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Development and analytical validation of a 25-gene next generation sequencing panel that includes the BRCA1 and BRCA2 genes to assess hereditary cancer risk

Overview of attention for article published in BMC Cancer, April 2015
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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 (88th percentile)
  • High Attention Score compared to outputs of the same age and source (94th percentile)

Mentioned by

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1 blog
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6 X users
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1 patent
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1 weibo user

Citations

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95 Dimensions

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116 Mendeley
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Title
Development and analytical validation of a 25-gene next generation sequencing panel that includes the BRCA1 and BRCA2 genes to assess hereditary cancer risk
Published in
BMC Cancer, April 2015
DOI 10.1186/s12885-015-1224-y
Pubmed ID
Authors

Thaddeus Judkins, Benoît Leclair, Karla Bowles, Natalia Gutin, Jeff Trost, James McCulloch, Satish Bhatnagar, Adam Murray, Jonathan Craft, Bryan Wardell, Mark Bastian, Jeffrey Mitchell, Jian Chen, Thanh Tran, Deborah Williams, Jennifer Potter, Srikanth Jammulapati, Michael Perry, Brian Morris, Benjamin Roa, Kirsten Timms

Abstract

Germline DNA mutations that increase the susceptibility of a patient to certain cancers have been identified in various genes, and patients can be screened for mutations in these genes to assess their level of risk for developing cancer. Traditional methods using Sanger sequencing focus on small groups of genes and therefore are unable to screen for numerous genes from several patients simultaneously. The goal of the present study was to validate a 25-gene panel to assess genetic risk for cancer in 8 different tissues using next generation sequencing (NGS) techniques. Twenty-five genes associated with hereditary cancer syndromes were selected for development of a panel to screen for risk of these cancers using NGS. In an initial technical assessment, NGS results for BRCA1 and BRCA2 were compared with Sanger sequencing in 1864 anonymized DNA samples from patients who had undergone previous clinical testing. Next, the entire gene panel was validated using parallel NGS and Sanger sequencing in 100 anonymized DNA samples. Large rearrangement analysis was validated using NGS, microarray comparative genomic hybridization (CGH), and multiplex ligation-dependent probe amplification analyses (MLPA). NGS identified 15,877 sequence variants, while Sanger sequencing identified 15,878 in the BRCA1 and BRCA2 comparison study of the same regions. Based on these results, the NGS process was refined prior to the validation of the full gene panel. In the validation study, NGS and Sanger sequencing were 100% concordant for the 3,923 collective variants across all genes for an analytical sensitivity of the NGS assay of >99.92% (lower limit of 95% confidence interval). NGS, microarray CGH and MLPA correctly identified all expected positive and negative large rearrangement results for the 25-gene panel. This study provides a thorough validation of the 25-gene NGS panel and indicates that this analysis tool can be used to collect clinically significant information related to risk of developing hereditary cancers.

X Demographics

X Demographics

The data shown below were collected from the profiles of 6 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 116 Mendeley readers of this research output. Click here to see the associated Mendeley record.

Geographical breakdown

Country Count As %
United States 1 <1%
Brazil 1 <1%
Unknown 114 98%

Demographic breakdown

Readers by professional status Count As %
Researcher 28 24%
Student > Master 16 14%
Student > Ph. D. Student 12 10%
Student > Postgraduate 8 7%
Other 8 7%
Other 20 17%
Unknown 24 21%
Readers by discipline Count As %
Biochemistry, Genetics and Molecular Biology 36 31%
Medicine and Dentistry 26 22%
Agricultural and Biological Sciences 22 19%
Nursing and Health Professions 2 2%
Economics, Econometrics and Finance 2 2%
Other 4 3%
Unknown 24 21%
Attention Score in Context

Attention Score in Context

This research output has an Altmetric Attention Score of 15. 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 01 June 2019.
All research outputs
#2,119,684
of 22,799,071 outputs
Outputs from BMC Cancer
#361
of 8,296 outputs
Outputs of similar age
#29,192
of 263,851 outputs
Outputs of similar age from BMC Cancer
#13
of 257 outputs
Altmetric has tracked 22,799,071 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 8,296 research outputs from this source. They receive a mean Attention Score of 4.3. This one has done particularly well, scoring higher than 95% 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 263,851 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 88% of its contemporaries.
We're also able to compare this research output to 257 others from the same source and published within six weeks on either side of this one. This one has done particularly well, scoring higher than 94% of its contemporaries.