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We review six frequently-used methods, i.e. global weight thresholding method (GWTM), k-core decomposition method (KCDM), minimum spanning tree method (MSTM), primary linkage analysis method (PLAM), multiple linkage analysis method (MLAM), and the disparity filter algorithm method (DFAM), and elaborate their analytical essence by applying them to extract the backbone of the SAAN.
In these, we used multiple computational techniques, including those based on phenotype [ 35, 39], for disease gene prioritization, using sets of genes defined by multiple linkage analysis data available through the biomedical literature as starting point.
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Enrichment over the whole set of probed genes and heuristic multiple linkage clustering analysis was performed using the same tools and Benjamini-Hochberg correction was applied to correct for multiple testing on the data set.
Additionally, we selected six susceptibility loci that had been identified in multiple genetic linkage analysis studies (Table 5).
Whole-genome multiple regression linkage analysis in R/qtl was performed for males (N = 96) and females (N = 72), or both genders together (Figure 6C).
Joint linkage analysis, using multiple segregating populations, could overcome some of the inherent limitations associated with single population linkage analysis and genome-wide association mapping [ 8].
Combining the linkage analysis from multiple reconstructed partial pedigrees with the association analysis over the remaining unrelated individuals can potentially increase the power of such studies.
Exactly 10 years ago, in November 1989, a small group of cancer geneticists and epidemiologists convened in Lyon, France, to initiate a joint effort with the aim being to find breast cancer predisposition genes through linkage analysis in multiple case families.
Xu et al (2001) exclude a major contribution of HPC2/ELAC2 as a high-prevalence, high-penetrance major gene for PrCa after performing linkage analysis in multiple case PrCa families and mutation screening (using DHPLC) of all coding exons of the gene in 93 probands.
Model-based linkage analysis in multiple-case families, followed by positional cloning, led to the identification of BRCA1 and BRCA2.
Although this pattern suggests that there are multiple segregating loci in the strains, linkage analysis of the RIAILs yielded only a single QTL on chromosome II at genome-wide significance (II:2808858 with LOD = 3.255; genome-wide P = 0.036).
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