Programs for calculating the statistical powers of detecting susceptibility genes in case-control studies based on multistage designs.
BACKGROUND
A two-stage association study is the most commonly used method among multistage designs to efficiently identify disease susceptibility genes. Recently, some SNP studies have utilized more than two stages to detect disease genes. However, there are few available programs for calculating statistical powers and positive predictive values (PPVs) of arbitrary n-stage designs.


RESULTS
We developed programs for a multistage case-control association study using R language. In our programs, input parameters include numbers of samples and candidate loci, genome-wide false positive rate and proportions of samples and loci to be selected at the k-th stage (k=1,..., n). The programs output statistical powers, PPVs and numbers of typings in arbitrary n-stage designs. The programs can contribute to prior simulations under various conditions in planning a genome-wide association study.
Kitamura
Nobutaka
N
Department of Medical Informatics, Niigata University Medical and Dental Hospital, Niigata, Japan. nktmr@m12.alpha-net.ne.jp
Akazawa
Kouhei
K
Miyashita
Akinori
A
Kuwano
Ryozo
R
Toyabe
Shin-ichi
S
Nakamura
Junichiro
J
Nakamura
Norihito
N
Sato
Tatsuhiko
T
Hoque
M Aminul
MA
D000465:Algorithms; D016022:Case-Control Studies; D020022:Genetic Predisposition to Disease; D055106:Genome-Wide Association Study; D006801:Humans; D015233:Models, Statistical; D020641:Polymorphism, Single Nucleotide; D011237:Predictive Value of Tests; D012984:Software