Evidence map›Paper›PMID 29298978›Full record

ArticleNature communications2018

A machine learning approach to integrate big data for precision medicine in acute myeloid leukemia.

Su-In Lee, Safiye Celik, Benjamin A Logsdon, Scott M Lundberg, Timothy J Martins, Vivian G Oehler, Elihu H Estey, Chris P Miller, Sylvia Chien, Jin Dai and 3 more

Open access · goldAbstract read
In one paragraph

Article in Nature communications, 2018. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 130 papers, 1 of them a synthesis that pooled it.

0numbers the graph read from it
0cells of the map it votes in
130citing papers in PubMed, 1 pooled it
8.5field-weighted citation impact, top 2% 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

130 citing papers in PubMed, 1 synthesis or guideline pooled it, 339 citations in OpenAlex.

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70 more citing papers are in PubMed but not listed here.

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

13 authors at 2 institutions in 1 country.

Su-In LeePaul G. Allen School of Computer Science and Engineering, University of Washington, 185 E Stevens Way NE, Seattle, WA, 98195, USA. suinlee@cs.washington.edu.ORCID http://orcid.org/0000-0001-5833-5215
Safiye CelikPaul G. Allen School of Computer Science and Engineering, University of Washington, 185 E Stevens Way NE, Seattle, WA, 98195, USA.
Benjamin A LogsdonSage Bionetworks, 1100 Fairview Ave N, Seattle, WA, 98109, USA.ORCID http://orcid.org/0000-0002-0572-2569
Scott M LundbergPaul G. Allen School of Computer Science and Engineering, University of Washington, 185 E Stevens Way NE, Seattle, WA, 98195, USA.
Timothy J MartinsQuellos High Throughput Screening Core, University of Washington, 850 Republican Street, Seattle, WA, 98109, USA.ORCID http://orcid.org/0000-0002-2133-7281
Vivian G OehlerClinical Research Division, Fred Hutchinson Cancer Research Center, 1100 Fairview Ave N, Seattle, WA, 98109, USA.
Elihu H EsteyClinical Research Division, Fred Hutchinson Cancer Research Center, 1100 Fairview Ave N, Seattle, WA, 98109, USA.
Chris P MillerDivision of Hematology, Department of Medicine and Institute for Stem Cell and Regenerative Medicine, University of Washington, 850 Republican Street, Seattle, WA, 98109, USA.
Sylvia ChienDivision of Hematology, Department of Medicine and Institute for Stem Cell and Regenerative Medicine, University of Washington, 850 Republican Street, Seattle, WA, 98109, USA.
Jin DaiDivision of Hematology, Department of Medicine and Institute for Stem Cell and Regenerative Medicine, University of Washington, 850 Republican Street, Seattle, WA, 98109, USA.
Akanksha SaxenaDivision of Hematology, Department of Medicine and Institute for Stem Cell and Regenerative Medicine, University of Washington, 850 Republican Street, Seattle, WA, 98109, USA.
C Anthony BlauCenter for Cancer Innovation, University of Washington, 850 Republican Street, Seattle, WA, 98109, USA.
Pamela S BeckerCenter for Cancer Innovation, University of Washington, 850 Republican Street, Seattle, WA, 98109, USA.ORCID http://orcid.org/0000-0001-6235-9463
University of Washington · USSage Bionetworks · US

Funding

Tumor mutation signaturesP01CA077852 · NCI · UNIVERSITY OF WASHINGTON · PI SIDOROVA, JULIA · 1999 to 2019
$26.0M
EXPERIMENTAL PATHOLOGY OF CARDIOVASCULAR DISEASET32HL007312 · NHLBI · UNIVERSITY OF WASHINGTON · PI MAJESKY, MARK W., SCHWARTZ, STEPHEN MARK · 1985 to 2019
$11.8M
NCI NIH HHS P01 CA077852NHLBI NIH HHS T32 HL007312
6 · The paper itself

Abstract

Cancers that appear pathologically similar often respond differently to the same drug regimens. Methods to better match patients to drugs are in high demand. We demonstrate a promising approach to identify robust molecular markers for targeted treatment of acute myeloid leukemia (AML) by introducing: data from 30 AML patients including genome-wide gene expression profiles and in vitro sensitivity to 160 chemotherapy drugs, a computational method to identify reliable gene expression markers for drug sensitivity by incorporating multi-omic prior information relevant to each gene's potential to drive cancer. We show that our method outperforms several state-of-the-art approaches in identifying molecular markers replicated in validation data and predicting drug sensitivity accurately. Finally, we identify SMARCA4 as a marker and driver of sensitivity to topoisomerase II inhibitors, mitoxantrone, and etoposide, in AML by showing that cell lines transduced to have high SMARCA4 expression reveal dramatically increased sensitivity to these agents.

Indexed as

Machine LearningAlgorithmsAntineoplastic AgentsBiomarkers, TumorCell LineDatasets as TopicDNA HelicasesDrug Resistance, NeoplasmEtoposideHumansLeukemia, Myeloid, AcuteNuclear ProteinsPrecision MedicineTopoisomerase II InhibitorsTranscription FactorsAntineoplastic AgentsBiomarkers, TumorDNA HelicasesEtoposideNuclear ProteinsSMARCA4 protein, humanTopoisomerase II InhibitorsTranscription Factors

Identifiers

PMID29298978
PMCPMC5752671
OpenAlexW2777794149

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.