This study performed on a large series of mutation carriers allows estimating the contribution to LFS of de novo mutations to at least 14% (48/336) and suggests that approximately one-fifth of these de novo mutations occur during embryonic development. Considering the medical impact of mutation identification, medical laboratories in charge of testing should ensure the detection of mosaic mutations.

The detection of Copy Number Variations (CNVs) from NGS data is under-exploited as chip-based or targeted techniques are still commonly used. We assessed the performances of a workflow centered on CANOES, a bioinformatics tool based on read depth information. We applied our workflow to gene panel (GP) and Whole Exome Sequencing (WES) data, and compared CNV calls to Quantitative Multiplex PCR of Short Fluorescent fragments (QMSPF) or array Comparative Genomic Hybridization (aCGH) results. From GP data of 3,776 samples, we reached an overall Positive Predictive Value (PPV) of 87.8%. This dataset included a complete comprehensive QMPSF comparison of 4 genes (60 exons) on which we obtained 100% sensitivity and specificity. From WES data, we first compared 137 samples to aCGH and filtered comparable events (exonic CNVs encompassing enough aCGH probes) and obtained an 87.25% sensitivity. The overall PPV was 86.4% following the targeted confirmation of candidate CNVs from 1,056 additional WES. In addition, our CANOES-centered workflow on WES data allowed the detection of CNVs of any size that were missed by aCGH. Overall, switching to a NGS-only approach should be costeffective as it allows a reduction in overall costs together with likely stable diagnostic yields. Our bioinformatics pipeline is available at : https://gitlab.bioinfo-diag.fr/nc4gpm/canoes-centeredworkflow.

In the Li-Fraumeni syndrome (LFS) resulting from germline TP53 mutations, the MDM2 SNP309G allele has been shown to be associated with an earlier age of tumour onset, however the significance of this association is controversial. The 285C variation, also located in the MDM2 promoter, has been shown to reduce the strength of Sp1 binding to MDM2 promoter, antagonizing the effect of the 309G variation. In this study, we investigated the interaction of the MDM2 SNP285 and 309 in a large series of 195 LFS patients. Although we observed a lower mean age of tumour onset in patients with MDM2 SNP309 T/G or G/G genotype (23.1 years) than in patients with T/T genotype (27.3 years), the difference was not statistically significant. In contrast, patients with the 285-309 G-G haplotype develop tumours 5 years earlier than patients harbouring other haplotypes (p = 0.044). This result shows that the MDM2 285-309 G-G is a higher risk haplotype in patients with germline TP53 mutations. This study confirms that the MDM2 309G variation is deleterious when its effect is not neutralized by the 285C variation and illustrates the interfering effects of SNPs located within a gene acting as modifier factor in a Mendelian disease.