The Development of a Fuzzy Logic System Using MATLAB for Early Detection of Hereditary Cancer in BRCA1/2 Negative Cases

Eligibility Criteria and Genetic Testing Results from a High-Risk Cohort for Hereditary Breast and Ovarian Cancer Syndrome in Southeastern Ontario

DNA-based screening and population health: a points to consider statement for programs and sponsoring organizations from the American College of Medical Genetics and Genomics (ACMG)

Background: The usefulness of prophylactic surgery and surveillance for hereditary breast cancer has been demonstrated, and germline testing for BRCA1 and BRCA2 had been covered by insurance since 2020 in Japan. In addition to BRCA1 and BRCA2, several other genes are also associated with an increased risk of developing breast cancer, such as PALB2, ATM, BARD1, CHEK2, PTEN, and TP53. Next-generation sequencing-enabled multigene panel tensing provides information about these gene variants at the same time, and at a low cost. Although germline testing of BRCA1 and BRCA2 has become widespread in Japan, multi-panel gene testing for germline variants has been conducted only in a limited number of facilities, partly due to the difficulty associated with dealing with the gene variant information obtained from the test. The aim of this study was to clarify the current status of multigene panel testing in our institute, and reveal the characteristics of the variants detected in patients with, or predisposed to, hereditary breast cancer. Methods: This retrospective study included 37 individuals who underwent next-generation sequencing-based multigene panel testing in order to investigate any inherited genetic variants due to a suspicion of hereditary breast cancer. Eighteen patients had a diagnosis of breast cancer with a family history of breast and/or ovarian cancer, nine patients had a diagnosis of breast cancer without family history of breast or ovarian cancer, and 10 patients had a family history of breast cancer but had not developed breast cancer themselves. Results: Utilizing mutigene panel testing, at least one alteration was found in 24 genes, and a total of 39 variants were found in the 37 patients. Of these 37 patients, nine (24.3%) had a pathogenic/likely pathogenic variant with or without other variants of uncertain significance (VUS), 15 (40.5%) had VUS, and 13 (35.1%) had negative genetic test results. Among the nine patients with pathogenic/likely pathogenic variants, seven had variants in either BRCA1 or BRCA2 (one BRCA1 pathogenic variant, five BRCA2 pathogenic variants, and one BRCA2 likely pathogenic variant), while the remaining positive results were attributed to other genes (one MLH1 pathogenic variant, and one SDHB pathogenic variant). VUS included BRCA1 and BRCA2, as well as other breast cancer-associated genes, such as ATM (n=2), CDH1 (n=2), NF1 (n=2), PALB2 (n=1), CHEK2 (n=1), NBN (n=1), and RAD51D (n=1). VUS also included other cancer syndrome-related genes, such as MLH1 (n=2), MUTYH (n=2), APC (n=1), and RET (n=1). Conclusion: Multigene panel tests in our institute revealed pathogenic/likely pathogenic variants in 24.3% of individuals who suspected hereditary breast cancer. As expected, multigene panel tests also revealed more VUS than pathogenic variants and 40.5% individuals were detected with VUS, which included many genes associated with hereditary breast cancer and other cancer syndromes, in addition to BRCA1 and BRCA2. Individuals with VUS will need to cope with new information if the interpretation of the variant changes in the future. We need to be aware of the characteristics and limitations of this type of panel testing, and to properly utilize the test results and information obtained for good quality patient care. Citation Format: Yusa Atake, Masayuki Nagahashi, Haruka Kanaoka, Akira Hattori, Ayako Bun, Reiko Fukui, Hiromi Ozawa, Yukie Fujimoto, Tomoko Higuchi, Michiko Imamura, Keiko Murase, Yuichi Takatsuka, Mina Kashima, Chiho Okada, Chinatsu Kinjo, Mikako Miyata, Ayako Miyazaki, Mako Ueda, Hiroshi Tsubamoto, Hideaki Sawai, Yasuo Miyoshi. Germline variants detected by next-generation sequencing-based multigene panel testing in patients with suspected hereditary breast cancer at a University Hospital in Japan [abstract]. In: Proceedings of the 2022 San Antonio Breast Cancer Symposium; 2022 Dec 6-10; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2023;83(5 Suppl):Abstract nr P5-12-02.

Points to consider: is there evidence to support BRCA1/2 and other inherited breast cancer genetic testing for all breast cancer patients? A statement of the American College of Medical Genetics and Genomics (ACMG)

BACKGROUND: Germline genetic testing is routinely incorporated into clinical care for breast cancer patients to inform management decisions and reduce risk for developing subsequent cancers. While the diagnostic yield of cancer genetic testing has increased over the years due to adoption of multigene panels, a substantial portion of breast cancer patients remain without a molecular diagnosis yet are suspected to have a genetic mutation that could not be detected and/or classified with standard DNA testing techniques. We assessed the ability of a novel genetic testing approach involving simultaneous DNA and RNA analysis to increase the diagnostic yield and decrease the number of variants of unknown significance (VUS). METHODS: Women with a personal history of breast cancer were ascertained from a larger cohort of patients referred for concurrent RNA sequencing alongside DNA hereditary cancer panel testing by ordering clinicians from 18 collaborating medical centers across the United States. Test result classifications were evaluated for women whose testing included sixteen clinically-actionable hereditary breast and/or ovarian cancer (HBOC) genes (ATM, BRCA1, BRCA2, BRIP1, CDH1, CHEK2, MLH1, MSH2, MSH6, NF1, PALB2, PMS2, PTEN, RAD51C, RAD51D, and TP53). RESULTS: In this cohort of 746 breast cancer patients, the addition of RNA sequencing increased the pathogenic variant detection rate from 8% to 9% across sixteen HBOC genes. These RNA-related positive results included two pathogenic variants in BRCA1 occurring outside the standard analytical range of DNA testing and three VUS (one each in ATM, BRCA2, and PMS2) that were reclassified as likely pathogenic as a result of additional information provided by RNA sequencing. In addition, two VUS were reclassified to benign/likely benign (one each in MSH2 and BRCA2). Together, these five variant reclassifications contributed to a 3% relative decrease in the number of unique VUS classifications (reduced from 182 to 177 unique VUS). In addition, 31 previously-tested patients received reclassification reports. CONCLUSIONS: Concurrent DNA and RNA genetic testing has shown immediate promise in this pilot study, leading to the identification of five breast cancer patients with mutations in clinically actionable genes that would otherwise have received inconclusive or negative results with DNA testing alone. By increasing the detection of germline pathogenic variants and reducing VUS classifications, concurrent DNA and RNA genetic testing increases the diagnostic yield and clinical impact of hereditary cancer testing for breast cancer patients. Citation Format: Holly LaDuca, Lily Hoang, Jill Dolinsky, Jessica Profato, Amal Yussuf, Carolyn Horton, Cara Dresbold, Cassie Garcia, Catherine Koptiuch, Danielle Dondanville, Danielle McKenna, Danielle Menashe, Deborah Wham, Deepika Nathan, Diane Samad, Elizabeth Hoodfar, Gayle Patel, Jen Moore, Jennifer Geurts, John Lee, Kara Milliron, Khateriaa Pyrtel, Meagan Farmer, Meredith Seidel, Morgan Depas, Nichole Morman, Olivia Tan, Rebekah Krukenberg, Rob Pilarski, Samantha Stachowiak, Sandra Jenkinson, Sara Pirzadeh-Miller, Shraddha Gaonkar, Tiffani Demarco, Brigette Tippin Davis, Elizabeth C Chao, Rachid Karam. Concurrent DNA and RNA genetic testing identifies more patients with hereditary breast cancer than DNA testing alone [abstract]. In: Proceedings of the 2019 San Antonio Breast Cancer Symposium; 2019 Dec 10-14; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2020;80(4 Suppl):Abstract nr P6-08-08.

Pathogenic germline mutations occurring in the BRCA1 (MIM:113705) and BRCA2 (MIM: 600185), which always result in truncated protein or nonsense-mediated mRNA decay, have been identified to increase the risk of hereditary breast, ovarian, pancreatic, prostate, and melanoma cancers. Recent studies show that BRCA1/2 germline mutations also contribute to half of all hereditary breast and ovarian cancer (HBOC).In this case series, we reported a novel frameshift mutation of the BRCA1 gene. This novel frameshift mutation occurs in exon10 of BRCA1 and may result in a lack of the serine cluster domain and BRCA1 C-terminus domain, which mediates the function of BRCA1 in DNA repair and are responsible for activation function of BRCA1. The mutation was present in a Chinese hereditary male/female breast and ovarian cancer family characterized by a high incidence of breast cancer and/or ovarian cancer among the relatives and by a high incidence of triple negative breast cancer (TNBC).Our findings speculate that BRCA1 E1148Rfs*7 mutation may be related to the occurrence of HBOC and even TNBC. Interestingly, three cases of TNBC with this novel BRCA1 mutation in this case series showed a good disease-free survival, one of them has a disease-free survival up to 7 years. Therefore, further study is required to confirm that whether this mutation is associated with good prognosis of HBOC.

Women with one or more first-degree female relatives with a history of breast cancer have a two-fold increased risk of developing breast cancer. This risk increases with the number of affected family members, particularly for those diagnosed at a young age or with bilateral disease. Segregation analyses of breast cancer families led to the identification of inactivating mutations in the BRCA1 and BRCA2 breast cancer susceptibility genes. Pathogenic variants resulting in truncation of these proteins, along with a small number of pathogenic missense variants, have been associated with 55% to 65% lifetime risk of breast cancer in the general population and up to 85% lifetime risks among women with a strong family history of the disease. In contrast, the influence on cancer risk of many rare variants of uncertain significance (VUS) is not known. Mutations in several genes in addition to BRCA1 and BRCA2 have been implicated in predisposition to breast cancer through family segregation studies. These include moderate risk mutations (relative risk between 2.0 and 5.0) in CHEK2 and ATM, high-risk mutations (relative risk greater than 5.0) in PALB2, and high-risk mutations in CDH1, PTEN, STK11, and TP53 that are associated with hereditary diffuse gastric cancer, Cowden, Peutz-Jeghers, and Li-Fraumeni syndromes. However, risks of breast and other cancers associated with mutations in these and other genes that have been suggested to predispose to cancer have not been established or have very broad confidence intervals. Despite the absence of accurate risk estimates clinical testing with gene panels for hereditary cancer gene mutations has become an integral component of medical management for high-risk families and individuals with triple negative breast cancer. To estimate breast cancer risks several large studies of breast cancer patients from the general population and from high-risk families are underway. These studies are expected to identify the subset of panel genes that are associated with increased risk of breast cancer or breast cancer subtypes and to establish more accurate risks of breast and other cancers. In addition, classification of the clinical relevance of VUS in BRCA1, BRCA2, and other predisposition genes remains a significant problem, with patients unable to benefit from enhanced risk assessment, prevention, and clinical management. Thousands of VUS in BRCA1 and BRCA2 have already been identified through clinical testing and many more in BRCA1, BRCA2, and other predisposition genes are being identified through panel-based genetic testing and tumor sequencing studies. Efforts to classify VUS as neutral or pathogenic have focused on large case-control studies and quantitative multifactorial models based on family history of cancer and pathology. However, more recent studies have established the utility of validated functional assays for VUS assessment. Hundreds of BRCA1 and BRCA2 VUS have been reclassified by commercial testing laboratories or by the ENIGMA consortium that serves as the expert review panel for variants in these genes for the ClinVar (https://www.ncbi.nlm.nih.gov/clinvar/) and BRCA Exchange (http://brcaexchange.org) publically accessible websites. Common genetic variants associated with breast cancer risk have also been identified through genome-wide association studies (GWAS). The magnitude of these associations have ranged from 1.03 to 1.29 in women of European ancestry. While the majority of the 179 known breast cancer variants are associated with estrogen receptor (ER) positive breast cancer, 21 of these show specific associations with ER negative or triple negative (ER negative, PR negative, HER2 negative) breast cancer. The variants in risk loci account for approximately 19% of the familial relative risk of breast cancer. Several studies have recently established that polygenic risk scores derived from these risk variants improve personalized risk assessment by identifying women at increased or reduced risk of breast cancer in the general population and by modifying risks of breast cancer among BRCA1 and BRCA2 mutation carriers. In summary, germline genetic studies have substantially changed the landscape of breast cancer, identifying mutations associated with moderate and high risks of breast cancer in up to 5% of population-based breast cancer cases and 35% of high-risk families and providing personalization of underlying breast cancer risk for all women. Citation Format: Couch FJ. OI-1 Decoding breast cancer predisposition genes [abstract]. In: Proceedings of the 2016 San Antonio Breast Cancer Symposium; 2016 Dec 6-10; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2017;77(4 Suppl):Abstract nr OI-1.

Introduction Current guidelines for cancer risk management for hereditary breast cancer focus on individuals with pathogenic/likely pathogenic variants (P/LP) in high penetrance genes. There is little consensus on prophylactic mastectomy for low/moderate penetrance genes or variants of uncertain significance (VUS). Furthermore, many guidelines for enhanced breast cancer screening are targeted to unaffected carriers, but not breast cancer survivors. Given the increasing use of multigene panel testing, more patients are receiving results of P/LP in low/moderate penetrance genes or VUSs. We aimed to investigate how multigene panel results impacted surgical and screening decisions among breast cancer patients. Methods We conducted a retrospective analysis of women diagnosed with stage 0-III breast cancer at Columbia University Irving Medical Center in 2013 or later, who received germline genetic testing. Clinical data were extracted from the electronic health record (EHR), tumor registry, and genetic testing portals. Patients were excluded if they had stage IV disease at diagnosis, had bilateral mastectomy before 2013, or had missing genetic test results or surgical reports. For the screening analysis, patients were excluded if they had bilateral mastectomy or did not have breast imaging in the EHR. Surgery type was defined by the most advanced breast surgery received. Enhanced screening was defined as use of breast ultrasound or MRI in the absence of breast symptoms and in the setting of a normal mammogram. Univariable and multivariable analyses were performed to assess the association between clinical factors and receipt of bilateral mastectomy or enhanced screening. Results Among 715 evaluable women, about two-thirds were 50 years or younger, with 45% white, 12% black, 27% Hispanic, 11% Asian, and 4% other. Most patients (69.5%) had benign/likely benign (B/LB) genetic test results, while 91 (12.7%) had P/LP and 127 (17.8%) had VUS. VUS rates were higher among racial/ethnic minorities (27% Asian, 25% Hispanic, 19% black) compared to white women (10%). About 31% of women underwent bilateral mastectomy, 25% unilateral mastectomy, and 45% lumpectomy. Bilateral mastectomy rates among patients with P/LP variants were higher compared to those with VUS or B/LB results (66% vs. 27% vs. 26%), particularly P/LP in high-penetrance genes (76%) compared to other genes (45%). On multivariable analysis, compared to patients with B/LB genetic results, P/LP was significantly associated with bilateral mastectomy (odds ratio [OR]=5.72, 95% confidence interval [CI]=3.43-9.53). Younger age at diagnosis and family history of breast cancer were also associated with bilateral mastectomy. Among patients with breast cancer screening data, almost half (43%) received enhanced screening (59% ultrasound, 25% MRI, 16% both). On multivariable analysis, patients with P/LP variants and age of diagnosis under 50 were more likely to receive enhanced screening (OR=4.43, 95% CI=1.59-12.33 and OR=1.92, 95% CI=1.09-3.38, respectively). Hispanic women compared to non-Hispanic whites and those with Medicaid rather than private health insurance were less likely to undergo enhanced screening. Conclusions We demonstrated that detection of P/LP variants on multigene panel testing influences surgical and screening decisions among breast cancer patients. Patients with VUS, a group enriched for racial/ethnic minorities, appropriately have similar surgical and screening decisions as those with B/LB results. Our findings suggest adequate genetic counseling and communication of cancer risk to multi-ethnic breast cancer survivors. Citation Format: Vicky Ro, Tarsha Jones, Meghna S Trivedi, Julia E McGuinness, Thomas Silverman, Wendy K Chung, Rita Kukafka, Katherine D Crew. Impact of genetic testing for hereditary breast cancer on screening and risk-reducing surgeries among multi-ethnic breast cancer survivors [abstract]. In: Proceedings of the 2020 San Antonio Breast Cancer Virtual Symposium; 2020 Dec 8-11; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2021;81(4 Suppl):Abstract nr PS8-08.

Background: Hereditary cancer syndromes explain 5-10% of all cancer cases. Germline pathogenic variants in BRCA1 and BRCA2 genes (BRCA) are present in 2-3% of all breast cancer (BC), and 15% of all ovarian cancer (OC) cases. BRCA1 and BRCA2 pathogenic variants (PV) represent 25-28% of BC and 40% of OC patients with a positive familial history. BRCAs are the most studied genes for the prevalence, family history, preventive surgeries, and target treatment options in both BC and OC. There are other genes, important in the diagnosis, pathogenesis, and treatment options of the patients: TP53, PALB2, CHEK2, among others. This study aims to identify the prevalence of non- BRCA genes related to the development of hereditary breast and ovarian cancer syndrome in patients of Northeast Mexico. Methods: This is a multicenter study that recruited patients from two reference oncology centers in Nuevo Leon, Mexico: the CECIL (The CUCC Early Cancer Detection Clinic) Hereditary Cancer Registry and Hereditary Cancer Program from Tec Salud. From March of 2016 to March of 2023, a total of 872 patients meeting NCCN criteria were evaluated by Medical Geneticists from both centers and were tested with NGS multigene cancer panels. Results: A total of 665 (76.26%) patients with a clinical diagnosis of HBOC (Hereditary Breast Hereditary Cancer Syndrome) were included. We found 310 (46.6%) patients had at least one variant, 180 (58%) with at least one pathogenic variant, and 130 (41%) with a VUS (a variant of uncertain significance). BRCA1 was found in 79 (43.8%) and BRCA2 in 32 (17.7%) of all PV. Non-BRCA PV were found in 69 (38.3%) patients: 4 ATM, 2 BLM, 3 BRIP1, 22 CHEK2, 4 CDKN2A, 5 MUTYH, 10 PALB2, 4 RAD51C, 2 SDHA, 2 TP53, 2 WRN, CDH1, CDK4, DICER, MSH3, NBN, PTEN, RAD50, USH2A one of each. Is remarkable that 19 of the 22 patients with CHEK2 and 5 of the 10 patients with PALB2 had the recurrent PV c.707T>C and c.2167_2168del, respectively. Conclusions: Non-BRCA PV in Northern Mexico corresponds to one-third of the BC and OC cases, including HRD (homologous recombination deficiency) genes. HDR patient carriers are potential targets of iPARP therapies. This project reinforces the fact that multigene panels should be employed to ensure a complete diagnosis in hereditary cancer patients. Citation Format: Carlos H. Burciaga-Flores, Diana C. Perez-Ibave, Maria L. Garza-Rodriguez, Oscar Vidal-Gutierrez, Cynthia M. Villarreal-Garza, Dione Aguilar y Mendez. Non-BRCA variants in hereditary breast and ovarian cancer patients in the Northern Mexico population [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2024; Part 1 (Regular Abstracts); 2024 Apr 5-10; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2024;84(6_Suppl):Abstract nr 3947.

Genetic testing outcome disparities in minority racial and ethnic sub-populations within a hereditary breast and ovarian cancer program serving a diverse, urban-based population (191)

BACKGROUND: Breast cancer patients with BRCA 1 or 2 gene mutations demonstrate a high lifetime incidence of a second breast cancer in the contralateral breast. These patients may benefit from a bilateral mastectomy (BLM) with an intent of risk reduction. If provided in the right window between cancer diagnosis and definitive treatment, genetic cancer risk assessment would aid high-risk patients in making an informed decision with respect to planning appropriate surgery. OBJECTIVE: The purpose of this study is to assess the feasibility of BRCA 1 and BRCA 2 gene mutation testing in the pre-operative setting and to determine whether test results altered final surgical decision. METHODS: Newly diagnosed breast cancer patients referred to the cancer genetics clinic between April 2009 to March 2010 were identified. All patients were sent for genetic cancer risk assessment due to the presence of clinical features suggestive of hereditary breast cancer based on current guidelines. A retrospective chart review of the patients was performed. RESULTS: 81 patients were identified. 6 patients were excluded as they went on to have surgery in a different hospital and were lost to follow up. 3 patients did not meet criteria for genetic testing. 1 patient was excluded as she was scheduled for a BLM prior to being seen in our clinic, and 1 patient was receiving neoadjuvant chemotherapy and hadn't had surgery at the time of data collection. Of the remaining 70 patients, the mean age was 48 years (29-74 years) with 81% being of caucasian race and 11% having Ashkenazi-Jewish ethnicity. 30% had two or more first degree and 68% had two or more second degree relatives with cancer. 29% had a first degree relative who had died of cancer. 74% had a diagnosis of invasive breast cancer, where as 26% only had in-situ disease. Further, 21% had grade 1, 37% with grade 2 and rest with grade 3 tumors. 81% tested negative for BRCA gene mutations, 9% were positive for either BRCA 1/2, 6% had variants of uncertain significance(VUS) and 4% didn't undergo genetic testing for various reasons. It took an average of 9.3 days (4-31 days) to obtain results. 54% of women aged 40 years or younger chose BLM versus 25% of women over 40 (p=0.015). 6.7% of women with low grade breast cancer underwent BLM versus 54% with moderate grade and 34% with high grade cancer (p=0.0098). Based on the BRCA results, 83% of BRCA positive women chose BLM versus 33% of BRCA negative (true negative and VUS) patients (p=0.024). A negative result had a greater influence in favor of a unilateral surgery in 67% of BRCA negative patients. In contrast, majority of women who underwent BLM were not influenced solely by their gene test results. CONCLUSIONS: Amongst newly diagnosed breast cancer patients, genetic testing for hereditary breast and/or ovarian cancer syndromes can influence surgical decision in a risk-appropriate way. Our results show that genetic cancer risk assessment can be effectively incorporated in newly diagnosed breast cancer patients and can help guide the decision about the optimal surgery without a significant delay. A negative BRCA gene result seemed to help patients reach a decision favoring unilateral surgery. Citation Information: Cancer Res 2010;70(24 Suppl):Abstract nr P2-10-03.

BACKGROUND: Breast cancer (BC) is the most common cancer and the second leading cause of cancer-related deaths worldwide. Mutations in tumor suppressor genes BRCA1 and BRCA2 are the most common cause of hereditary breast and ovarian cancer. Additionally, carriers of germline BRCA1/2 mutations also have an elevated risk of other malignancies. Identification of mutations within these genes is essential for determining early cancer detection and risk-reducing strategies in carriers and establishing a therapeutic approach in breast cancer patients. The aims of this study were to evaluate the prevalence and spectrumof germline BRCA1 and BRCA2 variants in peruvian breast cancer patients. METHODS: Patients with HER2Neu negative BC referred to ONCOGENOMICS laboratory from 2019 to2021 to assessed poly (adenosine diphosphate-ribose) polymerase (PARP) inhibitor treatment were included in the study. Blood samples were collected to assess the status of germline BRCA1 and BRCA2. Next Generation Sequencing (NGS) was performed using the Ampliseq for Illumina BRCA panel and run on the Illumina MiSeq. The Human Genome Variation Society (HGVS) nomenclature guidelines (http://varnomen.hgvs.org/) were used to annotate identified variants and the ClinVar database (www.ncbi.nlm.nih.gov/clinvar/) was used to determine the clinical significance of all reported variants. Current American College of Medical Genetics (ACMG) guidelines were also used for further classification. RESULTS: A total of 155 HER2Neu negative BC cases were evaluated. Median age at BRCA1/2 evaluation was 51 (23-82) years, 78.1% (121) were negative HR status (triple-negative BC, TNBC); 21.9% (34) were positive HR status; 33.5% (52) were clinical stage III and 66.5% (103) were clinical stage IV. Most patients were from Lima-Callao (65.8%) followed by patients from the coast (23.9%), highlands (9%) and rainforest(1.3%). Only 18.7% of patients were from public health centers. The prevalence of pathogenic (P) and likely pathogenic (LP) variants in BRCA1/2 was 13.5% (21) (13 in BRCA1 and 8 in BRCA2). The pathogenic variant in BRCA1 c.2105dupT (p.Leu702Phefs*10) was found in 3 cases (2 Lima-Callao and 1 coast). All variants identified in BRCA1 were in TNBC. In BRCA2, half of pathogenic variants were found in TNBC. The prevalence of variants of uncertain significance (VUS) was 6.4% (10). In BRCA2, we identified 7 VUS and the variant c.5465A>T (p.Asn1822Ile) was found in 3 cases with positive HR status. Only one VUS was found in BRCA1. CONCLUSION: BRCA1 and BRCA2 germline mutations were identified in 13.5% of peruvian HER2Neu negative BC patients. A higher rate of P/LP variants was found in BRCA1. TNBC patients demostrated a higher prevalence in BRCA1 variants. Citation Format: Joseph A Pinto, Yomali Ferreyra, Alicia M Cock-Rada, Franco Doimi, Jhoysi Casas, Jhajaira Araujo, Gina Rosas, Leny Bravo, Carolina Belmar-López. Landscape of germline BRCA1 and BRCA2 mutations in breast cancer in Peru [abstract]. In: Proceedings of the 2021 San Antonio Breast Cancer Symposium; 2021 Dec 7-10; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2022;82(4 Suppl):Abstract nr P3-12-24.

ACMG SF v3.0 list for reporting of secondary findings in clinical exome and genome sequencing: a policy statement of the American College of Medical Genetics and Genomics (ACMG)

Background: The CHEK2 gene codes for checkpoint protein Kinase 2 (CHK2), an effector in the ATM-CHK2-p53 DNA damage repair pathway in double-stranded DNA breaks. Initially, germline pathogenic variants were associated with moderate risk for breast carcinoma, but later studies linked alterations in the gene to other types of cancer. The aim of our study was to establish a clinical-molecular correlation of profiles of patients carrying pathogenic variants and variants of uncertain significance (VUS) in CHEK2 with a diagnosis of breast carcinoma, in patients treated in our hospital. And to describe whether the pathogenic variant c.1100del present different clinical or immunohistochemical characteristics than the rest, also considering the particularity of being an island population. Methodology: We have collected data from genetic studies performed in patients from our hospital, covering a population of 580,000 inhabitants, in Santa Cruz de Tenerife ( Canary Islands, Spain), between 2017 and 2023.Out of 952 patients with suspected hereditary cancer, 81 had CHEK2 mutations. In patients with CHEK2 mutations and breast cancer we established three groups for clinical molecular analysis: 1) pathogenic variant c.1100del, 2) other pathogenic variants and 3) VUS, to be correlated with age, histology, ER, PR, Ki, grade (G), HER2, second tumour or recurrence, subtype, HER2 low, aggressive clinic, neuropathy, haematological and digestive toxicity. The germline genetic study performed covered 77 genes related to hereditary cancer using the SureSelect HS library preparation kit (Agilent Technologies). The classification of the variants identified was performed according to the American College of Medical Genetics (ACMG) criteria. Results: In the 952 genetic studies performed, 8.5% of cases had CHEK2 mutations, 2.62% were related to breast carcinoma (N=26) of which 54% had the pathogenic variant “c.1100del”, 16% “other” pathogenic variants and 30% VUS. The mean age at diagnosis was 42 years, being lower than 38 years in pathogenic variants other than c.1100del. Histologically, infiltrating ductal carcinoma (85%) and mucinous carcinomas (12%), ER+ (93%), PR+ (77%), HER 2+ (31%), HER2 low (44%), G2-3 (84%) and Ki >15% (70%) were predominant. Second diagnoses were tumour or recurrence in 40%, being higher in the group of pathogenic variants other than c.1100del (50%), and showing aggressive clinical course in 26%. The predominant subtype was luminal B (50%), HER2+ (31%), luminal A (12 %) and triple negative (7%), although in the cluster analysis patients with pathogenic variant c.1100del HER2+ were higher (38%) and luminal B (38%), while in pathogenic variants other than c.1100del and VUS the luminal subtype was predominant (75%). Chemotherapy toxicity: neuropathy (35%), haematological and digestive toxicity (50%). Conclusion: Our results are consistent with other reported series, being related with all breast carcinoma subtypes, mainly luminal B and HER2+ and with triple negative at a lesser extend. Considering HER2 low patients were about 75% of patients with CHEK2 mutations, a molecular mechanism that correlates a truncating mutation in CHK2 and HER2 overexpression can be hypothesized. In the cluster analysis, HER2+ (38%), and luminal B (38%) subtypes predominate in patients with pathogenic variant c.1100del, while in pathogenic variants other than c.1100del and VUS the luminal B subtype predominates (75%), as well as recurrence or second tumours in 50% of cases. On the other hand, considering that this is an island population, the possible effect of geographical isolation and the resulting inbreeding in the past, these facts do not seem to elicit differences comparing to the rest of the continental population, although the increase in pathogenic variants in CHEK2 were observed in patients from the small island of La Gomera. The relationship between CHEK2 and HER2 in breast cancer is an area of active research. Relative frequency in groups of CHEK2 variants Relative frequency in CHEK2 “ pathogenic variants c.1100 del (53%)”, “other”pathogenic variants no c.1100 del (15 %)" and VUS (30%). Relative frequency of breast cancer subtypes according to CHEK2 variants. HER2+: 30,8%. Luminal A: 11,5% . Luminal B: 50%. Triple negative: 7,7% . Histology, ER, PR, Ki, HER2 and HER2 low Histology , infiltrating ductal carcinoma (84%), ER+ (92%), PR (77%), Ki >15% (70%), HER2+ (31%), HER2 low (45%) Citation Format: Natalia Pérez-Rodríguez, Carol Prieto-Morin, Maria del Carmen Maeso, Lina Pérez-Mendez. Clinical-molecular correlation in breast cancer with pathogenic variants in CHEK2. Is there a relationship with HER2+ breast cancer? [abstract]. In: Proceedings of the 2023 San Antonio Breast Cancer Symposium; 2023 Dec 5-9; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2024;84(9 Suppl):Abstract nr PO1-08-06.

Background: Genetic testing and genetic counseling for patients with breast cancer are routinely practiced as recommended by many professional societies and international guidelines including the National Comprehensive Cancer Network (NCCN). In addition to its major impact on cancer prevention, knowledge generated may impact cancer management, too. In this study, we evaluate the prevalence and patterns of germline mutations among at-risk breast cancer patients using commercially available next generation sequencing (NGS)-based multi-gene panel (MGP). Patients and Methods: Consecutive at-risk breast cancer patients, as recommended by the NCCN guidelines, were offered genetic testing using a 20-gene NGS-based panel performed at a reference genetic lab. Prior to testing, patients underwent extensive counseling by one of the investigators or their primary oncologist. Genetic variants were classified as benign or likely benign (negative), pathogenic or likely pathogenic (positive) or variants of uncertain significance (VUS). Clinical and pathological data were obtained from patients’ medical records, and detailed familial lineage for three generations was obtained by a cancer genetic counselor. Results: Between November 2019 and March 2021, a total of 714 patients were enrolled, the median age (range) was 39 (19-78) years. Among the whole group, 91 (12.7%) patients had pathogenic/likely pathogenic variants, mostly in BRCA1 and BRCA2 (n=50, 54.9%). However, 41 (45.1%) had pathogenic variants in genes other than BRCA1 or BRCA2; mostly in TP53, PALB2, CHECK2, BRIP2, ATM and MSH6.Mutation rates were significantly higher among a group of 182 women diagnosed at any age, with one or more close relatives with breast cancer (18.7% compared to 10.7%, p=0.007), and among 287 younger patients (diagnosed at age ≤ 50 years) with one or more close relatives with breast, ovarian, pancreatic, or prostate cancer (Gleason score ≥7); 17.1% vs. 9.8%, p=0.008. Additionally, patients with triple-negative disease (n=92) had higher pathogenic mutations; 17.4% vs. 12.1%, p=0.03. Variants of uncertain significance (VUS) were observed among 213 (29.8%) and majority (n=160, 75.1%) were in genes other than BRCA1 or BRCA2. Conclusions: Pathogenic mutations in genes other than BRCA1 or BRCA2 are relatively common and could have been missed, if genetic testing was restricted to BRCA1 or BRCA2. Patients with triple-negative disease and those with additional positive family history, have the highest mutation rates. On the other hand, expanding genetic testing using MGP resulted in a significantly higher rate of VUS, a finding that may increase the anxiety of patients and physicians, alike. Citation Format: Hikmat Abdel-Razeq, Rama Almasri, Lama Abujamous, Mahmoud Al-Masri, Majd Hamed Allah, Faris Tamimi, Sarah Edaily, Fawzi Abuhijla, Osama Salama, Hazem Abdulelah, Rayan Bater. Guideline-based multi-gene panel (MGP) testing for germline pathogenic variants among patients diagnosed with breast cancer: Regional perspectives [abstract]. In: Proceedings of the 2021 San Antonio Breast Cancer Symposium; 2021 Dec 7-10; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2022;82(4 Suppl):Abstract nr P3-07-06.