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Depletion of somatic mutations in splicing-associated sequences in cancer genomes

Overview of attention for article published in Genome Biology (Online Edition), November 2017
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About this Attention Score

  • In the top 25% of all research outputs scored by Altmetric
  • High Attention Score compared to outputs of the same age (85th percentile)
  • Average Attention Score compared to outputs of the same age and source

Mentioned by

blogs
1 blog
twitter
8 tweeters

Citations

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11 Dimensions

Readers on

mendeley
43 Mendeley
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Title
Depletion of somatic mutations in splicing-associated sequences in cancer genomes
Published in
Genome Biology (Online Edition), November 2017
DOI 10.1186/s13059-017-1337-5
Pubmed ID
Authors

Laurence D. Hurst, Nizar N. Batada

Abstract

An important goal of cancer genomics is to identify systematically cancer-causing mutations. A common approach is to identify sites with high ratios of non-synonymous to synonymous mutations; however, if synonymous mutations are under purifying selection, this methodology leads to identification of false-positive mutations. Here, using synonymous somatic mutations (SSMs) identified in over 4000 tumours across 15 different cancer types, we sought to test this assumption by focusing on coding regions required for splicing. Exon flanks, which are enriched for sequences required for splicing fidelity, have ~ 17% lower SSM density compared to exonic cores, even after excluding canonical splice sites. While it is impossible to eliminate a mutation bias of unknown cause, multiple lines of evidence support a purifying selection model above a mutational bias explanation. The flank/core difference is not explained by skewed nucleotide content, replication timing, nucleosome occupancy or deficiency in mismatch repair. The depletion is not seen in tumour suppressors, consistent with their role in positive tumour selection, but is otherwise observed in cancer-associated and non-cancer genes, both essential and non-essential. Consistent with a role in splicing modulation, exonic splice enhancers have a lower SSM density before and after controlling for nucleotide composition; moreover, flanks at the 5' end of the exons have significantly lower SSM density than at the 3' end. These results suggest that the observable mutational spectrum of cancer genomes is not simply a product of various mutational processes and positive selection, but might also be shaped by negative selection.

Twitter Demographics

The data shown below were collected from the profiles of 8 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 43 Mendeley readers of this research output. Click here to see the associated Mendeley record.

Geographical breakdown

Country Count As %
Unknown 43 100%

Demographic breakdown

Readers by professional status Count As %
Student > Ph. D. Student 13 30%
Researcher 10 23%
Student > Doctoral Student 4 9%
Student > Bachelor 3 7%
Student > Postgraduate 3 7%
Other 6 14%
Unknown 4 9%
Readers by discipline Count As %
Biochemistry, Genetics and Molecular Biology 19 44%
Agricultural and Biological Sciences 13 30%
Physics and Astronomy 2 5%
Computer Science 1 2%
Medicine and Dentistry 1 2%
Other 1 2%
Unknown 6 14%

Attention Score in Context

This research output has an Altmetric Attention Score of 14. 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 November 2017.
All research outputs
#1,875,709
of 20,160,781 outputs
Outputs from Genome Biology (Online Edition)
#1,718
of 3,919 outputs
Outputs of similar age
#47,529
of 338,068 outputs
Outputs of similar age from Genome Biology (Online Edition)
#152
of 241 outputs
Altmetric has tracked 20,160,781 research outputs across all sources so far. Compared to these this one has done particularly well and is in the 90th percentile: it's in the top 10% of all research outputs ever tracked by Altmetric.
So far Altmetric has tracked 3,919 research outputs from this source. They typically receive a lot more attention than average, with a mean Attention Score of 27.0. This one has gotten more attention than average, scoring higher than 56% 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 338,068 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 241 others from the same source and published within six weeks on either side of this one. This one is in the 37th percentile – i.e., 37% of its contemporaries scored the same or lower than it.