Combining information from linkage and association mapping for next-generation sequencing longitudinal family data.
BMC Proc
; 8(Suppl 1 Genetic Analysis Workshop 18Vanessa Olmo): S34, 2014.
Article
en En
| MEDLINE
| ID: mdl-25519382
ABSTRACT
In this analysis, we investigate the contributions that linkage-based methods, such as identical-by-descent mapping, can make to association mapping to identify rare variants in next-generation sequencing data. First, we identify regions in which cases share more segments identical-by-descent around a putative causal variant than do controls. Second, we use a two-stage mixed-effect model approach to summarize the single-nucleotide polymorphism data within each region and include them as covariates in the model for the phenotype. We assess the impact of linkage disequilibrium in determining identical-by-descent states between individuals by using markers with and without linkage disequilibrium for the first part and the impact of imputation in testing for association by using imputed genome-wide association studies or raw sequence markers for the second part. We apply the method to next-generation sequencing longitudinal family data from Genetic Association Workshop 18 and identify a significant region at chromosome 3 40249244-41025167 (p-value = 2.3 × 10(-3)).
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1
Colección:
01-internacional
Base de datos:
MEDLINE
Tipo de estudio:
Risk_factors_studies
Idioma:
En
Revista:
BMC Proc
Año:
2014
Tipo del documento:
Article
País de afiliación:
Países Bajos