Biology subjects

Oxtoby, N.

Publications and source records attributed to Oxtoby, N..

3 recordsLinked to original sources

bioRxiv2025

Incorporating Multi-threshold Polygenic Risk in Hippocampal-based Normative Models Improves Cognitive Decline Prediction

Predicting cognitive decline using MRI measures of brain volume is challenging. Normative models capture the evolution of biomarkers over time in a healthy group, quantifying an individuals deviation from that norm. Here, we improve the precision of normative models for hippocampal volume, a key cognitive biomarker, by integrating multi-threshold polygenic scores (PGS) that capture genetic predisposition to its variability. We built Gaussian Process Regression (GPR) models on genetic, imaging, and demographic data from 23,997 UK Biobank (UKBB) participants, validating on 3,000 out-of-sample participants from the Alzheimers Disease Neuroimaging Initiative (ADNI) and the European Prevention of Alzheimers Disease (EPAD) cohorts. The genetically-informed models improved associations significantly across five experimental designs and 13 key neurocognitive measures, including Mini-Mental State Examination (MMSE), Clinical Dementia Rating (CDR), Alzheimers Disease Assessment Scale (ADAS), and importantly, improving prediction of future cognitive decline. These findings underscore the value of integrating multi-threshold PGS with neuroimaging-based predictive models for improving prognostication in neurodegenerative diseases.

bioinformatics↗

bioRxiv2023

Fed-ComBat: A Generalized Federated Framework for Batch Effect Harmonization in Collaborative Studies

The use of multi-centric analyses is crucial for obtaining sufficient sample sizes and representative clinical populations in experimental studies. In this setting, data harmonization techniques are typically employed to address systematic biases and ensure the interoperability of the data. State-of-the-art harmonisation approaches are based on the statistical theory of random effect modeling, allowing to account for either linear of non-linear biases and batch effects. However, optimizing these statistical methods generally requires data centralization at some point during the analysis pipeline, therefore introducing the risk of exposing individual patient information while posing significant data governance issues. To overcome this challenge, in this paper we present Fed-ComBat, a federated framework for batch effect harmonization on decentralized data. Fed-ComBat enables the preservation of nonlinear covariate effects without requiring centralization of data and without prior parametric hypothesis on the variables to account for. We demonstrate the effectiveness of Fed-ComBat against a comprehensive panel of existing approaches based on the state-of-the-art ComBat, along with distributed and nonlinear variants. Our experiments are based on extensive simulated data, and on the analysis of multiple cohorts based on 7 neuroimaging studies comprising healthy controls (CI) and subjects with various disorders such as Parkinsons disease (PD), Alzheimers disease (AD), and autism spectrum disorder (ASD). Our results show that in a federated settings, Fed-ComBat harmonization exhibits comparable results to centralized methods for both linear and nonlinear cases. On real data, harmonized trajectories of the thickness of the right hippocampus across lifespan measured on a set of 7 public studies show comparable results between centralized and federated models and are consistent with the literature when using a nonlinear model. The code is publicly available at: https://gitlab.inria.fr/greguig/fedcombat

neuroscience↗

bioRxiv2021

Multi view based imaging genetics analysis on Parkinson disease

Longitudinal studies integrating imaging and genetic data have recently become widespread among bioinformatics researchers. Combining such heterogeneous data allows a better understanding of complex diseases origins and causes. Through a multi-view based workflow proposal, we show the common steps and tools used in imaging genetics analysis, interpolating genotyping, neuroimaging and transcriptomic data. We describe the advantages of existing methods to analyze heterogeneous datasets, using Parkinsons Disease (PD) as a case study. Parkinsons disease is associated with both genetic and neuroimaging factors, however such imaging genetics associations are at an early investigation stage. Therefore it is desirable to have a free and open source workflow that integrates different analysis flows in order to recover potential genetic biomarkers in PD, as in other complex diseases.

bioinformatics↗