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Using next-generation sequencing for high resolution multiplex analysis of copy number variation from nanogram quantities of DNA from formalin-fixed paraffin-embedded specimens

Overview of attention for article published in Nucleic Acids Research, June 2010
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Mentioned by

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105 patents

Citations

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94 Dimensions

Readers on

mendeley
178 Mendeley
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4 CiteULike
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2 Connotea
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Title
Using next-generation sequencing for high resolution multiplex analysis of copy number variation from nanogram quantities of DNA from formalin-fixed paraffin-embedded specimens
Published in
Nucleic Acids Research, June 2010
DOI 10.1093/nar/gkq510
Pubmed ID
Authors

Henry M. Wood, Ornella Belvedere, Caroline Conway, Catherine Daly, Rebecca Chalkley, Melissa Bickerdike, Claire McKinley, Phil Egan, Lisa Ross, Bruce Hayward, Joanne Morgan, Leslie Davidson, Ken MacLennan, Thian K. Ong, Kostas Papagiannopoulos, Ian Cook, David J. Adams, Graham R. Taylor, Pamela Rabbitts

Abstract

The use of next-generation sequencing technologies to produce genomic copy number data has recently been described. Most approaches, however, reply on optimal starting DNA, and are therefore unsuitable for the analysis of formalin-fixed paraffin-embedded (FFPE) samples, which largely precludes the analysis of many tumour series. We have sought to challenge the limits of this technique with regards to quality and quantity of starting material and the depth of sequencing required. We confirm that the technique can be used to interrogate DNA from cell lines, fresh frozen material and FFPE samples to assess copy number variation. We show that as little as 5 ng of DNA is needed to generate a copy number karyogram, and follow this up with data from a series of FFPE biopsies and surgical samples. We have used various levels of sample multiplexing to demonstrate the adjustable resolution of the methodology, depending on the number of samples and available resources. We also demonstrate reproducibility by use of replicate samples and comparison with microarray-based comparative genomic hybridization (aCGH) and digital PCR. This technique can be valuable in both the analysis of routine diagnostic samples and in examining large repositories of fixed archival material.

Mendeley readers

The data shown below were compiled from readership statistics for 178 Mendeley readers of this research output. Click here to see the associated Mendeley record.

Geographical breakdown

Country Count As %
United States 5 3%
United Kingdom 5 3%
Netherlands 4 2%
Brazil 2 1%
Finland 1 <1%
Sweden 1 <1%
France 1 <1%
Belgium 1 <1%
Spain 1 <1%
Other 2 1%
Unknown 155 87%

Demographic breakdown

Readers by professional status Count As %
Researcher 53 30%
Student > Ph. D. Student 38 21%
Student > Master 14 8%
Professor > Associate Professor 14 8%
Other 10 6%
Other 37 21%
Unknown 12 7%
Readers by discipline Count As %
Agricultural and Biological Sciences 85 48%
Medicine and Dentistry 41 23%
Biochemistry, Genetics and Molecular Biology 20 11%
Computer Science 7 4%
Engineering 2 1%
Other 8 4%
Unknown 15 8%

Attention Score in Context

This research output has an Altmetric Attention Score of 3. 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 May 2021.
All research outputs
#5,840,385
of 17,921,525 outputs
Outputs from Nucleic Acids Research
#10,360
of 23,990 outputs
Outputs of similar age
#35,690
of 103,185 outputs
Outputs of similar age from Nucleic Acids Research
#63
of 170 outputs
Altmetric has tracked 17,921,525 research outputs across all sources so far. This one is in the 47th percentile – i.e., 47% of other outputs scored the same or lower than it.
So far Altmetric has tracked 23,990 research outputs from this source. They typically receive a little more attention than average, with a mean Attention Score of 5.8. This one is in the 26th percentile – i.e., 26% 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 103,185 tracked outputs that were published within six weeks on either side of this one in any source. This one is in the 41st percentile – i.e., 41% of its contemporaries scored the same or lower than it.
We're also able to compare this research output to 170 others from the same source and published within six weeks on either side of this one. This one is in the 48th percentile – i.e., 48% of its contemporaries scored the same or lower than it.