OR04: Molecular diagnosis of inherited colorectal cancer using NGS panel

Stéphanie Baert-Desurmont, Françoise Charbonnier, Sophie Coutant, Myriam Vezain, Raphaël Lanos, Jacqueline Bou, Emilie Bouvignies, Steeve Fourneaux, Sandrine Manase, Stéphanie Vasseur, Gaëlle Bougeard, Jacques Mauillon, Isabelle Tournier, Thierry Frebourg

Department of Genetics Rouen University Hospital and Inserm U1079, Rouen University, Normandy Centre for Genomics and Personalized Medicine, Rouen, France

Aim

We have developed and optimized a massive parallel sequencing strategy for the diagnosis of inherited forms of colorectal cancer (CRC).

Method

This strategy is based on (1) a panel of 10 genes involved in Mendelian forms of CRC (MLH1, MSH2, MSH6, PMS2, APC, MUTYH, STK11, SMAD4, BMPR1A, PTEN), (2) a quick capture of exonic and intronic sequences using Sureselect Agilent QXT, (3) sequencing on MiSeq and NextSeq 500 Illumina platforms, (4) double bioinformatics pipelines including CASAVA (Illumina) and BWA-GATK (Broad Institute) softwares for alignment and variant calling, Alamut Batch (Interactive BioSoftware) for annotation, completed by CANOES software for the rearrangement detection, (5) automatically generated quality reports and (6) systematic control of the genotypes, using Sanger sequencing or QMPSF for the positive cases and Multiplex SNaPshot analysis of SNPs for the negative cases.

Results

Analysis of 1200 index cases allowed us to identify a deleterious mutation in 18% of the patients and the mutation detection rate reached 32% in Lynch syndrome suspected by tumour analyses.

Conclusion

The main advantages of this strategy are the reduction of molecular diagnosis delay, the correction of the diagnosis in cases of overlapping phenotypes (MUTYH biallelic mutations mimicking Lynch syndrome) and the detection of mosaics and cryptic alterations.

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