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X Demographics
Mendeley readers
Attention Score in Context
| Title |
Tools for translational epigenetic studies involving formalin-fixed paraffin-embedded human tissue: applying the Infinium HumanMethyation450 Beadchip assay to large population-based studies
|
|---|---|
| Published in |
BMC Research Notes, October 2015
|
| DOI | 10.1186/s13104-015-1487-z |
| Pubmed ID | |
| Authors |
Ee Ming Wong, JiHoon E. Joo, Catriona A. McLean, Laura Baglietto, Dallas R. English, Gianluca Severi, John L. Hopper, Roger L. Milne, Liesel M. FitzGerald, Graham G. Giles, Melissa C. Southey |
| Abstract |
Large population-based translational epigenetic studies are emerging due to recent technological advances that have made molecular analyses possible. For example, the Infinium HumanMethylation450 Beadchip (HM450K) has enabled studies of genome-wide methylation on a scale not previously possible. However, application of the HM450K to DNA extracted from formalin-fixed paraffin-embedded (FFPE) tumour material has been more challenging than application to high quality DNA extracted from blood. To facilitate the application of this assay consistently across a large number of FFPE tumour-enriched DNA samples we have devised a modification to the HM450K protocol for FFPE that includes an additional quality control (QC) checkpoint. QC checkpoint 3 was designed to assess the presence of DNA after bisulfite conversion and restoration, just prior to application of the HM450K assay. DNA was extracted from 474 archival FFPE breast tumour material. Five samples did not have a detectable amount of DNA with an additional 42 failing to progress past QC checkpoint 3. Genome-wide methylation was measured for the remaining 428 tumour-enriched DNA. Of these, only 4 samples failed our stringent HM450K data criteria thus representing a 99 % success rate. Using prior knowledge about methylation marks associated with breast cancer we further explored the quality of the data. Twenty probes in the BRCA1 promoter region showed increased methylation in triple-negative breast cancers compared to Luminal A, Luminal B and HER2-positive breast cancer subtypes. Validation of this observation in published data from The Cancer Genome Atlas (TCGA) Network (obtained from DNA extracted from fresh frozen tumour samples) confirms the quality of the data obtained from the improved protocol. The modified protocol is suitable for the analysis of FFPE tumour-enriched DNA and can be systematically applied to hundreds of samples. This protocol will have utility in population-based translational epigenetic studies and is applicable to a wide variety of translated studies interested in analysis of methylation and its role in the predisposition to disease and disease progression. |
X Demographics
The data shown below were collected from the profiles of 19 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 | 3 | 16% |
| United Kingdom | 3 | 16% |
| Belgium | 1 | 5% |
| Singapore | 1 | 5% |
| Tunisia | 1 | 5% |
| France | 1 | 5% |
| Unknown | 9 | 47% |
Demographic breakdown
| Type | Count | As % |
|---|---|---|
| Members of the public | 15 | 79% |
| Scientists | 4 | 21% |
Mendeley readers
The data shown below were compiled from readership statistics for 28 Mendeley readers of this research output. Click here to see the associated Mendeley record.
Geographical breakdown
| Country | Count | As % |
|---|---|---|
| Unknown | 28 | 100% |
Demographic breakdown
| Readers by professional status | Count | As % |
|---|---|---|
| Student > Ph. D. Student | 6 | 21% |
| Other | 4 | 14% |
| Student > Bachelor | 3 | 11% |
| Researcher | 3 | 11% |
| Student > Master | 2 | 7% |
| Other | 6 | 21% |
| Unknown | 4 | 14% |
| Readers by discipline | Count | As % |
|---|---|---|
| Medicine and Dentistry | 9 | 32% |
| Biochemistry, Genetics and Molecular Biology | 6 | 21% |
| Agricultural and Biological Sciences | 3 | 11% |
| Pharmacology, Toxicology and Pharmaceutical Science | 2 | 7% |
| Business, Management and Accounting | 1 | 4% |
| Other | 2 | 7% |
| Unknown | 5 | 18% |
Attention Score in Context
This research output has an Altmetric Attention Score of 12. 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 October 2015.
All research outputs
#3,077,825
of 25,393,528 outputs
Outputs from BMC Research Notes
#417
of 4,514 outputs
Outputs of similar age
#40,576
of 289,784 outputs
Outputs of similar age from BMC Research Notes
#8
of 187 outputs
Altmetric has tracked 25,393,528 research outputs across all sources so far. Compared to these this one has done well and is in the 87th percentile: it's in the top 25% of all research outputs ever tracked by Altmetric.
So far Altmetric has tracked 4,514 research outputs from this source. They typically receive a little more attention than average, with a mean Attention Score of 6.1. This one has done particularly well, scoring higher than 90% 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 289,784 tracked outputs that were published within six weeks on either side of this one in any source. This one has done well, scoring higher than 85% of its contemporaries.
We're also able to compare this research output to 187 others from the same source and published within six weeks on either side of this one. This one has done particularly well, scoring higher than 96% of its contemporaries.