Evidence map›Paper›PMID 42155441›Full record

ArticleCell genomics2026

FastGxC: Fast and powerful context-specific eQTL mapping in bulk and single-cell data.

Lena Krockenberger, Andrew Lu, Mike Thompson, Lise A Tucker, Cuining Liu, M Grace Gordon, Amanda Ramste, Ivan Carcamo-Orive, Joshua W Knowles, Andy Dahl and 3 more

Abstract read
PubMed Full text at PMC Publisher
In one paragraph

Article in Cell genomics, 2026. 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. Review
  2. Article
  3. 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

13 authors.

Lena KrockenbergerBioinformatics Interdepartmental Graduate Program, University of California, Los Angeles, Los Angeles, CA 90095, USA; Department of Pathology and Laboratory Medicine, University of California, Los Angeles, Los Angeles, CA 90095, USA.
Andrew LuUCLA-Caltech Medical Scientist Training Program, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA 90095, USA.
Mike ThompsonSystems and Synthetic Biology, Centre for Genomic Regulation, The Barcelona Institute for Science and Technology (BIST), 08003 Barcelona, Spain.
Lise A TuckerDepartment of Pathology and Laboratory Medicine, University of California, Los Angeles, Los Angeles, CA 90095, USA.
Cuining LiuBioinformatics Interdepartmental Graduate Program, University of California, Los Angeles, Los Angeles, CA 90095, USA; Department of Human Genetics, University of California, Los Angeles, Los Angeles, CA 90095, USA.
M Grace GordonBiological and Medical Informatics Graduate Program, University of California, San Francisco, San Francisco, CA 94143, USA.
Amanda RamsteInstitute for Molecular Medicine Finland (FIMM), HiLIFE, University of Helsinki, 00290 Helsinki, Finland; Division of Cardiovascular Medicine, Cardiovascular Institute, Diabetes Research Center, Stanford University School of Medicine, Stanford, CA 94305, USA.
Ivan Carcamo-OriveDepartment of Endocrinology, Metabolism, Nutrition, and Kidney Disease, Biobizkaia Health Research Institute, 48903 Barakaldo, Spain; IKERBASQUE, Basque Foundation for Science, 48009 Bilbao, Spain.
Joshua W KnowlesDivision of Cardiovascular Medicine, Cardiovascular Institute, Diabetes Research Center, Stanford University School of Medicine, Stanford, CA 94305, USA.
Andy DahlSection of Genetic Medicine, University of Chicago, Chicago, IL 60637, USA.
Chun Jimmie YeDivision of Rheumatology, Department of Medicine, University of California, San Francisco, San Francisco, CA 94143, USA.
Noah ZaitlenDepartment of Human Genetics, University of California, Los Angeles, Los Angeles, CA 90095, USA; Department of Computational Medicine, University of California, Los Angeles, Los Angeles, CA 90095, USA; Department of Neurology, University of California, Los Angeles, Los Angeles, CA 90095, USA.
Brunilda BalliuDepartment of Pathology and Laboratory Medicine, University of California, Los Angeles, Los Angeles, CA 90095, USA; Department of Computational Medicine, University of California, Los Angeles, Los Angeles, CA 90095, USA; Department of Biostatistics, University of California, Los Angeles, Los Angeles, CA 90095, USA. Electronic address: bballiu@ucla.edu.

Funding

Stanford Islet Research CoreP30DK116074 · NIDDK · STANFORD UNIVERSITY · PI Seung K Kim · 2017 to 2026
$19.5M
Leveraging genetic variation to dissect gene regulatory networks of reprogramming to pluripotencyU01HG012079 · NHGRI · UNIVERSITY OF CALIFORNIA LOS ANGELES · PI Chongyuan Luo, Kathrin Plath · 2021 to 2026
$6.9M
Methods for Genome-wide Association Studies in Admixed PopulationsR01HG006399 · NHGRI · HARVARD UNIVERSITY D/B/A HARVARD SCHOOL OF PUBLIC HEALTH · PI PRICE, ALKES L · 2011 to 2024
$6.3M
Optimizing imputation for diverse populations in a distributed frameworkU01HG009080 · NHGRI · STANFORD UNIVERSITY · PI KENNY, EIMEAR ELIZABETH · 2016 to 2020
$5.2M
Mapping gene-by-environment interactions using multiplexed single cell RNA-sequencingR01HG011239 · NHGRI · UNIVERSITY OF CALIFORNIA, SAN FRANCISCO · PI YE, CHUN JIMMIE · 2020 to 2023
$4.1M
SINGLE-CELL MULTI-OMIC APPROACHES TO MECHANISTICALLY CHARACTERIZE PSYCHIATRIC DISORDER RISK LOCI IN THE HUMAN BRAINR01MH125252 · NIMH · UNIVERSITY OF CALIFORNIA LOS ANGELES · PI LUO, CHONGYUAN · 2021 to 2025
$3.7M
Improved methods for inference of genotype-specific response to environmental toxinsR01ES029929 · NIEHS · PRINCETON UNIVERSITY · PI AYROLES, JULIEN, CLARK, ANDREW G · 2019 to 2023
$3.6M
Genetic regulation and immunological function of ERAP2 haplotypesR01AI136972 · NIAID · UNIVERSITY OF CALIFORNIA, SAN FRANCISCO · PI YE, CHUN JIMMIE · 2018 to 2022
$3.5M
(PQ3) A functional genomic approach to identification and interpretation of germline-tumor genetic interactionsR01CA227237 · NCI · DANA-FARBER CANCER INST · PI GUSEV, ALEXANDER, ZAITLEN, NOAH A · 2018 to 2022
$3.5M
Characterization of novel insulin resistance genes by gene editing, high-throughput phenotyping and in vivo studiesR01DK120565 · NIDDK · STANFORD UNIVERSITY · PI KNOWLES, JOSHUA WILEY · 2019 to 2023
$3.2M
Genomic Approaches to Population Health in Multi-Ethnic Hospital SystemsR01HG011345 · NHGRI · UNIVERSITY OF COLORADO DENVER · PI ARBOLEDA, VALERIE A, GIGNOUX, CHRISTOPHER R · 2020 to 2023
$3.1M
Epigenomics of asthma risk factors and clinical subtypes in minority childrenR01HL155024 · NHLBI · UNIVERSITY OF CALIFORNIA, SAN FRANCISCO · PI BORRELL, LUISA N, ZAITLEN, NOAH A · 2021 to 2024
$2.9M
NCI NIH HHS R01 CA227237NHGRI NIH HHS R01 HG006399NHGRI NIH HHS R01 HG011239NHGRI NIH HHS R01 HG011345NHGRI NIH HHS U01 HG009080NHGRI NIH HHS U01 HG012079NHLBI NIH HHS R01 HL155024NIAID NIH HHS R01 AI136972NIAMS NIH HHS R01 AR071522NIDDK NIH HHS P30 DK116074NIDDK NIH HHS R01 DK106236NIDDK NIH HHS R01 DK116750NIDDK NIH HHS R01 DK120565NIDDK NIH HHS R01 DK132775NIDDK NIH HHS R01 DK137889NIEHS NIH HHS R01 ES029929NIGMS NIH HHS R35 GM133531NIMH NIH HHS R01 MH122688NIMH NIH HHS R01 MH125252
6 · The paper itself

Abstract

Context-specific expression quantitative trait loci (eQTLs) mediate genetic risk for complex diseases, but current methods limit their characterization and interpretation. We introduce FastGxC, a method for efficiently mapping context-specific eQTLs by leveraging correlation structure in multi-tissue bulk and single-cell RNA sequencing studies. In simulations, FastGxC is nine times more powerful and 10

Indexed as

Chromosome MappingQuantitative Trait LociSequence Analysis, RNASingle-Cell Gene Expression AnalysisHumansLeukocytes, Mononuclearcomplex traitscontext-specific eQTLsgenotype-by-context interactionsGxCregulatory variationsingle-cell RNA-seq

Identifiers

PMID42155441
PMCPMC13261669

What OpenQuestion holds

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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.