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On the association analysis of CNV data: a fast and robust family-based association method

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Authors
Liu, Meiling; Moon, Sanghoon; Wang, Longfei; Kim, Sulgi; Kim, Yeon-Jung; Hwang, Mi Yeong; Kim, Young Jin; Elston, Robert C; Kim, Bong-Jo; Won, Sungho
Issue Date
2017-04-18
Publisher
BimMed Central
Citation
BMC Bioinformatics, 18(1):217
Keywords
CNVAssociation analysisScore testHematocrit
Abstract
Background
Copy number variation (CNV) is known to play an important role in the genetics of complex diseases and several methods have been proposed to detect association of CNV with phenotypes of interest. Statistical methods for CNV association analysis can be categorized into two different strategies. First, the copy number is estimated by maximum likelihood and association of the expected copy number with the phenotype is tested. Second, the observed probe intensity measurements can be directly used to detect association of CNV with the phenotypes of interest.

Results
For each strategy we provide a statistic that can be applied to extended families. The computational efficiency of the proposed methods enables genome-wide association analysis and we show with simulation studies that the proposed methods outperform other existing approaches. In particular, we found that the first strategy is always more efficient than the second strategy no matter whether copy numbers for each individual are well identified or not. With the proposed methods, we performed genome-wide CNV association analyses of hematological trait, hematocrit, on 521 Korean family samples.

Conclusions
We found that statistical analysis with the expected copy number is more powerful than the statistic with the probe intensity measurements regardless of the accuracy of the estimation of copy numbers.
Language
English
URI
https://doi.org/10.1186/s12859-017-1622-z

http://hdl.handle.net/10371/117009
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Graduate School of Public Health (보건대학원)Dept. of Public Health (보건학과)Journal Papers (저널논문_보건학과)
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