Evidence map›Paper›PMID 40781774›Full record

ArticleHGG advances2025

Genotyping TOMM40'523 poly-T polymorphisms using whole-genome sequencing.

Ricardo A Vialle, Lei Yu, Yan Li, Roberto T Raittz, Jose M Farfel, Philip L De Jager, Julie A Schneider, Lisa L Barnes, Shinya Tasaki, David A Bennett

Abstract read
PubMed Full text at PMC Publisher
In one paragraph

Article in HGG advances, 2025. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Not yet cited in PubMed.

0numbers the graph read from it
0cells of the map it votes in
0citing papers in PubMed
–field-weighted citation impact
1 · What the graph read from it

What it found

Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.

The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.

2 · The registry

The trial behind it

Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.

Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.

3 · Its place in the literature

Who cites it

0 citing papers in PubMed.

No citing paper in PubMed yet.

4 · The record

Corrections and comments

5 · Who and what money

Authors and funding

10 authors.

Ricardo A VialleRush Alzheimer's Disease Center, Rush University Medical Center, 1750 West Harrison Street, Chicago, IL 60612, USA; Graduate Program in Bioinformatics, Professional and Technical Education Sector (SEPT), Universidade Federal do Paraná (UFPR), R. Dr. Alcides Vieira Arcoverde 1225, Curitiba, Paraná 81520-260, Brazil. Electronic address: ricardo_a_vialle@rush.edu.
Lei YuRush Alzheimer's Disease Center, Rush University Medical Center, 1750 West Harrison Street, Chicago, IL 60612, USA.
Yan LiRush Alzheimer's Disease Center, Rush University Medical Center, 1750 West Harrison Street, Chicago, IL 60612, USA.
Roberto T RaittzGraduate Program in Bioinformatics, Professional and Technical Education Sector (SEPT), Universidade Federal do Paraná (UFPR), R. Dr. Alcides Vieira Arcoverde 1225, Curitiba, Paraná 81520-260, Brazil; Department of Biochemistry, Universidade Federal do Paraná (UFPR), Avenida Coronel Francisco H. dos Santos, 100, Curitiba, Paraná 81531-980, Brazil.
Jose M FarfelRush Alzheimer's Disease Center, Rush University Medical Center, 1750 West Harrison Street, Chicago, IL 60612, USA.
Philip L De JagerCenter for Translational and Computational Neuroimmunology, Department of Neurology, Columbia University Irving Medical Center, 630 West 168th Street, PH 19, New York, NY 10032, USA.
Julie A SchneiderRush Alzheimer's Disease Center, Rush University Medical Center, 1750 West Harrison Street, Chicago, IL 60612, USA.
Lisa L BarnesRush Alzheimer's Disease Center, Rush University Medical Center, 1750 West Harrison Street, Chicago, IL 60612, USA.
Shinya TasakiRush Alzheimer's Disease Center, Rush University Medical Center, 1750 West Harrison Street, Chicago, IL 60612, USA.
David A BennettRush Alzheimer's Disease Center, Rush University Medical Center, 1750 West Harrison Street, Chicago, IL 60612, USA.

Funding

Whole Genome Sequencing and Admixture Analyses of Neuropathologic Traits in White, Black, and Latino Americans and BraziliansR01AG075927 · NIA · RUSH UNIVERSITY MEDICAL CENTER · PI DAVID ALAN BENNETT · 2023 to 2026
$14.9M
NIA NIH HHS R01 AG075927
6 · The paper itself

Abstract

The TOMM40'523 poly-T repeat polymorphism (rs10524523) has been associated with cognitive decline and Alzheimer's disease (AD) progression. Challenges in processing whole-genome sequencing (WGS) data traditionally require additional PCR and targeted sequencing assays to genotype these polymorphisms. We introduce a computational pipeline that integrates multiple short tandem repeat (STR) detection tools in an ensemble machine learning model using XGBoost. Using a sample of 1,202 participants from 4 cohort studies, we benchmarked our method against PCR-based measures. Our ensemble model outperformed individual STR tools, improving repeat length estimation accuracy (R

Indexed as

Genotyping TechniquesMembrane Transport ProteinsPolymorphism, Single NucleotidePoly TWhole Genome SequencingAlzheimer DiseaseCognitive DysfunctionFemaleGenotypeHumansMaleMitochondrial Precursor Protein Import Complex ProteinsMembrane Transport ProteinsMitochondrial Precursor Protein Import Complex ProteinsPoly TTOMM40 protein, humanAPOEmachine learningTOMM40WGSXGBoost

Identifiers

PMID40781774
PMCPMC12536653

What OpenQuestion holds

Textmetadata
LicenceCC BY-NC-ND
Read underepoch 390

Registered trials

None linked

Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.