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Comparing gene expression data from formalin-fixed, paraffin embedded tissues and qPCR with that from snap-frozen tissue and microarrays for modeling outcomes of patients with ovarian carcinoma

Overview of attention for article published in BMC Clinical Pathology, September 2015
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About this Attention Score

  • In the top 25% of all research outputs scored by Altmetric
  • Among the highest-scoring outputs from this source (#11 of 113)
  • Good Attention Score compared to outputs of the same age (78th percentile)

Mentioned by

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11 tweeters

Citations

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5 Dimensions

Readers on

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25 Mendeley
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Title
Comparing gene expression data from formalin-fixed, paraffin embedded tissues and qPCR with that from snap-frozen tissue and microarrays for modeling outcomes of patients with ovarian carcinoma
Published in
BMC Clinical Pathology, September 2015
DOI 10.1186/s12907-015-0017-1
Pubmed ID
Authors

William H. Bradley, Kevin Eng, Min Le, A. Craig Mackinnon, Christina Kendziorski, Janet S. Rader

Abstract

Previously, we have used clinical and gene expression data from The Cancer Genome Atlas (TCGA) to model a pathway-based index predicting outcomes in ovarian carcinoma. This data were obtained from snap-frozen tissue measured with the Affymetrix U133 platform. In the current study, we correlate the data used to model with data derived from TaqMan qPCR both snap frozen and paraffin embedded (FFPE) samples. To compare the effect of preservation methods on gene expression measured by qPCR, we assessed 18 patient and tumor sample matched snap-frozen and FFPE ovarian carcinoma samples. To compare gene measurement technologies, we correlated qPCR data from 10 patients with tumor sample matched snap-frozen ovarian carcinoma samples with the microarray data from TCGA. We normalized results to the average expression of three housekeeping genes. We scaled and centered the data for comparison to the Affymetrix output. For the 18 specimens, gene expression data obtained from snap-frozen tissue correlated highly with that from FFPE samples in our TaqMan assay (r > 0.82). For the 10 duplicate TCGA specimens, the reported microarray data correlated well (r = 0.6) with our qPCR data, and ranges of expression along pathways were similar. Gene expression data obtained by qPCR from FFPE serous ovarian carcinoma samples can be used to assess in the pathway-based predictive model. The normalization procedures described control variations in expression, and the range calculated along a specific pathway can be interpreted for a patient's risk profile.

Twitter Demographics

The data shown below were collected from the profiles of 11 tweeters who shared this research output. Click here to find out more about how the information was compiled.

Mendeley readers

The data shown below were compiled from readership statistics for 25 Mendeley readers of this research output. Click here to see the associated Mendeley record.

Geographical breakdown

Country Count As %
United Kingdom 1 4%
Unknown 24 96%

Demographic breakdown

Readers by professional status Count As %
Student > Ph. D. Student 6 24%
Researcher 4 16%
Student > Master 4 16%
Other 3 12%
Professor 2 8%
Other 3 12%
Unknown 3 12%
Readers by discipline Count As %
Medicine and Dentistry 6 24%
Biochemistry, Genetics and Molecular Biology 6 24%
Agricultural and Biological Sciences 4 16%
Nursing and Health Professions 1 4%
Mathematics 1 4%
Other 2 8%
Unknown 5 20%

Attention Score in Context

This research output has an Altmetric Attention Score of 6. 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
#2,867,787
of 12,913,752 outputs
Outputs from BMC Clinical Pathology
#11
of 113 outputs
Outputs of similar age
#54,103
of 247,388 outputs
Outputs of similar age from BMC Clinical Pathology
#1
of 1 outputs
Altmetric has tracked 12,913,752 research outputs across all sources so far. Compared to these this one has done well and is in the 77th percentile: it's in the top 25% of all research outputs ever tracked by Altmetric.
So far Altmetric has tracked 113 research outputs from this source. They receive a mean Attention Score of 3.0. This one has done well, scoring higher than 89% 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 247,388 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 78% of its contemporaries.
We're also able to compare this research output to 1 others from the same source and published within six weeks on either side of this one. This one has scored higher than all of them