood glucose levels in a regression framework utilising physical activity and contemporaneous blood glucose levels, comparing Ramadan to non-Ramadan days.

RESULTS

The median age of participants was 51 years (IQR 49-52); median BMI was 33.2 kg/m² (IQR 33.0-35.9) and median HbA1c was 7.3% (IQR 6.7-7.8). The optimal model using physical activity achieved an R² of 0.548 and a mean absolute error (MAE) of 30.30. The addition of electronic health record (ehr) information increased R² to 0.636 and reduced MAE to 26.89 and the time of the day feature further increased R² to 0.768 and reduced MAE to 20.55. Combining all the features together resulted in an optimal XGBoost model with an R² of 0.836 and MAE of 17.47. This model accurately estimated normal glucose levels in 2584/2715 (95.2%) readings and hyperglycaemic events in 852/1031 (82.6%) readings, but fewer hypoglycaemic events (48/172 (27.9%)). The optimal XGBoost model prioritized age, gender, BMI and HbA1c followed by glucose levels and physical activity. Interestingly, the blood glucose level prediction by our model was influenced by use of SGLT2i.

CONCLUSION

XGBoost, a machine learning AI algorithm achieves high predictive performance for normal and hyperglycaemic excursions, but has limited predictive value for hypoglycaemia in patients on multiple therapies who fast during Ramadan.

Obesity in Qatar: A Case-Control Study on the Identification of Associated Risk Factors

Obesity is an emerging public health problem in the Western world as well as in the Gulf region. Qatar, a tiny wealthy county, is among the top-ranked obese countries with a high obesity rate among its population. Compared to Qatar's severity of this health crisis, only a limited number of studies focused on the systematic identification of potential risk factors using multimodal datasets. This study aims to develop machine learning (ML) models to distinguish healthy from obese individuals and reveal potential risk factors associated with obesity in Qatar. We designed a case-control study focused on 500 Qatari subjects, comprising 250 obese and 250 healthy individuals- the later forming the control group. We obtained the most extensive collection of clinical measurements for the Qatari population from the Qatar Biobank (QBB) repertoire, including (i) Physio-clinical Biomarkers, (ii) Spirometry, (iii) VICORDER, (iv) DXA scan composition, and (v) DXA scan densitometry readings. We developed several machine learning (ML) models to distinguish healthy from obese individuals and applied multiple feature selection techniques to identify potential risk factors associated with obesity. The proposed ML model achieved over 90% accuracy, thereby outperforming the existing state of the art models. The outcome from the ablation study on multimodal clinical datasets revealed physio-clinical measurements as the most influential risk factors in distinguishing healthy versus obese subjects. Furthermore, multiple feature ranking techniques confirmed known obesity risk factors (c-peptide, insulin, albumin, uric acid) and identified potential risk factors linked to obesity-related comorbidities such as diabetes (e.g., HbA1c, glucose), liver function (e.g., alkaline phosphatase, gamma-glutamyl transferase), lipid profile (e.g., triglyceride, low density lipoprotein cholesterol, high density lipoprotein cholesterol), etc. Most of the DXA measurements (e.g., bone area, bone mineral composition, bone mineral density, etc.) were significantly (p-value < 0.05) higher in the obese group. Overall, the net effect of hypothesized protective factors of obesity on bone mass seems to have surpassed the hypothesized harmful factors. All the identified factors warrant further investigation in a clinical setup to understand their role in obesity.

Predicting hypertension using machine learning: Findings from Qatar Biobank Study

Background and objective

Hypertension, a global burden, is associated with several risk factors and can be treated by lifestyle modifications and medications. Prediction and early diagnosis is important to prevent related health complications. The objective is to construct and compare predictive models to identify individuals at high risk of developing hypertension without the need of invasive clinical procedures.

Methods

This is a cross-sectional study using 987 records of Qataris and long-term residents aged 18₊ years from Qatar Biobank. Percentages were used to summarize data and chi-square tests to assess associations. Predictive models of hypertension were constructed and compared using three supervised machine learning algorithms: decision tree, random forest, and logistics regression using 5-fold cross-validation. The performance of algorithms was assessed using accuracy, positive predictive value (PPV), sensitivity, F-measure, and area under the receiver operating characteristic curve (AUC). Stata and Weka were used for analysis.

Results

Age, gender, education level, employment, tobacco use, physical activity, adequate consumption of fruits and vegetables, abdominal obesity, history of diabetes, history of high cholesterol, and mother’s history high blood pressure were important predictors of hypertension. All algorithms showed more or less similar performances: Random forest (accuracy = 82.1%, PPV = 81.4%, sensitivity = 82.1%), logistic regression (accuracy = 81.1%, PPV = 80.1%, sensitivity = 81.1%) and decision tree (accuracy = 82.1%, PPV = 81.2%, sensitivity = 82.1%. In terms of AUC, compared to logistic regression, while random forest performed similarly, decision tree had a significantly lower discrimination ability (p-value<0.05) with AUC’s equal to 85.0, 86.9, and 79.9, respectively.

Conclusions

Machine learning provides the chance of having a rapid predictive model using non-invasive predictors to screen for hypertension. Future research should consider improving the predictive accuracy of models in larger general populations, including more important predictors and using a variety of algorithms.

Association of low serum magnesium with diabetes and hypertension: Findings from Qatar Biobank study

AIM

We aimed to examine the association between serum magnesium and diabetes and hypertension among Qatari adults.

METHODS

In the cross-sectional study, we used data from 9693 Qatari participants aged 20 years and above attending the Qatar Biobank (QBB) Study. Blood samples were analyzed in a central lab. Habitual food consumption was assessed by a food frequency questionnaire. Reduced rank regression was used to construct magnesium related dietary pattern (MRDP) using serum magnesium as a response variable. Diabetes was defined by blood glucose, HbA1c or known diabetes. Prediabetes was defined as HbA1c between 5.7% and 6.4%. Subclinical magnesium deficiency was defined as serum magnesium <0.85 mmol/L.

RESULTS

The prevalence of diabetes, prediabetes and subclinical magnesium deficiency was 18.9%, 11.5% and 59.5%, respectively. Across the quartiles of serum magnesium from high to low, the prevalence ratios (PR 95%CI) for diabetes were 1.00, 1.35, 1.88, and 2.70 (95%CI 2.38-3.05), respectively (p for trend <0.001). The presence of hypertension significantly increased the probability of diabetes along a wide range of low serum magnesium. A low intake of MRDP was also positively associated with diabetes and high HbA1c.

CONCLUSION

Subclinical magnesium deficiency is common in Qatar and associates with diabetes, prediabetes and hypertension in Qatari adults.