Optimal peeling order for pedigrees with incomplete genotypic information

MQScore_SNP software for multipoint parametric linkage analysis of quantitative traits in large pedigrees

We describe software for multipoint parametric linkage analysis of quantitative traits using information about SNP genotypes. A mixed model of major gene and polygene inheritance is implemented in this software. Implementation of several algorithms to avoid computational underflow and decrease running time permits application of our software to the analysis of very large pedigrees collected in human genetically isolated populations. We tested our software by performing linkage analysis of adult height in a large pedigree from a Dutch isolated population. Three significant and four suggestive loci were identified with the help of our programs, whereas variance-component-based linkage analysis, which requires the pedigree fragmentation, demonstrated only three suggestive peaks. The software package MQScore_SNP is available at http://mga.bionet.nsc.ru/soft/index.html.

Linkage analysis of adult height in a large pedigree from a Dutch genetically isolated population

Despite extensive research of genetic determinants of human adult height, the genes identified up until now allow to predict only a small proportion of the trait's variance. To identify new genes we analyzed 2,486 genotyped and phenotyped individuals in a large pedigree including 23,612 members in 18 generations. The pedigree was derived from a young genetically isolated Dutch population, where genetic heterogeneity is expected to be low and linkage disequilibrium has been shown to be increased. Complex segregation analysis confirmed high heritability of adult height, and suggested mixed model of height inheritance in this population. The estimates of the model parameters obtained from complex segregation analysis were used in parametric linkage analysis, which highlighted three genome-wide significant and additionally at least four suggestive loci involved in height. Significant peaks were located at the chromosomal regions 1p32 (LOD score = 3.35), 2p16 (LOD score = 3.29) and 16q24 (LOD score = 3.94). For the latter region, a strong association signal (FDR q < 0.05) was obtained for 19 SNPs, 17 of them were located in the CDH13 (cadherin 13) gene of which one (rs1035569) explained 1.5% of the total height variance.