Optimal two-stage design for case-control association analysis incorporating genotyping errors.

Annals of Human Genetics
Yijun ZuoH Liang

Abstract

Two-stage design is a cost effective approach for identifying disease genes in genetic studies and it has received much attention recently. In general, there are two types of two-stage designs that differ on the methods and samples used to measure allele frequencies in the first stage: (1) Individual genotyping is used in the first stage; (2) DNA pooling is used in the first stage. In this paper, we focus on the latter. Zuo et al. (2006) investigated statistical power of such a design, among other things, but the cost of the study was not taken into account. The purpose of this paper is to study the optimal design under the given overall cost. We investigate how to allocate the resources to the two stages. Note that in addition to the measurement errors associated with DNA pooling, genotyping errors are also unavoidable with individual genotyping. Therefore, we discuss the optimal design combining genotyping errors associated with individual genotyping. The joint statistical distributions of test statistics in the first and second stages are derived. For a fixed cost, our results show that the optimal design requires no additional samples in the second stage but only that the samples in the first stage be re-used. When the seco...Continue Reading

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Citations

Sep 17, 2008·The Pharmacogenomics Journal·C M BromleyUNKNOWN Industry Pharmacogenomics Working Group
Dec 5, 2008·Biostatistics·Jiexun WangGuohua Zou
Apr 7, 2009·Annals of Human Genetics·Nathan TintleStephen Finch
Jun 6, 2009·Statistical Applications in Genetics and Molecular Biology·Bryce BorchersNathan L Tintle
Jan 22, 2014·Progress in Neuro-psychopharmacology & Biological Psychiatry·P H KuoR B Lu
Mar 23, 2011·Human Genetics·Charleston W K ChiangJoel N Hirschhorn
Feb 10, 2016·Canadian Journal of Anaesthesia = Journal Canadien D'anesthésie·Miklos D KertaiUNKNOWN PEGASUS Investigative Team
Nov 16, 2010·Journal of Clinical Epidemiology·Hsiao-Yuan Huang, Wen-Chung Lee
Jun 17, 2010·Genetic Epidemiology·Su Yeon KimRasmus Nielsen
Feb 19, 2011·American Journal of Hypertension·Chong ShenDongfeng Gu
Mar 19, 2013·Statistical Applications in Genetics and Molecular Biology·Irene S L ZengRalph A H Stewart
Jan 1, 2014·Microarrays·Yi-Hsuan ChenPo-Hsiu Kuo

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