TY - CHAP
T1 - Testing departure from Hardy-Weinberg proportions
AU - Wang, Jian
AU - Shete, Sanjay
N1 - Publisher Copyright:
© 2017, Springer Science+Business Media LLC.
PY - 2017
Y1 - 2017
N2 - The Hardy-Weinberg principle, one of the most important principles in population genetics, was originally developed for the study of allele frequency changes in a population over generations. It is now, however, widely used in studies of human diseases to detect inbreeding, population stratification, and genotyping errors. For assessment of deviation from Hardy-Weinberg proportions in data, the most popular approaches include the asymptotic Pearson’s chi-squared goodness-of-fit test and the exact test. Pearson’s chi-squared goodness-of-fit test is simple and straightforward, but is very sensitive to a small sample size or rare allele frequency. The exact test of Hardy-Weinberg proportions is preferable in these situations. The exact test can be performed through complete enumeration of heterozygote genotypes or on the basis of the Markov chain Monte Carlo procedure. In this chapter, we describe the Hardy-Weinberg principle and the commonly used Hardy-Weinberg proportion tests and their applications, and we demonstrate how the chi-squared test and exact test of Hardy-Weinberg proportions can be performed step-by-step using the popular software programs SAS, R, and PLINK, which have been widely used in genetic association studies, along with numerical examples. We also discuss approaches for testing Hardy-Weinberg proportions in case–control study designs that are better than traditional approaches for testing Hardy-Weinberg proportions in controls only. Finally, we note that deviation from the Hardy-Weinberg proportions in affected individuals can provide evidence for an association between genetic variants and diseases.
AB - The Hardy-Weinberg principle, one of the most important principles in population genetics, was originally developed for the study of allele frequency changes in a population over generations. It is now, however, widely used in studies of human diseases to detect inbreeding, population stratification, and genotyping errors. For assessment of deviation from Hardy-Weinberg proportions in data, the most popular approaches include the asymptotic Pearson’s chi-squared goodness-of-fit test and the exact test. Pearson’s chi-squared goodness-of-fit test is simple and straightforward, but is very sensitive to a small sample size or rare allele frequency. The exact test of Hardy-Weinberg proportions is preferable in these situations. The exact test can be performed through complete enumeration of heterozygote genotypes or on the basis of the Markov chain Monte Carlo procedure. In this chapter, we describe the Hardy-Weinberg principle and the commonly used Hardy-Weinberg proportion tests and their applications, and we demonstrate how the chi-squared test and exact test of Hardy-Weinberg proportions can be performed step-by-step using the popular software programs SAS, R, and PLINK, which have been widely used in genetic association studies, along with numerical examples. We also discuss approaches for testing Hardy-Weinberg proportions in case–control study designs that are better than traditional approaches for testing Hardy-Weinberg proportions in controls only. Finally, we note that deviation from the Hardy-Weinberg proportions in affected individuals can provide evidence for an association between genetic variants and diseases.
KW - Case–control genetic association study
KW - Exact test
KW - Genetic association study
KW - Genotyping error
KW - Hardy-Weinberg proportions
KW - PLINK
KW - Pearson’s chi-squared goodness-of-fit test
KW - Population stratification
KW - Quality control
KW - R
KW - SAS/genetics
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U2 - 10.1007/978-1-4939-7274-6_6
DO - 10.1007/978-1-4939-7274-6_6
M3 - Chapter
C2 - 28980243
AN - SCOPUS:85030685534
T3 - Methods in Molecular Biology
SP - 83
EP - 115
BT - Methods in Molecular Biology
PB - Humana Press Inc.
ER -