IDEAS home Printed from https://ideas.repec.org/a/plo/pone00/0062495.html
   My bibliography  Save this article

SNP Set Association Analysis for Genome-Wide Association Studies

Author

Listed:
  • Min Cai
  • Hui Dai
  • Yongyong Qiu
  • Yang Zhao
  • Ruyang Zhang
  • Minjie Chu
  • Juncheng Dai
  • Zhibin Hu
  • Hongbing Shen
  • Feng Chen

Abstract

Genome-wide association study (GWAS) is a promising approach for identifying common genetic variants of the diseases on the basis of millions of single nucleotide polymorphisms (SNPs). In order to avoid low power caused by overmuch correction for multiple comparisons in single locus association study, some methods have been proposed by grouping SNPs together into a SNP set based on genomic features, then testing the joint effect of the SNP set. We compare the performances of principal component analysis (PCA), supervised principal component analysis (SPCA), kernel principal component analysis (KPCA), and sliced inverse regression (SIR). Simulated SNP sets are generated under scenarios of 0, 1 and ≥2 causal SNPs model. Our simulation results show that all of these methods can control the type I error at the nominal significance level. SPCA is always more powerful than the other methods at different settings of linkage disequilibrium structures and minor allele frequency of the simulated datasets. We also apply these four methods to a real GWAS of non-small cell lung cancer (NSCLC) in Han Chinese population

Suggested Citation

  • Min Cai & Hui Dai & Yongyong Qiu & Yang Zhao & Ruyang Zhang & Minjie Chu & Juncheng Dai & Zhibin Hu & Hongbing Shen & Feng Chen, 2013. "SNP Set Association Analysis for Genome-Wide Association Studies," PLOS ONE, Public Library of Science, vol. 8(5), pages 1-10, May.
    • Handle: RePEc:plo:pone00:0062495
    DOI: 10.1371/journal.pone.0062495
    as

    Download full text from publisher

    File URL: https://journals.plos.org/plosone/article?id=10.1371/journal.pone.0062495
    Download Restriction: no
    File URL: https://journals.plos.org/plosone/article/file?id=10.1371/journal.pone.0062495&type=printable
    Download Restriction: no
    File URL: https://libkey.io/10.1371/journal.pone.0062495?utm_source=ideas
    LibKey link: if access is restricted and if your library uses this service, LibKey will redirect you to where you can use your library subscription to access this item
    ---><---

    References listed on IDEAS

    as
    1. Bair, Eric & Hastie, Trevor & Paul, Debashis & Tibshirani, Robert, 2006. "Prediction by Supervised Principal Components," Journal of the American Statistical Association, American Statistical Association, vol. 101, pages 119-137, March.
    2. Audrey E Hendricks & Josée Dupuis & Mayetri Gupta & Mark W Logue & Kathryn L Lunetta, 2012. "A Comparison of Gene Region Simulation Methods," PLOS ONE, Public Library of Science, vol. 7(7), pages 1-12, July.
    3. Yang Zhao & Feng Chen & Rihong Zhai & Xihong Lin & Nancy Diao & David C Christiani, 2012. "Association Test Based on SNP Set: Logistic Kernel Machine Based Test vs. Principal Component Analysis," PLOS ONE, Public Library of Science, vol. 7(9), pages 1-11, September.
    Full references (including those not matched with items on IDEAS)

    Most related items

    These are the items that most often cite the same works as this one and are cited by the same works as this one.
    1. Qiuyi Zhang & Yang Zhao & Ruyang Zhang & Yongyue Wei & Honggang Yi & Fang Shao & Feng Chen, 2016. "A Comparative Study of Five Association Tests Based on CpG Set for Epigenome-Wide Association Studies," PLOS ONE, Public Library of Science, vol. 11(6), pages 1-13, June.
    2. Eric Hillebrand & Huiyu Huang & Tae-Hwy Lee & Canlin Li, 2018. "Using the Entire Yield Curve in Forecasting Output and Inflation," Econometrics, MDPI, vol. 6(3), pages 1-27, August.
    3. Tomohiro Ando & Ruey S. Tsay, 2009. "Model selection for generalized linear models with factor‐augmented predictors," Applied Stochastic Models in Business and Industry, John Wiley & Sons, vol. 25(3), pages 207-235, May.
    4. Kui Shen & Nan Song & Youngchul Kim & Chunqiao Tian & Shara D Rice & Michael J Gabrin & W Fraser Symmans & Lajos Pusztai & Jae K Lee, 2012. "A Systematic Evaluation of Multi-Gene Predictors for the Pathological Response of Breast Cancer Patients to Chemotherapy," PLOS ONE, Public Library of Science, vol. 7(11), pages 1-9, November.
    5. Xiuli Du & Xiaohu Jiang & Jinguan Lin, 2023. "Multinomial Logistic Factor Regression for Multi-source Functional Block-wise Missing Data," Psychometrika, Springer;The Psychometric Society, vol. 88(3), pages 975-1001, September.
    6. Wang Zhu & Wang C.Y., 2010. "Buckley-James Boosting for Survival Analysis with High-Dimensional Biomarker Data," Statistical Applications in Genetics and Molecular Biology, De Gruyter, vol. 9(1), pages 1-33, June.
    7. Caroline Jardet & Baptiste Meunier, 2022. "Nowcasting world GDP growth with high‐frequency data," Journal of Forecasting, John Wiley & Sons, Ltd., vol. 41(6), pages 1181-1200, September.
    8. Tommaso Proietti, 2016. "On the Selection of Common Factors for Macroeconomic Forecasting," Advances in Econometrics, in: Dynamic Factor Models, volume 35, pages 593-628, Emerald Group Publishing Limited.
    9. Federico Pavone & Juho Piironen & Paul-Christian Bürkner & Aki Vehtari, 2023. "Using reference models in variable selection," Computational Statistics, Springer, vol. 38(1), pages 349-371, March.
    10. Kawano, Shuichi & Fujisawa, Hironori & Takada, Toyoyuki & Shiroishi, Toshihiko, 2015. "Sparse principal component regression with adaptive loading," Computational Statistics & Data Analysis, Elsevier, vol. 89(C), pages 192-203.
    11. Jianqing Fan & Yang Feng & Jiancheng Jiang & Xin Tong, 2016. "Feature Augmentation via Nonparametrics and Selection (FANS) in High-Dimensional Classification," Journal of the American Statistical Association, Taylor & Francis Journals, vol. 111(513), pages 275-287, March.
    12. Cem Cakmakli & Dick van Dijk, 2010. "Getting the Most out of Macroeconomic Information for Predicting Stock Returns and Volatility," Tinbergen Institute Discussion Papers 10-115/4, Tinbergen Institute.
    13. Zambom, Adriano Zanin & Akritas, Michael G., 2015. "Nonparametric significance testing and group variable selection," Journal of Multivariate Analysis, Elsevier, vol. 133(C), pages 51-60.
    14. Hatem Jemmali & Mohamed Salah Matoussi, 2012. "A Multidimensional Analysis of Water Poverty at A Local Scale- Application of Improved Water Poverty Index for Tunisia," Working Papers 730, Economic Research Forum, revised 2012.
    15. Hojin Yang & Hongtu Zhu & Joseph G. Ibrahim, 2018. "MILFM: Multiple index latent factor model based on high‐dimensional features," Biometrics, The International Biometric Society, vol. 74(3), pages 834-844, September.
    16. Travaglini, Guido, 2010. "Supervised Principal Components and Factor Instrumental Variables. An Application to Violent CrimeTrends in the US, 1982-2005," MPRA Paper 22077, University Library of Munich, Germany.
    17. Myoungsoo Kim & Wonik Choi & Youngjun Jeon & Ling Liu, 2019. "A Hybrid Neural Network Model for Power Demand Forecasting," Energies, MDPI, vol. 12(5), pages 1-17, March.
    18. Anish Agarwal & Keegan Harris & Justin Whitehouse & Zhiwei Steven Wu, 2023. "Adaptive Principal Component Regression with Applications to Panel Data," Papers 2307.01357, arXiv.org, revised Oct 2023.
    19. Cheng, Cheng, 2009. "Internal validation inferences of significant genomic features in genome-wide screening," Computational Statistics & Data Analysis, Elsevier, vol. 53(3), pages 788-800, January.
    20. Seungchul Baek & Yen‐Yi Ho & Yanyuan Ma, 2020. "Using sufficient direction factor model to analyze latent activities associated with breast cancer survival," Biometrics, The International Biometric Society, vol. 76(4), pages 1340-1350, December.

    More about this item

    Statistics

    Access and download statistics

    Corrections

    All material on this site has been provided by the respective publishers and authors. You can help correct errors and omissions. When requesting a correction, please mention this item's handle: RePEc:plo:pone00:0062495. See general information about how to correct material in RePEc.

    If you have authored this item and are not yet registered with RePEc, we encourage you to do it here. This allows to link your profile to this item. It also allows you to accept potential citations to this item that we are uncertain about.

    If CitEc recognized a bibliographic reference but did not link an item in RePEc to it, you can help with this form .

    If you know of missing items citing this one, you can help us creating those links by adding the relevant references in the same way as above, for each refering item. If you are a registered author of this item, you may also want to check the "citations" tab in your RePEc Author Service profile, as there may be some citations waiting for confirmation.

    For technical questions regarding this item, or to correct its authors, title, abstract, bibliographic or download information, contact: plosone (email available below). General contact details of provider: https://journals.plos.org/plosone/ .

    Please note that corrections may take a couple of weeks to filter through the various RePEc services.

    IDEAS is a RePEc service. RePEc uses bibliographic data supplied by the respective publishers.