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BMC Genet. 2006 Feb 10;7:8.

Analysis of case-parent trios at a locus with a deletion allele: association of GSTM1 with autism.

Author information

  • 1Departments of Statistics and Genetics, 110 Frelinghuysen Rd, Rutgers University, Piscataway, NJ 08854, USA. buyske@stat.rutgers.edu

Abstract

BACKGROUND:

Certain loci on the human genome, such as glutathione S-transferase M1 (GSTM1), 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 GSTM1 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 GSTM1 deletion genotype with autism.

PMID:
16472391
PMCID:
PMC1382247
DOI:
10.1186/1471-2156-7-8
[PubMed - indexed for MEDLINE]
Free PMC Article
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