title: Testing genetic association with rare and common variants in family data.
abstract: With the advance of next-generation sequencing technologies in recent years, rare genetic variant data have now become available for genetic epidemiology studies. For family samples, however, only a few statistical methods for association analysis of rare genetic variants have been developed. Rare variant approaches are of great interest, particularly for family data, because samples enriched for trait-relevant variants can be ascertained and rare variants are putatively enriched through segregation. To facilitate the evaluation of existing and new rare variant testing approaches for analyzing family data, Genetic Analysis Workshop 18 (GAW18) provided genotype and next-generation sequencing data and longitudinal blood pressure traits from extended pedigrees of Mexican American families from the San Antonio Family Study. Our GAW18 group members analyzed real and simulated phenotype data from GAW18 by using generalized linear mixed-effects models or principal components to adjust for familial correlation or by testing binary traits using a correction factor for familial effects. With one exception, approaches dealt with the extended pedigrees in their original state using information based on the kinship matrix or alternative genetic similarity measures. For simulated data our group demonstrated that the family-based kernel machine score test is superior in power to family-based single-marker or burden tests, except in a few specific scenarios. For real data three contributions identified significant associations. They substantially reduced the number of tests before performing the association analysis. We conclude from our real data analyses that further development of strategies for targeted testing or more focused screening of genetic variants is strongly desirable.
authors.affiliation: Department of Biostatistics, Boston University School of Public Health, Boston, Massachusetts, United States of America.
authors.forename: Han
authors.initials: H
authors.lastname: Chen
authors.forename: Dörthe
authors.initials: D
authors.lastname: Malzahn
authors.forename: Brunilda
authors.initials: B
authors.lastname: Balliu
authors.forename: Cong
authors.initials: C
authors.lastname: Li
authors.forename: Julia N
authors.initials: JN
authors.lastname: Bailey
mesh_terms: D001794:Blood Pressure / Q000235:genetics; D056726:Genetic Association Studies; D005820:Genetic Testing; D014644:Genetic Variation; D005838:Genotype; D059014:High-Throughput Nucleotide Sequencing; D006801:Humans; D006973:Hypertension / Q000235:genetics / Q000473:pathology; D016014:Linear Models; D010375:Pedigree; D010641:Phenotype; D020641:Polymorphism, Single Nucleotide; D025341:Principal Component Analysis; D017422:Sequence Analysis, DNA
keywords: Extended pedigrees; family-based association test; kernel machine score test; linear mixed-effects model; principal components; rare variant analysis
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