Dataset Information

Bayesian linkage analysis of categorical traits for arbitrary pedigree designs.

ABSTRACT:

Background

Pedigree studies of complex heritable diseases often feature nominal or ordinal phenotypic measurements and missing genetic marker or phenotype data.

Methodology

We have developed a Bayesian method for Linkage analysis of Ordinal and Categorical traits (LOCate) that can analyze complex genealogical structure for family groups and incorporate missing data. LOCate uses a Gibbs sampling approach to assess linkage, incorporating a simulated tempering algorithm for fast mixing. While our treatment is Bayesian, we develop a LOD (log of odds) score estimator for assessing linkage from Gibbs sampling that is highly accurate for simulated data. LOCate is applicable to linkage analysis for ordinal or nominal traits, a versatility which we demonstrate by analyzing simulated data with a nominal trait, on which LOCate outperforms LOT, an existing method which is designed for ordinal traits. We additionally demonstrate our method's versatility by analyzing a candidate locus (D2S1788) for panic disorder in humans, in a dataset with a large amount of missing data, which LOT was unable to handle.

Conclusion

LOCate's accuracy and applicability to both ordinal and nominal traits will prove useful to researchers interested in mapping loci for categorical traits.

SUBMITTER: Brisbin A

PROVIDER: S-EPMC2928726 | biostudies-literature | 2010 Aug

REPOSITORIES: biostudies-literature

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Publications

Bayesian linkage analysis of categorical traits for arbitrary pedigree designs.

Brisbin Abra A Weissman Myrna M MM Fyer Abby J AJ Hamilton Steven P SP Knowles James A JA Bustamante Carlos D CD Mezey Jason G JG

PloS one 20100826 8

<h4>Background</h4>Pedigree studies of complex heritable diseases often feature nominal or ordinal phenotypic measurements and missing genetic marker or phenotype data.<h4>Methodology</h4>We have developed a Bayesian method for Linkage analysis of Ordinal and Categorical traits (LOCate) that can analyze complex genealogical structure for family groups and incorporate missing data. LOCate uses a Gibbs sampling approach to assess linkage, incorporating a simulated tempering algorithm for fast mixi ...[more]

PMID: 20865038

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Project description:Least-cost modeling for focal species is the most widely used method for designing conservation corridors and linkages. However, these designs depend on today's land covers, which will be altered by climate change. We recently proposed an alternative approach based on land facets (recurring landscape units of relatively uniform topography and soils). The rationale is that corridors with high continuity of individual land facets will facilitate movement of species associated with each facet today and in the future. Conservation practitioners might like to know whether a linkage design based on land facets is likely to provide continuity of modeled breeding habitat for species needing connectivity today, and whether a linkage for focal species provides continuity and interspersion of land facets. To address these questions, we compared linkages designed for focal species and land facets in three landscapes in Arizona, USA. We used two variables to measure linkage utility, namely distances between patches of modeled breeding habitat for 5-16 focal species in each linkage, and resistance profiles for focal species and land facets between patches connected by the linkage. Compared to focal species designs, linkage designs based on land facets provided as much or more modeled habitat connectivity for 25 of 28 species-landscape combinations, failing only for the three species with the most narrowly distributed habitat. Compared to land facets designs, focal species linkages provided lower connectivity for about half the land facets in two landscapes. In areas where a focal species approach to linkage design is not possible, our results suggest that conservation practitioners may be able to implement a land facets approach with some confidence that the linkage design would serve most potential focal species. In areas where focal species designs are possible, we recommend using the land facet approach to complement, rather than replace, focal species approaches.

Dataset Information

Bayesian linkage analysis of categorical traits for arbitrary pedigree designs.

Background

Methodology

Conclusion

Publications

Bayesian linkage analysis of categorical traits for arbitrary pedigree designs.

Similar Datasets

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