Evidence map›Paper›PMID 32383980›Full record

ArticleJCO clinical cancer informatics2020

Imaging-AMARETTO: An Imaging Genomics Software Tool to Interrogate Multiomics Networks for Relevance to Radiography and Histopathology Imaging Biomarkers of Clinical Outcomes.

Olivier Gevaert, Mohsen Nabian, Shaimaa Bakr, Celine Everaert, Jayendra Shinde, Artur Manukyan, Ted Liefeld, Thorin Tabor, Jishu Xu, Joachim Lupberger and 10 more

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

Article in JCO clinical cancer informatics, 2020. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 7 papers.

0numbers the graph read from it
0cells of the map it votes in
7citing papers in PubMed
1.3field-weighted citation impact, top 20% 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

7 citing papers in PubMed, 14 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

20 authors at 9 institutions in 2 countries.

Olivier GevaertStanford Center for Biomedical Informatics Research, Department of Medicine and Biomedical Data Science, Stanford University, Stanford, CA.
Mohsen NabianCell Circuits Program, Broad Institute of MIT and Harvard, Cambridge, MA.
Shaimaa BakrStanford Center for Biomedical Informatics Research, Department of Medicine and Biomedical Data Science, Stanford University, Stanford, CA.
Celine EveraertCell Circuits Program, Broad Institute of MIT and Harvard, Cambridge, MA.
Jayendra ShindeStanford Center for Biomedical Informatics Research, Department of Medicine and Biomedical Data Science, Stanford University, Stanford, CA.
Artur ManukyanCell Circuits Program, Broad Institute of MIT and Harvard, Cambridge, MA.
Ted LiefeldDepartment of Medicine, University of California, San Diego, San Diego, CA.
Thorin TaborDepartment of Medicine, University of California, San Diego, San Diego, CA.
Jishu XuCell Circuits Program, Broad Institute of MIT and Harvard, Cambridge, MA.
Joachim LupbergerINSERM, U1110, Institut de Recherche sur les Maladies Virales et Hépatiques, Université de Strasbourg, Institut Hopitalo-Universitaire, Hôpitaux Universitaires de Strasbourg, Strasbourg, France.
Brian J HaasCell Circuits Program, Broad Institute of MIT and Harvard, Cambridge, MA.
Thomas F BaumertINSERM, U1110, Institut de Recherche sur les Maladies Virales et Hépatiques, Université de Strasbourg, Institut Hopitalo-Universitaire, Hôpitaux Universitaires de Strasbourg, Strasbourg, France.
Mikel HernaezCarl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Champaign, IL.
Michael ReichDepartment of Medicine, University of California, San Diego, San Diego, CA.
Francisco J QuintanaCell Circuits Program, Broad Institute of MIT and Harvard, Cambridge, MA.
Erik J UhlmannAnn Romney Center for Neurologic Diseases, Department of Neurology, Brigham and Women's Hospital, Harvard Medical School, Boston, MA.
Anna M KrichevskyAnn Romney Center for Neurologic Diseases, Department of Neurology, Brigham and Women's Hospital, Harvard Medical School, Boston, MA.
Jill P MesirovDepartment of Medicine, University of California, San Diego, San Diego, CA.
Vincent CareyCell Circuits Program, Broad Institute of MIT and Harvard, Cambridge, MA.
Nathalie PochetCell Circuits Program, Broad Institute of MIT and Harvard, Cambridge, MA.
Broad Institute · USUniversity of California, San Diego · USHarvard University · USStanford University · USBrigham and Women's Hospital · USInserm · FRRush University Medical Center · USUniversité de Strasbourg · FRUniversity of Illinois Urbana-Champaign · US

Funding

Trinity: Transcriptome assembly for genetic and functional analysis of cancerU24CA180922 · NCI · BROAD INSTITUTE, INC. · PI HAAS, BRIAN · 2013 to 2022
$7.5M
Supporting Integrative Genomic Analysis Users with GenePatternR01GM074024 · NIGMS · UNIVERSITY OF CALIFORNIA, SAN DIEGO · PI MESIROV, JILL P. · 2005 to 2019
$6.6M
Organoid-based Discovery of Oncogenic Drivers and Treatment Resistance MechanismsU01CA217851 · NCI · STANFORD UNIVERSITY · PI CURTIS, CHRISTINA N, JI, HANLEE P · 2017 to 2021
$4.7M
GenePattern and GenePattern Notebook: Integrative 'Omic Analysis for Cancer ResearchU24CA248457 · NCI · UNIVERSITY OF CALIFORNIA, SAN DIEGO · PI MESIROV, JILL P., TAMAYO, PABLO · 2020 to 2024
$4.6M
Modeling KRAS-Dependent Synthetic Lethality in Human Colon OrganoidsU01CA199241 · NCI · STANFORD UNIVERSITY · PI KUO, CALVIN J, SHOKAT, KEVAN M. · 2016 to 2019
$4.3M
Supporting and evolving Gene Set Enrichment Analysis and the Molecular Signatures Database for cancer researchU24CA220341 · NCI · UNIVERSITY OF CALIFORNIA, SAN DIEGO · PI MESIROV, JILL P., TAMAYO, PABLO · 2018 to 2022
$3.4M
GenePattern Notebooks for Cancer ResearchU24CA194107 · NCI · UNIVERSITY OF CALIFORNIA, SAN DIEGO · PI MESIROV, JILL P. · 2015 to 2019
$2.8M
Radiogenomics Framework for Non-Invasive Personalized MedicineR01EB020527 · NIBIB · STANFORD UNIVERSITY · PI GEVAERT, OLIVIER · 2015 to 2018
$2.3M
Developing miR-10b targeting for glioblastomaR01CA215072 · NCI · BRIGHAM AND WOMEN'S HOSPITAL · PI KRICHEVSKY, ANNA M. · 2018 to 2022
$2.0M
Accelerating Cancer Genomics with Cloud-scale BioconductorU01CA214846 · NCI · BRIGHAM AND WOMEN'S HOSPITAL · PI CAREY, VINCENT JAMES · 2017 to 2019
$1.3M
Platform and portal development for accessible, reproducible cancer genomics researchR50CA243876 · NCI · UNIVERSITY OF CALIFORNIA, SAN DIEGO · PI LIEFELD, JOHN THEODORE · 2019 to 2023
$1.1M
Radiogenomics framework for non-invasive personalized medicineR56EB020527 · NIBIB · STANFORD UNIVERSITY · PI GEVAERT, OLIVIER · 2019 to 2019
$444k
NCI NIH HHS R01 CA215072NCI NIH HHS R21 CA209940NCI NIH HHS R50 CA243876NCI NIH HHS U01 CA199241NCI NIH HHS U01 CA214846NCI NIH HHS U01 CA217851NCI NIH HHS U24 CA180922NCI NIH HHS U24 CA194107NCI NIH HHS U24 CA220341NCI NIH HHS U24 CA248457NIAID NIH HHS R03 AI131066NIBIB NIH HHS R01 EB020527NIBIB NIH HHS R56 EB020527NIGMS NIH HHS R01 GM074024
6 · The paper itself

Abstract

purposeThe availability of increasing volumes of multiomics, imaging, and clinical data in complex diseases such as cancer opens opportunities for the formulation and development of computational imaging genomics methods that can link multiomics, imaging, and clinical data.

methodsHere, we present the Imaging-AMARETTO algorithms and software tools to systematically interrogate regulatory networks derived from multiomics data within and across related patient studies for their relevance to radiography and histopathology imaging features predicting clinical outcomes.

resultsTo demonstrate its utility, we applied Imaging-AMARETTO to integrate three patient studies of brain tumors, specifically, multiomics with radiography imaging data from The Cancer Genome Atlas (TCGA) glioblastoma multiforme (GBM) and low-grade glioma (LGG) cohorts and transcriptomics with histopathology imaging data from the Ivy Glioblastoma Atlas Project (IvyGAP) GBM cohort. Our results show that Imaging-AMARETTO recapitulates known key drivers of tumor-associated microglia and macrophage mechanisms, mediated by

conclusionOur network-based imaging genomics tools serve as hypothesis generators that facilitate the interrogation of known and uncovering of novel hypotheses for follow-up with experimental validation studies. We anticipate that our Imaging-AMARETTO imaging genomics tools will be useful to the community of biomedical researchers for applications to similar studies of cancer and other complex diseases with available multiomics, imaging, and clinical data.

Indexed as

GlioblastomaImaging GenomicsBiomarkersHumansRadiographySoftwareBiomarkers

Identifiers

PMID32383980
PMCPMC7265792
OpenAlexW3021232069

What OpenQuestion holds

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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.