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The effect of rare variants on inflation of the test statistics in case–control analyses

Overview of attention for article published in BMC Bioinformatics, February 2015
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  • Above-average Attention Score compared to outputs of the same age (57th percentile)

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1 Facebook page

Citations

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6 Dimensions

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24 Mendeley
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Title
The effect of rare variants on inflation of the test statistics in case–control analyses
Published in
BMC Bioinformatics, February 2015
DOI 10.1186/s12859-015-0496-1
Pubmed ID
Authors

Ailith Pirie, Angela Wood, Michael Lush, Jonathan Tyrer, Paul DP Pharoah

Abstract

The detection of bias due to cryptic population structure is an important step in the evaluation of findings of genetic association studies. The standard method of measuring this bias in a genetic association study is to compare the observed median association test statistic to the expected median test statistic. This ratio is inflated in the presence of cryptic population structure. However, inflation may also be caused by the properties of the association test itself particularly in the analysis of rare variants. We compared the properties of the three most commonly used association tests: the likelihood ratio test, the Wald test and the score test when testing rare variants for association using simulated data. We found evidence of inflation in the median test statistics of the likelihood ratio and score tests for tests of variants with less than 20 heterozygotes across the sample, regardless of the total sample size. The test statistics for the Wald test were under-inflated at the median for variants below the same minor allele frequency. In a genetic association study, if a substantial proportion of the genetic variants tested have rare minor allele frequencies, the properties of the association test may mask the presence or absence of bias due to population structure. The use of either the likelihood ratio test or the score test is likely to lead to inflation in the median test statistic in the absence of population structure. In contrast, the use of the Wald test is likely to result in under-inflation of the median test statistic which may mask the presence of population structure.

Twitter Demographics

The data shown below were collected from the profiles of 4 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 24 Mendeley readers of this research output. Click here to see the associated Mendeley record.

Geographical breakdown

Country Count As %
United States 2 8%
Belgium 1 4%
Unknown 21 88%

Demographic breakdown

Readers by professional status Count As %
Researcher 10 42%
Student > Master 5 21%
Student > Ph. D. Student 5 21%
Student > Doctoral Student 2 8%
Student > Bachelor 1 4%
Other 1 4%
Readers by discipline Count As %
Biochemistry, Genetics and Molecular Biology 9 38%
Agricultural and Biological Sciences 9 38%
Computer Science 3 13%
Medicine and Dentistry 1 4%
Unknown 2 8%

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 25 February 2015.
All research outputs
#7,866,469
of 14,573,111 outputs
Outputs from BMC Bioinformatics
#2,952
of 5,420 outputs
Outputs of similar age
#87,864
of 216,288 outputs
Outputs of similar age from BMC Bioinformatics
#1
of 1 outputs
Altmetric has tracked 14,573,111 research outputs across all sources so far. This one is in the 44th percentile – i.e., 44% of other outputs scored the same or lower than it.
So far Altmetric has tracked 5,420 research outputs from this source. They receive a mean Attention Score of 4.9. This one is in the 43rd percentile – i.e., 43% of its peers scored the same or lower than it.
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We're also able to compare this research output to 1 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