After the completion of this step of linkage, a telephone survey was conducted to confirm the possible links found.
After this step of linkage, we repeated the telephone survey process, then obtaining 19 treatment confirmations as exact matches.
For the different steps of the linkage analysis; e.g. data formatting, detection of Mendelian inconsistencies, mistyping analysis, LD removal and single to multipoint linkage analysis, we have chosen the following programs that can handle large pedigrees and many SNPs where required; Alohomora [ 32], Mega2 [ 33], MENDEL [ 30], SNPLINK [ 29] and SimWalk2 [ 31].
Tables 6 and 7 provide a roadmap to parameters used in sequential steps of the linkage mapping analyses.
A two-step approach of linkage analysis using single nucleotide polymorphism (SNP) microarrays to detect high logarithm of odds (LOD) score regions and subsequent targeted re-sequencing of regions of interest has been utilized in many genomic studies to intensify the power of detection [ 7].
Briefly, this process consists of nine steps, including standardisation of linkage variables, determination of the quality of coding and quality assessment of linked data [ 22].
Steps for the construction of linkage maps included testing for distorted segregation, clustering SNPs, calculation of recombination fractions and LOD (logarithm of the odds) scores, ordering of SNPs, and inference of parental phase.
Sensitivity analyses using Cox models did not show any noteworthy difference of survival in function of linkage step or certainty of a correct link, when sex, age and wave was adjusted for.
The construction of linkage maps is a primary step towards the description and understanding of the structure and evolution of whole genomes.
We consider that the present strategy might be a valid second step for identifying high penetrance genes, specifically when the regions of interest show significant evidence of linkage.
