Evidence map›Paper›PMID 29635542›Full record

ArticleAnnals of oncology : official journal of the European Society for Medical Oncology2018

Targeted methylation sequencing of plasma cell-free DNA for cancer detection and classification.

L Liu, J M Toung, A F Jassowicz, R Vijayaraghavan, H Kang, R Zhang, K M Kruglyak, H J Huang, T Hinoue, H Shen and 21 more

Registry-linked trialOpen access · bronzeAbstract read
PubMed Full text at PMC Publisher
In one paragraph

Article in Annals of oncology : official journal of the European Society for Medical Oncology, 2018. The graph could read no effect estimate from its abstract, so it casts no vote on the map. It is linked to trial NCT05227261 (Assessment of a Novel Blood Test in Early Detection of the Five Common Cancers Based on the Investigation of the Circulating Tumour DNA), which is not on this map. Cited by 93 papers, 2 of them syntheses that pooled it.

0numbers the graph read from it
0cells of the map it votes in
93citing papers in PubMed, 2 pooled it
4.8field-weighted citation impact, top 3% 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.

NCT05227261 completednot on this mapstarted 2022, after this paper: background citation

Assessment of a Novel Blood Test in Early Detection of the Five Common Cancers Based on the Investigation of the Circulating Tumour DNA

TypeobservationalSponsorGene SolutionsRan2022 to 2024Enrolled9,057ConditionsCancer, Lung, Cancer, Breast, Cancer Liver, Cancer, Colorectal
3 · Its place in the literature

Who cites it

93 citing papers in PubMed, 2 syntheses or guidelines pooled it, 151 citations in OpenAlex.

  1. Pooled it
  2. Circulating Cell-Free DNA and Colorectal Cancer: A Systematic Review.International journal of molecular sciences · 2018
    Pooled it
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33 more citing papers are in PubMed but not listed here.

4 · The record

Corrections and comments

5 · Who and what money

Authors and funding

31 authors at 2 institutions in 1 country.

L LiuIllumina, Inc., San Diego, The University of Texas MD Anderson Cancer Center, Houston, USA. Electronic address: lliu3@illumina.com.
J M ToungIllumina, Inc., San Diego, The University of Texas MD Anderson Cancer Center, Houston, USA.
A F JassowiczDepartment of Investigational Cancer Therapeutics (Phase I Clinical Trials Program), The University of Texas MD Anderson Cancer Center, Houston, USA.
R VijayaraghavanIllumina, Inc., San Diego, The University of Texas MD Anderson Cancer Center, Houston, USA.
H KangIllumina, Inc., San Diego, The University of Texas MD Anderson Cancer Center, Houston, USA.
R ZhangIllumina, Inc., San Diego, The University of Texas MD Anderson Cancer Center, Houston, USA.
K M KruglyakIllumina, Inc., San Diego, The University of Texas MD Anderson Cancer Center, Houston, USA.
H J HuangDepartment of Investigational Cancer Therapeutics (Phase I Clinical Trials Program), The University of Texas MD Anderson Cancer Center, Houston, USA.
T HinoueVan Andel Research Institute, Grand Rapids, The University of Texas MD Anderson Cancer Center, Houston, USA.
H ShenVan Andel Research Institute, Grand Rapids, The University of Texas MD Anderson Cancer Center, Houston, USA.
N S SalathiaIllumina, Inc., San Diego, The University of Texas MD Anderson Cancer Center, Houston, USA.
D S HongDepartment of Investigational Cancer Therapeutics (Phase I Clinical Trials Program), The University of Texas MD Anderson Cancer Center, Houston, USA.
A NaingDepartment of Investigational Cancer Therapeutics (Phase I Clinical Trials Program), The University of Texas MD Anderson Cancer Center, Houston, USA.
V SubbiahDepartment of Investigational Cancer Therapeutics (Phase I Clinical Trials Program), The University of Texas MD Anderson Cancer Center, Houston, USA.
S A Piha-PaulDepartment of Investigational Cancer Therapeutics (Phase I Clinical Trials Program), The University of Texas MD Anderson Cancer Center, Houston, USA.
M BibikovaIllumina, Inc., San Diego, The University of Texas MD Anderson Cancer Center, Houston, USA.
G GrangerIllumina, Inc., San Diego, The University of Texas MD Anderson Cancer Center, Houston, USA.
B BarnesIllumina, Inc., San Diego, The University of Texas MD Anderson Cancer Center, Houston, USA.
R ShenIllumina, Inc., San Diego, The University of Texas MD Anderson Cancer Center, Houston, USA.
K GutekunstIllumina, Inc., San Diego, The University of Texas MD Anderson Cancer Center, Houston, USA.
S FuDepartment of Investigational Cancer Therapeutics (Phase I Clinical Trials Program), The University of Texas MD Anderson Cancer Center, Houston, USA.
A M TsimberidouDepartment of Investigational Cancer Therapeutics (Phase I Clinical Trials Program), The University of Texas MD Anderson Cancer Center, Houston, USA.
C LuDepartment of Thoracic/Head and Neck Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, USA.
C EngDepartment of Gastrointestinal Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, USA.
S L MoulderDepartment of Breast Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, USA.
E S KopetzDepartment of Gastrointestinal Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, USA.
R N AmariaDepartment of Melanoma Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, USA.
F Meric-BernstamDepartment of Investigational Cancer Therapeutics (Phase I Clinical Trials Program), The University of Texas MD Anderson Cancer Center, Houston, USA.
P W LairdVan Andel Research Institute, Grand Rapids, The University of Texas MD Anderson Cancer Center, Houston, USA.
J-B FanIllumina, Inc., San Diego, The University of Texas MD Anderson Cancer Center, Houston, USA.
F JankuDepartment of Investigational Cancer Therapeutics (Phase I Clinical Trials Program), The University of Texas MD Anderson Cancer Center, Houston, USA. Electronic address: fjanku@mdanderson.org.
The University of Texas MD Anderson Cancer Center · USVan Andel Institute · US

Funding

Tumor Evolution and Metastasis ProgramP30CA016672 · NCI · UNIVERSITY OF TX MD ANDERSON CAN CTR · PI DIANE BODURKA · 1985 to 2026
$290.8M
Center for Clinical and Translational Sciences (CCTS)UL1TR000371 · NCATS · UNIVERSITY OF TEXAS HLTH SCI CTR HOUSTON · PI MCPHERSON, DAVID D · 2012 to 2016
$13.4M
NCATS NIH HHS UL1 TR000371NCI NIH HHS P30 CA016672
6 · The paper itself

Abstract

Background: Targeted methylation sequencing of plasma cell-free DNA (cfDNA) has a potential to expand liquid biopsies to patients with tumors without detectable oncogenic alterations, which can be potentially useful in early diagnosis. Patients and methods: We developed a comprehensive methylation sequencing assay targeting 9223 CpG sites consistently hypermethylated according to The Cancer Genome Atlas. Next, we carried out a clinical validation of our method using plasma cfDNA samples from 78 patients with advanced colorectal cancer, non-small-cell lung cancer (NSCLC), breast cancer or melanoma and compared results with patients' outcomes. Results: Median methylation scores in plasma cfDNA samples from patients on therapy were lower than from patients off therapy (4.74 versus 85.29; P = 0.001). Of 68 plasma samples from patients off therapy, methylation scores detected the presence of cancer in 57 (83.8%), and methylation-based signatures accurately classified the underlying cancer type in 45 (78.9%) of these. Methylation scores were most accurate in detecting colorectal cancer (96.3%), followed by breast cancer (91.7%), melanoma (81.8%) and NSCLC (61.1%), and most accurate in classifying the underlying cancer type in colorectal cancer (88.5%), followed by NSCLC (81.8%), breast cancer (72.7%) and melanoma (55.6%). Low methylation scores versus high were associated with longer survival (10.4 versus 4.4 months, P < 0.001) and longer time-to-treatment failure (2.8 versus 1.6 months, P = 0.016). Conclusions: Comprehensive targeted methylation sequencing of 9223 CpG sites in plasma cfDNA from patients with common advanced cancers detects the presence of cancer and underlying cancer type with high accuracy. Methylation scores in plasma cfDNA correspond with treatment outcomes.

Indexed as

DNA MethylationAdolescentAdultAgedBiomarkers, TumorCase-Control StudiesCell-Free Nucleic AcidsCombined Modality TherapyDNA, NeoplasmFemaleFollow-Up StudiesHumansMaleMiddle AgedNeoplasmsPrognosisBiomarkers, TumorCell-Free Nucleic AcidsDNA, Neoplasm

Identifiers

PMID29635542
PMCPMC6005020
OpenAlexW2798012507

What Socratic holds

Textmetadata
Read underepoch 390

Registered trials

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.