Evidence map›Paper›PMID 34425859›Full record

ArticleGenome biology2021

Integrative approach identifies SLC6A20 and CXCR6 as putative causal genes for the COVID-19 GWAS signal in the 3p21.31 locus.

Silva Kasela, Zharko Daniloski, Sailalitha Bollepalli, Tristan X Jordan, Benjamin R tenOever, Neville E Sanjana, Tuuli Lappalainen

Open access · goldAbstract read
In one paragraph

Article in Genome biology, 2021. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 34 papers, 2 of them syntheses that pooled it.

0numbers the graph read from it
0cells of the map it votes in
34citing papers in PubMed, 2 pooled it
3.0field-weighted citation impact, top 7% 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

34 citing papers in PubMed, 2 syntheses or guidelines pooled it, 51 citations in OpenAlex.

  1. Pooled it
  2. Pooled it
  3. Article
  4. Article
  5. Article
  6. rs71327024 Associated with COVID-19 Hospitalization ReducesInternational journal of molecular sciences · 2023
    Article
  7. Article
  8. Single-cell genomics meets human genetics.Nature reviews. Genetics · 2023
    Review
  9. Article
  10. Host Genetic Factors, Comorbidities and the Risk of Severe COVID-19.Journal of epidemiology and global health · 2023
    Article
  11. Article
  12. Article
  13. Review
  14. Article
  15. Review
  16. Article
  17. COVID-19 Molecular Pathophysiology: Acetylation of Repurposing Drugs.International journal of molecular sciences · 2022
    Review
  18. Article
  19. The human genetic epidemiology of COVID-19.Nature reviews. Genetics · 2022
    Review
  20. Article
4 · The record

Corrections and comments

5 · Who and what money

Authors and funding

7 authors at 2 institutions in 1 country.

Silva KaselaNew York Genome Center, New York, NY, USA. skasela@nygenome.org.ORCID 0000-0003-4362-0034
Zharko DaniloskiNew York Genome Center, New York, NY, USA.
Sailalitha BollepalliNew York Genome Center, New York, NY, USA.
Tristan X JordanDepartment of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY, USA.
Benjamin R tenOeverDepartment of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY, USA.
Neville E SanjanaNew York Genome Center, New York, NY, USA.
Tuuli LappalainenNew York Genome Center, New York, NY, USA. tlappalainen@nygenome.org.
New York Genome Center · USIcahn School of Medicine at Mount Sinai · US

Funding

Clinical and Translational Science AwardUL1TR001873 · NCATS · COLUMBIA UNIVERSITY HEALTH SCIENCES · PI REILLY, MUREDACH P · 2016 to 2025
$99.0M
New York Center for Collaborative Research In Common Disease Genomics: Genome Aggregation and Joint Variant Calling for CCDG Freeze2UM1HG008901 · NHGRI · NEW YORK GENOME CENTER · PI MANIATIS, THOMAS P, WIGLER, MICHAEL H · 2016 to 2020
$56.6M
Statistical models for fine-mapping and interpretation of schizophrenia-associated lociR01MH106842 · NIMH · NEW YORK GENOME CENTER · PI BUSSEMAKER, HARMEN J, LAPPALAINEN, TUULI · 2015 to 2024
$5.0M
Predicting the functional impact of non-coding mutations using patient-specific gene regulatory networksR01CA218668 · NCI · WEILL MEDICAL COLL OF CORNELL UNIV · PI EKTA KHURANA, Neville Sanjana · 2018 to 2026
$4.7M
In situ functional genomics to understand transcriptional regulationDP2HG010099 · NHGRI · NEW YORK GENOME CENTER · PI SANJANA, NEVILLE · 2017 to 2022
$4.4M
The biology of the nuclear export protein in influenza A virus replicationR01AI123155 · NIAID · ICAHN SCHOOL OF MEDICINE AT MOUNT SINAI · PI TENOEVER, BENJAMIN R. · 2017 to 2020
$2.4M
Integration of omics data to improve interpretation of genetic risk variants in lung diseaseR01HL142028 · NHLBI · COLUMBIA UNIVERSITY HEALTH SCIENCES · PI BARR, R GRAHAM, LAPPALAINEN, TUULI · 2018 to 2019
$790k
American Heart Association 20POST35220040Defense Sciences Office, DARPA D18AP00053Defense Sciences Office, DARPA HR0011-20-2-0040NCATS NIH HHS UL1 TR001873NCI NIH HHS R01 CA218668NCI NIH HHS R01CA218668NHGRI NIH HHS DP2HG010099NHGRI NIH HHS UM1 HG008901NHGRI NIH HHS UM1HG008901NHLBI NIH HHS R01 HL142028NHLBI NIH HHS R01HL142028NIAID NIH HHS R01 AI123155NIH HHS R01AI123155NIMH NIH HHS R01 MH106842NIMH NIH HHS R01MH106842
6 · The paper itself

Abstract

To date, the locus with the most robust human genetic association to COVID-19 severity is 3p21.31. Here, we integrate genome-scale CRISPR loss-of-function screens and eQTLs in diverse cell types and tissues to pinpoint genes underlying COVID-19 risk. Our findings identify SLC6A20 and CXCR6 as putative causal genes that modulate COVID-19 risk and highlight the usefulness of this integrative approach to bridge the divide between correlational and causal studies of human biology.

Indexed as

Quantitative Trait LociChromosomes, Human, Pair 3COVID-19HumansMembrane Transport ProteinsPhenotypeReceptors, CXCR6CXCR6 protein, humanMembrane Transport ProteinsReceptors, CXCR6SLC6A20 protein, humanCOVID-19CRISPReQTLGWASSARS-CoV-2

Identifiers

PMID34425859
PMCPMC8381345
OpenAlexW3194226878

What OpenQuestion holds

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LicenceCC BY
Read underepoch 390

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.