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A pipeline combining multiple strategies for prioritizing heterozygous variants for the identification of candidate genes in exome datasets

Overview of attention for article published in Human Genomics, May 2017
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  • Good Attention Score compared to outputs of the same age (67th percentile)

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Title
A pipeline combining multiple strategies for prioritizing heterozygous variants for the identification of candidate genes in exome datasets
Published in
Human Genomics, May 2017
DOI 10.1186/s40246-017-0107-5
Pubmed ID
Authors

Teresa Requena, Alvaro Gallego-Martinez, Jose A. Lopez-Escamez

Abstract

The identification of disease-causing variants in autosomal dominant diseases using exome-sequencing data remains a difficult task in small pedigrees. We combined several strategies to improve filtering and prioritizing of heterozygous variants using exome-sequencing datasets in familial Meniere disease: an in-house Pathogenic Variant (PAVAR) score, the Variant Annotation Analysis and Search Tool (VAAST-Phevor), Exomiser-v2, CADD, and FATHMM. We also validated the method by a benchmarking procedure including causal mutations in synthetic exome datasets. PAVAR and VAAST were able to select the same sets of candidate variants independently of the studied disease. In contrast, Exomiser V2 and VAAST-Phevor had a variable correlation depending on the phenotypic information available for the disease on each family. Nevertheless, all the selected diseases ranked a limited number of concordant variants in the top 10 ranking, using the three systems or other combined algorithm such as CADD or FATHMM. Benchmarking analyses confirmed that the combination of systems with different approaches improves the prediction of candidate variants compared with the use of a single method. The overall efficiency of combined tools ranges between 68 and 71% in the top 10 ranked variants. Our pipeline prioritizes a short list of heterozygous variants in exome datasets based on the top 10 concordant variants combining multiple systems.

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Mendeley readers

Mendeley readers

The data shown below were compiled from readership statistics for 70 Mendeley readers of this research output. Click here to see the associated Mendeley record.

Geographical breakdown

Country Count As %
China 1 1%
Unknown 69 99%

Demographic breakdown

Readers by professional status Count As %
Researcher 11 16%
Student > Ph. D. Student 9 13%
Student > Master 9 13%
Other 8 11%
Student > Bachelor 6 9%
Other 12 17%
Unknown 15 21%
Readers by discipline Count As %
Biochemistry, Genetics and Molecular Biology 24 34%
Medicine and Dentistry 13 19%
Agricultural and Biological Sciences 7 10%
Engineering 3 4%
Computer Science 2 3%
Other 4 6%
Unknown 17 24%
Attention Score in Context

Attention Score in Context

This research output has an Altmetric Attention Score of 5. 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 29 April 2018.
All research outputs
#7,121,912
of 25,382,440 outputs
Outputs from Human Genomics
#171
of 564 outputs
Outputs of similar age
#105,549
of 327,324 outputs
Outputs of similar age from Human Genomics
#5
of 7 outputs
Altmetric has tracked 25,382,440 research outputs across all sources so far. This one has received more attention than most of these and is in the 71st percentile.
So far Altmetric has tracked 564 research outputs from this source. They typically receive more attention than average, with a mean Attention Score of 8.0. This one has gotten more attention than average, scoring higher than 69% 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 327,324 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 67% of its contemporaries.
We're also able to compare this research output to 7 others from the same source and published within six weeks on either side of this one. This one has scored higher than 2 of them.