Evidence map›Paper›PMID 31040117›Full record

ArticleGenetics2019

Examining the Impact of Imputation Errors on Fine-Mapping Using DNA Methylation QTL as a Model Trait.

V Kartik Chundru, Riccardo E Marioni, James G D Prendergast, Costanza L Vallerga, Tian Lin, Allan J Beveridge, SGPD Consortium, Jacob Gratten, David A Hume, Ian J Deary and 3 more

Open access · bronzeAbstract read
PubMed Full text at PMC Publisher
In one paragraph

Article in Genetics, 2019. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 1 paper.

0numbers the graph read from it
0cells of the map it votes in
1citing papers in PubMed
0.5field-weighted citation impact, top 27% of its field
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

1 citing paper in PubMed, 4 citations in OpenAlex.

  1. Article
4 · The record

Corrections and comments

PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.

5 · Who and what money

Authors and funding

13 authors at 5 institutions in 2 countries.

V Kartik ChundruInstitute for Molecular Bioscience, The University of Queensland, Brisbane, Queensland 4072, Australia v.chundru@uq.edu.au.ORCID 0000-0002-6348-5565
Riccardo E MarioniCentre for Cognitive Ageing and Cognitive Epidemiology, Department of Psychology, University of Edinburgh, EH8 9JZ, United Kingdom.ORCID 0000-0003-4430-4260
James G D PrendergastThe Roslin Institute, University of Edinburgh, Midlothian EH25 9RG, United Kingdom.ORCID 0000-0001-8916-018X
Costanza L VallergaInstitute for Molecular Bioscience, The University of Queensland, Brisbane, Queensland 4072, Australia.ORCID 0000-0001-9493-6800
Tian LinInstitute for Molecular Bioscience, The University of Queensland, Brisbane, Queensland 4072, Australia.
Allan J BeveridgeGlasgow Polyomics, Wolfson Wohl Cancer Research Centre, University of Glasgow, Bearsden G61 1QH, United Kingdom.
SGPD Consortium
Jacob GrattenInstitute for Molecular Bioscience, The University of Queensland, Brisbane, Queensland 4072, Australia.ORCID 0000-0003-1293-409X
David A HumeMater Research Institute, The University of Queensland, Brisbane, Queensland 4102, Australia.ORCID 0000-0002-2615-1478
Ian J DearyCentre for Cognitive Ageing and Cognitive Epidemiology, Department of Psychology, University of Edinburgh, EH8 9JZ, United Kingdom.ORCID 0000-0002-1733-263X
Naomi R WrayInstitute for Molecular Bioscience, The University of Queensland, Brisbane, Queensland 4072, Australia.ORCID 0000-0001-7421-3357
Peter M VisscherInstitute for Molecular Bioscience, The University of Queensland, Brisbane, Queensland 4072, Australia.ORCID 0000-0002-2143-8760
Allan F McRaeORCID 0000-0001-5286-5485
University of Queensland · AUUniversity of Edinburgh · GBMater Research · AURoslin Institute · GBUniversity of Glasgow · GB

Funding

Biotechnology and Biological Sciences Research Council BB/F019394/1Chief Scientist OfficeMedical Research Council G0700704Medical Research Council MR/K026992/1Medical Research Council MR/M01311/1Wellcome Trust
6 · The paper itself

Abstract

Genetic variants disrupting DNA methylation at CpG dinucleotides (CpG-SNP) provide a set of known causal variants to serve as models to test fine-mapping methodology. We use 1716 CpG-SNPs to test three fine-mapping approaches (Bayesian imputation-based association mapping, Bayesian sparse linear mixed model, and the J-test), assessing the impact of imputation errors and the choice of reference panel by using both whole-genome sequence (WGS), and genotype array data on the same individuals (

Indexed as

DNA MethylationQuantitative Trait LociCpG IslandsGenome-Wide Association StudyHumansPolymorphism, Single NucleotideQuantitative Trait, HeritableReference StandardsReproducibility of ResultsWhole Genome SequencingCpG-SNPsDNA-methylationfine-mappingimputation

Identifiers

PMID31040117
PMCPMC6614908
OpenAlexW2943738111

What OpenQuestion holds

Textmetadata
LicenceCC BY
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.