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X Demographics
Mendeley readers
Attention Score in Context
| Title |
Genome-scale methylation assessment did not identify prognostic biomarkers in oral tongue carcinomas
|
|---|---|
| Published in |
Clinical Epigenetics, July 2016
|
| DOI | 10.1186/s13148-016-0235-0 |
| Pubmed ID | |
| Authors |
Annette M. Lim, Nicholas C. Wong, Ruth Pidsley, Elena Zotenko, June Corry, Alexander Dobrovic, Susan J. Clark, Danny Rischin, Benjamin Solomon |
| Abstract |
DNA methylation profiling of heterogeneous head and neck squamous cell carcinoma (HNSCC) cohorts has been reported to predict patient outcome. We investigated if a prognostic DNA methylation profile could be found in tumour tissue from a single uniform subsite, the oral tongue. The methylation status of 109 comprehensively annotated oral tongue squamous cell carcinoma (OTSCC) formalin-fixed paraffin-embedded (FFPE) samples from a single institution were examined with the Illumina HumanMethylation450K (HM450K) array. Data pre-processing, quality control and analysis were performed using R packages. Probes mapping to SNPs, sex chromosomes and unreliable probes were accounted for prior to downstream analyses. The relationship between methylation and patient survival was examined using both agnostic approaches and feature selection. The cohort was enlarged by incorporation of 331 The Cancer Genome Atlas (TCGA) HNSCC samples, which included 91 TCGA OTSCC samples with HM450K and survival data available. Given the use of FFPE-derived DNA, we defined different cohorts for separate analyses. Overall, similar results were found between cohorts. With an unsupervised approach, no distinct hypermethylated group of samples was identified and nor was a prognostic methylation profile identified. The use of multiple downstream feature selection approaches, including a linear models for microarray data (LIMMA), centroid feature selection (CFS), and recursive feature elimination (RFE) support vector machines, similarly failed to identify a significant methylation signature informative for patient prognosis or any clinicopathological data available. Furthermore, we were unable to confirm the prognostic methylation profiles or specific prognostic loci reported within the literature for HNSCC. With genome-scale assessment of DNA methylation using HM450K in one of the largest OTSCC cohorts to date, we were unable to identify a hypermethylated group of tumours or a prognostic methylation signature. This suggests that either DNA methylation in isolation is not likely to be of prognostic value or larger cohorts are required to identify such a biomarker for OTSCC. |
X Demographics
The data shown below were collected from the profiles of 8 X users who shared this research output. Click here to find out more about how the information was compiled.
Geographical breakdown
| Country | Count | As % |
|---|---|---|
| United States | 2 | 25% |
| Australia | 1 | 13% |
| United Kingdom | 1 | 13% |
| France | 1 | 13% |
| Unknown | 3 | 38% |
Demographic breakdown
| Type | Count | As % |
|---|---|---|
| Members of the public | 5 | 63% |
| Scientists | 3 | 38% |
Mendeley readers
The data shown below were compiled from readership statistics for 41 Mendeley readers of this research output. Click here to see the associated Mendeley record.
Geographical breakdown
| Country | Count | As % |
|---|---|---|
| Uruguay | 1 | 2% |
| Unknown | 40 | 98% |
Demographic breakdown
| Readers by professional status | Count | As % |
|---|---|---|
| Other | 6 | 15% |
| Student > Bachelor | 6 | 15% |
| Researcher | 5 | 12% |
| Student > Doctoral Student | 4 | 10% |
| Student > Postgraduate | 4 | 10% |
| Other | 9 | 22% |
| Unknown | 7 | 17% |
| Readers by discipline | Count | As % |
|---|---|---|
| Medicine and Dentistry | 17 | 41% |
| Agricultural and Biological Sciences | 5 | 12% |
| Biochemistry, Genetics and Molecular Biology | 3 | 7% |
| Engineering | 3 | 7% |
| Nursing and Health Professions | 2 | 5% |
| Other | 3 | 7% |
| Unknown | 8 | 20% |
Attention Score in Context
This research output has an Altmetric Attention Score of 4. This is our high-level measure of the quality and quantity of online attention that it has received. This Attention Score, as well as the ranking and number of research outputs shown below, was calculated when the research output was last mentioned on 23 July 2016.
All research outputs
#6,816,146
of 22,880,691 outputs
Outputs from Clinical Epigenetics
#463
of 1,259 outputs
Outputs of similar age
#108,899
of 393,699 outputs
Outputs of similar age from Clinical Epigenetics
#25
of 47 outputs
Altmetric has tracked 22,880,691 research outputs across all sources so far. This one has received more attention than most of these and is in the 69th percentile.
So far Altmetric has tracked 1,259 research outputs from this source. They typically receive a little more attention than average, with a mean Attention Score of 6.5. This one has gotten more attention than average, scoring higher than 61% of its peers.
Older research outputs will score higher simply because they've had more time to accumulate mentions. To account for age we can compare this Altmetric Attention Score to the 393,699 tracked outputs that were published within six weeks on either side of this one in any source. This one has gotten more attention than average, scoring higher than 71% of its contemporaries.
We're also able to compare this research output to 47 others from the same source and published within six weeks on either side of this one. This one is in the 42nd percentile – i.e., 42% of its contemporaries scored the same or lower than it.