Results of integrative germline analyses performed in this study.

<p>VUS included in-frame deletions, sequence variants with uncertain effect on splicing and missense variants. Evidence of a pathogenic, possibly pathogenic defect in 28 probands with VUS derived from previous studies (see <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0081194#pone.0081194.s007" target="_blank">Table S5</a>). In one additional case (360#2916) availability of RNA allowed ASE analysis that helped to characterize a VUS shared also by another proband (986#3487, see Results). ASE analysis was conducted in 22 individuals, including 12 with ascertained germline defect that are not shown in the figure. <i>APC</i> and MUTYH screening was conducted in a subset of patients negative for MMR defects (see Methods). Inclusion of ASE analysis and screening for <i>APC</i> and MUTYH sequence variants in the integrative analyses increased the number of probands with germline alterations detected.</p

ASE values observed.

<p>ASE values between the 2 dashed lines correspond to less than twofold imbalances in allelic ratios (see Methods). </p