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This approach was tested by the authors on a subset of genes representative of those that might be selected by a linkage analysis study, and not the full complement of genes in the Ensembl database, as in the current study.
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We started by performing a linkage analysis in a collection of 36 families with the aim to identify both general and family specific linked chromosomal regions.
GLA1BLUP EBV were obtained by fitting a linkage analysis based relationship matrix, G LA1, [ 14, 15] for which the probabilities of paternal/maternal inheritance were obtained using the LDMIP program [ 6].
We also carried out a linkage analysis followed by a case-note review within one hospital in Scotland.
To investigate discrepancies in more detail we also carried out a linkage analysis followed by a case-note review within one hospital in Scotland for data entered between 1st Jan 2010-31st October 2010.
All together, this work underlines several chromosomal regions which could play a role in resistance mechanism to malaria infection: 12q22 which have already been pointed out by a previous linkage analysis and three new regions (6p25.1, 20p11q11 and 9q34).
The Mss1 locus had been detected by a targeted linkage analysis with chromosome 10 simple sequence length polymorphisms after the discovery that ENU-induced MPNST of (BDIV × BDIX) F1 rats had been shown previously to display losses of heterozygosity on this chromosome usually losing the BDIV resistance allele.
In an earlier study, we mapped QTL for skatole, as detected by a (human) sensory panel, by linkage analysis with a low density microsatellite marker map with the closest marker SW1353 mapping to SSC6: 9.872 Mbp (Sscrofa10.2 coordinates) [ 13].
These data lead to the assumption that the remaining predisposing genes can be found neither by GWAS nor by linkage analysis.
This approach ranks each candidate gene in a genomic interval (identified by linkage analysis) by their interactions to genes known to be involved in the phenotype/disease in the protein-protein interaction network [ 5].
The detailed clinical and morphologic characterization of the members of family DU-11 afforded the identification of a disease-related genomic locus on chromosome 14q by a genome-wide linkage analysis.
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