RGD Reference Report - Novel case-control test in a founder population identifies P-selectin as an atopy-susceptibility locus. - Rat Genome Database

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Novel case-control test in a founder population identifies P-selectin as an atopy-susceptibility locus.

Authors: Bourgain, C  Hoffjan, S  Nicolae, R  Newman, D  Steiner, L  Walker, K  Reynolds, R  Ober, C  McPeek, MS 
Citation: Bourgain C, etal., Am J Hum Genet. 2003 Sep;73(3):612-26. Epub 2003 Aug 15.
RGD ID: 1599904
Pubmed: PMID:12929084   (View Abstract at PubMed)
PMCID: PMC1180685   (View Article at PubMed Central)
DOI: DOI:10.1086/378208   (Journal Full-text)

To avoid problems related to unknown population substructure, association studies may be conducted in founder populations. In such populations, however, the relatedness among individuals may be considerable. Neglecting such correlations among individuals can lead to seriously spurious associations. Here, we propose a method for case-control association studies of binary traits that is suitable for any set of related individuals, provided that their genealogy is known. Although we focus here on large inbred pedigrees, this method may also be used in outbred populations for case-control studies in which some individuals are relatives. We base inference on a quasi-likelihood score (QLS) function and construct a QLS test for allelic association. This approach can be used even when the pedigree structure is far too complex to use an exact-likelihood calculation. We also present an alternative approach to this test, in which we use the known genealogy to derive a correction factor for the case-control association chi2 test. We perform analytical power calculations for each of the two tests by deriving their respective noncentrality parameters. The QLS test is more powerful than the corrected chi2 test in every situation considered. Indeed, under certain regularity conditions, the QLS test is asymptotically the locally most powerful test in a general class of linear tests that includes the corrected chi2 test. The two methods are used to test for associations between three asthma-associated phenotypes and 48 SNPs in 35 candidate genes in the Hutterites. We report a highly significant novel association (P=2.10-6) between atopy and an amino acid polymorphism in the P-selectin gene, detected with the QLS test and also, but less significantly (P=.0014), with the transmission/disequilibrium test.

RGD Manual Disease Annotations    Click to see Annotation Detail View
TermQualifierEvidenceWithReferenceNotesSourceOriginal Reference(s)
atopic dermatitis  IAGP 1599904atopy and bronchial hyperresponsiveness and OMIM:147050 DNA:point_mutation:CDS:amino acid Val640LeuRGD 
atopic dermatitis  ISOSELP (Homo sapiens)1599904; 1599904atopy and bronchial hyperresponsiveness and OMIM:147050RGD 
Bronchial Hyperreactivity  IAGP 1599904atopy and bronchial hyperresponsiveness and OMIM:147050 DNA:point_mutation:CDS:amino acid Val640LeuRGD 
Bronchial Hyperreactivity  ISOSELP (Homo sapiens)1599904; 1599904atopy and bronchial hyperresponsiveness and OMIM:147050RGD 
Immediate Hypersensitivity  IAGP 1599904atopy and bronchial hyperresponsiveness and OMIM:147050 DNA:point_mutation:CDS:amino acid Val640LeuRGD 
Immediate Hypersensitivity  ISOSELP (Homo sapiens)1599904; 1599904atopy and bronchial hyperresponsiveness and OMIM:147050RGD 

Objects Annotated

Genes (Rattus norvegicus)
Selp  (selectin P)

Genes (Mus musculus)
Selp  (selectin, platelet)

Genes (Homo sapiens)
SELP  (selectin P)


Additional Information