Analysis of case-parent trios at a locus with a deletion allele: Association of GSTMI with autism

Steven Buyske, Tanishia A. Williams, Audrey E. Mars, Edward S. Stenroos, Sue X. Ming, Rong Wang, Madhura Sreenath, Marivic F. Factura, Chitra Reddy, George H. Lambert, William G. Johnson

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Abstract

Background: Certain loci on the human genome, such as glutathione S-transferase MI (GSTMI), do not permit heterozygotes to be reliably determined by commonly used methods. Association of such a locus with a disease is therefore generally tested with a case-control design. When subjects have already been ascertained in a case-parent design however, the question arises as to whether the data can still be used to test disease association at such a locus. Results: A likelihood ratio test was constructed that can be used with a case-parents design but has somewhat less power than a Pearson's chi-squared test that uses a case-control design. The test is illustrated on a novel dataset showing a genotype relative risk near 2 for the homozygous GSTMI deletion genotype and autism. Conclusion: Although the case-control design will remain the mainstay for a locus with a deletion, the likelihood ratio test will be useful for such a locus analyzed as part of a larger case-parent study design. The likelihood ratio test has the advantage that it can incorporate complete and incomplete case-parent trios as well as independent cases and controls. Both analyses support (p = 0.046 for the proposed test, p = 0.028 for the case-control analysis) an association of the homozygous GSTMI deletion genotype with autism.

Original languageEnglish (US)
JournalBMC genetics
Volume7
DOIs
StatePublished - Feb 10 2006

All Science Journal Classification (ASJC) codes

  • Genetics(clinical)
  • Genetics

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    Buyske, S., Williams, T. A., Mars, A. E., Stenroos, E. S., Ming, S. X., Wang, R., Sreenath, M., Factura, M. F., Reddy, C., Lambert, G. H., & Johnson, W. G. (2006). Analysis of case-parent trios at a locus with a deletion allele: Association of GSTMI with autism. BMC genetics, 7. https://doi.org/10.1186/1471-2156-7-8