Chapter 11: Genome-Wide Association Studies

  • William S. Bush mail,

    Affiliation: Department of Biomedical Informatics, Center for Human Genetics Research, Vanderbilt University Medical School, Nashville, Tennessee, United States of America

  • Jason H. Moore

    Affiliation: Departments of Genetics and Community Family Medicine, Institute for Quantitative Biomedical Sciences, Dartmouth Medical School, Lebanon, New Hampshire, United States of America


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minor allele frequency example is incorrect

Posted by sfyoung on 14 May 2013 at 18:08 GMT

The second paragraph in section 2.1 claims that "a SNP with a minor allele (G) frequency of 0.40 implies that 40% of a population has the G allele versus the more common allele (the major allele), which is found in 60% of the population." That is incorrect unless referring to a haploid population. For a locus that is in Hardy-Weinberg Equilibrium in a diploid population, an allele that is at a frequency of 0.4 will be present in 64% of the population [1 - (1 - 0.4) ^2] and absent in 36% of the population [(1 - 0.4) ^2]. The correct statement would be that a SNP with a minor allele frequency of 0.40 implies that 40% of the alleles in the population are the minor allele.

The error is repeated in the second paragraph of section 2.3,
"For example, if a SNP with 40% frequency in the population causes a highly deleterious amino acid substitution that directly leads to a disease phenotype, nearly 40% of the population would have that phenotype." Actually, if the SNP causes a deleterious amino acid substitution, then about 64% of the population would have at least one copy of the deleterious amino acid.

Otherwise, I liked the article.

No competing interests declared.