OSCR

Genome wide association study meta-analysis of neuropathologic lesions of Alzheimer's disease and related dementias in a multi-site autopsy cohort.

Code ↔ Paper

4 matches between paragraphs of the paper and lines of its authors' code, computed by the harvester (lexical-v1). Click a colored paragraph or line to see its counterpart.

The 4 matches · 2 of them tie a paragraph to a whole file, not to given lines: weak matches, whose lines are not tinted
  1. [1] § Methods › Statistical analyses › Single variant GWAS meta-analysis. ↔ postMETAL_qqMh.R, the whole file · a weak match · score 0.63 · genomic inflation factor, Manhattan, Mb, QQ, meta, APOE
  2. [2] § Methods › Statistical analyses › Single variant GWAS meta-analysis. ↔ postMETAL_qqMh.R, the whole file · a weak match · score 0.53 · genomic inflation factors, QQ, METAL, APOE, model, GWAS
  3. [3] § Results › GWS associations with ADNC ↔ Phenotype Harmonization (PHC)/ACT_Harmonization_Script_20230123.R, lines 137–176 · score 0.53 · ADNC variables, ABC score, Braak stage, NIA
  4. [4] § Results › GWS associations with ADNC ↔ Phenotype Harmonization (PHC)/NACC_Freeze2_Harmonization_Script_20231020.R, lines 166–207 · score 0.53 · ADNC variables, ABC score, Braak stage, NIA

Paper

Loaded from Europe PMC by your browser, not stored by OSCR: doi.org · Europe PMC

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The authors' code

R · 29 lines · 1.6 KB · MIT · 2 matches

  1. library("data.table")
  2. library("R.utils")
  3. library("GWASTools")
  4. library("dplyr")
  5. Args <- commandArgs(TRUE)
  6. resloc <- as.character(Args[2])
  7. phenoname <- as.character(Args[1])
  8. # Running the loop
  9. for(method in c("M1","M2")){
  10. for(pn in phenoname){
  11. res <- fread(paste0("/hihg/studies/AD/analysis/projects/ADGC/Neuropath/GWAS_Results/",resloc,"/",pn,"/METAL/METAL_",pn,"_chrall.",method,".final.tbl"),header=TRUE,sep="\t")
  12. res <- res %>% mutate(CHR = as.numeric(gsub("chr","",CHROM)), P_value = as.numeric(P_value)) %>% arrange(CHR,POS)
  13. res <- res[!is.na(res$P_value),]
  14. medGIF <- median(qchisq(1-res[!(res$CHROM %in% "chr19" & (res$POS >= 44*10^6 | res$POS <= 46*10^6)),]$P_value,1))/qchisq(0.5,1)
  15. fwrite(as.data.frame(t(c(signif(medGIF,digits=4),method))),paste0("/hihg/studies/AD/analysis/projects/ADGC/Neuropath/GWAS_Results/",resloc,"/",pn,"/METAL/GenomicInflationFactor.",method,".txt"),append=TRUE,row.names=FALSE,col.names=FALSE)
  16. png(paste0("/hihg/studies/AD/analysis/projects/ADGC/Neuropath/GWAS_Results/",resloc,"/",pn,"/METAL/",pn,".",method,".qq.png"))
  17. qqPlot(res[!(res$CHROM %in% "chr19" & (res$POS >= 44*10^6 | res$POS <= 46*10^6)),]$P_value)+title(paste0("QQ plot for phenotype ",pn,"\n Dataset: Meta-Analyzed - model ",method))+text(4,0.5,bquote(lambda== .(signif(medGIF,digits=4))))+text(4,0,"note: APOE (chr19:44Mb-46Mb) excluded",cex=0.75)
  18. dev.off()
  19. png(paste0("/hihg/studies/AD/analysis/projects/ADGC/Neuropath/GWAS_Results/",resloc,"/",pn,"/METAL/",pn,".",method,".Mh.png"))
  20. manhattanPlot(res$P_value,chromosome=res$CHROM)+title(paste0("Manhattan plot for ",pn,"\n Dataset: Meta-Analyzed - model ",method))
  21. dev.off()
  22. }
  23. }

postMETAL_qqMh.R at commit aaac6db, under MIT · at the source

Overview

Authors: Brenna Cholerton1, Dana Godrich2, Jeremy Pasteris3, Joe Rivero4, Eden R Martin2,3, Brian W Kunkle2,3, Adam C Naj5,6,7, Kara L Hamilton-Nelson3, Hui Wang5,6, Wan-Ping Lee5,6, Logan Dumitrescu8,9, Timothy J Hohman8,9,10, Richard Mayeux11,12,13,14, Eric B Larson15, Paul K Crane16, C Dirk Keene17, Caitlin S Latimer17, Shubhabrata Mukherjee18, Julia K Kofler19, M Ilyas Kamboh20,21,22
and 11 other authorsDavid A Bennett23, Laura Molina-Porcel24,25, Michael Cuccaro2,3, Margaret A Pericak-Vance2,3, Tatjana Rundek26, William K Scott2,3, Walter Kukull27, Gerard Schellenberg5,6, Alzheimer’s Disease Genetics Consortium, Gary W Beecham4, Thomas J Montine1
27 affiliations
  1. Department of Pathology, Stanford University School of Medicine, Stanford, California, United States of America
  2. Dr. John T Macdonald Foundation Department of Human Genetics, Miller School of Medicine, University of Miami, Miami, Florida, United States of America
  3. John P. Hussman Institute for Human Genomics, Miller School of Medicine, University of Miami, Miami, Florida, United States of America
  4. Department of Biostatistics and Data Science, Wake Forest University School of Medicine, Winston-Salem, North Carolina, United States of America
  5. Department of Pathology and Laboratory Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
  6. Penn Neurodegeneration Genomics Center, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
  7. Department of Biostatistics, Epidemiology, and Informatics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, United States of America
  8. Vanderbilt Memory & Alzheimer’s Center, Vanderbilt University Medical Center, Nashville, Tennessee, United States of America
  9. Vanderbilt Genetics Institute, Vanderbilt University Medical Center, Nashville, Tennessee, United States of America
  10. Department of Neurology, Vanderbilt University Medical Center, Nashville, Tennessee, United States of America
  11. Taub Institute on Alzheimer’s Disease and the Aging Brain, Department of Neurology, Columbia University, New York City, New York, United States of America
  12. Gertrude H. Sergievsky Center, Columbia University, New York City, New York, United States of America
  13. Department of Neurology, College of Physicians and Surgeons, Columbia University and the New York Presbyterian Hospital, New York City, New York, United States of America
  14. Department of Epidemiology, Mailman School of Public Health, Columbia University, New York City, New York, United States of America
  15. Kaiser Permanente Washington Health Research Institute, Seattle, Washington, United States of America
  16. Department of Medicine, Division of General Internal Medicine, University of Washington, Harborview Medical Center, Seattle, Washington, United States of America
  17. Department of Laboratory Medicine and Pathology, University of Washington, Seattle, Washington, United States of America
  18. Division of General Internal Medicine, Department of Medicine, University of Washington, Seattle, United States of America
  19. Department of Pathology, University of Pittsburgh, Pittsburgh, Pennsylvania, United States of America
  20. Department of Human Genetics, University of Pittsburgh School of Public Health, Pittsburgh, Pennsylvania, United States of America
  21. Department of Psychiatry, School of Medicine, University of Pittsburgh, Pittsburgh, Pennsylvania, United States of America
  22. Department of Epidemiology, University of Pittsburgh School of Public Health, Pittsburgh, Pennsylvania, United States of America
  23. Rush Alzheimer’s Disease Center, Rush University Medical Center, Chicago, Illinois, United States of America
  24. Alzheimer’s Disease and Other Cognitive Disorders Unit, Neurology Service, Hospital Clínic, Fundació Recerca Clínic Barcelona (FRCB), Institut d’Investigacions Biomediques August Pi I Sunyer (IDIBAPS), University of Barcelona, Barcelona, Spain
  25. Neurological Tissue Bank of the Biobanc-Hospital Clínic-IDIBAPS, Barcelona, Spain
  26. Department of Neurology, Evelyn F. McKnight Brain Institute, University of Miami Miller School of Medicine, Miami, Florida, United States of America
  27. Department of Epidemiology, University of Washington, Seattle, Washington, United States of America
Journal: PLoS genetics, volume 22, issue 6, article e1012170
Dates: received 24 July 2025; accepted 18 May 2026; published online 29 June 2026
Type: Research article · Language: English
License: CC BY
Identifiers: DOI 10.1371/journal.pgen.1012170 · PMID 42371968 · PMCID PMC13340787 · OpenAlex W7166556253
Open access: gold, a free copy (OpenAlex)
Status: code verified
Categories: genetics / omics (modality), histology / microscopy (modality), human (organism), Alzheimer's / dementia (population), Parkinson's (population), clinical / translational (subfield)
Methods: Smoothing, state filtering, decompositions, Machine learning, Connectivity
MeSH: Alzheimer Disease*, Dementia*, Genome-Wide Association Study*, Aged, Aged, 80 and over, Apolipoproteins E, Autopsy, Cohort Studies, Female, Genetic Predisposition to Disease, Humans, Linkage Disequilibrium, Male, Parkinson Disease, Polymorphism, Single Nucleotide (* major topic)
Topic: Genetic Associations and Epidemiology (Genetics, Biochemistry, Genetics and Molecular Biology), according to OpenAlex
Funding: National Institute on Aging (AG023651, AG062695, AG010491, AG019085, AG008702, AG015473, AG041797, AG066567, AG016976, AG021547, AG026395, AG032984, AG0064877, AG010161, AG036528, AG007562, AG019757, AG0066468, AG027944, AG041689); NIA NIH HHS (P30 AG066509)
Citations: cited by 2 papers (Europe PMC); 84 references in the paper

Abstract

Understanding the genetic foundations of dementia is critical to unraveling its complex molecular basis. Given that a clinical diagnosis of Alzheimer’s disease (AD) dementia often results from interplay between multiple underlying neuropathologic co-morbidities, previous genome-wide association studies (GWAS) of clinically diagnosed AD are restricted in their ability to translate genetic associations to potential targeted therapeutics. The current study seeks to address these limitations by presenting the largest GWAS to date (n = 12,509) of neuropathologic hallmarks of AD and AD related dementias (ADRDs). We further performed a candidate-variant analysis using loci previously identified in GWAS of clinically diagnosed AD dementia and Parkinson’s disease (PD). Finally, we conducted heritability and genetic correlation analyses using linkage disequilibrium (LD) score regression. We found broad genome-wide significant associations with APOE across AD and ADRDs but not cerebrovascular disease and vascular brain injury. We further identified 12 significant loci across 10 neuropathologic phenotypes, including 5 loci previously implicated in GWAS of clinical AD and ADRDs (variants on BIN1, PICALM/ EED, TMEM106B, GRN, and SNCA/ SNCA-AS1) and 7 novel genome-wide associations (variants on EPHA5, PSMG1, LINC00276, VAPA, LINC00290, DOCK4 and SLAIN2/ SLC10A4). Our analysis of AD and PD clinical candidate variants demonstrated several that were associated with AD neuropathologic change and Lewy body disease, as well as substantial overlap with neuropathologic lesions other than the primary neuropathologic hallmarks of these diseases. Heritability analyses demonstrated heritability that was high for amyloid plaques (78%) relative to prior clinical AD heritability analyses, intermediate for TDP-43 inclusions (41%), and low for remaining AD and ADRD pathologic features. This study underscores the importance of investigating the underlying neuropathologic hallmarks of AD and ADRDs as a step toward refining the translation of genetic associations to biomarker interpretation and development of targeted therapeutics.

Reproduced under the paper's license (CC BY), from the paper cited above.

Repository

Its files are read in the Code ↔ Paper reader above, with 4 matches between paragraphs and lines of code.

beecham-lab/ADRD-Neuropathology-Scripts

License: MIT
State: the link answers, verified on 27 September 2026
Evidence: files inventoried
Commit: aaac6db6e2416623cc48afa88cda1957c938c096, 1 July 2026
Languages: Shell (47), R (12)
Size: 61 files, 59 scripts
Software Heritage: not archived
Found in: “Data Availability”
Holds: README, license file
Not found: CITATION.cff, environment file, tests, continuous integration, documentation
Tools: SAMtools (44 files), data.table (10 files), tidyverse (10 files), BCFtools (2 files), ggplot2 (1 file)
Availability: 1 check, the latest on 27 September 2026: the link answers
  • 27 September 2026: the link answers
61 files

The paper's code and data availability statement is in the Data section.

Tracing map

Proposed by the machine: these links were found in the paper and verified at the source, without human review. The map will receive a Zenodo DOI once one of the paper's authors has validated it with their ORCID.

What the map holds:

  • 1 repository of the authors' code, each at its verified commit, with its license and how the link was found in the paper;
  • 59 scripts, each with its path and the digest of its content;
  • 4 matches between paragraphs of the paper and lines of the code (method lexical-v1);
  • neither the text of the paper nor the code itself.

Its JSON (tracing-map.json) is deposited on Zenodo with its DOI once the map is validated.

Data

No dataset and no data link were found in the paper.

Data Availability

Genotype and phenotype data are available through the contributing cohorts. ROSMAP data can be requested at https://www.radc.rush.edu and https://www.synapse.org. ADGC data can be requested from NIAGADS at https://www.niagads.org/resources/related-projects/alzheimers-disease-genetics-consortium-adgc-collection. NACC neuropathology data can be requested at https://naccdata.org/. ACT data can be requested at https://actagingresearch.org/. Harmonized neuropathology data are available through NIAGADS at https://dss.niagads.org/datasets/ng00067/. IDIBAPS data can be requested at https://www.clinicbarcelona.org/en/idibaps. TGen data can be requested at https://www.tgen.org/. NIA-LOAD data can be requested at https://www.ncbi.nlm.nih.gov/projects/gap/cgi-bin/study.cgi?study_id=phs000168.v2.p2. Analysis-related scripts are available at https://github.com/beecham-lab/ADRD-Neuropathology-Scripts/.

Reproduced under the paper's license (CC BY), from the paper cited above.

Versions

The history of this record: each version stored by the harvester or made by a correction of its authors or of the maintainers of its code, and what changed in its facts. The texts of the paper (its abstract, its availability statements) are not part of it; versions that changed only those are not listed.

Version 1, 27 September 2026: the first record

Recorded: type, language, journal, volume, issue, pages, dates, 31 authors, 15 MeSH terms, 2 funders, 81 references.

Cite

This paper

Cholerton, B., Godrich, D., Pasteris, J., Rivero, J., Martin, E. R., Kunkle, B. W., Naj, A. C., Hamilton-Nelson, K. L., Wang, H., Lee, W.-P., Dumitrescu, L., Hohman, T. J., Mayeux, R., Larson, E. B., Crane, P. K., Keene, C. D., Latimer, C. S., Mukherjee, S., Kofler, J. K., . . . Montine, T. J. (2026). Genome wide association study meta-analysis of neuropathologic lesions of Alzheimer's disease and related dementias in a multi-site autopsy cohort. PLoS genetics, 22(6), e1012170. https://doi.org/10.1371/journal.pgen.1012170

BibTeX

@article{cholerton2026genome,
author = {Cholerton, Brenna and Godrich, Dana and Pasteris, Jeremy and Rivero, Joe and Martin, Eden R and Kunkle, Brian W and Naj, Adam C and Hamilton-Nelson, Kara L and Wang, Hui and Lee, Wan-Ping and Dumitrescu, Logan and Hohman, Timothy J and Mayeux, Richard and Larson, Eric B and Crane, Paul K and Keene, C Dirk and Latimer, Caitlin S and Mukherjee, Shubhabrata and Kofler, Julia K and Kamboh, M Ilyas and Bennett, David A and Molina-Porcel, Laura and Cuccaro, Michael and Pericak-Vance, Margaret A and Rundek, Tatjana and Scott, William K and Kukull, Walter and Schellenberg, Gerard and {Alzheimer’s Disease Genetics Consortium} and Beecham, Gary W and Montine, Thomas J},
title = {{Genome wide association study meta-analysis of neuropathologic lesions of Alzheimer's disease and related dementias in a multi-site autopsy cohort}},
journal = {PLoS genetics},
year = {2026},
month = jun,
volume = {22},
number = {6},
pages = {e1012170},
publisher = {PLOS},
issn = {1553-7390},
doi = {10.1371/journal.pgen.1012170},
url = {https://doi.org/10.1371/journal.pgen.1012170},
pmid = {42371968},
pmcid = {PMC13340787}
}

RIS

TY - JOUR
AU - Cholerton, Brenna
AU - Godrich, Dana
AU - Pasteris, Jeremy
AU - Rivero, Joe
AU - Martin, Eden R
AU - Kunkle, Brian W
AU - Naj, Adam C
AU - Hamilton-Nelson, Kara L
AU - Wang, Hui
AU - Lee, Wan-Ping
AU - Dumitrescu, Logan
AU - Hohman, Timothy J
AU - Mayeux, Richard
AU - Larson, Eric B
AU - Crane, Paul K
AU - Keene, C Dirk
AU - Latimer, Caitlin S
AU - Mukherjee, Shubhabrata
AU - Kofler, Julia K
AU - Kamboh, M Ilyas
AU - Bennett, David A
AU - Molina-Porcel, Laura
AU - Cuccaro, Michael
AU - Pericak-Vance, Margaret A
AU - Rundek, Tatjana
AU - Scott, William K
AU - Kukull, Walter
AU - Schellenberg, Gerard
AU - Alzheimer’s Disease Genetics Consortium
AU - Beecham, Gary W
AU - Montine, Thomas J
TI - Genome wide association study meta-analysis of neuropathologic lesions of Alzheimer's disease and related dementias in a multi-site autopsy cohort
T2 - PLoS genetics
J2 - PLoS Genet
PY - 2026
DA - 2026/06/29
VL - 22
IS - 6
SP - e1012170
SN - 1553-7390
PB - PLOS
DO - 10.1371/journal.pgen.1012170
UR - https://doi.org/10.1371/journal.pgen.1012170
LA - en
ER -

CSL-JSON

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