Presence Of Germline Variants Research Articles

Comparison of survival outcomes between olaparib and niraparib maintenance therapy in BRCA-mutated, newly diagnosed advanced ovarian cancer

IntroductionThis multicenter retrospective cohort study aimed to compare survival outcomes and adverse events between maintenance therapy with two poly (ADP-ribose) polymerase (PARP) inhibitors, olaparib and niraparib, in patients with BRCA-mutated, newly diagnosed advanced epithelial ovarian cancer (EOC) who responded to platinum-based chemotherapy. MethodsWe enrolled stage III-IV EOC patients with germline and/or somatic BRCA1/2 mutations that had received maintenance therapy with olaparib or niraparib. A 3:1 propensity score matching was conducted using two variables: residual disease size and the presence of germline variants. The primary outcome was progression-free survival (PFS), and the secondary outcomes were time to first subsequent therapy (TFST), overall survival (OS), and treatment-emergent adverse events (TEAEs). ResultsIn the propensity score-matched analysis, 80 patients who received olaparib and 31 patients who received niraparib were matched (3:1). In the propensity score-matched cohort, median PFS with olaparib vs. niraparib was not reached vs 31.5 months (HR, 1.08; 95% CI, 0.47–2.52; p = 0.854). The median TFST was not reached vs 31.8 months (HR, 1.20; 95% CI, 0.51–2.81; p = 0.682), and neither olaparib nor niraparib reached the median OS (HR, 0.42; 95% CI, 0.01–17.61; p = 0.649). In terms of the incidence rates of any-grade hematologic or non-hematologic TEAEs, higher rates of thrombocytopenia (p = 0.021) and neutropenia (p = 0.011) were observed in the niraparib group. ConclusionAdvanced EOC patients with BRCA1/2 mutations exhibited no significant difference in OS between olaparib and niraparib, indicating the need to consider individualized strategies for selecting PARP inhibitors based on adverse event profiles.

Abstract B147: The relationship between germline variants and clinicopathological characteristics in triple negative breast cancer patients from Colombia

Abstract Introduction: Triple-negative breast cancer (TNBC) is the molecular subtype with the worst prognosis among breast tumors. It has been shown that the presence of germline variants can influence disease onset, progression, tumor biology, and other outcomes, however, to this date, the differences in clinical-pathological features according to germline variants in an admixed population like Colombian women, have not been yet explored. Therefore, the aim of this study was to explore the relationship between clinical-pathological characteristics and germline mutations in TNBC patients from Colombia. Methodology: This is a descriptive analysis that included 47 Colombian women with confirmed diagnosis of hereditary TNBC treated at the National Cancer Institute of Colombia, from 2008 to 2022. Germline mutations in 105 genes were assessed using the TruSigth multi-gene panel, and patients were divided according to the identified mutation into the following groups: BRCA1 carriers (n=18), BRCA2 carriers (n=13), homologous recombination (HR) gene carriers (n=13), and carriers of mutations in other genes (n=3). Fisher’s and Pearson’s chi-squared tests were used for categorical variables, and differences were considered statistically significant if p<0.05. Results: Among our cohort, the identified mutation with the highest prevalence was the c.5123C>A p. (Ala1708Glu) in the BRCA1 gene (36,9%). Regarding clinical-pathological features, we observed statistically significant differences in the distribution of germline mutations by age at diagnosis (p=0.042), body mass index (BMI) (p=0.04), and tumor differentiation (p=0.01). Women younger than 50 years at diagnosis had the highest frequency of BRCA1 (23,9%) mutations. Overweight (BMI: 25-30) and obese (BMI>30) patients presented a higher proportion of mutations in the BRCA1 (15,2%) and BRCA2 (13,0%) genes, compared to patients with mutations in HR repair pathways (8,6%) and mutations in other genes (2,2%).  This is interesting as previous reports have shown an association between BRCA1/2 mutations with BMI and chronic inflammation, which could influence the development and progression of breast cancer. Poorly differentiated tumors (Bloom-Richardson: III) were more frequently observed in patients with BRCA1 mutations (32,6%), followed by patients with mutations in the HR genes (17,4%).  It is possible that this is related to the genetic changes that germline mutations induce within the tumor, which ultimately lead to a less differentiated disease. Conclusion: Our study confirms the greater proportion of mutations in BRCA1/2 genes in TNBCs among the Colombian population. The characterization of clinical-pathological characteristics of germline mutation-related tumors may help improve diagnosis, prognosis assessment, and targeted therapeutic approaches. Further studies with larger patient cohorts are needed to confirm our findings. Additionally, large-scale studies are also warranted to elucidate the landscape of germline mutations relevant to the Colombian population, along with its clinical implications. Citation Format: Yina Tatiana Zambrano Ordonez, Laura Rey Vargas, Paula Daniela Morales, Silvia Juliana Serrano. The relationship between germline variants and clinicopathological characteristics in triple negative breast cancer patients from Colombia [abstract]. In: Proceedings of the 16th AACR Conference on the Science of Cancer Health Disparities in Racial/Ethnic Minorities and the Medically Underserved; 2023 Sep 29-Oct 2;Orlando, FL. Philadelphia (PA): AACR; Cancer Epidemiol Biomarkers Prev 2023;32(12 Suppl):Abstract nr B147.

Germ line variants in patients with acute myeloid leukemia without a suspicion of hereditary hematologic malignancy syndrome

AbstractGerm line predisposition in acute myeloid leukemia (AML) has gained attention in recent years because of a nonnegligible frequency and an impact on management of patients and their relatives. Risk alleles for AML development may be present in patients without a clinical suspicion of hereditary hematologic malignancy syndrome. In this study we investigated the presence of germ line variants (GVs) in 288 genes related to cancer predisposition in 47 patients with available paired, tumor-normal material, namely bone marrow stroma cells (n = 29), postremission bone marrow (n = 17), and saliva (n = 1). These patients correspond to 2 broad AML categories with heterogeneous genetic background (AML myelodysplasia related and AML defined by differentiation) and none of them had phenotypic abnormalities, previous history of cytopenia, or strong cancer aggregation. We found 11 pathogenic or likely pathogenic variants, 6 affecting genes related to autosomal dominant cancer predisposition syndromes (ATM, DDX41, and CHEK2) and 5 related to autosomal recessive bone marrow failure syndromes (FANCA, FANCM, SBDS, DNAJC21, and CSF3R). We did not find differences in clinical characteristics nor outcome between carriers of GVs vs noncarriers. Further studies in unselected AML cohorts are needed to determine GV incidence and penetrance and, in particular, to clarify the role of ATM nonsense mutations in AML predisposition.

Defining germline genetics of germ cell tumor: Implications for genetic testing and clinical management.

5007 Background: Epidemiologic studies on germ cell tumors (GCT) in men have shown GCT has a high heritability. Yet, the genetic mechanisms underlying development of GCT in men remain unknown. We sought to determine the prevalence of pathogenic or likely pathogenic (P/LP) germline variants in cancer predisposition genes in men with GCT and identify clinical and pathologic factors associated with the presence of P/LP variants. Methods: We retrospectively identified men with testicular (T) or mediastinal (M) GCT who underwent matched tumor--germline sequencing of ≥ 310 genes as part of an institutional genomic profiling initiative from 04/2015 to 12/2020. Presence of germline variants in clinically actionable genes associated with hereditary cancer syndromes were analyzed. Clinicopathologic characteristics, including primary site, histology and family history were assessed by the presence of P/LP variants and compared using Fisher’s exact test. Results: The study included 480 men, 70 (15%) with M-GCT and 410 (85%) with T-GCT. The median age of diagnosis was 30 years (interquartile range 24 – 39). A total of 81% had non-seminoma; 5% had localized disease; 46%, 14%, and 34% had good, intermediate, and poor risk advanced disease, respectively; 6% had family history of GCT. Among men with T-GCT, 4% had bilateral T-GCT. P/LP variants in clinically actionable genes were identified in 58 (12%) men in the entire cohort. Men with M-GCT had higher frequency of P/LP variants compared to those with T-GCT (15/70 [21%] vs 43/410 [10%], p = 0.02). A total of 7 (10%) men with M-GCT and 20 (5%) with T-GCT had P/LP variants in moderate or high penetrance cancer predisposition genes (p = 0.09). Most P/LP variants in both M-GCT (11/15, 73%) and T-GCT (33/43, 77%) were in genes involved in DNA damage repair pathways. The spectrum of moderate or high penetrance DNA damage repair genes identified is shown in the Table 1. Family history and histology (seminoma vs. non-seminoma) were not associated with the presence of a P/LP variants in the overall cohort (p = 0.8 and 0.7, respectively). Bilateral disease was not associated with the presence of P/LP variants in men with T-GCT (p = 0.4). Conclusions: Approximately 1 in 5 men with M-GCT carried a P/LP variant in a clinically actionable cancer susceptibility gene and 10% had a P/LP variant in a high-risk gene such as TP53 and PMS2. As men with GCT tend to develop disease in early adulthood, identification of germline P/LP variant has significant implications for enhanced cancer screening and surveillance, cascade testing for at-risk family members, and potential preconception genetic counseling. [Table: see text]

Abstract P3-07-05: Genetic profile of germline mutations in unselected women with breast cancer in a Colombian population

Abstract Introduction In Colombia Breast cancer (BC), is the most frequent and has the highest mortality rate among all types of cancer. There are few studies of the genomic profile in unselected affected population by BC in Colombia. Some of these studies have only tested the presence of variants reported as founders named “Colombian Profile”.We conducted a large-scale genomic analysis using Whole Exome Sequencing (WES) to evaluate germline mutations in unselected BC patients. Methods This trial included 299 unselected BC female patients aged over 18 years old, without personal and family history of germline BC risk mutations.The protocol was approved by the IRC and EC of Fundación Cardioinfantil (FCI). All patients signed informed consent before recruitment.Genomic DNA was extracted from peripheral blood samples and was used to WES (Novogene Inc. Beijing, China). The variants were filtered using VarSeq v2.1.1 software, following the criteria: missense, non-sense, frameshift, and intronic variants, we additionally considered a MAF ≤0.01 for ATM, CHEK2, and PALB2 genes.Clinical significance of each variant was annotated according to the ACMG/AMP and ENIGMA guidelines.MLPA was assessed using the commercial kit SALSA MLPA Probemix P002-D1 for BRCA1 and P090-C1 for BRCA2 (MRC-Holland, Amsterdam).This study was financially supported by an unrestricted grant from Pfizer. Results This abstract is the first report from 299 patients. To determine the presence of germline variants in the patients a WES was performed. Here we describe the pathogenic and probably pathogenic mutations in BRCA1, BRCA2, ATM, CHEK2, PALB2. We found BRCA1/2 alterations were found in 3.7% of the patients (11 patients, IC 95% 1.7-5.6%), 5 patients in BRCA1 and 6 patients in BRCA2 (1.7% IC 95% 0.7-4%, and 2% IC 95% 0.9-4.4% respectively). We found 29 patients had mutations unrelated to BRCA1/2 (9.5% IC 95% 5.8-11.7%). The most frequently affected gene was ATM (17 patients, 5.7% IC95% 3.6-9%). Discussion and conclusion We found that 12.2% of the population of the study were carriers of a pathogenic/likely pathogenic variant in the evaluated genes, and interestingly 9.5% of them corresponded to non-BRCA1/2 genes. ATM variants have a prevalence of 5.7% in the whole population and represent 42% of all the variants. Other mutations in genes like BRCA2, ATM and CHEK2 were exclusive in non-TNBC. Meanwhile, BRCA1 and PALB2 mutations had higher frequencies in TNBC. We identified five novel mutations.We demonstrate that LGRs are not an important molecular cause in non-hereditary cases of BC.27% of the carriers of mutations in BRCA1/2 did not fulfilled NCCN criteria and 82% of the mutations are not described in “Colombian Profile”. These findings demonstrate the particular genetic profile in an unselected population with breast cancer, and this highlights the importance of WES as a molecular diagnostic tool. We think that universal germline testing in cancer should be considered. Baseline demographic and clinical characteristics Demographic and clinical characteristics of patients with pathogenic and likely pathogenic mutationsVariableBRCA1 n (%, IC 95%)BRCA2 n (%, IC 95%)ATM n (%, IC 95%)PALB2 n (%, IC 95%)CHEK2 n (%, IC 95%)Median age37.4 (22.4 – 54.3)45.5 (36.2 – 54.7)53.1 (45.4 – 60.7)55.8 (27.9 – 83.5)NA*Age≤ 50 years4 (80, 11.1 – 99.2%)4 (66.7, 14.8 – 95.8%)8 (47.1, 23.5 – 80%)2 (50, 24.7 – 97.5)NA*> 50 years1 (20, 0.7 – 88.9%)2 (33.3, 4 – 85%)9 (52.9, 28 – 76.5%)2 (50, 24.7 – 97.5)OverweightYes4 (80, 11 – 99-2%)(33.3, 4 – 85%)9 (52.9, 28 – 76.5%) 3 (75, 0.4 – 99.5%)NA*No1 (20, 0.8 – 88.9%)(66.7, 14.9 – 94.8%)8 (47, 23.5 – 80%)1 (25, 0.4 – 95.9%)Estrogen receptor(+)2 (0.9%, 0.2 – 3.5%)5 (2.2%, 0.9 – 5.3%)16 (7.1%, 4.4 – 11.3%)3 (1.3%, 0.4 – 4.1%)3 (1.3%, 0.4 – 4.1%)(-)3 (4.3%, 1.4 – 12.6%)1 (1.4%, 0.2 – 9.6%)1 (1.4%, 0,2 – 9.6%)1 (1.4%, 0.2 – 9.6%)1 (1.4%, 0.2 – 9.6%)Progesterone receptor(+)2 (0.9%, 0.2 – 3.5%)5 (2.2%, 0.9 – 5.3%)13 (6%, 3.7 – 10.5%)3 (1.3%, 0.4 – 4.1%)4 (1.9%, 0.7 – 5%)(-)3 (4.3%, 1.4 – 12.6%)1 (1.4%, 0,2 – 9.6%)4 (4%, 1.7 – 11.7%)1 (1.4%, 0.2 – 9.6%)0HER-2 3+Yes1 (1.3%, 0.2 – 8.5%)1 (1.3%, 0.2 – 8.5%)4 (5%, 1.9 – 12.7%)1 (1.3%, 0.2 – 8.5%)2 (2.5%, 0.6 – 9.6%)No4 (1.9%, 0.7 – 4.9%)5 (2.3, 0.1 – 5.5%)13 (6%, 3.5- 10.2%)3 (1.4%, 0.4 – 4.3%)2 (0.9%, 0.2 – 3.7%)ER/Pgr y HER-2 negativeYes2 (5.1, 1.3 – 18.7%)001 (2.5%, 0-3 – 16.5%)0No3 (1.2%, 0.4 – 3.6%)6 (2.3%, 1 – 5.1%)17 (6.6%, 4-2 – 10.4%)3 (1.2%, 0.4 – 3.6%)4 (1.6%, 0.6 – 4.1%)Ki67<20%0 1 (16.7, 0.9 – 81%) 5 (29.4, 11.5 – 57.1)0NA*≥20%5 (100%)5 (83.3, 18.6 – 99%)12 (70.6, 42.8 – 88.5%)4 (100%)Median tumoral size mm (min-max)24 (19.6 – 47.8)21 (12.5 – 29.5)24.9 (19.6 – 30.3)27.6 (0 – 59)NA* Lymph nodes involvementYes1 (0.7%, 0.1 – 4.6%)2 (1.3%, 0.3 – 5.2%)10 (6.7%, 3.6 – 12.1%)3 (2%, 0.6 – 6.1%)4 (2.7%, 1 – 7%)1No4 (2.7%, 1 – 7%)4 (2.7%, 1 – 7%)7 (4.7%, 2.2 – 9.5%)1 (0.7%, 0.1 – 4.6%)0MetastasisYes00001 (9%, 1.1 – 46.6%)2No5 (1.9%, 0.8 – 4.5%)6 (2.3%, 1 – 5%)17 (5.7%, 3.5 – 9.3%)4 (1.5 – 0.5 – 4%)3 (1.1%, 0.4 – 3.5%)Clinical stage (AJCC)I2 (40, 3.7 – 91.9%)1 (16.7, 0.9 – 81.3%)4 (23.5, 81 – 51.8%)0NA*II2(40 3.7 – 91.9%)4 (66.7, 14.8 – 95.8%)7 (41.2, 19.3 – 67.3%)4 (100%)III1 (20, 0.7 – 88.9%)1 (16.7, 0.9 – 81.3%)6 (23-3, 15.2 – 62.3%)0IV0000Family history for cancerYes4 (80, 11.1 – 99.2%)5 (83.3, 9 – 81.4%)13 (76.5 – 48.2 – 91.9%)2 (50, 2- 97.5%)NA*No1 (20, 0.7 – 88-9)1 (16.7, 0.9 – 81.4%)4 (23, 8 – 51.8%)2 (50, 2- 97.5%)NCCN criteriaYes4 (2.4%, 0.9 – 6.3%)4 (2.4%, 0.9 – 6.3%)NA*NA*NA*No1 (0.8%, 0.1 – 5.9%)2 (1.7%, 0.4 – 6.6%)Colombian profileYes1 (50%, 19 – 98%)31(50%, 19 – 98%)3NA*NA*NA*No4 (13.5%, 5 – 35.5%)5 (17%, 7 – 40%) Citation Format: Diana Carolina Sierra-Díaz, Adrien Morel, Dora Janeth Fonseca, Nora Contreras, Mariana Angulo-Aguado, Valentina Balaguera, Kevin Llinás-Caballero, Isabel Munevar, Mariana Borras, Mauricio Lema, Henry Idrobo, Daniela Trujillo, Norma Serrano, Ana Isabel Orduz, Diego Lopera, Jaime Gonzalez, Gustavo Rojas, Paula Londoño, Ray Manneh, Catalina Quintero, Paul Laissue, Rodrigo Cabrera, Carlos M Restrepo, William Mantilla. Genetic profile of germline mutations in unselected women with breast cancer in a Colombian population [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 P3-07-05.

The Role of the Rare Variants in the Genes Encoding the Alpha-Ketoglutarate Dehydrogenase in Alzheimer's Disease.

There is increasing evidence that several mitochondrial abnormalities are present in the brains of patients with Alzheimer’s disease (AD). Decreased alpha-ketoglutarate dehydrogenase complex (αKGDHc) activity was identified in some patients with AD. The αKGDHc is a key enzyme in the Krebs cycle. This enzyme is very sensitive to the harmful effect of reactive oxygen species, which gives them a critical role in the Alzheimer and mitochondrial disease research area. Previously, several genetic risk factors were described in association with AD. Our aim was to analyze the associations of rare damaging variants in the genes encoding αKGDHc subunits and AD. The three genes (OGDH, DLST, DLD) encoding αKGDHc subunits were sequenced from different brain regions of 11 patients with histologically confirmed AD and the blood of further 35 AD patients. As a control group, we screened 134 persons with whole-exome sequencing. In all subunits, a one–one rare variant was identified with unknown significance based on American College of Medical Genetics and Genomics (ACMG) classification. Based on the literature research and our experience, R263H mutation in the DLD gene seems likely to be pathogenic. In the different cerebral areas, the αKGDHc mutational profile was the same, indicating the presence of germline variants. We hypothesize that the heterozygous missense R263H in the DLD gene may have a role in AD as a mild genetic risk factor.

Germline alterations in cancer susceptibility genes in women with high-risk bladder cancer: Implications for germline testing and clinical management.

418 Background: Gender differences exist in bladder cancer incidence, stage at diagnosis, and outcomes. Women have lower incidence of bladder cancer but are diagnosed with more advanced disease at presentation. They also have less favorable outcomes even after adjusting for tumor stage and treatment modality. The biologic mechanisms underlying gender disparities in bladder cancer remain unknown. Methods: We leveraged a prospective matched tumor-normal genomic profiling initiative to determine the prevalence and spectrum of pathogenic/likely pathogenic (P/LP) germline variants in women with bladder cancer. Germline DNA was tested for mutations in ≥77 cancer susceptibility genes using next-generation sequencing in 686 patients with bladder cancer. Mutation frequency and clinical characteristics were assessed by gender. Results: A total of 184 (27%) women and 502 (73%) men with bladder cancer underwent germline testing; median age of diagnosis was 66 ± 11.3 and 65 ± 11.3 years, respectively. Twenty-two women (12%) had bladder cancer diagnosis at age ≤ 50 years. Both groups had similar rate of tobacco exposure (57% vs 63%, p = 0.1), family history of bladder cancer (10% vs 10%, p = 0.5), and disease stage at diagnosis (non-muscle invasive bladder cancer [NMIBC] 54% vs 54%, MIBC 38% vs 39%, and metastatic disease 8% vs 6%, p = 0.7). Women had more non-urothelial carcinoma histology than men (adenocarcinoma 5% vs. 1%; squamous cell carcinoma 1% vs 0.2%, p = 0.001). More P/LP germline variants were found in women than men (38 [21%] vs. 70 [14%], p = 0.04). Twenty-eight women (15%) had P/LP variants in DNA-damage repair (DDR) genes; 23 (13%) carried moderate/high penetrance germline mutations, the most common were BRCA1/ 2, CHEK2, NBN, ATM, and MITF. Current clinical guideline for referral for genetic testing failed to identify 12 (52%) women with moderate/high penetrance germline mutations. Nine women (5%) carried germline mutations associated with increased risk of ovarian/endometrial cancers ( BRCA1/ 2 [5], ATM [2], MLH1 [1], TP53 [1]). Conclusions: Deleterious germline alterations are commonly present in women with high-risk bladder cancer. The presence of germline variants in some genes, such as BRCA1/2, can guide cancer screening and risk-reducing surgeries for patients and their families. Women with high-risk bladder cancer should be evaluated for suitability of germline testing, especially those who desire preservation of uterus and ovaries at the time of radical cystectomy, to rule out the presence of P/LP variants that increase risk of future gynecologic malignancies.

Abstract P2-10-12: Relationship between predicted risks of carrying breast cancer susceptibility genes and the presence of germline variants in Japanese patients with primary breast cancer

Abstract Background: Breast cancer risk models are used to predict the risk of carrying a variant, for one of the most common breast cancer susceptibility genes such as BRCA1 and BRCA2, and the lifetime risk of developing breast cancer. The prediction of harboring a germline variant of the BRCA gene and the development of breast or ovarian cancer over time affects the decision-making for undergoing genetic testing and screening using imaging techniques as the common practice. For instance, the American Cancer Society and the National Comprehensive Cancer Network (NCCN) recommends screening using MRI in women with 20% or greater lifetime risk of having breast cancer. We aimed to investigate the prediction of these risks in Japanese women, particularly on the relationship between the presence of pathogenic germline variants and breast cancer susceptibility genes, using a cohort of 1016 primary breast cancer patients. Patients and Methods: We analyzed a cohort of Japanese patients with primary breast cancer who were treated at the Kyoto University Hospital and the related institutions or hospitals from the period of 2011 to 2016. The germline variants were examined for a set of 13 breast cancer susceptibility genes, using targeted-capture sequencing of pooled DNA, and it was found that 66 out of 1016 patients had pathogenic variants. These included 11 functionally well-established genes (BRCA1, BRCA2, TP53, PTEN, CDH1, STK11, NF1, PALB2, ATM, CHEK2, and NBN) and two additional genes (BARD1 and BRIP1), which are recommended for the screening of high-risk patients with hereditary breast cancer in the NCCN guidelines. Using this cohort, we studied the association of the calculated risk of carrying a germline variant of BRCA1/ BRCA2, using the Tyrer-Cuzick model Breast Cancer Risk Evaluation Tool, within the laboratory germline test results. Results: Pathogenic germline variants of BRCA1/ BRCA2 were carried by 54 (5.3%) out of the 1016 patients (12 cases of BRCA1 and 42 cases of BRCA2). According to the NCCN guidelines, which focus on Genetic/ Familial High-Risk Assessment: Breast and Ovarian, it was found that 500 out of 1016 (49.2%)patients were categorized for considering germline testing. In fact, 38 (7.6%) of the 500 patients, harbored a pathogenic germline variant of BRCA1/ BRCA2. In the remaining 516 patients, 16 (3.1%) harbored the pathogenic germline variant of BRCA1/ BRCA2. The predictive risks of the Tyrer-Cuzick model Breast Cancer Risk Evaluation Tool were recorded as follows: Area under the ROC curve, BRCA1 (area 0.750, 95% CI- 0.581-0.919), BRCA2 (area 0.741, 95% CI- 0.661-0.820), BRCA1 or BRCA2 (Area 0.749, 95% CI: 0.675-0.822), suggesting that the Tyrer-Cuzick model may be useful for the Japanese population. In the mammography breast density analysis, 484 patients showed almost entirely fat or scattered fibroglandular breast tissue, and 362 cases had heterogeneous or extreme fibroglandular breast tissue. In this study, the correlations of breast tissue density with age and breast or ovarian cancer familial history have been reported in greater detail. Discussion and Conclusions: In a retrospective cohort of 1016 Japanese patients with primary breast cancer, 5.3% had pathogenic germline variants of BRCA1/ BRCA2. In a group recommended by NCCN guidelines for considering genetic testing, the BRCA1/ BRCA2 variant rate was 7.6%. Predictive risks calculated by the Tyrer-Cuzick model similar with the known data. Further data are reported. Citation Format: Noriko Senda, Nobuko Kawaguchi-Sakita, Masahiro Kawashima, Yukiko Inagaki-Kawata, Kenichi Yoshida, Tomomi Nishimura, Masahiro Takada, Eiji Suzuki, Yuki Kataoka, Fumiaki Sato, Yoshiaki Matsumoto, Masae Torii, Hiroshi Yoshibayashi, Kazuhiro Yamagami, Shigeru Tsuyuki, Akira Yamauchi, Nobuhiko Shinkura, Hironori Kato, Yoshio Moriguchi, Ryuji Okamura, Norimichi Kan, Hirofumi Suwa, Shingo Sakata, Susumu Mashima, Fumiaki Yotsumoto, Tsuyoshi Tachibana, Mitsuru Tanaka, Takashi Inamoto, Masahiro Sugimoto, Seishi Ogawa, Masakazu Toi. Relationship between predicted risks of carrying breast cancer susceptibility genes and the presence of germline variants in Japanese patients with primary breast cancer [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 P2-10-12.

Abstract 1589: Breast cancer subtype GWAS in Peruvian breast cancer patients

Abstract Background: We previously investigated genetic ancestry associations with breast cancer subtypes in Peruvian women. We found that women with human epidermal growth factor receptor 2 (HER2) over-expressing tumors had higher Indigenous American ancestry than women with other subtypes. We found a suggestive association between African ancestry and triple negative breast cancer (TNBC). We hypothesized that these associations could be due to the presence of germline variants in the Indigenous American genome or the African genome predisposing women to HER2 over-expression or TNBC respectively. We conducted genome wide association analyses to explore this hypothesis. Methods: Blood samples and clinical data were collected from 1195 women with breast cancer at the Instituto Nacional de Enfermedades Neoplasicas in Lima, Peru. Genotypic profiles for 821 women were generated using the Affymetrix Precision Medicine Research Array. Four major breast cancer subtypes were identified using immunohistochemical markers (luminal A, luminal B, triple negative, and HER2 over-expressing). Genetic ancestry was determined using ADMIXTURE. Genome wide association analyses were conducted in PLINK. Results: Three polymorphisms with the lowest p values in the TNBC GWAS are of interest. A variant, rs16910137, at 10q26, is located in an intron of the Glutaredoxin 3 gene (GLRX3 or TXNL2, OR = 2.45, P = 8.60*10-07). The protein encoded by this gene may inhibit apoptosis and play a role in cellular growth. It has also been described as a biomarker for TNBC. Our own RNA-seq data for TXNL2 in 52 Colombian women with breast cancer showed that the expression level of this gene is higher in women with triple negative (N=9) compared to luminal tumors (N=43) (P=0.06). The other two variants, rs12327440 and rs13381183, are located in an intron of the Mitogen-Activated Protein Kinase 4 (MAPK4) gene at 18q21 (OR = 0.44 and 1.94 respectively, P = 4.92*10-07 and 7.230*10-06). RNA-seq data for MAPK4 suggestively showed that the expression level is higher in women with TNBC compared to luminal tumors (P=0.18). The variant in the HER2 over-expressing GWAS with the lowest p value, rs11594103, at 10p11 is located upstream of the Enhancer Of Polycomb Homolog 1 (EPC1) gene (OR = 2.38, P = 8.03*10-07). The encoded protein has been linked to apoptosis and DNA repair among other functions and suggested as involved in the activation of metastasis. Conclusions: Our data suggests that a germline variant within the GLRX3/TXNL2 gene might be associated with the risk of developing TNBC compared to other subtypes. This is particularly interesting in the light that previous work suggested that TXNL2 autoantibodies could be biomarker of TNBC. The MAPK4 and EPC1 genes have been previously implicated in multiple types of cancer and our results indicate that they may play a role in the etiology of specific breast cancer subtypes. This supports the importance of conducting genetic association studies in diverse samples. Citation Format: Katie M. Marker, Tatiana Vidaurre, Jeannie Navarro Vasquez, Valentina Zavala, Silvia Serrano Gomez, Lizeth Tamayo, Renzo Meza Florez, S Casavilca, M Calderon, JE Abugattas, Henry Gómez, Hugo Fuentes, CL Monge Pimentel, Sikai Song, Daniel Cherry, Scott Huntsman, Donglei Hu, Elad Ziv, Laura Fejerman. Breast cancer subtype GWAS in Peruvian breast cancer patients [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2019; 2019 Mar 29-Apr 3; Atlanta, GA. Philadelphia (PA): AACR; Cancer Res 2019;79(13 Suppl):Abstract nr 1589.

Exploration of germline variants responsible for adverse events of crizotinib in anaplastic lymphoma kinase-positive non-small cell lung cancer by target-gene panel sequencing

ObjectivesCrizotinib is a standard treatment for advanced anaplastic lymphoma kinase (ALK)- or ROS1-fusion-gene-positive non-small cell lung cancer; however, serious adverse events (AEs), including elevated alanine aminotransferase (ALT)/aspartate aminotransferase (AST) and interstitial lung disease (ILD), develop occasionally. Here, we evaluated relationships between clinically significant crizotinib-associated AEs and germline variations. Materials and MethodsDNA obtained from 75 patients allowed selection of 147 genes according to function, exon identification and sequencing, and determination of germline single nucleotide variants (SNVs). Correlations between clinically significant AEs and presence of germline variants were estimated by Fisher’s exact test. ResultsWe defined clinically significant AEs as grade 4 hematological toxicity, grade ≥3 non-hematological toxicity, and any grade of ILD. These AEs were observed in 26 patients (35%), with elevated AST/ALT (15%) the most common, followed by neutropenia (5%), ILD (4%), and thromboembolic events (4%). Nonsynonymous SNVs in epoxide hydrolase 1 (EPHX1) [odds ratio (OR): 3.86; p = 0.0009) and transcription factor 7-like 2 (TCF7L2) (OR: 2.51; p = 0.025) were associated with the presence of clinically significant AEs. ConclusionNonsynonymous EPHX1 and TCF7L2 SNVs might be associated with clinically significant crizotinib-associated AEs. These data indicated that target-gene sequencing could be feasible for predicting anticancer-agent toxicity, and that germline multi-gene information might be useful for predicting patient-specific AEs to promote precision medicine.

A Dominantly Inherited 5′ UTR Variant Causing Methylation-Associated Silencing of BRCA1 as a Cause of Breast and Ovarian Cancer

Pathogenic variants in BRCA1 or BRCA2 are identified in ∼20% of families with multiple individuals affected by early-onset breast and/or ovarian cancer. Extensive searches for additional highly penetrant genes or alternative mutational mechanisms altering BRCA1 or BRCA2 have not explained the missing heritability. Here, we report a dominantly inherited 5′ UTR variant associated with epigenetic BRCA1 silencing due to promoter hypermethylation in two families affected by breast and ovarian cancer. BRCA1 promoter methylation of ten CpG dinucleotides in families who are affected by breast and/or ovarian cancer but do not have germline BRCA1 or BRCA2 pathogenic variants was assessed by pyrosequencing and clonal bisulfite sequencing. RNA and DNA sequencing of BRCA1 from lymphocytes was undertaken to establish allelic expression and the presence of germline variants. BRCA1 promoter hypermethylation was identified in 2 of 49 families in which multiple women are affected by grade 3 breast cancer or high-grade serous ovarian cancer. Soma-wide BRCA1 promoter hypermethylation was confirmed in blood, buccal mucosa, and hair follicles. Pyrosequencing showed that DNA was ∼50% methylated, consistent with the silencing of one allele, which was confirmed by clonal bisulfite sequencing. RNA sequencing revealed the allelic loss of BRCA1 expression in both families and that this loss of expression segregated with the heterozygous variant c.−107A>T in the BRCA1 5′ UTR. Our results establish a mechanism whereby familial breast and ovarian cancer is caused by an in cis 5′ UTR variant associated with epigenetic silencing of the BRCA1 promoter in two independent families. We propose that methylation analyses be undertaken to establish the frequency of this mechanism in families affected by early-onset breast and/or ovarian cancer without a BRCA1 or BRCA2 pathogenic variant.

Abstract P3-09-05: Clinical outcome of patients with advanced triple negative breast cancer with germline and somatic variants in homologous recombination gene

Abstract Background: Variants in homologous recombination (HR) genes other than BRCA1/2 may cause a BRCA-like phenotype triple negative breast cancer (TNBC), which includes the sensitivity to platinums and DNA repair inhibitors. Evaluation of HR proficiency may influence the clinical management of TNBC. Our aim was to evaluate germline and somatic HR gene variants in advanced TNBC patients (pts) and clinical outcome. Methods: Our cohort included advanced TNBC pts unselected for family history or age at diagnosis, enrolled in an institutional molecular screening program (NCT01505400). DNA from matched blood and FFPE tumor samples was assessed using a lab developed next generation sequencing Hereditary Cancer Panel (NGS-HCP) that includes all exons of 52 cancer predisposition genes, with 20 HR genes (Illumina MiSeq/NextSeq, germline coverage 100x, somatic coverage 500x). Medical records were reviewed for clinical outcome, pathology and prior germline BRCA1/2 testing results. All pts consented for research on banked samples and return of pathogenic germline variants was optional. Log rank test was used to determine time from surgery with curative intent to relapse (TTR) and overall survival from diagnosis to death (OS) differences based on presence of HR variants. Results: We included 32 pts who consented for return of pathogenic germline variants and had sufficient DNA for NGS-HCP analysis. Median age at diagnosis was 45 years (range 21-80). Initial stages at diagnosis were: I (12.5%), II (62.5%), III (19%) and IV (6%). Germline HR variants were detected in 17 pts (53%) with a median number of variants per patient of 1 (range 0-6). Five pts had likely pathogenic or pathogenic variants in HR genes: BRCA1 (2), BRCA2 (1) FANCC (1) and FANCC + BML (1). Another patient had a BRCA1 pathogenic variant previously detected by Multiplex Ligation-dependent Probe Amplification but was not detected by NGS-HCP. 26 variants of unknown significance (VUS) were identified in 13 HR genes, including FANCA (6), FANCF (3) and BRCA1 (3). Only one patient had a somatic HR variant in FANCA not found in the germline. 30 pts (94%) had somatic TP53 variants. Sporadic somatic BRCA1/2 variants were not seen. BRCA1/2 variants present in the tumor were equivalent to those detected in blood of BRCA1/2 carriers. Median (m) TTR was 17 months (range 1-119) and mOS was 49 months (range 8-123). Presence of likely pathogenic or pathogenic germline variants was not associated with TTR (p=0.78) and OS (p=0.23). Presence of germline VUS, likely pathogenic or pathogenic variants also did not correlate with TTR (p=0.72) and OS (p=0.47) Conclusions: In our cohort of pts with advanced TNBC, 12% had germline pathogenic variants in BRCA1/2, similar to the previously reported rate in early stage TNBC pts. Prevalence of likely pathogenic or pathogenic variants in non-BRCA HR genes was 6%. The presence of germline variants in HR genes was not associated with clinical outcome, however, the number of patients included was small and we had limited power to detect survival differences.Background: Variants in homologous recombination (HR) genes other than BRCA1/2 may cause a BRCA-like phenotype triple negative breast cancer (TNBC), which includes the sensitivity to platinums and DNA repair inhibitors. Evaluation of HR proficiency may influence the clinical management of TNBC. Our aim was to evaluate germline and somatic HR gene variants in advanced TNBC patients (pts) and clinical outcome. Methods: Our cohort included advanced TNBC pts unselected for family history or age at diagnosis, enrolled in an institutional molecular screening program (NCT01505400). DNA from matched blood and FFPE tumor samples was assessed using a lab developed next generation sequencing Hereditary Cancer Panel (NGS-HCP) that includes all exons of 52 cancer predisposition genes, with 20 HR genes (Illumina MiSeq/NextSeq, germline coverage 100x, somatic coverage 500x). Medical records were reviewed for clinical outcome, pathology and prior germline BRCA1/2 testing results. All pts consented for research on banked samples and return of pathogenic germline variants was optional. Log rank test was used to determine time from surgery with curative intent to relapse (TTR) and overall survival from diagnosis to death (OS) differences based on presence of HR variants. Results: We included 32 pts who consented for return of pathogenic germline variants and had sufficient DNA for NGS-HCP analysis. Median age at diagnosis was 45 years (range 21-80). Initial stages at diagnosis were: I (12.5%), II (62.5%), III (19%) and IV (6%). Germline HR variants were detected in 17 pts (53%) with a median number of variants per patient of 1 (range 0-6). Five pts had likely pathogenic or pathogenic variants in HR genes: BRCA1 (2), BRCA2 (1) FANCC (1) and FANCC + BML (1). Another patient had a BRCA1 pathogenic variant previously detected by Multiplex Ligation-dependent Probe Amplification but was not detected by NGS-HCP. 26 variants of unknown significance (VUS) were identified in 13 HR genes, including FANCA (6), FANCF (3) and BRCA1 (3). Only one patient had a somatic HR variant in FANCA not found in the germline. 30 pts (94%) had somatic TP53 variants. Sporadic somatic BRCA1/2 variants were not seen. BRCA1/2 variants present in the tumor were equivalent to those detected in blood of BRCA1/2 carriers. Median (m) TTR was 17 months (range 1-119) and mOS was 49 months (range 8-123). Presence of likely pathogenic or pathogenic germline variants was not associated with TTR (p=0.78) and OS (p=0.23). Presence of germline VUS, likely pathogenic or pathogenic variants also did not correlate with TTR (p=0.72) and OS (p=0.47) Conclusions: In our cohort of pts with advanced TNBC, 12% had germline pathogenic variants in BRCA1/2, similar to the previously reported rate in early stage TNBC pts. Prevalence of likely pathogenic or pathogenic variants in non-BRCA HR genes was 6%. The presence of germline variants in HR genes was not associated with clinical outcome, however, the number of patients included was small and we had limited power to detect survival differences. Citation Format: Stjepanovic N, Kim RH, Wilson M, Mandilaras V, Berman H, Amir E, Cescon D, Elser C, Randall Armel S, McCuaig J, Volenik A, Demsky R, Chow H, Misyura M, Wang L, Oza AM, Kamel-Reid S, Stockley T, Bedard PL. Clinical outcome of patients with advanced triple negative breast cancer with germline and somatic variants in homologous recombination gene [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 P3-09-05.