Evidence map›Paper›PMID 32774784›Full record

ArticleComputational and structural biotechnology journal2020

Finding new cancer epigenetic and genetic biomarkers from cell-free DNA by combining SALP-seq and machine learning.

Shicai Liu, Jian Wu, Qiang Xia, Hongde Liu, Weiwei Li, Xinyi Xia, Jinke Wang

Abstract read
PubMed Full text at PMC Publisher
In one paragraph

Article in Computational and structural biotechnology journal, 2020. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 14 papers.

0numbers the graph read from it
0cells of the map it votes in
14citing papers in PubMed
–field-weighted citation impact
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

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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

14 citing papers in PubMed.

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  11. Computational challenges in detection of cancer using cell-free DNA methylation.Computational and structural biotechnology journal · 2022
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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

7 authors.

Shicai LiuState Key Laboratory of Bioelectronics, Southeast University, Nanjing 210096, China.
Jian WuState Key Laboratory of Bioelectronics, Southeast University, Nanjing 210096, China.
Qiang XiaState Key Laboratory of Bioelectronics, Southeast University, Nanjing 210096, China.
Hongde LiuState Key Laboratory of Bioelectronics, Southeast University, Nanjing 210096, China.
Weiwei LiJinling Hospital, Nanjing University School of Medicine, Nanjing 210002, China.
Xinyi XiaJinling Hospital, Nanjing University School of Medicine, Nanjing 210002, China.
Jinke WangState Key Laboratory of Bioelectronics, Southeast University, Nanjing 210096, China.

Funding

No grant is acknowledged in the PubMed record.

6 · The paper itself

Abstract

The effective non-invasive diagnosis and prognosis are critical for cancer treatment. The plasma cell-free DNA (cfDNA) provides a good material for cancer liquid biopsy and its worth in this field is increasingly explored. Here we describe a new pipeline for effectively finding new cfDNA-based biomarkers for cancers by combining SALP-seq and machine learning. Using the pipeline, 30 cfDNA samples from 26 esophageal cancer (ESCA) patients and 4 healthy people were analyzed as an example. As a result, 103 epigenetic markers (including 54 genome-wide and 49 promoter markers) and 37 genetic markers were identified for this cancer. These markers provide new biomarkers for ESCA diagnosis, prognosis and therapy. Importantly, these markers, especially epigenetic markers, not only shed important new insights on the regulatory mechanisms of this cancer, but also could be used to classify the cfDNA samples. We therefore developed a new pipeline for effectively finding new cfDNA-based biomarkers for cancers by combining SALP-seq and machine learning. In this study, we also discovered new clinical worth of cfDNA distinct from other reported characters.

Indexed as

ATAC-seq, Assay for Transposase-Accessible Chromatin-sequencing and high-throughput sequencingAUC, Area Under CurveBiomarkersCell-free DNAcfDNA, cell-free DNAcfMeDIP-seq, cell-free methylated DNA immunoprecipitation and high-throughput sequencingCTC, circulating tumor cellctDNA, cell-free tumor DNAESCA, esophageal cancerEsophageal cancermiRNA, microRNAmRNA, messenger RNANext generation sequencingNGS, next generation sequencingNIPT, noninvasive prenatal testingPCA, principal component analysisSALP-seqSALP-seq, Single strand Adaptor Library Preparation-sequencingSNP, single nucleotide polymorphismSNV, single nucleotide variantTCGA, The Cancer Genome AtlasTFBS, TF binding siteTF, transcription factorTi, transitionsTSS, transcription start siteTv, transversion

Identifiers

PMID32774784
PMCPMC7387736

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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.