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A workflow to increase verification rate of chromosomal structural rearrangements using high-throughput next-generation sequencing

Overview of attention for article published in Biotechniques, July 2014
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About this Attention Score

  • Above-average Attention Score compared to outputs of the same age (61st percentile)

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1 Google+ user

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Title
A workflow to increase verification rate of chromosomal structural rearrangements using high-throughput next-generation sequencing
Published in
Biotechniques, July 2014
DOI 10.2144/000114189
Pubmed ID
Authors

Kelly Quek, Katia Nones, Ann-Marie Patch, J. Lynn Fink, Felicity Newell, Nicole Cloonan, David Miller, Muhammad Z. H. Fadlullah, Karin Kassahn, Angelika N. Christ, Timothy J. C. Bruxner, Suzanne Manning, Ivon Harliwong, Senel Idrisoglu, Craig Nourse, Ehsan Nourbakhsh, Shivangi Wani, Anita Steptoe, Matthew Anderson, Oliver Holmes, Conrad Leonard, Darrin Taylor, Scott Wood, Qinying Xu, Peter Wilson, Andrew V. Biankin, John V. Pearson, Nic Waddell, Sean M. Grimmond

Abstract

Somatic rearrangements, which are commonly found in human cancer genomes, contribute to the progression and maintenance of cancers. Conventionally, the verification of somatic rearrangements comprises many manual steps and Sanger sequencing. This is labor intensive when verifying a large number of rearrangements in a large cohort. To increase the verification throughput, we devised a high-throughput workflow that utilizes benchtop next-generation sequencing and in-house bioinformatics tools to link the laboratory processes. In the proposed workflow, primers are automatically designed. PCR and an optional gel electrophoresis step to confirm the somatic nature of the rearrangements are performed. PCR products of somatic events are pooled for Ion Torrent PGM and/or Illumina MiSeq sequencing, the resulting sequence reads are assembled into consensus contigs by a consensus assembler, and an automated BLAT is used to resolve the breakpoints to base level. We compared sequences and breakpoints of verified somatic rearrangements between the conventional and high-throughput workflow. The results showed that next-generation sequencing methods are comparable to conventional Sanger sequencing. The identified breakpoints obtained from next-generation sequencing methods were highly accurate and reproducible. Furthermore, the proposed workflow allows hundreds of events to be processed in a shorter time frame compared with the conventional workflow.

Twitter Demographics

The data shown below were collected from the profiles of 2 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 35 Mendeley readers of this research output. Click here to see the associated Mendeley record.

Geographical breakdown

Country Count As %
United States 1 3%
Singapore 1 3%
Australia 1 3%
Unknown 32 91%

Demographic breakdown

Readers by professional status Count As %
Student > Ph. D. Student 9 26%
Researcher 9 26%
Professor 4 11%
Student > Master 4 11%
Other 3 9%
Other 5 14%
Unknown 1 3%
Readers by discipline Count As %
Agricultural and Biological Sciences 14 40%
Biochemistry, Genetics and Molecular Biology 8 23%
Medicine and Dentistry 4 11%
Computer Science 1 3%
Immunology and Microbiology 1 3%
Other 3 9%
Unknown 4 11%

Attention Score in Context

This research output has an Altmetric Attention Score of 2. 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 11 July 2014.
All research outputs
#3,681,971
of 8,073,544 outputs
Outputs from Biotechniques
#165
of 289 outputs
Outputs of similar age
#66,678
of 178,135 outputs
Outputs of similar age from Biotechniques
#1
of 3 outputs
Altmetric has tracked 8,073,544 research outputs across all sources so far. This one has received more attention than most of these and is in the 53rd percentile.
So far Altmetric has tracked 289 research outputs from this source. They receive a mean Attention Score of 2.7. This one is in the 41st percentile – i.e., 41% 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 178,135 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 61% of its contemporaries.
We're also able to compare this research output to 3 others from the same source and published within six weeks on either side of this one. This one has scored higher than all of them