Dataset Information

Optimizing timing and cost-effective use of plasma biomarkers in Alzheimer's disease.

ABSTRACT:

Background and objectives

Early and cost-effective identification of amyloid positivity is crucial for Alzheimer's disease (AD) diagnosis. While amyloid PET is the gold standard, plasma biomarkers such as phosphorylated tau 217 (pTau217) provide a potential alternative. This study evaluates the diagnostic accuracy of a combined-panel approach using machine learning models and evaluated the biomarker significance.

Methods

We enrolled 371 participants, including AD (n = 143), non-AD (n = 159), and cognitively unimpaired (CU, n = 69) controls. Combined panels of pTau217, pTau181, glial fibrillary acidic protein (GFAP), neurofilament light chain (NFL), Aβ42/40, and total tau were measured prior to the amyloid PET scan. The multiclass logistic (LR) regression, support vector machines, decision trees, and random forests (RF)-were applied to classify amyloid positivity (A+) at all stages or at early clinical stages (1-3). In AD, we tested whether the biomarker may define the clinical stagings.

Results

When benchmarked against amyloid PET, plasma biomarker-based stratification achieves an optimal balance between diagnostic accuracy and cost-effectiveness. The multi-class LR performed equivalently with RF model in identifying A+. The combined plasma panel reached an > 92% accuracy in identifying A+, with performance increasing to 93.4% at early clinical stages. We ranked the importance of individual biomarkers and pTau217 alone achieved comparable accuracy (> 90%) and was the top-ranked biomarker in the LR or RF model. NFL and GFAP correlated significantly with Mini-Mental State Examination; however, these plasma biomarkers did not enhance clinical staging stratification.

Discussion

The use of multiclass LR model enhances amyloid classification, particularly at earlier clinical stages. While the combined-panel approach is most accurate, pTau217 alone provides a cost-effective alternative for screening. These findings support the integration of plasma biomarkers and ML into clinical workflows for early detection and patient stratification.

SUBMITTER: Chang HI

PROVIDER: S-EPMC12366151 | biostudies-literature | 2025 Aug

REPOSITORIES: biostudies-literature

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Publications

Optimizing timing and cost-effective use of plasma biomarkers in Alzheimer's disease.

Chang Hsin-I HI Ma Mi-Chia MC Huang Kuo-Lun KL Huang Chung-Gue CG Huang Shu-Hua SH Huang Chi-Wei CW Lin Kun-Ju KJ Chang Chiung-Chih CC

Alzheimer's research & therapy 20250820 1

<h4>Background and objectives</h4>Early and cost-effective identification of amyloid positivity is crucial for Alzheimer's disease (AD) diagnosis. While amyloid PET is the gold standard, plasma biomarkers such as phosphorylated tau 217 (pTau217) provide a potential alternative. This study evaluates the diagnostic accuracy of a combined-panel approach using machine learning models and evaluated the biomarker significance.<h4>Methods</h4>We enrolled 371 participants, including AD (n = 143), non-AD ...[more]

PMID: 40830505

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Project description:Background: Genetic and genomic selection programs require large numbers of phenotypes observed for animals in shared environments. Direct measurements of phenotypes like meat quality, methane emission, and disease susceptibility are difficult and expensive to measure at scale but are critically important to livestock production. Our work leans on our understanding of the “Central Dogma” of molecular genetics to leverage molecular intermediates as cheaply-measured proxies of organism-level phenotypes. The rapidly declining cost of next-generation sequencing presents opportunities for population-level molecular phenotyping. While the cost of whole transcriptome sequencing has declined recently, its required sequencing depth still makes it an expensive choice for wide-scale molecular phenotyping. We aim to optimize 3′ mRNA sequencing (3′ mRNA-Seq) approaches for collecting cost-effective proxy molecular phenotypes for cattle from easy-to-collect tissue samples (i.e., whole blood). We used matched 3′ mRNA-Seq samples for 15 Holstein male calves in a heat stress trail to identify the 1) best library preparation kit (Takara SMART-Seq v4 3′ DE and Lexogen QuantSeq) and 2) optimal sequencing depth (0.5 to 20 million reads/sample) to capture gene expression phenotypes most cost-effectively. Results: Takara SMART-Seq v4 3′ DE outperformed Lexogen QuantSeq libraries across all metrics: number of quality reads, expressed genes, informative genes, differentially expressed genes, and 3′ biased intragenic variants. Serial downsampling analyses identified that as few as 8.0 million reads per sample could effectively capture most of the between-sample variation in gene expression. However, progressively more reads did provide marginal increases in recall across metrics. These 3′ mRNA-Seq reads can also capture animal genotypes that could be used as the basis for downstream imputation. The 10 million read downsampled groups called an average of 104,386 SNPs and 20,131 INDELs, many of which segregate at moderate minor allele frequencies in the population. Conclusion: This work demonstrates that 3′ mRNA-Seq with Takara SMART-Seq v4 3′ DE can provide an incredibly cost-effective (<$25/sample) approach to quantifying molecular phenotypes (gene expression) while discovering sufficient variation for use in genotype imputation. Ongoing work is evaluating the accuracy of imputation and the ability of much larger datasets to predict individual animal phenotypes.

Dataset Information

Optimizing timing and cost-effective use of plasma biomarkers in Alzheimer's disease.

Background and objectives

Methods

Results

Discussion

Publications

Optimizing timing and cost-effective use of plasma biomarkers in Alzheimer's disease.

Similar Datasets

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