N13: Identification Of Genetic Variants In Early-Onset And Familial Cancers By Targeted Next Generation Sequencing

M. Dominguez-Valentin1, S. Nakken1, H. Tubeuf2, D. Vodak1, P. O. Ekstrøm1, A. M. Nissen3, 4, M. Morak3, 4, E. Holinski-Feder3, 4, A. Holth5, B. Davidson5, 6, A. Martins2, P. Møller7, 8, E. Hovig1

1 – Department of Tumor Biology, Institute for Cancer Research, Oslo University Hospital, Oslo, Norway. 2 – Inserm-U1245, UNIROUEN, Normandie Univ, Normandy Centre for Genomic and Personalized Medicine, Rouen, France. 3 – Medizinische Klinik und Poliklinik IV, Campus Innenstadt, Klinikum der Universität München, Ziemssenstr. 1, Munich, Germany. 4 – MGZ—Medizinisch Genetisches Zentrum, Munich, Germany. 5 – Department of Pathology, Oslo University Hospital, Norwegian Radium Hospital, Oslo, Norway. 6 – University of Oslo, Faculty of Medicine, Institute of Clinical Medicine, N-0316 Oslo, Norway. 7 – Department of Human Medicine, Universität Witten/Herdecke, Germany. 8 – Department of Medical Genetics and Tumor Biology, Oslo University Hospital, Norway.


Aim: To study the potential contribution of genes other than BRCA1/2, PTEN, TP53 and MMR to the biological and clinical characteristics of early-onset and familial cancers in Norwegian families.

Method: The Hereditary Cancer Biobank from the Norwegian Radium Hospital was used to identify early-onset families and individuals with a high risk of developing breast, gynecological and colorectal cancers. Forty-four cancer susceptibility genes were selected and analyzed by our in-house designed TruSeq amplicon-based assay for targeted sequencing. Protein- and RNA splicing-dedicated in silico analyses were performed for all variants of unknown significance (VUS). Variants predicted as the more likely to affect splicing were experimentally analyzed by a minigene assay (PMID: 29458332, 29371908, 28608266).

Results: We analyzed 176 early onset and familial cases who harbored 5% (8/175) class 5 variants in the genes ATM (3), CHEK2 (2), MSH6, MUTYH and MAP3K1. Out of the 18 VUS tested in the minigene splicing assay, ATM c.3806A>G, NOTCH3 c.14090C>T and MSH2 c.815C>T showed a significant effect on RNA splicing.

Conclusion: Our study provides new information on genetic loci that may affect the risk of developing cancer in these patients and their families, demonstrating that genes presently not routinely tested in molecular diagnostic settings may be important for capturing cancer predisposition in these families.