Evidence map›Paper›PMID 40291654›Full record

ArticlebioRxiv : the preprint server for biology2025

Polymorphic tandem repeats influence cell type-specific gene expression across the human immune landscape.

Hope A Tanudisastro, Anna S E Cuomo, Ben Weisburd, Matthew Welland, Eleanor Spenceley, Michael Franklin, Angli Xue, Blake Bowen, Kristof Wing, Owen Tang and 41 more

Abstract readPreprint
PubMed Full text at PMC Publisher
In one paragraph

Article in bioRxiv : the preprint server for biology, 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

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

51 authors.

Hope A TanudisastroCentre for Population Genomics, Garvan Institute of Medical Research, and UNSW Sydney, Sydney, NSW, Australia.ORCID 0000-0002-4561-305X
Anna S E CuomoCentre for Population Genomics, Garvan Institute of Medical Research, and UNSW Sydney, Sydney, NSW, Australia.ORCID 0000-0001-5168-6979
Ben WeisburdProgram in Medical and Population Genetics, Broad Institute of MIT and Harvard, Cambridge, MA, USA.ORCID 0000-0001-9898-9109
Matthew WellandCentre for Population Genomics, Garvan Institute of Medical Research, and UNSW Sydney, Sydney, NSW, Australia.
Eleanor SpenceleyFaculty of Medicine and Health, University of New South Wales, Sydney, NSW, Australia.
Michael FranklinCentre for Population Genomics, Garvan Institute of Medical Research, and UNSW Sydney, Sydney, NSW, Australia.
Angli XueFaculty of Medicine and Health, University of New South Wales, Sydney, NSW, Australia.ORCID 0000-0002-0285-0426
Blake BowenFaculty of Medicine and Health, University of New South Wales, Sydney, NSW, Australia.
Kristof WingMenzies Institute for Medical Research, University of Tasmania, Hobart, TAS, Australia.ORCID 0000-0002-7136-9484
Owen TangFaculty of Medicine and Health, University of Sydney, Sydney, NSW, Australia.
Michael GrayFaculty of Medicine and Health, University of Sydney, Sydney, NSW, Australia.
Andre L M ReisFaculty of Medicine and Health, University of New South Wales, Sydney, NSW, Australia.
Jonathan MargoliashDepartment of Medicine, University of California San Diego, CA, USA.ORCID 0000-0001-7292-8076
Nehir E KurtasMassachusetts General Hospital, Boston, MA, USA.ORCID 0000-0001-8498-3400
Jeffrey M PullinMRC Biostatistics Unit, University of Cambridge, UK.ORCID 0000-0003-3651-5471
Arthur S LeeMassachusetts General Hospital, Boston, MA, USA.ORCID 0000-0002-4513-4630
Harrison BrandMassachusetts General Hospital, Boston, MA, USA.
Michael HarperCentre for Population Genomics, Garvan Institute of Medical Research, and UNSW Sydney, Sydney, NSW, Australia.
Katalina BobowikCentre for Population Genomics, Garvan Institute of Medical Research, and UNSW Sydney, Sydney, NSW, Australia.ORCID 0000-0002-7030-3969
Michael SilkCentre for Population Genomics, Garvan Institute of Medical Research, and UNSW Sydney, Sydney, NSW, Australia.ORCID 0000-0001-5855-8750
John MarshallCentre for Population Genomics, Garvan Institute of Medical Research, and UNSW Sydney, Sydney, NSW, Australia.
Vivian BakirisCentre for Population Genomics, Garvan Institute of Medical Research, and UNSW Sydney, Sydney, NSW, Australia.
Bindu Swapna MadalaCentre for Population Genomics, Garvan Institute of Medical Research, and UNSW Sydney, Sydney, NSW, Australia.
Caitlin UrenCentre for Population Genomics, Garvan Institute of Medical Research, and UNSW Sydney, Sydney, NSW, Australia.
Caitlin BartieFaculty of Medicine and Health, University of New South Wales, Sydney, NSW, Australia.
Anne SenabouthFaculty of Medicine and Health, University of New South Wales, Sydney, NSW, Australia.ORCID 0000-0002-8798-9821
Harriet DashnowDepartment of Biomedical Informatics, University of Colorado Anschutz Medical Campus, Aurora, CO, USA.ORCID 0000-0001-8433-6270
Liam FearnleyPopulation Health and Immunity Division, The Walter and Eliza Hall Institute of Medical Research, Parkville, VIC 3052, Australia.ORCID 0000-0003-2198-5411
Alejandro Martin-TrujilloDepartment of Genetics and Genomics Sciences and Minidich Child Health and Development Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA.
Egor DolzhenkoPacific Biosciences of California, Menlo Park, CA, USA.ORCID 0000-0002-3296-0677
Zhen QiaoFaculty of Medicine and Health, University of New South Wales, Sydney, NSW, Australia.ORCID 0000-0002-4401-774X
Stuart M GrieveImaging and Phenotyping Laboratory, Charles Perkins Centre, Faculty of Medicine and Health, The University of Sydney, Australia.
Tung NguyenFaculty of Medicine and Health, University of Sydney, Sydney, NSW, Australia.
Eyal Ben-DavidIllumina Artificial Intelligence Laboratory, Illumina, San Diego, CA, USA.
Ling ChenIllumina Artificial Intelligence Laboratory, Illumina, San Diego, CA, USA.
Kyle Kai-How FarhIllumina Artificial Intelligence Laboratory, Illumina, San Diego, CA, USA.ORCID 0000-0001-6947-8537
Michael TalkowskiMassachusetts General Hospital, Boston, MA, USA.ORCID 0000-0003-2889-0992
Stephen I AlexanderFaculty of Medicine and Health, University of Sydney, Sydney, NSW, Australia.ORCID 0000-0002-3609-4446
Owen M SiggsFaculty of Medicine and Health, University of New South Wales, Sydney, NSW, Australia.ORCID 0000-0003-2840-4851
Leonhard GruenschlossCentre for Population Genomics, Garvan Institute of Medical Research, and UNSW Sydney, Sydney, NSW, Australia.
Hannah R NicholasCentre for Population Genomics, Garvan Institute of Medical Research, and UNSW Sydney, Sydney, NSW, Australia.ORCID 0000-0002-2239-9249
Jennifer PiscionereCentre for Population Genomics, Garvan Institute of Medical Research, and UNSW Sydney, Sydney, NSW, Australia.ORCID 0000-0002-1091-8734
Cas SimonsCentre for Population Genomics, Garvan Institute of Medical Research, and UNSW Sydney, Sydney, NSW, Australia.ORCID 0000-0003-3147-8042
Chris WallaceMRC Biostatistics Unit, University of Cambridge, UK.ORCID 0000-0001-9755-1703
Melissa GymrekDepartment of Medicine, University of California San Diego, CA, USA.ORCID 0000-0002-6086-3903
Ira W DevesonFaculty of Medicine and Health, University of New South Wales, Sydney, NSW, Australia.ORCID 0000-0003-3861-0472
Alex W HewittMenzies Institute for Medical Research, University of Tasmania, Hobart, TAS, Australia.ORCID 0000-0002-5123-5999
Gemma A FigtreeFaculty of Medicine and Health, University of Sydney, Sydney, NSW, Australia.ORCID 0000-0002-5080-6083
Katrina M de LangeCentre for Population Genomics, Garvan Institute of Medical Research, and UNSW Sydney, Sydney, NSW, Australia.
Joseph E PowellFaculty of Medicine and Health, University of New South Wales, Sydney, NSW, Australia.ORCID 0000-0002-5070-4124
Daniel G MacArthurCentre for Population Genomics, Garvan Institute of Medical Research, and UNSW Sydney, Sydney, NSW, Australia.ORCID 0000-0002-5771-2290

Funding

Systematic characterization of tandem repeat variants contributing to complex traitsR01HG010885 · NHGRI · UNIVERSITY OF CALIFORNIA, SAN DIEGO · PI Alon Goren, Melissa Gymrek · 2020 to 2026
$4.8M
Revealing new short tandem repeat variation in the human population across sequencing technologies: towards rare disease diagnosis and discoveryR00HG012796 · NHGRI · UNIVERSITY OF COLORADO DENVER · PI Harriet Dashnow · 2024 to 2026
$747k
NHGRI NIH HHS R00 HG012796NHGRI NIH HHS R01 HG010885
6 · The paper itself

Abstract

Tandem repeats (TRs) - highly polymorphic, repetitive sequences dispersed across the human genome - are crucial regulators of gene expression and diverse biological processes, but have remained underexplored relative to other classes of genetic variation due to historical challenges in their accurate calling and analysis. Here, we leverage whole genome and single-cell RNA sequencing from over 5.4 million blood-derived cells from 1,925 individuals to explore the impact of variation in over 1.7 million polymorphic TR loci on blood cell type-specific gene expression. We identify over 62,000 single-cell expression quantitative trait TR loci (sc-eTRs), 16.6% of which are specific to one of 28 distinct immune cell types. Further fine-mapping uncovers 4,283 sc-eTRs as candidate causal drivers of gene expression in 13.6% of genes tested genome-wide. We show through colocalization that TRs are likely mediators of genetic associations with immune-mediated and hematological traits in over 700 genes, and further identify novel TRs warranting investigation in rare disease cohorts. TRs are critical, yet long-overlooked, contributors to cell type-specific gene expression, with implications for understanding rare disease pathogenesis and the genetic architecture of complex traits.

Identifiers

PMID40291654
PMCPMC12026411

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LicenceCC BY
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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 OpenQuestion graph.