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High-depth whole genome sequencing of an Ashkenazi Jewish reference panel: enhancing sensitivity, accuracy, and imputation

Overview of attention for article published in Human Genetics, April 2018
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  • Above-average Attention Score compared to outputs of the same age and source (58th percentile)

Mentioned by

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3 tweeters

Citations

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22 Mendeley
Title
High-depth whole genome sequencing of an Ashkenazi Jewish reference panel: enhancing sensitivity, accuracy, and imputation
Published in
Human Genetics, April 2018
DOI 10.1007/s00439-018-1886-z
Pubmed ID
Authors

Todd Lencz, Jin Yu, Cameron Palmer, Shai Carmi, Danny Ben-Avraham, Nir Barzilai, Susan Bressman, Ariel Darvasi, Judy H. Cho, Lorraine N. Clark, Zeynep H. Gümüş, Vijai Joseph, Robert Klein, Steven Lipkin, Kenneth Offit, Harry Ostrer, Laurie J. Ozelius, Inga Peter, Gil Atzmon, Itsik Pe’er

Abstract

While increasingly large reference panels for genome-wide imputation have been recently made available, the degree to which imputation accuracy can be enhanced by population-specific reference panels remains an open question. Here, we sequenced at full-depth (≥ 30×), across two platforms (Illumina X Ten and Complete Genomics, Inc.), a moderately large (n = 738) cohort of samples drawn from the Ashkenazi Jewish population. We developed a series of quality control steps to optimize sensitivity, specificity, and comprehensiveness of variant calls in the reference panel, and then tested the accuracy of imputation against target cohorts drawn from the same population. Quality control (QC) thresholds for the Illumina X Ten platform were identified that permitted highly accurate calling of single nucleotide variants across 94% of the genome. QC procedures also identified numerous regions that are poorly mapped using current reference or alternate assemblies. After stringent QC, the population-specific reference panel produced more accurate and comprehensive imputation results relative to publicly available, large cosmopolitan reference panels, especially in the range of rare variants that may be most critical to further progress in mapping of complex phenotypes. The population-specific reference panel also permitted enhanced filtering of clinically irrelevant variants from personal genomes.

Twitter Demographics

The data shown below were collected from the profiles of 3 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 22 Mendeley readers of this research output. Click here to see the associated Mendeley record.

Geographical breakdown

Country Count As %
Unknown 22 100%

Demographic breakdown

Readers by professional status Count As %
Unspecified 6 27%
Researcher 5 23%
Professor > Associate Professor 3 14%
Student > Ph. D. Student 3 14%
Other 2 9%
Other 3 14%
Readers by discipline Count As %
Unspecified 7 32%
Biochemistry, Genetics and Molecular Biology 6 27%
Agricultural and Biological Sciences 3 14%
Neuroscience 3 14%
Mathematics 1 5%
Other 2 9%

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 03 February 2019.
All research outputs
#7,500,639
of 13,322,622 outputs
Outputs from Human Genetics
#2,093
of 2,547 outputs
Outputs of similar age
#132,207
of 269,504 outputs
Outputs of similar age from Human Genetics
#5
of 12 outputs
Altmetric has tracked 13,322,622 research outputs across all sources so far. This one is in the 42nd percentile – i.e., 42% of other outputs scored the same or lower than it.
So far Altmetric has tracked 2,547 research outputs from this source. They receive a mean Attention Score of 4.7. This one is in the 17th percentile – i.e., 17% 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 269,504 tracked outputs that were published within six weeks on either side of this one in any source. This one is in the 49th percentile – i.e., 49% of its contemporaries scored the same or lower than it.
We're also able to compare this research output to 12 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 58% of its contemporaries.