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A new bioinformatics tool to help assess the significance of BRCA1 variants

Overview of attention for article published in Human Genomics, July 2018
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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 (#18 of 311)
  • High Attention Score compared to outputs of the same age (88th percentile)

Mentioned by

blogs
1 blog
twitter
14 tweeters
facebook
1 Facebook page

Citations

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5 Dimensions

Readers on

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20 Mendeley
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Title
A new bioinformatics tool to help assess the significance of BRCA1 variants
Published in
Human Genomics, July 2018
DOI 10.1186/s40246-018-0168-0
Pubmed ID
Authors

Isabelle Cusin, Daniel Teixeira, Monique Zahn-Zabal, Valentine Rech de Laval, Anne Gleizes, Valeria Viassolo, Pierre O. Chappuis, Pierre Hutter, Amos Bairoch, Pascale Gaudet

Abstract

Germline pathogenic variants in the breast cancer type 1 susceptibility gene BRCA1 are associated with a 60% lifetime risk for breast and ovarian cancer. This overall risk estimate is for all BRCA1 variants; obviously, not all variants confer the same risk of developing a disease. In cancer patients, loss of BRCA1 function in tumor tissue has been associated with an increased sensitivity to platinum agents and to poly-(ADP-ribose) polymerase (PARP) inhibitors. For clinical management of both at-risk individuals and cancer patients, it would be important that each identified genetic variant be associated with clinical significance. Unfortunately for the vast majority of variants, the clinical impact is unknown. The availability of results from studies assessing the impact of variants on protein function may provide insight of crucial importance. We have collected, curated, and structured the molecular and cellular phenotypic impact of 3654 distinct BRCA1 variants. The data was modeled in triple format, using the variant as a subject, the studied function as the object, and a predicate describing the relation between the two. Each annotation is supported by a fully traceable evidence. The data was captured using standard ontologies to ensure consistency, and enhance searchability and interoperability. We have assessed the extent to which functional defects at the molecular and cellular levels correlate with the clinical interpretation of variants by ClinVar submitters. Approximately 30% of the ClinVar BRCA1 missense variants have some molecular or cellular assay available in the literature. Pathogenic variants (as assigned by ClinVar) have at least some significant functional defect in 94% of testable cases. For benign variants, 77% of ClinVar benign variants, for which neXtProt Cancer variant portal has data, shows either no or mild experimental functional defects. While this does not provide evidence for clinical interpretation of variants, it may provide some guidance for variants of unknown significance, in the absence of more reliable data. The neXtProt Cancer variant portal ( https://www.nextprot.org/portals/breast-cancer ) contains over 6300 observations at the molecular and/or cellular level for BRCA1 variants.

Twitter Demographics

The data shown below were collected from the profiles of 14 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 20 Mendeley readers of this research output. Click here to see the associated Mendeley record.

Geographical breakdown

Country Count As %
Unknown 20 100%

Demographic breakdown

Readers by professional status Count As %
Researcher 7 35%
Student > Master 3 15%
Student > Bachelor 3 15%
Student > Ph. D. Student 2 10%
Student > Doctoral Student 1 5%
Other 1 5%
Unknown 3 15%
Readers by discipline Count As %
Biochemistry, Genetics and Molecular Biology 9 45%
Medicine and Dentistry 3 15%
Computer Science 2 10%
Immunology and Microbiology 2 10%
Agricultural and Biological Sciences 1 5%
Other 0 0%
Unknown 3 15%

Attention Score in Context

This research output has an Altmetric Attention Score of 19. 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 20 September 2019.
All research outputs
#1,066,085
of 15,882,393 outputs
Outputs from Human Genomics
#18
of 311 outputs
Outputs of similar age
#31,468
of 276,455 outputs
Outputs of similar age from Human Genomics
#1
of 1 outputs
Altmetric has tracked 15,882,393 research outputs across all sources so far. Compared to these this one has done particularly well and is in the 93rd percentile: it's in the top 10% of all research outputs ever tracked by Altmetric.
So far Altmetric has tracked 311 research outputs from this source. They typically receive a little more attention than average, with a mean Attention Score of 6.6. This one has done particularly well, scoring higher than 94% 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 276,455 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 88% 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