Using artificial intelligence to learn optimal regimen plan for Alzheimer's disease

BACKGROUND

Alzheimer's disease (AD) is a progressive neurological disorder with no specific curative medications. Sophisticated clinical skills are crucial to optimize treatment regimens given the multiple coexisting comorbidities in the patient population.

OBJECTIVE

Here, we propose a study to leverage reinforcement learning (RL) to learn the clinicians' decisions for AD patients based on the longitude data from electronic health records.

METHODS

In this study, we selected 1736 patients from the Alzheimer's Disease Neuroimaging Initiative (ADNI) database. We focused on the two most frequent concomitant diseases-depression, and hypertension, thus creating 5 data cohorts (ie, Whole Data, AD, AD-Hypertension, AD-Depression, and AD-Depression-Hypertension). We modeled the treatment learning into an RL problem by defining states, actions, and rewards. We built a regression model and decision tree to generate multiple states, used six combinations of medications (ie, cholinesterase inhibitors, memantine, memantine-cholinesterase inhibitors, hypertension drugs, supplements, or no drugs) as actions, and Mini-Mental State Exam (MMSE) scores as rewards.

RESULTS

Given the proper dataset, the RL model can generate an optimal policy (regimen plan) that outperforms the clinician's treatment regimen. Optimal policies (ie, policy iteration and Q-learning) had lower rewards than the clinician's policy (mean -3.03 and -2.93 vs. -2.93, respectively) for smaller datasets but had higher rewards for larger datasets (mean -4.68 and -2.82 vs. -4.57, respectively).

CONCLUSIONS

Our results highlight the potential of using RL to generate the optimal treatment based on the patients' longitude records. Our work can lead the path towards developing RL-based decision support systems that could help manage AD with comorbidities.

Association of the fibronectin type III domain-containing protein 5 rs1746661 single nucleotide polymorphism with reduced brain glucose metabolism in elderly humans

Fibronectin type III domain-containing protein 5 (FNDC5) and its derived hormone, irisin, have been associated with metabolic control in humans, with described FNDC5 single nucleotide polymorphisms being linked to obesity and metabolic syndrome. Decreased brain FNDC5/irisin has been reported in subjects with dementia due to Alzheimer's disease. Since impaired brain glucose metabolism develops in ageing and is prominent in Alzheimer's disease, here, we examined associations of a single nucleotide polymorphism in the FNDC5 gene (rs1746661) with brain glucose metabolism and amyloid-β deposition in a cohort of 240 cognitively unimpaired and 485 cognitively impaired elderly individuals from the Alzheimer's Disease Neuroimaging Initiative. In cognitively unimpaired elderly individuals harbouring the FNDC5 rs1746661(T) allele, we observed a regional reduction in low glucose metabolism in memory-linked brain regions and increased brain amyloid-β PET load. No differences in cognition or levels of cerebrospinal fluid amyloid-β42, phosphorylated tau and total tau were observed between FNDC5 rs1746661(T) allele carriers and non-carriers. Our results indicate that a genetic variant of FNDC5 is associated with low brain glucose metabolism in elderly individuals and suggest that FNDC5 may participate in the regulation of brain metabolism in brain regions vulnerable to Alzheimer's disease pathophysiology. Understanding the associations between genetic variants in metabolism-linked genes and metabolic brain signatures may contribute to elucidating genetic modulators of brain metabolism in humans.

Longitudinal changes in hippocampal texture from healthy aging to Alzheimer's disease

Early detection of Alzheimer's disease is essential to develop preventive treatment strategies. Detectible change in brain volume emerges relatively late in the pathogenic progression of disease, but microstructural changes caused by early neuropathology may cause subtle changes in the MR signal, quantifiable using texture analysis. Texture analysis quantifies spatial patterns in an image, such as smoothness, randomness and heterogeneity. We investigated whether the MRI texture of the hippocampus, an early site of Alzheimer's disease pathology, is sensitive to changes in brain microstructure before the onset of cognitive impairment. We also explored the longitudinal trajectories of hippocampal texture across the Alzheimer's continuum in relation to hippocampal volume and other biomarkers. Finally, we assessed the ability of texture to predict future cognitive decline, over and above hippocampal volume. Data were acquired from the Alzheimer's Disease Neuroimaging Initiative. Texture was calculated for bilateral hippocampi on 3T T1-weighted MRI scans. Two hundred and ninety-three texture features were reduced to five principal components that described 88% of total variance within cognitively unimpaired participants. We assessed cross-sectional differences in these texture components and hippocampal volume between four diagnostic groups: cognitively unimpaired amyloid-β- (n = 406); cognitively unimpaired amyloid-β+ (n = 213); mild cognitive impairment amyloid-β+ (n = 347); and Alzheimer's disease dementia amyloid-β+ (n = 202). To assess longitudinal texture change across the Alzheimer's continuum, we used a multivariate mixed-effects spline model to calculate a 'disease time' for all timepoints based on amyloid PET and cognitive scores. This was used as a scale on which to compare the trajectories of biomarkers, including volume and texture of the hippocampus. The trajectories were modelled in a subset of the data: cognitively unimpaired amyloid-β- (n = 345); cognitively unimpaired amyloid-β+ (n = 173); mild cognitive impairment amyloid-β+ (n = 301); and Alzheimer's disease dementia amyloid-β+ (n = 161). We identified a difference in texture component 4 at the earliest stage of Alzheimer's disease, between cognitively unimpaired amyloid-β- and cognitively unimpaired amyloid-β+ older adults (Cohen's d = 0.23, Padj = 0.014). Differences in additional texture components and hippocampal volume emerged later in the disease continuum alongside the onset of cognitive impairment (d = 0.30-1.22, Padj < 0.002). Longitudinal modelling of the texture trajectories revealed that, while most elements of texture developed over the course of the disease, noise reduced sensitivity for tracking individual textural change over time. Critically, however, texture provided additional information than was provided by volume alone to more accurately predict future cognitive change (d = 0.32-0.63, Padj < 0.0001). Our results support the use of texture as a measure of brain health, sensitive to Alzheimer's disease pathology, at a time when therapeutic intervention may be most effective.

The status of digital pathology and associated infrastructure within Alzheimer's Disease Centers

Digital pathology (DP) has transformative potential, especially for Alzheimer disease and related disorders. However, infrastructure barriers may limit adoption. To provide benchmarks and insights into implementation barriers, a survey was conducted in 2019 within National Institutes of Health's Alzheimer's Disease Centers (ADCs). Questions covered infrastructure, funding sources, and data management related to digital pathology. Of the 35 ADCs to which the survey was sent, 33 responded. Most respondents (81%) stated that their ADC had digital slide scanner access, with the most frequent brand being Aperio/Leica (62.9%). Approximately a third of respondents stated there were fees to utilize the scanner. For DP and machine learning (ML) resources, 41% of respondents stated none was supported by their ADC. For scanner purchasing and operations, 50% of respondents stated they received institutional support. Some were unsure of the file size of scanned digital images (37%) and total amount of storage space files occupied (50%). Most (76%) were aware of other departments at their institution working with ML; a similar (76%) percentage were unaware of multiuniversity or industry partnerships. These results demonstrate many ADCs have access to a digital slide scanner; additional investigations are needed to further understand hurdles to implement DP and ML workflows.

Longitudinal progression of choroid plexus enlargement is associated with female sex, cognitive decline and ApoE E4 homozygote status

Introduction

Choroid plexus (CP)-related mechanisms have been implicated in the pathogenesis of neurodegenerative diseases, including Alzheimer's disease. In this pilot study, we aimed to elucidate the association between longitudinal changes in CP volume, sex and cognitive impairment.

Methods

We assessed longitudinal changes in CP volume in a cohort of n = 613 subjects across n = 2,334 datapoints from ADNI 2 and ADNI-GO, belonging to cognitively unimpaired (CN), stable mild cognitive impairment (MCI), clinically diagnosed Alzheimer's disease dementia (AD) or convertor (to either AD or MCI) subgroups. CP volume was automatically segmented and used as a response variable in linear mixed effect models with random intercept clustered by patient identity. Temporal effects of select variables were assessed by interactions and subgroup analyses.

Results

We found an overall significant increase of CP volume in time (14.92 mm³ per year, 95% confidence interval, CI (11.05, 18.77), p < 0.001). Sex-disaggregated results showed an annual rate of increase 9.48 mm³ in males [95% CI (4.08, 14.87), p < 0.001], and 20.43 mm³ in females [95% CI (14.91, 25.93), p < 0.001], indicating more than double the rate of increase in females, which appeared independent of other temporal variables. The only diagnostic group with a significant CP increase as compared to CN was the convertors group, with an increase of 24.88 mm³/year [95% CI (14, 35.82), p < 0.001]. ApoE exhibited a significant temporal effect, with the E4 homozygote group's CP increasing at more than triple the rate of non-carrier or heterozygote groups [40.72, 95% CI (25.97, 55.46), p < 0.001 vs. 12.52, 95% CI (8.02, 17.02), p < 0.001 for ApoE E4 homozygotes and E4 non-carriers, respectively], and may have modified the diagnostic group relationship.

Conclusion

Our results contribute to potential mechanisms for sex differences in cognitive impairment with a novel finding of twice the annual choroid plexus enlargement in females and provide putative support for CP-related mechanisms of cognitive deterioration and its relationship to ApoE E4.

SPARE-Tau: A flortaucipir machine-learning derived early predictor of cognitive decline

BACKGROUND

Recently, tau PET tracers have shown strong associations with clinical outcomes in individuals with cognitive impairment and cognitively unremarkable elderly individuals. flortaucipir PET scans to measure tau deposition in multiple brain areas as the disease progresses. This information needs to be summarized to evaluate disease severity and predict disease progression. We, therefore, sought to develop a machine learning-derived index, SPARE-Tau, which successfully detects pathology in the earliest disease stages and accurately predicts progression compared to a priori-based region of interest approaches (ROI).

METHODS

587 participants of the Alzheimer's Disease Neuroimaging Initiative (ADNI) cohort had flortaucipir scans, structural MRI scans, and an Aβ biomarker test (CSF or florbetapir PET) performed on the same visit. We derived the SPARE-Tau index in a subset of 367 participants. We evaluated associations with clinical measures for CSF p-tau, SPARE-MRI, and flortaucipir PET indices (SPARE-Tau, meta-temporal, and average Braak ROIs). Bootstrapped multivariate adaptive regression splines linear regression analyzed the association between the biomarkers and baseline ADAS-Cog13 scores. Bootstrapped multivariate linear regression models evaluated associations with clinical diagnosis. Cox-hazards and mixed-effects models investigated clinical progression and longitudinal ADAS-Cog13 changes. The Aβ positive cognitively unremarkable participants, not included in the SPARE-Tau training, served as an independent validation group.

RESULTS

Compared to CSF p-tau, meta-temporal, and averaged Braak tau PET ROIs, SPARE-Tau showed the strongest association with baseline ADAS-cog13 scores and diagnosis. SPARE-Tau also presented the strongest association with clinical progression in cognitively unremarkable participants and longitudinal ADAS-Cog13 changes. Results were confirmed in the Aβ+ cognitively unremarkable hold-out sample participants. CSF p-tau showed the weakest cross-sectional associations and longitudinal prediction.

DISCUSSION

Flortaucipir indices showed the strongest clinical association among the studied biomarkers (flortaucipir, florbetapir, structural MRI, and CSF p-tau) and were predictive in the preclinical disease stages. Among the flortaucipir indices, the machine-learning derived SPARE-Tau index was the most sensitive clinical progression biomarker. The combination of different biomarker modalities better predicted cognitive performance.

Autosomal dominant and sporadic late onset Alzheimer's disease share a common in vivo pathophysiology

The extent to which the pathophysiology of autosomal dominant Alzheimer's disease corresponds to the pathophysiology of 'sporadic' late onset Alzheimer's disease is unknown, thus limiting the extrapolation of study findings and clinical trial results in autosomal dominant Alzheimer's disease to late onset Alzheimer's disease. We compared brain MRI and amyloid PET data, as well as CSF concentrations of amyloid-β42, amyloid-β40, tau and tau phosphorylated at position 181, in 292 carriers of pathogenic variants for Alzheimer's disease from the Dominantly Inherited Alzheimer Network, with corresponding data from 559 participants from the Alzheimer's Disease Neuroimaging Initiative. Imaging data and CSF samples were reprocessed as appropriate to guarantee uniform pipelines and assays. Data analyses yielded rates of change before and after symptomatic onset of Alzheimer's disease, allowing the alignment of the ∼30-year age difference between the cohorts on a clinically meaningful anchor point, namely the participant age at symptomatic onset. Biomarker profiles were similar for both autosomal dominant Alzheimer's disease and late onset Alzheimer's disease. Both groups demonstrated accelerated rates of decline in cognitive performance and in regional brain volume loss after symptomatic onset. Although amyloid burden accumulation as determined by PET was greater after symptomatic onset in autosomal dominant Alzheimer's disease than in late onset Alzheimer's disease participants, CSF assays of amyloid-β42, amyloid-β40, tau and p-tau181 were largely overlapping in both groups. Rates of change in cognitive performance and hippocampal volume loss after symptomatic onset were more aggressive for autosomal dominant Alzheimer's disease participants. These findings suggest a similar pathophysiology of autosomal dominant Alzheimer's disease and late onset Alzheimer's disease, supporting a shared pathobiological construct.

Residual reserve index modifies the effect of amyloid pathology on fluorodeoxyglucose metabolism: Implications for efficiency and capacity in cognitive reserve

Background

The residual approach to measuring cognitive reserve (using the residual reserve index) aims to capture cognitive resilience conferred by cognitive reserve, but may be confounded by factors representing brain resilience. We sought to distinguish between brain and cognitive resilience by comparing interactions between the residual reserve index and amyloid, tau, and neurodegeneration [“AT(N)”] biomarkers when predicting executive function. We hypothesized that the residual reserve index would moderate at least one path from an AT(N) biomarker to executive function (consistent with cognitive resilience), as opposed to moderating a path between two AT(N) biomarkers (suggestive of brain resilience).

Methods

Participants (N = 332) were from the Alzheimer’s Disease Neuroimaging Initiative. The residual reserve index represented the difference between observed and predicted memory performance (a positive residual reserve index suggests higher cognitive reserve). AT(N) biomarkers were: CSF β-amyloid_1–42/β-amyloid_1–40 (A), plasma phosphorylated tau-181 (T), and FDG metabolism in AD-specific regions ([N]). AT(N) biomarkers (measured at consecutive time points) were entered in a sequential mediation model testing the indirect effects from baseline amyloid to executive function intercept (third annual follow-up) and slope (baseline to seventh follow-up), via tau and/or FDG metabolism. The baseline residual reserve index was entered as a moderator of paths between AT(N) biomarkers (e.g., amyloid-tau), and paths between AT(N) biomarkers and executive function.

Results

The residual reserve index interacted with amyloid pathology when predicting FDG metabolism: the indirect effect of amyloid → FDG metabolism → executive function intercept and slope varied as a function of the residual reserve index. With lower amyloid pathology, executive function performance was comparable at different levels of the residual reserve index, but a higher residual reserve index was associated with lower FDG metabolism. With higher amyloid pathology, a higher residual reserve index predicted better executive function via higher FDG metabolism.

Conclusion

The effect of the residual reserve index on executive function performance via FDG metabolism was consistent with cognitive resilience. This suggests the residual reserve index captures variation in cognitive reserve; specifically, neural efficiency, and neural capacity to upregulate metabolism to enhance cognitive resilience in the face of greater amyloid pathology. Implications for future research include the potential bidirectionality between neural efficiency and amyloid accumulation.

Causal links among amyloid, tau, and neurodegeneration

Amyloid-β pathology is associated with greater tau pathology and facilitates tau propagation from the medial temporal lobe to the neocortex, where tau is closely associated with local neurodegeneration. The degree of the involvement of amyloid-β versus existing tau pathology in tau propagation and neurodegeneration has not been fully elucidated in human studies. Careful quantification of these effects can inform the development and timing of therapeutic interventions. We conducted causal mediation analyses to investigate the relative contributions of amyloid-β and existing tau to tau propagation and neurodegeneration in two longitudinal studies of individuals without dementia: the Baltimore Longitudinal Study of Aging (N = 103, age range 57-96) and the Alzheimer's Disease Neuroimaging Initiative (N = 122, age range 56-92). As proxies of neurodegeneration, we investigated cerebral blood flow, glucose metabolism, and regional volume. We first confirmed that amyloid-β moderates the association between tau in the entorhinal cortex and in the inferior temporal gyrus, a neocortical region exhibiting early tau pathology (amyloid group × entorhinal tau interaction term β  = 0.488, standard error [SE] = 0.126, P < 0.001 in the Baltimore Longitudinal Study of Aging; β  = 0.619, SE = 0.145, P < 0.001 in the Alzheimer's Disease Neuroimaging Initiative). In causal mediation analyses accounting for this facilitating effect of amyloid, amyloid positivity had a statistically significant direct effect on inferior temporal tau as well as an indirect effect via entorhinal tau (average direct effect =0.47, P < 0.001 and average causal mediation effect =0.44, P = 0.0028 in Baltimore Longitudinal Study of Aging; average direct effect =0.43, P = 0.004 and average causal mediation effect =0.267, P = 0.0088 in Alzheimer's Disease Neuroimaging Initiative). Entorhinal tau mediated up to 48% of the total effect of amyloid on inferior temporal tau. Higher inferior temporal tau was associated with lower colocalized cerebral blood flow, glucose metabolism, and regional volume, whereas amyloid had only an indirect effect on these measures via tau, implying tau as the primary driver of neurodegeneration (amyloid-cerebral blood flow average causal mediation effect =-0.28, P = 0.021 in Baltimore Longitudinal Study of Aging; amyloid-volume average causal mediation effect =-0.24, P < 0.001 in Alzheimer's Disease Neuroimaging Initiative). Our findings suggest targeting amyloid or medial temporal lobe tau might slow down neocortical spread of tau and subsequent neurodegeneration, but a combination therapy may yield better outcomes.

Validation of and Demographically Adjusted Normative Data for the Learning Ratio Derived from the RAVLT in Robustly Intact Older Adults

BACKGROUND

The learning ratio (LR) is a novel learning slope score that was developed to identify learning more accurately by considering the proportion of information learned after the first trial of a multi-trial learning task. Specifically, LR is the number of items learned after trial one divided by the number of items yet to be learned. Although research on LR has been promising, convergent validation, clinical characterization, and demographic norming of this LR metric are warranted to understand its clinical utility when derived from the Rey Auditory Verbal Learning Test (RAVLT).

METHOD

Data from 674 robustly cognitively intact older participants from the Alzheimer's Disease Neuroimaging Initiative (aged 54- 89) were used to calculate the LR metric. Comparison of LR's relationship with standard memory measures was undertaken relative to other traditional learning slope metrics. In addition, retest reliability at 6, 12, and 24 months was examined, and demographically adjusted normative comparisons were developed.

RESULTS

Lower LR scores were associated with poorer performances on memory measures, and LR scores outperformed traditional learning slope calculations across all analyses. Retest reliability exceeded acceptability thresholds across time, and demographically adjusted normative equations suggested better performance for cognitively intact participants than those with mild cognitive impairment.

CONCLUSIONS

These results suggest that this LR score possesses sound retest reliability and can better reflect learning capacity than traditional learning slope calculations. With the added development and validation of regression-based normative comparisons, these findings support the use of the RAVLT LR as a clinical tool to inform clinical decision-making and treatment.

A Hybrid Deep Learning Method for Early and Late Mild Cognitive Impairment Diagnosis With Incomplete Multimodal Data

Multimodality neuroimages have been widely applied to diagnose mild cognitive impairment (MCI). However, the missing data problem is unavoidable. Most previously developed methods first train a generative adversarial network (GAN) to synthesize missing data and then train a classification network with the completed data. These methods independently train two networks with no information communication. Thus, the resulting GAN cannot focus on the crucial regions that are helpful for classification. To overcome this issue, we propose a hybrid deep learning method. First, a classification network is pretrained with paired MRI and PET images. Afterward, we use the pretrained classification network to guide a GAN by focusing on the features that are helpful for classification. Finally, we synthesize the missing PET images and use them with real MR images to fine-tune the classification model to make it better adapt to the synthesized images. We evaluate our proposed method on the ADNI dataset, and the results show that our method improves the accuracies obtained on the validation and testing sets by 3.84 and 5.82%, respectively. Moreover, our method increases the accuracies for the validation and testing sets by 7.7 and 9.09%, respectively, when we synthesize the missing PET images via our method. An ablation experiment shows that the last two stages are essential for our method. We also compare our method with other state-of-the-art methods, and our method achieves better classification performance.

Combined Structural MR and Diffusion Tensor Imaging Classify the Presence of Alzheimer's Disease With the Same Performance as MR Combined With Amyloid Positron Emission Tomography: A Data Integration Approach

Background: In recent years, classification frameworks using imaging data have shown that multimodal classification methods perform favorably over the use of a single imaging modality for the diagnosis of Alzheimer's Disease. The currently used clinical approach often emphasizes the use of qualitative MRI and/or PET data for clinical diagnosis. Based on the hypothesis that classification of isolated imaging modalities is not predictive of their respective value in combined approaches, we investigate whether the combination of T1 Weighted MRI and diffusion tensor imaging (DTI) can yield an equivalent performance as the combination of quantitative structural MRI (sMRI) with amyloid-PET. Methods: We parcellated the brain into regions of interest (ROI) following different anatomical labeling atlases. For each region of interest different metrics were extracted from the different imaging modalities (sMRI, PiB-PET, and DTI) to be used as features. Thereafter, the feature sets were reduced using an embedded-based feature selection method. The final reduced sets were then used as input in support vector machine (SVM) classifiers. Three different base classifiers were created, one for each imaging modality, and validated using internal (n = 41) and external data from the ADNI initiative (n = 330 for sMRI, n = 148 for DTI and n = 55 for PiB-PET) sources. Finally, the classifiers were ensembled using a weighted method in order to evaluate the performance of different combinations. Results: For the base classifiers the following performance levels were found: sMRI-based classifier (accuracy, 92%; specificity, 97% and sensitivity, 87%), PiB-PET (accuracy, 91%; specificity, 89%; and sensitivity, 92%) and the lowest performance was attained with DTI (accuracy, 80%; specificity, 76%; and sensitivity, 82%). From the multimodal approaches, when integrating two modalities, the following results were observed: sMRI+PiB-PET (accuracy, 98%; specificity, 98%; and sensitivity, 99%), sMRI+DTI (accuracy, 97%; specificity, 99%; and sensitivity, 94%) and PiB-PET+DTI (accuracy, 91%; specificity, 90%; and sensitivity, 93%). Finally, the combination of all imaging modalities yielded an accuracy of 98%, specificity of 97% and sensitivity of 99%. Conclusion: Although DTI in isolation shows relatively poor performance, when combined with structural MR, it showed a surprising classification performance which was comparable to MR combined with amyloid PET. These results are consistent with the notion that white matter changes are also important in Alzheimer's Disease.

Basal forebrain volume reliably predicts the cortical spread of Alzheimer's degeneration

Alzheimer's disease neurodegeneration is thought to spread across anatomically and functionally connected brain regions. However, the precise sequence of spread remains ambiguous. The prevailing model used to guide in vivo human neuroimaging and non-human animal research assumes that Alzheimer's degeneration starts in the entorhinal cortices, before spreading to the temporoparietal cortex. Challenging this model, we previously provided evidence that in vivo markers of neurodegeneration within the nucleus basalis of Meynert (NbM), a subregion of the basal forebrain heavily populated by cortically projecting cholinergic neurons, precedes and predicts entorhinal degeneration. There have been few systematic attempts at directly comparing staging models using in vivo longitudinal biomarker data, and none to our knowledge testing if comparative evidence generalizes across independent samples. Here we addressed the sequence of pathological staging in Alzheimer's disease using two independent samples of the Alzheimer's Disease Neuroimaging Initiative (n1 = 284; n2 = 553) with harmonized CSF assays of amyloid-β and hyperphosphorylated tau (pTau), and longitudinal structural MRI data over 2 years. We derived measures of grey matter degeneration in a priori NbM and the entorhinal cortical regions of interest. To examine the spreading of degeneration, we used a predictive modelling strategy that tests whether baseline grey matter volume in a seed region accounts for longitudinal change in a target region. We demonstrated that predictive spread favoured the NbM→entorhinal over the entorhinal→NbM model. This evidence generalized across the independent samples. We also showed that CSF concentrations of pTau/amyloid-β moderated the observed predictive relationship, consistent with evidence in rodent models of an underlying trans-synaptic mechanism of pathophysiological spread. The moderating effect of CSF was robust to additional factors, including clinical diagnosis. We then applied our predictive modelling strategy to an exploratory whole-brain voxel-wise analysis to examine the spatial specificity of the NbM→entorhinal model. We found that smaller baseline NbM volumes predicted greater degeneration in localized regions of the entorhinal and perirhinal cortices. By contrast, smaller baseline entorhinal volumes predicted degeneration in the medial temporal cortex, recapitulating a prior influential staging model. Our findings suggest that degeneration of the basal forebrain cholinergic projection system is a robust and reliable upstream event of entorhinal and neocortical degeneration, calling into question a prevailing view of Alzheimer's disease pathogenesis.

Quick assessment for systematic test statistic inflation/deflation due to null model misspecifications in genome-wide environment interaction studies

Gene-environment (GxE) interaction is one potential explanation for the missing heritability problem. A popular approach to genome-wide environment interaction studies (GWEIS) is based on regression models involving interactions between genetic variants and environment variables. Unfortunately, GWEIS encounters systematically inflated (or deflated) test statistics more frequently than a marginal association study. The problematic behavior may occur due to poor specification of the null model (i.e. the model without genetic effect) in GWEIS. Improved null model specification may resolve the problem, but the investigation requires many time-consuming analyses of genome-wide scans, e.g. by trying out several transformations of the phenotype. It is therefore helpful if we can predict such problematic behavior beforehand. We present a simple closed-form formula to assess problematic behavior of GWEIS under the null hypothesis of no genetic effects. It requires only phenotype, environment variables, and covariates, enabling quick identification of systematic test statistic inflation or deflation. Applied to real data from the Alzheimer’s Disease Neuroimaging Initiative (ADNI), our formula identified problematic studies from among hundreds GWEIS considering each metabolite as the environment variable in GxE interaction. Our formula is useful to quickly identify problematic GWEIS without requiring a genome-wide scan.

Early Prediction of Alzheimer's Disease Using Null Longitudinal Model-Based Classifiers

Incipient Alzheimer’s Disease (AD) is characterized by a slow onset of clinical symptoms, with pathological brain changes starting several years earlier. Consequently, it is necessary to first understand and differentiate age-related changes in brain regions in the absence of disease, and then to support early and accurate AD diagnosis. However, there is poor understanding of the initial stage of AD; seemingly healthy elderly brains lose matter in regions related to AD, but similar changes can also be found in non-demented subjects having mild cognitive impairment (MCI). By using a Linear Mixed Effects approach, we modelled the change of 166 Magnetic Resonance Imaging (MRI)-based biomarkers available at a 5-year follow up on healthy elderly control (HC, n = 46) subjects. We hypothesized that, by identifying their significant variant (vr) and quasi-variant (qvr) brain regions over time, it would be possible to obtain an age-based null model, which would characterize their normal atrophy and growth patterns as well as the correlation between these two regions. By using the null model on those subjects who had been clinically diagnosed as HC (n = 161), MCI (n = 209) and AD (n = 331), normal age-related changes were estimated and deviation scores (residuals) from the observed MRI-based biomarkers were computed. Subject classification, as well as the early prediction of conversion to MCI and AD, were addressed through residual-based Support Vector Machines (SVM) modelling. We found reductions in most cortical volumes and thicknesses (with evident gender differences) as well as in sub-cortical regions, including greater atrophy in the hippocampus. The average accuracies (ACC) recorded for men and women were: AD-HC: 94.11%, MCI-HC: 83.77% and MCI converted to AD (cAD)-MCI non-converter (sMCI): 76.72%. Likewise, as compared to standard clinical diagnosis methods, SVM classifiers predicted the conversion of cAD to be 1.9 years earlier for females (ACC:72.5%) and 1.4 years earlier for males (ACC:69.0%).