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Validation of OncoPanel: A Targeted Next-Generation Sequencing Assay for the Detection of Somatic Variants in Cancer

Overview of attention for article published in Archives of Pathology & Laboratory Medicine, March 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 (83rd percentile)
  • Average Attention Score compared to outputs of the same age and source

Mentioned by

blogs
1 blog
twitter
3 X users
patent
1 patent
facebook
1 Facebook page

Citations

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360 Dimensions

Readers on

mendeley
113 Mendeley
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Title
Validation of OncoPanel: A Targeted Next-Generation Sequencing Assay for the Detection of Somatic Variants in Cancer
Published in
Archives of Pathology & Laboratory Medicine, March 2017
DOI 10.5858/arpa.2016-0527-oa
Pubmed ID
Authors

Elizabeth P Garcia, Alissa Minkovsky, Yonghui Jia, Matthew D Ducar, Priyanka Shivdasani, Xin Gong, Azra H Ligon, Lynette M Sholl, Frank C Kuo, Laura E MacConaill, Neal I Lindeman, Fei Dong

Abstract

- The analysis of somatic mutations across multiple genes in cancer specimens may be used to aid clinical decision making. The analytical validation of targeted next-generation sequencing panels is important to assess accuracy and limitations. - To report the development and validation of OncoPanel, a custom targeted next-generation sequencing assay for cancer. - OncoPanel was designed for the detection of single-nucleotide variants, insertions and deletions, copy number alterations, and structural variants across 282 genes with evidence as drivers of cancer biology. We implemented a validation strategy using formalin-fixed, paraffin-embedded, fresh or frozen samples compared with results obtained by clinically validated orthogonal technologies. - OncoPanel achieved 98% sensitivity and 100% specificity for the detection of single-nucleotide variants, and 84% sensitivity and 100% specificity for the detection of insertions and deletions compared with single-gene assays and mass spectrometry-based genotyping. Copy number detection achieved 86% sensitivity and 98% specificity compared with array comparative genomic hybridization. The sensitivity of structural variant detection was 74% compared with karyotype, fluorescence in situ hybridization, and polymerase chain reaction. Sensitivity was affected by inconsistency in the detection of FLT3 and NPM1 alterations and IGH rearrangements due to design limitations. Limit of detection studies demonstrated 98.4% concordance across triplicate runs for variants with allele fraction greater than 0.1 and at least 50× coverage. - The analytical validation of OncoPanel demonstrates the ability of targeted next-generation sequencing to detect multiple types of genetic alterations across a panel of genes implicated in cancer biology.

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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 113 Mendeley readers of this research output. Click here to see the associated Mendeley record.

Geographical breakdown

Country Count As %
China 1 <1%
Unknown 112 99%

Demographic breakdown

Readers by professional status Count As %
Student > Ph. D. Student 21 19%
Researcher 20 18%
Other 15 13%
Student > Doctoral Student 7 6%
Student > Bachelor 6 5%
Other 11 10%
Unknown 33 29%
Readers by discipline Count As %
Medicine and Dentistry 36 32%
Biochemistry, Genetics and Molecular Biology 21 19%
Agricultural and Biological Sciences 10 9%
Computer Science 2 2%
Engineering 2 2%
Other 6 5%
Unknown 36 32%
Attention Score in Context

Attention Score in Context

This research output has an Altmetric Attention Score of 12. 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 27 October 2022.
All research outputs
#2,619,571
of 22,979,862 outputs
Outputs from Archives of Pathology & Laboratory Medicine
#662
of 2,557 outputs
Outputs of similar age
#50,897
of 310,507 outputs
Outputs of similar age from Archives of Pathology & Laboratory Medicine
#27
of 49 outputs
Altmetric has tracked 22,979,862 research outputs across all sources so far. Compared to these this one has done well and is in the 88th percentile: it's in the top 25% of all research outputs ever tracked by Altmetric.
So far Altmetric has tracked 2,557 research outputs from this source. They typically receive a lot more attention than average, with a mean Attention Score of 18.4. This one has gotten more attention than average, scoring higher than 74% 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 310,507 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 83% of its contemporaries.
We're also able to compare this research output to 49 others from the same source and published within six weeks on either side of this one. This one is in the 44th percentile – i.e., 44% of its contemporaries scored the same or lower than it.