Evidence map›Paper›PMID 35036860›Full record

ArticleiScience2022

Optical genome mapping identifies rare structural variations as predisposition factors associated with severe COVID-19.

Nikhil Shri Sahajpal, Chi-Yu Jill Lai, Alex Hastie, Ashis K Mondal, Siavash Raeisi Dehkordi, Caspar I van der Made, Olivier Fedrigo, Farooq Al-Ajli, Sawan Jalnapurkar, Marta Byrska-Bishop and 17 more

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

Article in iScience, 2022. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 11 papers.

0numbers the graph read from it
0cells of the map it votes in
11citing papers in PubMed
2.1field-weighted citation impact, top 11% 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

11 citing papers in PubMed, 22 citations in OpenAlex.

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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

27 authors at 12 institutions in 3 countries.

Nikhil Shri SahajpalDepartment of Pathology, Medical College of Georgia, Augusta University, 1120 15th Street, BF-207, Augusta, GA 30912, USA.
Chi-Yu Jill LaiBionano Genomics, Inc., San Diego, CA 92121, USA.
Alex HastieBionano Genomics, Inc., San Diego, CA 92121, USA.
Ashis K MondalDepartment of Pathology, Medical College of Georgia, Augusta University, 1120 15th Street, BF-207, Augusta, GA 30912, USA.
Siavash Raeisi DehkordiDepartment of Computer Science and Engineering, University of California at San Diego, San Diego, CA 92093, USA.
Caspar I van der MadeDepartment of Human Genetics, Radboud University Medical Center for Infectious Diseases (RCI), Department of Internal Medicine, Radboud Institute for Molecular Life Sciences, and Radboud Expertise Center for Immunodeficiency and Autoinflammation, Radboud University Medical Center, 6525 Nijmegen, the Netherlands.
Olivier FedrigoVertebrate Genome Lab, The Rockefeller University, New York, NY 10065, USA.
Farooq Al-AjliVertebrate Genome Lab, The Rockefeller University, New York, NY 10065, USA.
Sawan JalnapurkarDepartment of Medicine, Medical College of Georgia, Augusta University, GA 30912, USA.
Marta Byrska-BishopNew York Genome Center, New York, NY 10013, USA.
Rashmi Kanagal-ShamannaHematopathology, University of Texas M.D. Anderson Cancer Center, Houston 77030, USA.
Brynn LevyDepartment of Pathology and Cell Biology, Columbia University Medical Center, New York 10032, USA.
Maximilian SchieckDepartment of Human Genetics, Cluster of Excellence RESIST (EXC 2155), Hannover Medical School, Hannover 30625, Germany.
Thomas IlligDepartment of Human Genetics, Cluster of Excellence RESIST (EXC 2155), Hannover Medical School, Hannover 30625, Germany.
Silviu-Alin BacanuDepartment of Psychiatry, Virginia Commonwealth University, Richmond, VA 23284, USA.
Janet S ChouDivision of Immunology, Boston Children's Hospital, Boston, MA 02115, USA.
Adrienne G RandolphDepartment of Anesthesiology, Critical Care, and Pain Medicine, Boston Children's Hospital, Boston, MA 02115, USA.
Amyn M RojianiDepartment of Pathology, Medical College of Georgia, Augusta University, 1120 15th Street, BF-207, Augusta, GA 30912, USA.
Michael C ZodyNew York Genome Center, New York, NY 10013, USA.
Catherine A BrownsteinDivision of Genetics and Genomics, The Manton Center for Orphan Disease Research, Boston Children's Hospital, Harvard Medical School, Boston, MA 02115, USA.
Alan H BeggsDivision of Genetics and Genomics, The Manton Center for Orphan Disease Research, Boston Children's Hospital, Harvard Medical School, Boston, MA 02115, USA.
Vineet BafnaDepartment of Computer Science and Engineering, University of California at San Diego, San Diego, CA 92093, USA.
Erich D JarvisVertebrate Genome Lab, The Rockefeller University, New York, NY 10065, USA.
Alexander HoischenDepartment of Human Genetics, Radboud University Medical Center for Infectious Diseases (RCI), Department of Internal Medicine, Radboud Institute for Molecular Life Sciences, and Radboud Expertise Center for Immunodeficiency and Autoinflammation, Radboud University Medical Center, 6525 Nijmegen, the Netherlands.
Alka ChaubeyDepartment of Pathology, Medical College of Georgia, Augusta University, 1120 15th Street, BF-207, Augusta, GA 30912, USA.
Ravindra KolheDepartment of Pathology, Medical College of Georgia, Augusta University, 1120 15th Street, BF-207, Augusta, GA 30912, USA.
COVID19hostgenomesv Consortium
Augusta University · USBoston Children's Hospital · USBioNano Genomics (United States) · USMedizinische Hochschule Hannover · DENew York Genome Center · USRadboud University Nijmegen · NLRockefeller University · USUniversity of California San Diego · USColumbia University Irving Medical Center · USHoward Hughes Medical Institute · USThe University of Texas MD Anderson Cancer Center · USVirginia Commonwealth University · US

Funding

Computational methods for detecting patterns of complex genomic variationR01GM114362 · NIGMS · UNIVERSITY OF CALIFORNIA, SAN DIEGO · PI Vineet Bafna · 2016 to 2026
$3.1M
NIGMS NIH HHS R01 GM114362
6 · The paper itself

Abstract

Impressive global efforts have identified both rare and common gene variants associated with severe COVID-19 using sequencing technologies. However, these studies lack the sensitivity to accurately detect several classes of variants, especially large structural variants (SVs), which account for a substantial proportion of genetic diversity including clinically relevant variation. We performed optical genome mapping on 52 severely ill COVID-19 patients to identify rare/unique SVs as decisive predisposition factors associated with COVID-19. We identified 7 SVs involving genes implicated in two key host-viral interaction pathways: innate immunity and inflammatory response, and viral replication and spread in nine patients, of which SVs in

Indexed as

Genetic sampleGenomicsVirology

Identifiers

PMID35036860
PMCPMC8744399
OpenAlexW4206164526

What Socratic holds

Textmetadata
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 Socratic graph.