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Coverage and efficiency in current SNP chips

Overview of attention for article published in European Journal of Human Genetics, January 2014
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Title
Coverage and efficiency in current SNP chips
Published in
European Journal of Human Genetics, January 2014
DOI 10.1038/ejhg.2013.304
Pubmed ID
Authors

Ngoc-Thuy Ha, Saskia Freytag, Heike Bickeboeller

Abstract

To answer the question as to which commercial high-density SNP chip covers most of the human genome given a fixed budget, we compared the performance of 12 chips of different sizes released by Affymetrix and Illumina for the European, Asian, and African populations. These include Affymetrix' relatively new population-optimized arrays, whose SNP sets are each tailored toward a specific ethnicity. Our evaluation of the chips included the use of two measures, efficiency and cost-benefit ratio, which we developed as supplements to genetic coverage. Unlike coverage, these measures factor in the price of a chip or its substitute size (number of SNPs on chip), allowing comparisons to be drawn between differently priced chips. In this fashion, we identified the Affymetrix population-optimized arrays as offering the most cost-effective coverage for the Asian and African population. For the European population, we established the Illumina Human Omni 2.5-8 as the preferred choice. Interestingly, the Affymetrix chip tailored toward an Eastern Asian subpopulation performed well for all three populations investigated. However, our coverage estimates calculated for all chips proved much lower than those advertised by the producers. All our analyses were based on the 1000 Genome Project as reference population.

Twitter Demographics

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Mendeley readers

The data shown below were compiled from readership statistics for 103 Mendeley readers of this research output. Click here to see the associated Mendeley record.

Geographical breakdown

Country Count As %
Germany 1 <1%
Brazil 1 <1%
Costa Rica 1 <1%
Canada 1 <1%
Denmark 1 <1%
Unknown 98 95%

Demographic breakdown

Readers by professional status Count As %
Researcher 30 29%
Student > Ph. D. Student 27 26%
Student > Master 13 13%
Student > Postgraduate 7 7%
Student > Bachelor 7 7%
Other 10 10%
Unknown 9 9%
Readers by discipline Count As %
Agricultural and Biological Sciences 47 46%
Biochemistry, Genetics and Molecular Biology 23 22%
Medicine and Dentistry 9 9%
Computer Science 3 3%
Mathematics 2 2%
Other 5 5%
Unknown 14 14%

Attention Score in Context

This research output has an Altmetric Attention Score of 1. 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 14 August 2014.
All research outputs
#9,081,263
of 11,343,589 outputs
Outputs from European Journal of Human Genetics
#1,935
of 2,202 outputs
Outputs of similar age
#129,682
of 192,913 outputs
Outputs of similar age from European Journal of Human Genetics
#54
of 60 outputs
Altmetric has tracked 11,343,589 research outputs across all sources so far. This one is in the 11th percentile – i.e., 11% of other outputs scored the same or lower than it.
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We're also able to compare this research output to 60 others from the same source and published within six weeks on either side of this one. This one is in the 1st percentile – i.e., 1% of its contemporaries scored the same or lower than it.