Revisiting the Implications of Positive Germline Testing Results Using Multi-gene Panels in Breast Cancer Patients

BACKGROUND/AIM

The use of multi-gene panels for germline testing in breast cancer enables the estimation of cancer risk and guides risk-reducing management options. The aim of this study was to present data that demonstrate the different levels of actionability for multi-gene panels used in genetic testing of breast cancer patients and their family members.

MATERIALS AND METHODS

We performed an analysis in our clinical database to identify breast cancer patients undergoing genetic testing. We reviewed positive results in respect of risk estimation and management, cascade family testing, secondary findings and information for treatment decision-making.

RESULTS

A total of 415 positive test reports were identified with 57.1%, 18.1%, 10.8% and 13.5% of individuals having pathogenic/likely pathogenic variants in high, moderate, low and with insufficient evidence for breast cancer risk genes, respectively. Six point seven percent of individuals were double heterozygotes.

CONCLUSION

Germline findings in 92% of individuals are linked to evidence-based treatment information and risk estimates for predisposition to breast and/or other cancer types. The use of germline findings for treatment decision making expands the indication of genetic testing to include individuals that could benefit from targeted treatments.

Analysis of hereditary cancer syndromes by using a panel of genes: novel and multiple pathogenic mutations

Background

Hereditary cancer predisposition syndromes are responsible for approximately 5–10% of all diagnosed cancer cases. In the past, single-gene analysis of specific high risk genes was used for the determination of the genetic cause of cancer heritability in certain families. 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 predisposing gene variants. The purpose of this study was to investigate the extent and nature of variants in genes implicated in hereditary cancer predisposition in individuals referred for testing in our laboratory.

Methods

In total, 1197 individuals from Greece, Romania and Turkey were referred to our laboratory for genetic testing in the past 4 years. The majority of referrals included individuals with personal of family history of breast and/or ovarian cancer. The analysis of genes involved in hereditary cancer predisposition was performed using a NGS approach. Genomic DNA was enriched for targeted regions of 36 genes and sequencing was carried out using the Illumina NGS technology. The presence of large genomic rearrangements (LGRs) was investigated by computational analysis and Multiplex Ligation-dependent Probe Amplification (MLPA).

Results

A pathogenic variant was identified in 264 of 1197 individuals (22.1%) analyzed while a variant of uncertain significance (VUS) was identified in 34.8% of cases. Clinically significant variants were identified in 29 of the 36 genes analyzed. Concerning the mutation distribution among individuals with positive findings, 43.6% were located in the BRCA1/2 genes whereas 21.6, 19.9, and 15.0% in other high, moderate and low risk genes respectively. Notably, 25 of the 264 positive individuals (9.5%) carried clinically significant variants in two different genes and 6.1% had a LGR.

Conclusions

In our cohort, analysis of all the genes in the panel allowed the identification of 4.3 and 8.1% additional pathogenic variants in other high or moderate/low risk genes, respectively, enabling personalized management decisions for these individuals and supporting the clinical significance of multigene panel analysis in hereditary cancer predisposition.

Electronic supplementary material

The online version of this article (10.1186/s12885-019-5756-4) contains supplementary material, which is available to authorized users.

Abstract P4-03-07: Analysis of hereditary cancer syndromes by using a panel of genes: Novel and multiple pathogenic mutations

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.

[Malign melanoma of the small bowel as a cause of occult intestinal bleeding: case report]

Although the metastases from extra- abdominal tumors to the small bowel are rare, cutaneous melanoma is the most common source. A 78 year old man with occult intestinal bleeding due to malign melanoma of the small bowel was admitted to our clinics. The patient was managed successfully by small bowel resection with end to end anastomosis. Patient is alive three months after the surgery and is in pretty good condition.