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Haplotype‐Based Regression Analysis and Inference of Case–Control Studies with Unphased Genotypes and Measurement Errors in Environmental Exposures

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  • Iryna Lobach
  • Raymond J. Carroll
  • Christine Spinka
  • Mitchell H. Gail
  • Nilanjan Chatterjee

Abstract

Summary It is widely believed that risks of many complex diseases are determined by genetic susceptibilities, environmental exposures, and their interaction. Chatterjee and Carroll (2005, Biometrika92, 399–418) developed an efficient retrospective maximum‐likelihood method for analysis of case–control studies that exploits an assumption of gene–environment independence and leaves the distribution of the environmental covariates to be completely nonparametric. Spinka, Carroll, and Chatterjee (2005, Genetic Epidemiology29, 108–127) extended this approach to studies where certain types of genetic information, such as haplotype phases, may be missing on some subjects. We further extend this approach to situations when some of the environmental exposures are measured with error. Using a polychotomous logistic regression model, we allow disease status to have K+ 1 levels. We propose use of a pseudolikelihood and a related EM algorithm for parameter estimation. We prove consistency and derive the resulting asymptotic covariance matrix of parameter estimates when the variance of the measurement error is known and when it is estimated using replications. Inferences with measurement error corrections are complicated by the fact that the Wald test often behaves poorly in the presence of large amounts of measurement error. The likelihood‐ratio (LR) techniques are known to be a good alternative. However, the LR tests are not technically correct in this setting because the likelihood function is based on an incorrect model, i.e., a prospective model in a retrospective sampling scheme. We corrected standard asymptotic results to account for the fact that the LR test is based on a likelihood‐type function. The performance of the proposed method is illustrated using simulation studies emphasizing the case when genetic information is in the form of haplotypes and missing data arises from haplotype‐phase ambiguity. An application of our method is illustrated using a population‐based case–control study of the association between calcium intake and the risk of colorectal adenoma.

Suggested Citation

  • Iryna Lobach & Raymond J. Carroll & Christine Spinka & Mitchell H. Gail & Nilanjan Chatterjee, 2008. "Haplotype‐Based Regression Analysis and Inference of Case–Control Studies with Unphased Genotypes and Measurement Errors in Environmental Exposures," Biometrics, The International Biometric Society, vol. 64(3), pages 673-684, September.
    • Handle: RePEc:bla:biomet:v:64:y:2008:i:3:p:673-684
    DOI: 10.1111/j.1541-0420.2007.00930.x
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    References listed on IDEAS

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    1. Daowen Zhang & Marie Davidian, 2001. "Linear Mixed Models with Flexible Distributions of Random Effects for Longitudinal Data," Biometrics, The International Biometric Society, vol. 57(3), pages 795-802, September.
    2. Lin, D.Y. & Zeng, D., 2006. "Likelihood-Based Inference on Haplotype Effects in Genetic Association Studies," Journal of the American Statistical Association, American Statistical Association, vol. 101, pages 89-104, March.
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    Cited by:

    1. Yanyuan Ma & Raymond J. Carroll, 2016. "Semiparametric estimation in the secondary analysis of case–control studies," Journal of the Royal Statistical Society Series B, Royal Statistical Society, vol. 78(1), pages 127-151, January.
    2. Jun Zhang & Zhenghui Feng & Peirong Xu & Hua Liang, 2017. "Generalized varying coefficient partially linear measurement errors models," Annals of the Institute of Statistical Mathematics, Springer;The Institute of Statistical Mathematics, vol. 69(1), pages 97-120, February.
    3. Tianying Wang & Alex Asher, 2021. "Improved Semiparametric Analysis of Polygenic Gene–Environment Interactions in Case–Control Studies," Statistics in Biosciences, Springer;International Chinese Statistical Association, vol. 13(3), pages 386-401, December.

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