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Optimizing cancer genome sequencing and analysis.

Overview of attention for article published in Cell Systems, September 2015
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About this Attention Score

  • In the top 5% of all research outputs scored by Altmetric
  • Among the highest-scoring outputs from this source (#30 of 380)
  • High Attention Score compared to outputs of the same age (97th percentile)
  • Good Attention Score compared to outputs of the same age and source (71st percentile)

Mentioned by

news
1 news outlet
twitter
134 tweeters
facebook
1 Facebook page
googleplus
1 Google+ user
q&a
1 Q&A thread

Readers on

mendeley
216 Mendeley
citeulike
2 CiteULike
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Title
Optimizing cancer genome sequencing and analysis.
Published in
Cell Systems, September 2015
DOI 10.1016/j.cels.2015.08.015
Pubmed ID
Authors

Malachi Griffith, Christopher A. Miller, Obi L. Griffith, Kilannin Krysiak, Zachary L. Skidmore, Avinash Ramu, Jason R. Walker, Ha X. Dang, Lee Trani, David E. Larson, Ryan T. Demeter, Michael C. Wendl, Joshua F. McMichael, Rachel E. Austin, Vincent Magrini, Sean D. McGrath, Amy Ly, Shashikant Kulkarni, Matthew G. Cordes, Catrina C. Fronick, Robert S. Fulton, Christopher A. Maher, Li Ding, Jeffery M. Klco, Elaine R. Mardis, Timothy J. Ley, Richard K. Wilson, Griffith, Malachi, Miller, Christopher A, Griffith, Obi L, Krysiak, Kilannin, Skidmore, Zachary L, Ramu, Avinash, Walker, Jason R, Dang, Ha X, Trani, Lee, Larson, David E, Demeter, Ryan T, Wendl, Michael C, McMichael, Joshua F, Austin, Rachel E, Magrini, Vincent, McGrath, Sean D, Ly, Amy, Kulkarni, Shashikant, Cordes, Matthew G, Fronick, Catrina C, Fulton, Robert S, Maher, Christopher A, Ding, Li, Klco, Jeffery M, Mardis, Elaine R, Ley, Timothy J, Wilson, Richard K

Abstract

Tumors are typically sequenced to depths of 75-100× (exome) or 30-50× (whole genome). We demonstrate that current sequencing paradigms are inadequate for tumors that are impure, aneuploid or clonally heterogeneous. To reassess optimal sequencing strategies, we performed ultra-deep (up to ~312×) whole genome sequencing (WGS) and exome capture (up to ~433×) of a primary acute myeloid leukemia, its subsequent relapse, and a matched normal skin sample. We tested multiple alignment and variant calling algorithms and validated ~200,000 putative SNVs by sequencing them to depths of ~1,000×. Additional targeted sequencing provided over 10,000× coverage and ddPCR assays provided up to ~250,000× sampling of selected sites. We evaluated the effects of different library generation approaches, depth of sequencing, and analysis strategies on the ability to effectively characterize a complex tumor. This dataset, representing the most comprehensively sequenced tumor described to date, will serve as an invaluable community resource (dbGaP accession id phs000159).

Twitter Demographics

The data shown below were collected from the profiles of 134 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 216 Mendeley readers of this research output. Click here to see the associated Mendeley record.

Geographical breakdown

Country Count As %
United States 5 2%
Italy 3 1%
United Kingdom 3 1%
Netherlands 2 <1%
Germany 1 <1%
Australia 1 <1%
Brazil 1 <1%
Ireland 1 <1%
Sweden 1 <1%
Other 5 2%
Unknown 193 89%

Demographic breakdown

Readers by professional status Count As %
Researcher 73 34%
Student > Ph. D. Student 59 27%
Student > Master 21 10%
Student > Bachelor 15 7%
Other 14 6%
Other 34 16%
Readers by discipline Count As %
Agricultural and Biological Sciences 100 46%
Biochemistry, Genetics and Molecular Biology 49 23%
Medicine and Dentistry 24 11%
Computer Science 22 10%
Unspecified 10 5%
Other 11 5%

Attention Score in Context

This research output has an Altmetric Attention Score of 88. 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 17 May 2018.
All research outputs
#130,716
of 10,768,289 outputs
Outputs from Cell Systems
#30
of 380 outputs
Outputs of similar age
#5,018
of 242,760 outputs
Outputs of similar age from Cell Systems
#4
of 14 outputs
Altmetric has tracked 10,768,289 research outputs across all sources so far. Compared to these this one has done particularly well and is in the 98th percentile: it's in the top 5% of all research outputs ever tracked by Altmetric.
So far Altmetric has tracked 380 research outputs from this source. They typically receive a lot more attention than average, with a mean Attention Score of 28.0. This one has done particularly well, scoring higher than 92% 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 242,760 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 97% of its contemporaries.
We're also able to compare this research output to 14 others from the same source and published within six weeks on either side of this one. This one has gotten more attention than average, scoring higher than 71% of its contemporaries.