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Genome-wide association study of copy number variation with lung function identifies a novel signal of association near BANP for forced vital capacity

Overview of attention for article published in BMC Genetics, August 2016
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Title
Genome-wide association study of copy number variation with lung function identifies a novel signal of association near BANP for forced vital capacity
Published in
BMC Genetics, August 2016
DOI 10.1186/s12863-016-0423-0
Pubmed ID
Authors

Nick Shrine, Martin D. Tobin, Claudia Schurmann, María Soler Artigas, Jennie Hui, Terho Lehtimäki, Olli T. Raitakari, Craig E. Pennell, Qi Wei Ang, David P. Strachan, Georg Homuth, Sven Gläser, Stephan B. Felix, David M. Evans, John Henderson, Raquel Granell, Lyle J. Palmer, Jennifer Huffman, Caroline Hayward, Generation Scotland, Anders Malarstig, Bill Musk, Alan L. James, Louise V. Wain

Abstract

Genome-wide association studies of Single Nucleotide Polymorphisms (SNPs) have identified 55 SNPs associated with lung function. However, little is known about the effect of copy number variants (CNVs) on lung function, although CNVs represent a significant proportion of human genetic polymorphism. To assess the effect of CNVs on lung function quantitative traits, we measured copy number at 2788 previously characterised, common copy number variable regions in 6 independent cohorts (n = 24,237) using intensity data from SNP genotyping experiments. We developed a pipeline for genome-wide association analysis and meta-analysis of CNV genotypes measured across multiple studies using SNP genotype array intensity data from different platform technologies. We then undertook cohort-level genome-wide association studies of CNV with lung function in a subset of 4 cohorts (n < =12,403) with lung function measurements and meta-analysed the results. Follow-up was undertaken for CNVs which were well tagged by SNPs, in up to 146,871 individuals. We generated robust copy number calls for 1962 out of 2788 (70 %) known CNV regions genome-wide, with 1103 measured with compatible class frequencies in at least 2 cohorts. We report a novel CNV association (discovery P = 0.0007) with Forced Vital Capacity (FVC) downstream of BANP on chromosome 16 that shows evidence of replication by a tag SNP in two independent studies (replication P = 0.004). In addition, we provide suggestive evidence (discovery P = 0.0002) for a role of complex copy number variation at a previously reported lung function locus, containing the rootletin gene CROCC, that is not tagged by SNPs. We demonstrate how common CNV regions can be reliably and consistently called across cohorts, using an existing calling algorithm and rigorous quality control steps, using SNP genotyping array intensity data. Although many common biallelic CNV regions were well-tagged by common SNPs, we also identified associations with untagged mulitallelic CNV regions thereby illustrating the potential of our approach to identify some of the missing heritability of complex traits.

Twitter Demographics

The data shown below were collected from the profiles of 2 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 18 Mendeley readers of this research output. Click here to see the associated Mendeley record.

Geographical breakdown

Country Count As %
Canada 1 6%
Unknown 17 94%

Demographic breakdown

Readers by professional status Count As %
Student > Master 4 22%
Researcher 4 22%
Student > Doctoral Student 2 11%
Student > Ph. D. Student 2 11%
Other 1 6%
Other 1 6%
Unknown 4 22%
Readers by discipline Count As %
Biochemistry, Genetics and Molecular Biology 5 28%
Medicine and Dentistry 4 22%
Agricultural and Biological Sciences 1 6%
Psychology 1 6%
Nursing and Health Professions 1 6%
Other 1 6%
Unknown 5 28%

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 12 August 2016.
All research outputs
#5,720,149
of 10,558,904 outputs
Outputs from BMC Genetics
#335
of 771 outputs
Outputs of similar age
#121,957
of 263,811 outputs
Outputs of similar age from BMC Genetics
#16
of 40 outputs
Altmetric has tracked 10,558,904 research outputs across all sources so far. This one is in the 43rd percentile – i.e., 43% of other outputs scored the same or lower than it.
So far Altmetric has tracked 771 research outputs from this source. They receive a mean Attention Score of 3.3. This one has gotten more attention than average, scoring higher than 53% 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 263,811 tracked outputs that were published within six weeks on either side of this one in any source. This one has gotten more attention than average, scoring higher than 50% of its contemporaries.
We're also able to compare this research output to 40 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 52% of its contemporaries.