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Implementation of next generation sequencing into pediatric hematology-oncology practice: moving beyond actionable alterations

Overview of attention for article published in Genome Medicine, December 2016
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About this Attention Score

  • In the top 5% of all research outputs scored by Altmetric
  • High Attention Score compared to outputs of the same age (94th percentile)
  • Good Attention Score compared to outputs of the same age and source (76th percentile)

Mentioned by

news
1 news outlet
blogs
1 blog
twitter
41 tweeters
facebook
2 Facebook pages
googleplus
1 Google+ user
reddit
1 Redditor

Citations

dimensions_citation
106 Dimensions

Readers on

mendeley
243 Mendeley
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Title
Implementation of next generation sequencing into pediatric hematology-oncology practice: moving beyond actionable alterations
Published in
Genome Medicine, December 2016
DOI 10.1186/s13073-016-0389-6
Pubmed ID
Authors

Jennifer A. Oberg, Julia L. Glade Bender, Maria Luisa Sulis, Danielle Pendrick, Anthony N. Sireci, Susan J. Hsiao, Andrew T. Turk, Filemon S. Dela Cruz, Hanina Hibshoosh, Helen Remotti, Rebecca J. Zylber, Jiuhong Pang, Daniel Diolaiti, Carrie Koval, Stuart J. Andrews, James H. Garvin, Darrell J. Yamashiro, Wendy K. Chung, Stephen G. Emerson, Peter L. Nagy, Mahesh M. Mansukhani, Andrew L. Kung

Abstract

Molecular characterization has the potential to advance the management of pediatric cancer and high-risk hematologic disease. The clinical integration of genome sequencing into standard clinical practice has been limited and the potential utility of genome sequencing to identify clinically impactful information beyond targetable alterations has been underestimated. The Precision in Pediatric Sequencing (PIPseq) Program at Columbia University Medical Center instituted prospective clinical next generation sequencing (NGS) for pediatric cancer and hematologic disorders at risk for treatment failure. We performed cancer whole exome sequencing (WES) of patient-matched tumor-normal samples and RNA sequencing (RNA-seq) of tumor to identify sequence variants, fusion transcripts, relative gene expression, and copy number variation (CNV). A directed cancer gene panel assay was used when sample adequacy was a concern. Constitutional WES of patients and parents was performed when a constitutionally encoded disease was suspected. Results were initially reviewed by a molecular pathologist and subsequently by a multi-disciplinary molecular tumor board. Clinical reports were issued to the ordering physician and posted to the patient's electronic medical record. NGS was performed on tumor and/or normal tissue from 101 high-risk pediatric patients. Potentially actionable alterations were identified in 38% of patients, of which only 16% subsequently received matched therapy. In an additional 38% of patients, the genomic data provided clinically relevant information of diagnostic, prognostic, or pharmacogenomic significance. RNA-seq was clinically impactful in 37/65 patients (57%) providing diagnostic and/or prognostic information for 17 patients (26%) and identified therapeutic targets in 15 patients (23%). Known or likely pathogenic germline alterations were discovered in 18/90 patients (20%) with 14% having germline alternations in cancer predisposition genes. American College of Medical Genetics (ACMG) secondary findings were identified in six patients. Our results demonstrate the feasibility of incorporating clinical NGS into pediatric hematology-oncology practice. Beyond the identification of actionable alterations, the ability to avoid ineffective/inappropriate therapies, make a definitive diagnosis, and identify pharmacogenomic modifiers is clinically impactful. Taking a more inclusive view of potential clinical utility, 66% of cases tested through our program had clinically impactful findings and samples interrogated with both WES and RNA-seq resulted in data that impacted clinical decisions in 75% of cases.

Twitter Demographics

The data shown below were collected from the profiles of 41 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 243 Mendeley readers of this research output. Click here to see the associated Mendeley record.

Geographical breakdown

Country Count As %
Portugal 1 <1%
Brazil 1 <1%
South Africa 1 <1%
Belgium 1 <1%
United States 1 <1%
Unknown 238 98%

Demographic breakdown

Readers by professional status Count As %
Student > Ph. D. Student 26 11%
Researcher 23 9%
Other 21 9%
Student > Bachelor 20 8%
Student > Master 16 7%
Other 31 13%
Unknown 106 44%
Readers by discipline Count As %
Medicine and Dentistry 39 16%
Biochemistry, Genetics and Molecular Biology 29 12%
Agricultural and Biological Sciences 20 8%
Pharmacology, Toxicology and Pharmaceutical Science 8 3%
Computer Science 5 2%
Other 27 11%
Unknown 115 47%

Attention Score in Context

This research output has an Altmetric Attention Score of 37. 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 02 March 2019.
All research outputs
#785,655
of 19,844,828 outputs
Outputs from Genome Medicine
#159
of 1,295 outputs
Outputs of similar age
#22,113
of 407,179 outputs
Outputs of similar age from Genome Medicine
#27
of 110 outputs
Altmetric has tracked 19,844,828 research outputs across all sources so far. Compared to these this one has done particularly well and is in the 96th percentile: it's in the top 5% of all research outputs ever tracked by Altmetric.
So far Altmetric has tracked 1,295 research outputs from this source. They typically receive a lot more attention than average, with a mean Attention Score of 23.6. This one has done well, scoring higher than 87% 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 407,179 tracked outputs that were published within six weeks on either side of this one in any source. This one has done particularly well, scoring higher than 94% of its contemporaries.
We're also able to compare this research output to 110 others from the same source and published within six weeks on either side of this one. This one has done well, scoring higher than 76% of its contemporaries.