Evidence map›Paper›PMID 38254182›Full record

ArticleGenome biology2024

PICALO: principal interaction component analysis for the identification of discrete technical, cell-type, and environmental factors that mediate eQTLs.

Martijn Vochteloo, Patrick Deelen, Britt Vink, BIOS Consortium, Ellen A Tsai, Heiko Runz, Sergio Andreu-Sánchez, Jingyuan Fu, Alexandra Zhernakova, Harm-Jan Westra and 1 more

Abstract read
PubMed Full text at PMC Publisher
In one paragraph

Article in Genome biology, 2024. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 3 papers.

0numbers the graph read from it
0cells of the map it votes in
3citing 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

3 citing papers in PubMed.

  1. Article
  2. Review
  3. Methods and Insights from Single-Cell Expression Quantitative Trait Loci.Annual review of genomics and human genetics · 2023
    Review
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

11 authors.

Martijn VochtelooDepartment of Genetics, University Medical Center Groningen, University of Groningen, Groningen, The Netherlands.ORCID 0000-0002-6385-0550
Patrick DeelenDepartment of Genetics, University Medical Center Groningen, University of Groningen, Groningen, The Netherlands.ORCID 0000-0002-5654-3966
Britt VinkDepartment of Genetics, University Medical Center Groningen, University of Groningen, Groningen, The Netherlands.
BIOS Consortium
Ellen A TsaiTranslational Sciences, Research and Development, Biogen, Cambridge, MA, USA.ORCID 0000-0002-5625-1189
Heiko RunzTranslational Sciences, Research and Development, Biogen, Cambridge, MA, USA.ORCID 0000-0002-2133-7345
Sergio Andreu-SánchezDepartment of Genetics, University Medical Center Groningen, University of Groningen, Groningen, The Netherlands.ORCID 0000-0002-3503-9971
Jingyuan FuDepartment of Genetics, University Medical Center Groningen, University of Groningen, Groningen, The Netherlands.ORCID 0000-0001-5578-1236
Alexandra ZhernakovaDepartment of Genetics, University Medical Center Groningen, University of Groningen, Groningen, The Netherlands.ORCID 0000-0002-4574-0841
Harm-Jan Westra *Department of Genetics, University Medical Center Groningen, University of Groningen, Groningen, The Netherlands. h.j.westra@umcg.nl.ORCID 0000-0001-7038-567X
Lude Franke *Department of Genetics, University Medical Center Groningen, University of Groningen, Groningen, The Netherlands. l.h.franke@umcg.nl.ORCID 0000-0002-5159-8802

Funding

Vascular Structure and Function in Cognitive AgingP01AG003949 · NIA · YESHIVA UNIVERSITY · PI Richard B. LIPTON · 1985 to 2026
$73.9M
Alzheimer's Disease Genetics ConsortiumU01AG032984 · NIA · UNIVERSITY OF PENNSYLVANIA · PI SCHELLENBERG, GERARD DAVID · 2009 to 2024
$60.4M
SUPPLEMENT TO ALZHEIMERS DISEASE PATIENT REGISTRYU01AG006786 · NIA · MAYO CLINIC ROCHESTER · PI GRAFF-RADFORD, JONATHAN, JACK, CLIFFORD R. · 1986 to 2023
$49.6M
SUPPLEMENT TO RUSH ALZHEIMERS DISEASE CENTER COREP30AG010161 · NIA · RUSH UNIVERSITY MEDICAL CENTER · PI BENNETT, DAVID ALAN · 1991 to 2020
$49.1M
EPIDEMIOLOGY OF NEURAL RESERVE AND NEUROBIOLOGY IN AGINGR01AG017917 · NIA · RUSH UNIVERSITY MEDICAL CENTER · PI BENNETT, DAVID ALAN · 2001 to 2023
$43.3M
VESICULAR LOCALIZATION AND FUNCTION OF PRESENILIN 1 FRAGMENTP50AG005138 · NIA · MOUNT SINAI SCHOOL OF MEDICINE OF NYU · PI GROSSMAN, HILLEL · 1985 to 2019
$37.9M
THE PGRN/TDP-43 AXIS IN ALZHEIMER?S DISEASE AND NEURODEGENERATIONP50AG016574 · NIA · MAYO CLINIC ROCHESTER · PI PETERSEN, RONALD C · 1999 to 2018
$36.9M
Research Education ComponentP30AG019610 · NIA · SUN HEALTH RESEARCH INSTITUTE · PI REIMAN, ERIC MICHAEL · 2001 to 2020
$32.5M
Research Education ComponentP30AG072980 · NIA · BANNER HEALTH · PI ALIREZA ATRI · 2021 to 2026
$24.9M
Integrating the exposome and methylome to inform brain molecular changes in ADRD across established diverse cohorts.U01AG046139 · NIA · UNIVERSITY OF FLORIDA · PI ERTEKIN-TANER, NILUFER, FUNK, CORY · 2013 to 2022
$24.6M
University of Kentucky Alzheimer's Disease Research CenterP30AG072946 · NIA · UNIVERSITY OF KENTUCKY · PI LINDA J VAN ELDIK · 2021 to 2026
$23.5M
RISK FACTORS, PATHOLOGY, AND CLINICAL EXPRESSIONS OF ADR01AG015819 · NIA · RUSH UNIVERSITY MEDICAL CENTER · PI BENNETT, DAVID ALAN · 1998 to 2024
$21.4M
CCR NIH HHS HHSN261200800001CIntramural NIH HHS Z01 AG000949Intramural NIH HHS Z01 ES101986Intramural NIH HHS ZIA NS003154NCI NIH HHS HHSN261200800001ENHLBI NIH HHS HHSN268201000029CNIA NIH HHS P01 AG002219NIA NIH HHS P01 AG003949NIA NIH HHS P01 AG017216NIA NIH HHS P30 AG010161NIA NIH HHS P30 AG019610NIA NIH HHS P30 AG072946NIA NIH HHS P30 AG072980NIA NIH HHS P50 AG005138NIA NIH HHS P50 AG016574NIA NIH HHS P50 AG025711NIA NIH HHS R01 AG015819NIA NIH HHS R01 AG017917NIA NIH HHS R01 AG018023NIA NIH HHS R01 AG030146NIA NIH HHS R01 AG032990NIA NIH HHS R01 AG036836NIA NIH HHS U01 AG006786NIA NIH HHS U01 AG032984NIA NIH HHS U01 AG046139NIA NIH HHS U01 AG046152NIDA NIH HHS HHSN271201300031CNIDA NIH HHS R01 DA006227NIMH NIH HHS P50 MH066392NIMH NIH HHS P50 MH084053NIMH NIH HHS P50 MH106934NIMH NIH HHS R01 MH075916NIMH NIH HHS R01 MH080405NIMH NIH HHS R01 MH085542NIMH NIH HHS R01 MH090936NIMH NIH HHS R01 MH090937NIMH NIH HHS R01 MH090941NIMH NIH HHS R01 MH090948NIMH NIH HHS R01 MH090951NIMH NIH HHS R01 MH093725NIMH NIH HHS R01 MH094714NIMH NIH HHS R01 MH097276NIMH NIH HHS R01 MH101782NIMH NIH HHS R01 MH101810NIMH NIH HHS R01 MH101814NIMH NIH HHS R01 MH101819NIMH NIH HHS R01 MH101820NIMH NIH HHS R01 MH101822NIMH NIH HHS R01 MH101825NIMH NIH HHS R01 MH105472NIMH NIH HHS R01 MH105898NIMH NIH HHS R01 MH109677NIMH NIH HHS R01 MH109897NIMH NIH HHS R01 MH110921NIMH NIH HHS R21 MH102791NIMH NIH HHS R21 MH103877NIMH NIH HHS R21 MH105881NIMH NIH HHS R37 MH057881NIMH NIH HHS U01 MH103339NIMH NIH HHS U01 MH103340NIMH NIH HHS U01 MH103346NIMH NIH HHS U01 MH103365NIMH NIH HHS U01 MH103392NINDS NIH HHS R01 NS080820NINDS NIH HHS U24 NS072026
6 · The paper itself

Abstract

Expression quantitative trait loci (eQTL) offer insights into the regulatory mechanisms of trait-associated variants, but their effects often rely on contexts that are unknown or unmeasured. We introduce PICALO, a method for hidden variable inference of eQTL contexts. PICALO identifies and disentangles technical from biological context in heterogeneous blood and brain bulk eQTL datasets. These contexts are biologically informative and reproducible, outperforming cell counts or expression-based principal components. Furthermore, we show that RNA quality and cell type proportions interact with thousands of eQTLs. Knowledge of hidden eQTL contexts may aid in the inference of functional mechanisms underlying disease variants.

Indexed as

BrainQuantitative Trait LociCell CountPhenotypePrincipal Component AnalysisCell typeContexteQTLsHidden variable inferenceInteraction eQTLs

Identifiers

PMID38254182
PMCPMC10802033

What Socratic holds

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Registered trials

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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 Socratic graph.