SNP-based linkage analysis in extended pedigrees: comparison between two alternative approaches.
Hum Hered
; 78(1): 27-37, 2014.
Article
in En
| MEDLINE
| ID: mdl-24969533
ABSTRACT
BACKGROUND:
Linkage analysis on extended pedigrees is often challenged by the high computational demand of exact identity-by-descent (IBD) matrix reconstruction. When such an analysis becomes not feasible, two alternative solutions are contrasted a full pedigree analysis based on approximate IBD estimation versus a pedigree splitting followed by exact IBD estimation. A multiple splitting (MS) approach, which combines linkage results across different splitting configurations, has been proposed to increase the power of single-split solutions.METHODS:
To assess whether MS can achieve a comparable power to a full pedigree analysis, we compared the power of linkage on a very large pedigree in both simulated and real-case scenarios, using variance components linkage analysis of a dense SNP array.RESULTS:
Our results confirm that the power to detect linkage is affected by the pedigree size. The MS approach showed higher power than the single-split analysis, but it was substantially less powerful than the full pedigree approach in both scenarios, at any level of significance and variance explained by a quantitative trait locus.CONCLUSION:
The MS approach should always be preferred to analyses based on a single split but, when adequate computational resources are available, a full pedigree analysis is better than the MS analysis. Rather than focusing on how to best split a pedigree, it might be more valuable to identify computational solutions that can make the IBD estimation of dense-marker maps practically feasible, thus allowing a full pedigree analysis.
Full text:
1
Collection:
01-internacional
Database:
MEDLINE
Main subject:
Pedigree
/
Chromosome Mapping
/
Polymorphism, Single Nucleotide
/
Genetic Linkage
Type of study:
Prognostic_studies
Limits:
Female
/
Humans
/
Male
Language:
En
Journal:
Hum Hered
Year:
2014
Type:
Article
Affiliation country:
France