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A computational tool to detect DNA alterations tailored to formalin-fixed paraffin-embedded samples in cancer clinical sequencing

Overview of attention for article published in Genome Medicine, June 2018
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About this Attention Score

  • Good Attention Score compared to outputs of the same age (66th percentile)

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3 X users
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1 patent

Citations

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49 Mendeley
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Title
A computational tool to detect DNA alterations tailored to formalin-fixed paraffin-embedded samples in cancer clinical sequencing
Published in
Genome Medicine, June 2018
DOI 10.1186/s13073-018-0547-0
Pubmed ID
Authors

Mamoru Kato, Hiromi Nakamura, Momoko Nagai, Takashi Kubo, Asmaa Elzawahry, Yasushi Totoki, Yuko Tanabe, Eisaku Furukawa, Joe Miyamoto, Hiromi Sakamoto, Shingo Matsumoto, Kuniko Sunami, Yasuhito Arai, Yutaka Suzuki, Teruhiko Yoshida, Katsuya Tsuchihara, Kenji Tamura, Noboru Yamamoto, Hitoshi Ichikawa, Takashi Kohno, Tatsuhiro Shibata

Abstract

Advanced cancer genomics technologies are now being employed in clinical sequencing, where next-generation sequencers are used to simultaneously identify multiple types of DNA alterations for prescription of molecularly targeted drugs. However, no computational tool is available to accurately detect DNA alterations in formalin-fixed paraffin-embedded (FFPE) samples commonly used in hospitals. Here, we developed a computational tool tailored to the detection of single nucleotide variations, indels, fusions, and copy number alterations in FFPE samples. Elaborated multilayer noise filters reduced the inherent noise while maintaining high sensitivity, as evaluated in tumor-unmatched normal samples using orthogonal technologies. This tool, cisCall, should facilitate clinical sequencing in everyday diagnostics. It is available at https://www.ciscall.org .

X Demographics

X Demographics

The data shown below were collected from the profiles of 3 X users who shared this research output. Click here to find out more about how the information was compiled.
Mendeley readers

Mendeley readers

The data shown below were compiled from readership statistics for 49 Mendeley readers of this research output. Click here to see the associated Mendeley record.

Geographical breakdown

Country Count As %
Unknown 49 100%

Demographic breakdown

Readers by professional status Count As %
Researcher 13 27%
Student > Master 10 20%
Student > Ph. D. Student 9 18%
Other 3 6%
Lecturer 2 4%
Other 4 8%
Unknown 8 16%
Readers by discipline Count As %
Biochemistry, Genetics and Molecular Biology 12 24%
Agricultural and Biological Sciences 11 22%
Computer Science 5 10%
Medicine and Dentistry 4 8%
Social Sciences 2 4%
Other 6 12%
Unknown 9 18%
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 17 March 2022.
All research outputs
#6,322,840
of 23,347,114 outputs
Outputs from Genome Medicine
#1,045
of 1,458 outputs
Outputs of similar age
#109,336
of 330,136 outputs
Outputs of similar age from Genome Medicine
#20
of 25 outputs
Altmetric has tracked 23,347,114 research outputs across all sources so far. This one has received more attention than most of these and is in the 72nd percentile.
So far Altmetric has tracked 1,458 research outputs from this source. They typically receive a lot more attention than average, with a mean Attention Score of 25.9. This one is in the 27th percentile – i.e., 27% of its peers scored the same or lower than it.
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 330,136 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 66% of its contemporaries.
We're also able to compare this research output to 25 others from the same source and published within six weeks on either side of this one. This one is in the 20th percentile – i.e., 20% of its contemporaries scored the same or lower than it.