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Background Carriers with pathogenic variants in MSH2 have increased risk to develop colorectal, endometrium, ovarian, and other types of cancer. The PALB2 is associated with breast, ovarian, pancreatic, and prostate cancer. We describe the case of a 42‐year‐old female diagnosed with endometrial cancer at the age of 42 years with a strong family history of colorectal cancer, which was referred to our private diagnostic laboratory for genetic testing. Methods In this study, we performed next‐generation sequencing (NGS) using an amplicon based 26 genes panel. The presence of multi‐exonic copy number variations (CNVs) was investigated by computational analysis and Multiplex Ligation‐dependent Probe Amplification (MLPA). Results A gross deletion of the genomic region encompassing exons 11–16 of the MSH2 and the loss‐of‐function variant c.757_758delCT, p.(Leu253Ilefs*3) in the PALB2 were identified in the proband. Conclusions Multigene analysis using NGS technology allows the identification of pathogenic variants in genes that would normally not be tested based on the patient diagnosis. In our case these results explained not only the personal and/or family history of cancer but also allowed the surveillance for prevention of other cancer types. Moreover, the detection of large genomic rearrangements should be routinely included in hereditary cancer testing., We describe the case of a 42‐year‐old female diagnosed with endometrial cancer with a strong family history of colorectal cancer, which was referred to our private diagnostic laboratory for genetic testing. By next‐generation sequencing (NGS) and Multiplex Ligation‐dependent Probe Amplification (MLPA) analysis we identified a gross deletion of the genomic region encompassing exons 11–16 of the MSH2 gene and the loss‐of‐function variant c.757_758delCT, p.(Leu253Ilefs*3) in the PALB2 gene in our proband.

Gastrointestinal malignancies are among the leading causes of cancer-related deaths worldwide. Like all human malignancies they are characterized by accumulation of mutations which lead to inactivation of tumor suppressor genes or activation of oncogenes. Advances in Molecular Biology techniques have allowed for more accurate analysis of tumors' genetic profiling using new breakthrough technologies such as next generation sequencing (NGS), leading to the development of targeted therapeutical approaches based upon biomarker-selection. During the last 10 years tremendous advances in the development of targeted therapies for patients with advanced cancer have been made, thus various targeted agents, associated with predictive biomarkers, have been developed or are in development for the treatment of patients with gastrointestinal cancer patients. This review summarizes the advances in the field of molecular biomarkers in tumors of the gastrointestinal tract, with focus on the available NGS platforms that enable comprehensive tumor molecular profile analysis.

Background The application of the Next Generation Sequencing (NGS) technology has facilitated multigene panel testing for hereditary breast cancer (BC) in clinical practice. We performed a retrospective analysis of individuals referred for testing in our lab aiming to investigate the contribution of included genes and evaluate current genetic testing guidelines in BC. Methods In total, 1141 BC patients and 184 unaffected individuals with family history (FH) of BC were referred from physicians for testing using a multigene panel. Genomic DNA was enriched for targeted regions of 33 genes and sequencing was carried out using the Illumina NGS technology. The presence of large genomic rearrangements (LGRs) was investigated computationally and by Multiplex Ligation-dependent Probe Amplification (MLPA). Results A pathogenic variant (PV) was identified in 22% (291/1325) of analyzed individuals and in specific in 23.2% of BC patients and 14.1% of unaffected individuals (P = 0.006). Among individuals with PVs, 49.1% were located in the BRCA1/2 genes whereas 8.6%, 22.7% and 19.6% occurred in other high, moderate and low-risk genes respectively. Notably, 21 of the 291 positive individuals (7.2%) carried clinically significant variants in two different genes and 6.5% had a LGR. A retrospective analysis of positive individuals showed that 88.3% of BC patients met the NCCN criteria for further genetic risk evaluation compared to 80.8% of unaffected individuals with FH of BC (P = 0.269). In BRCA-positive cases, NCCN criteria were met in 92.3% of the referrals compared to 81.8% in individuals positive for other genes (P = 0.008). Conclusions Extended multigene panel testing in hereditary BC facilitates the detection of nearly twice as many individuals that could benefit from personalized management. In our cohort, the currently used selection criteria for HBOC failed to identify only 12.7% of individuals positive for pathogenic variants, suggesting strong selection strategies from physicians. However, our results indicate that selection criteria perform better for the identification of BRCA-positive BC patients and should be revised to facilitate towards the inclusion of BC patients with PVs in other genes. Legal entity responsible for the study The authors. Funding Has not received any funding. Disclosure All authors have declared no conflicts of interest.

BACKGOUND: Hereditary cancer predisposition syndromes are believed to be responsible for approximately 5-10% of all diagnosed cancer cases. In the past, single genes analysis of certain high risk genes was used for the determination of the genetic cause of cancer heritability in certain families. The selection of genes was mainly based on the family history of the individuals analyzed and included only highly associated genes (e.g. the BRCA1 and BRCA2 genes for families with breast cancer history. Nowadays though, the application of Next Generation Sequencing (NGS) technology has facilitated multigene panel analysis and is widely used in clinical practice, for the identification of individuals with cancer predisposition gene mutations. AIM: The aim of this study was to investigate the extent and nature of mutations in 36 genes implicated in hereditary cancer predisposition in individuals referred for testing in our lab. MATERIALS & METHODS: In total, 1197 individuals were referred for testing in our lab in the past four years from Greece, Romania and Turkey. The analysis of genes involved in hereditary cancer predisposition was performed using two NGS approaches. The first 451 individuals were analyzed using an amplicon based sequencing method (26 gene panel), while the following 746 individuals were analyzed using a capture based method (33 gene panel). Genomic DNA was enriched for targeted regions of 36 genes involved in hereditary predisposition to cancer included in both versions of the panel (APC, BMPR1A, BRCA1, BRCA2, CDH1, CDK4, CDKN2A, EPCAM, MEN1, MLH1, MSH2, MSH6, MUTYH, PALB2, PMS2, PTEN, RET, SMAD4, STK11, TP53, VHL, ATM, BRIP1, CHEK2, NBN, RAD51C, RAD51D, BARD1, BLM, CHEK1, ABRAXAS1 (FAM175A), MRE11 (MRE11A), NF1, RAD50, RAD51B, XRCC2). Sequencing was carried out using the Illumina NGS technology. Reads were aligned to the reference sequence (GRCh37), and sequence changes were identified and interpreted in the context of a single clinically relevant transcript. The presence of large genomic rearrangements was investigated by computational analysis of NGS results and the use of MLPA for 13 genes. All clinically significant observations were confirmed by orthogonal technologies. RESULTS: In total, a pathogenic mutation was identified in 259 of the 1197 individuals (21.6%) analyzed while a VUS was identified in 35.7% of the cases. Clinically significant mutations were identified in 29 of the genes analyzed. Concerning the mutation distribution among individuals with positive findings, 44.7% of them were located in BRCA1/2 genes whereas 20.9%, 19.9%, and 14.5% in high, moderate and low risk genes respectively. In addition to BRCA1 and BRCA2 genes other highly mutated genes were CHEK2 (10.6%), PALB2 (7.1%), MUTYH (7.1%) and ATM (4.3%). Of note is that 25 of the 259 positive individuals (9.7%) carried clinically significant mutations in two different genes and 5.8% had a large genomic rearrangement (LGR). CONCLUSIONS: Our results support the clinical significance of analysis of a panel of genes involved in hereditary cancer predisposition. In our cohort, analysis of this panel allowed for the identification of 8.3% additional pathogenic variants in moderate/low risk genes, enabling personalized management of these individuals. Citation Format: Tsoulos N, Tsaousis GN, Papadopoulou E, Agiannitopoulos K, Pepe G, Kambouri S, Apessos A, Diamantopoulos N, Floros T, Iosifidou R, Katopodi O, Koumarianou A, Markopoulos C, Papazisis K, Venizelos V, Xanthakis I, Xepapadakis G, Banu E, Eniu DT, Negru S, Stanculeanu DL, Ungureanu A, Ozmen V, Tansan S, Tekinel M, Yalcin S, Nasioulas G. Analysis of hereditary cancer syndromes by using a panel of genes: Novel and multiple pathogenic mutations [abstract]. In: Proceedings of the 2018 San Antonio Breast Cancer Symposium; 2018 Dec 4-8; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2019;79(4 Suppl):Abstract nr P4-03-07.

INTRODUCTION Hereditary breast cancer is estimated to account for approximately 10% of all breast cancer cases. In addition, an estimated 15-20% of those affected by breast cancer have a positive family history. Despite the fact that BRCA1 and BRCA2 are the two most significant genes in hereditary breast cancer predisposition, twenty years of analysis has highlighted the fact, that mutations in these two highly penetrant genes, are only present in approximately 20% of high risk families. Other genes, mutations in which are associated with high risk of breast cancer, were identified because of the strong association with familial cancer syndromes, in which breast cancer is one of the defining components. Technological advances in molecular biology and especially DNA sequencing, commonly designated as “Next Generation Sequencing – NGS” have aided in the concentrated efforts to identify new genes responsible for the missing heritability, allowing the application of this knowledge in the diagnostic setting. AIM The aim of this study was to investigate the extent and nature of mutations in 26 genes implicated in hereditary cancer predisposition in families of Romanian descent. MATERIALS & METHODS In total, 297 Romanian families have been analyzed by our group in the past three years. Genomic DNA was enriched for targeted regions of 26 genes involved in hereditary predisposition to cancer (ATM, BARD1, BLM, BRCA1, BRCA2, BRIP1, CDH1, CHEK2, EPCAM (only intron 8, exon 9 and 3'UTR), FAM175A, MEN1, MLH1, MRE11A, MSH2, MSH6, MUTYH, NBN, PALB2, PMS2, PTEN, RAD50, RAD51C, RAD51D, STK11, TP53, XRCC2). Sequencing was carried out using the Illumina NGS technology. Reads were aligned to the reference sequence (GRCh38), and sequence changes were identified and interpreted in the context of a single clinically relevant transcript. The presence of large genomic rearrangements was investigated by use of MLPA. All clinically significant observations were confirmed by orthogonal technologies. RESULTS In total, a pathogenic mutation was identified in 79 of the 297 families (26.6%) analyzed. Clinically significant mutations were identified in 17 of the genes included in the panel. The most commonly mutated genes in the Romanian population were BRCA1 and BRCA2, accounting for 50% of the mutations identified, followed by PALB2 (12%), CHEK2 (9.4%) and ATM, NBN and RAD50 which accounted for 3.5% of the mutations each. Of note is that 7 of the 79 affected families (8.8%) carried clinically significant mutations in two different genes. CONCLUSIONS Our results support the clinical significance of analysis of a panel of genes involved in hereditary cancer predisposition. In this series of patients, analysis of this panel allowed for the identification of 14% additional pathogenic variants. This is especially true in those cases where more than one pathogenic variant was identified. Citation Format: Tsoulos N, Apessos A, Agiannitopoulos K, Pepe G, Tsaousis G, Kambouri S, Eniu DT, Ungureanu A, Banu E, Ciule L, Blidaru A, Chiorean A, Stanculeanu DL, Mateescu D, Nasioulas G. Analysis of hereditary cancer syndromes by use of a panel of genes: More answers than questions [abstract]. In: Proceedings of the 2017 San Antonio Breast Cancer Symposium; 2017 Dec 5-9; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2018;78(4 Suppl):Abstract nr P3-03-03.