Evidence map›Paper›PMID 37664640›Full record

ArticleiScience2023

Machine learning reveals genetic modifiers of the immune microenvironment of cancer.

Bridget Riley-Gillis, Shirng-Wern Tsaih, Emily King, Sabrina Wollenhaupt, Jonas Reeb, Amy R Peck, Kelsey Wackman, Angela Lemke, Hallgeir Rui, Zoltan Dezso and 1 more

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

Article in iScience, 2023. 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
0.5field-weighted citation impact, top 29% 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

0 citing papers in PubMed, 2 citations in OpenAlex.

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

11 authors at 3 institutions in 2 countries.

Bridget Riley-GillisGenomics Research Center, AbbVie Inc, 1 North Waukegan Road, North Chicago, IL 60064, USA.
Shirng-Wern TsaihGenomic Sciences and Precision Medicine Center, Medical College of Wisconsin, Milwaukee, WI, USA.
Emily KingGenomics Research Center, AbbVie Inc, 1 North Waukegan Road, North Chicago, IL 60064, USA.
Sabrina WollenhauptInformation Research, AbbVie Deutschland GmbH & Co. KG, 67061, Knollstrasse, Ludwigshafen, Germany.
Jonas ReebInformation Research, AbbVie Deutschland GmbH & Co. KG, 67061, Knollstrasse, Ludwigshafen, Germany.
Amy R PeckGenomic Sciences and Precision Medicine Center, Medical College of Wisconsin, Milwaukee, WI, USA.
Kelsey WackmanGenomic Sciences and Precision Medicine Center, Medical College of Wisconsin, Milwaukee, WI, USA.
Angela LemkeGenomic Sciences and Precision Medicine Center, Medical College of Wisconsin, Milwaukee, WI, USA.
Hallgeir RuiDepartment of Pathology, Medical College of Wisconsin, Milwaukee, WI 53226, USA.
Zoltan DezsoGenomics Research Center, AbbVie Bay Area, 1000 Gateway Boulevard, South San Francisco, CA 94080, USA.
Michael J FlisterGenomics Research Center, AbbVie Inc, 1 North Waukegan Road, North Chicago, IL 60064, USA.
Medical College of Wisconsin · USAbbVie (United States) · USAbbVie (Germany) · DE

Funding

Leveraging genetic mapping for personalized targeting of breast cancer microenvironmentR01CA193343 · NCI · MEDICAL COLLEGE OF WISCONSIN · PI Amit Joshi · 2015 to 2026
$3.5M
Prolactin pathways and metastatic progression of ER-positive breast cancerR01CA188575 · NCI · THOMAS JEFFERSON UNIVERSITY · PI RUI, HALLGEIR · 2015 to 2019
$1.8M
NCI NIH HHS R01 CA188575NCI NIH HHS R01 CA193343Wellcome Trust
6 · The paper itself

Abstract

Heritability in the immune tumor microenvironment (iTME) has been widely observed yet remains largely uncharacterized. Here, we developed a machine learning approach to map iTME modifiers within loci from genome-wide association studies (GWASs) for breast cancer (BrCa) incidence. A random forest model was trained on a positive set of immune-oncology (I-O) targets, and then used to assign I-O target probability scores to 1,362 candidate genes in linkage disequilibrium with 155 BrCa GWAS loci. Cluster analysis of the most probable candidates revealed two subfamilies of genes related to effector functions and adaptive immune responses, suggesting that iTME modifiers impact multiple aspects of anticancer immunity. Two of the top ranking BrCa candidates,

Indexed as

Cancer systems biologyMicroenvironmentQuantitative genetics

Identifiers

PMID37664640
PMCPMC10470213
OpenAlexW4385686724

What OpenQuestion holds

Textmetadata
LicenceCC BY
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.