Improving Mutation Screening in Patients with Colorectal Cancer Predisposition Using Next-Generation Sequencing Jean-Marc Rey, Vincent Ducros, Pascal.

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Improving Mutation Screening in Patients with Colorectal Cancer Predisposition Using Next-Generation Sequencing Jean-Marc Rey, Vincent Ducros, Pascal Pujol, Qing Wang, Marie-Pierre Buisine, Hanaa Aissaoui, Thierry Maudelonde, Sylviane Olschwang The Journal of Molecular Diagnostics Volume 19, Issue 4, Pages 589-601 (July 2017) DOI: 10.1016/j.jmoldx.2017.04.005 Copyright © 2017 American Society for Investigative Pathology and the Association for Molecular Pathology Terms and Conditions

Figure 1 Depth of coverage comparison between overlapping (gray curve) and nonoverlapping (black curve) sequencing regions. The average of amplicon coverage was calculated after each run for one representative sample tested in the 28 runs. Runs 1 to 2 tested HNPCC MASTR Kit, generating 82 amplicons. Runs 3 to 28 tested HNPCC MASTR Plus Kit combined with FAP MASTR Kit, generating 136 amplicons. The Journal of Molecular Diagnostics 2017 19, 589-601DOI: (10.1016/j.jmoldx.2017.04.005) Copyright © 2017 American Society for Investigative Pathology and the Association for Molecular Pathology Terms and Conditions

Figure 2 Depth of coverage distribution across each targeted exon obtained from a representative patient sample. Horizontal black bars represent exons with their flanking intronic regions analyzed. Vertical solid bars represent the different depth of coverage obtained from overlapping or nonoverlapping amplicon sequencing. Values >500 and >1000 reflect overlapping sequencing regions for MMR and FAP genes, respectively. The Journal of Molecular Diagnostics 2017 19, 589-601DOI: (10.1016/j.jmoldx.2017.04.005) Copyright © 2017 American Society for Investigative Pathology and the Association for Molecular Pathology Terms and Conditions

Figure 3 c.942+3A>T in MSH2 intron 5 detected in one control sample and two patient samples with diagnostic report. The Journal of Molecular Diagnostics 2017 19, 589-601DOI: (10.1016/j.jmoldx.2017.04.005) Copyright © 2017 American Society for Investigative Pathology and the Association for Molecular Pathology Terms and Conditions

Figure 4 Mutation identified in a control sample in PMS2 exon 13 as c.2182_2184delinsG using NGS method (A) or c. 2186_2187del using Sanger method (B). The insG signal diluted in the background is pointed out by an arrow. The Journal of Molecular Diagnostics 2017 19, 589-601DOI: (10.1016/j.jmoldx.2017.04.005) Copyright © 2017 American Society for Investigative Pathology and the Association for Molecular Pathology Terms and Conditions

Figure 5 False deletion of MSH2 exon 11 using the MLPA method. In the upper part of the figure, MLPA analysis shows exon 11 deletion (red arrow) and Sanger analysis identifies a 2-bp deletion on MLPA probe hybridization site. In the lower part of the figure, a single run analysis identifies the point mutation, whereas CNV mode analysis shows a normal profile. The Journal of Molecular Diagnostics 2017 19, 589-601DOI: (10.1016/j.jmoldx.2017.04.005) Copyright © 2017 American Society for Investigative Pathology and the Association for Molecular Pathology Terms and Conditions

Figure 6 Pedigree of a patient assessed for MMR gene screening by the genetic counseling and showing MUTYH mutations (proband III-1, pointed out by an arrow). Siblings I-1 and I-6 developed colon cancer. The Journal of Molecular Diagnostics 2017 19, 589-601DOI: (10.1016/j.jmoldx.2017.04.005) Copyright © 2017 American Society for Investigative Pathology and the Association for Molecular Pathology Terms and Conditions