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Next generation mapping reveals novel large genomic rearrangements in prostate cancer

Overview of attention for article published in Oncotarget, March 2017
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  • In the top 5% of all research outputs scored by Altmetric
  • High Attention Score compared to outputs of the same age (95th percentile)
  • High Attention Score compared to outputs of the same age and source (98th percentile)

Mentioned by

news
6 news outlets
twitter
18 tweeters

Citations

dimensions_citation
34 Dimensions

Readers on

mendeley
80 Mendeley
Title
Next generation mapping reveals novel large genomic rearrangements in prostate cancer
Published in
Oncotarget, March 2017
DOI 10.18632/oncotarget.15802
Pubmed ID
Authors

Weerachai Jaratlerdsiri, Eva K.F. Chan, Desiree C. Petersen, Claire Yang, Peter I. Croucher, M.S. Riana Bornman, Palak Sheth, Vanessa M. Hayes

Abstract

Complex genomic rearrangements are common molecular events driving prostate carcinogenesis. Clinical significance, however, has yet to be fully elucidated. Detecting the full range and subtypes of large structural variants (SVs), greater than one kilobase in length, is challenging using clinically feasible next generation sequencing (NGS) technologies. Next generation mapping (NGM) is a new technology that allows for the interrogation of megabase length DNA molecules outside the detection range of single-base resolution NGS. In this study, we sought to determine the feasibility of using the Irys (Bionano Genomics Inc.) nanochannel NGM technology to generate whole genome maps of a primary prostate tumor and matched blood from a Gleason score 7 (4 + 3), ETS-fusion negative prostate cancer patient. With an effective mapped coverage of 35X and sequence coverage of 60X, and an estimated 43% tumor purity, we identified 85 large somatic structural rearrangements and 6,172 smaller somatic variants, respectively. The vast majority of the large SVs (89%), of which 73% are insertions, were not detectable ab initio using high-coverage short-read NGS. However, guided manual inspection of single NGS reads and de novo assembled scaffolds of NGM-derived candidate regions allowed for confirmation of 94% of these large SVs, with over a third impacting genes with oncogenic potential. From this single-patient study, the first cancer study to integrate NGS and NGM data, we hypothesise that there exists a novel spectrum of large genomic rearrangements in prostate cancer, that these large genomic rearrangements are likely early events in tumorigenesis, and they have potential to enhance taxonomy.

Twitter Demographics

The data shown below were collected from the profiles of 18 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 80 Mendeley readers of this research output. Click here to see the associated Mendeley record.

Geographical breakdown

Country Count As %
Germany 1 1%
Unknown 79 99%

Demographic breakdown

Readers by professional status Count As %
Researcher 23 29%
Student > Ph. D. Student 22 28%
Student > Bachelor 8 10%
Student > Master 6 8%
Student > Postgraduate 4 5%
Other 8 10%
Unknown 9 11%
Readers by discipline Count As %
Biochemistry, Genetics and Molecular Biology 26 33%
Agricultural and Biological Sciences 18 23%
Computer Science 6 8%
Medicine and Dentistry 4 5%
Engineering 2 3%
Other 10 13%
Unknown 14 18%

Attention Score in Context

This research output has an Altmetric Attention Score of 57. 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 07 April 2019.
All research outputs
#470,463
of 17,897,867 outputs
Outputs from Oncotarget
#165
of 13,552 outputs
Outputs of similar age
#13,227
of 268,778 outputs
Outputs of similar age from Oncotarget
#13
of 831 outputs
Altmetric has tracked 17,897,867 research outputs across all sources so far. Compared to these this one has done particularly well and is in the 97th percentile: it's in the top 5% of all research outputs ever tracked by Altmetric.
So far Altmetric has tracked 13,552 research outputs from this source. They receive a mean Attention Score of 4.6. This one has done particularly well, scoring higher than 98% 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 268,778 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 95% of its contemporaries.
We're also able to compare this research output to 831 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 98% of its contemporaries.