Evidence map›Paper›PMID 26087196›Full record

ArticleOncotarget2015

Somatic copy number alterations detected by ultra-deep targeted sequencing predict prognosis in oral cavity squamous cell carcinoma.

Chien-Hua Peng, Chun-Ta Liao, Ka-Pou Ng, An-Shun Tai, Shih-Chi Peng, Jen-Pao Yeh, Shu-Jen Chen, Kuo-Chien Tsao, Tzu-Chen Yen, Wen-Ping Hsieh

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

Article in Oncotarget, 2015. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 12 papers.

0numbers the graph read from it
0cells of the map it votes in
12citing papers in PubMed
1.5field-weighted citation impact, top 19% 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

12 citing papers in PubMed, 24 citations in OpenAlex.

  1. Detection ofBiomolecules · 2021
    Trial
  2. Article
  3. Review
  4. Article
  5. Article
  6. Article
  7. Article
  8. Article
  9. Article
  10. Article
  11. Article
  12. Observational
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

10 authors at 1 institution in 1 country.

Chien-Hua PengDepartments of Resource Center for Clinical Research, Chang Gung Memorial Hospital, Taoyuan, Taiwan, R.O.C.
Chun-Ta LiaoOtorhinolaryngology, Head and Neck Surgery, Chang Gung Memorial Hospital, Taoyuan, Taiwan, R.O.C.
Ka-Pou NgInstitute of Statistics, National Tsing Hua University, Hsinchu, Taiwan, R.O.C.
An-Shun TaiInstitute of Statistics, National Tsing Hua University, Hsinchu, Taiwan, R.O.C.
Shih-Chi PengDepartment of Nuclear Medicine and Molecular Imaging Center, Chang Gung Memorial Hospital, Taoyuan, Taiwan, R.O.C.
Jen-Pao YehInstitute of Statistics, National Tsing Hua University, Hsinchu, Taiwan, R.O.C.
Shu-Jen ChenDepartment of Biomedical Sciences, School of Medicine, Chang Gung University, Taoyuan, Taiwan, R.O.C.
Kuo-Chien TsaoMedical Biotechnology and Laboratory Science, Research Center for Emerging Viral Infections, Chang Gung Memorial Hospital, Taoyuan, Taiwan, R.O.C.
Tzu-Chen YenDepartment of Nuclear Medicine and Molecular Imaging Center, Chang Gung Memorial Hospital, Taoyuan, Taiwan, R.O.C.
Wen-Ping HsiehOtorhinolaryngology, Head and Neck Surgery, Chang Gung Memorial Hospital, Taoyuan, Taiwan, R.O.C.
National Tsing Hua University · TW

Funding

No grant is acknowledged in the PubMed record.

6 · The paper itself

Abstract

backgroundUltra-deep targeted sequencing (UDT-Seq) has advanced our knowledge on the incidence and functional significance of somatic mutations. However, the utility of UDT-Seq in detecting copy number alterations (CNAs) remains unclear. With the goal of improving molecular prognostication and identifying new therapeutic targets, we designed this study to assess whether UDT-Seq may be useful for detecting CNA in oral cavity squamous cell carcinoma (OSCC).

methodsWe sequenced a panel of clinically actionable cancer mutations in 310 formalin-fixed paraffin-embedded OSCC specimens. A linear model was developed to overcome uneven coverage across target regions and multiple samples. The 5-year rates of secondary primary tumors, local recurrence, neck recurrence, distant metastases, and survival served as the outcome measures. We confirmed the prognostic significance of the CNA signatures in an independent sample of 105 primary OSCC specimens.

resultsThe CNA burden across 10 targeted genes was found to predict prognosis in two independent cohorts. FGFR1 and PIK3CAamplifications were associated with prognosis independent of clinical risk factors. Genes exhibiting CNA were clustered in the proteoglycan metabolism, the FOXO signaling, and the PI3K-AKT signaling pathways, for which targeted drugs are already available or currently under development.

conclusionsUDT-Seq is clinically useful to identify CNA, which significantly improve the prognostic information provided by traditional clinicopathological risk factors in OSCC patients.

Indexed as

DNA Copy Number VariationsGene DosageBiomarkers, TumorCarcinoma, Squamous CellChi-Square DistributionDisease-Free SurvivalDisease ProgressionGene Expression ProfilingGene Expression Regulation, NeoplasticGenetic Predisposition to DiseaseHead and Neck NeoplasmsHigh-Throughput Nucleotide SequencingHumansKaplan-Meier EstimateLinear ModelsMouth NeoplasmsBiomarkers, Tumorbiomarkerclinically actionable genescopy number alterationoral cavity squamous cell carcinomaultradeep-targeted sequencing

Identifiers

PMID26087196
PMCPMC4637328
OpenAlexW1846702883

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.