Variants Of Uncertain Significance Research Articles

Outcomes of a universal germline screening program in a community urology practice.

The role of germline genetic testing in urologic oncology has expanded in recent years. However, implementation of genetic testing in community practices remains a challenge, often due to limited access to qualified genetics trained providers. In this study, we report outcomes of a universal germline screening program in a community urology practice. Between November 2021 and September 2022, all patients referred for urology clinic visits at Frederick Health (Frederick, MD, USA) were provided an online genetics screening questionnaire prior to the visit. Responses were compared against National Comprehensive Cancer Network (NCCN) criteria for germline testing. Those who met criteria were provided educational materials at the end of the questionnaire, and then counseled by a trained urologic oncologist (HC) in the clinic or referred to a genetic counselor prior to testing. Testing was performed with a 36-gene pan-cancer panel (CancerNext) or a 14-gene targeted prostate cancer panel (ProstateNext), with or without additional RNA analysis (RNAinsight) (Ambry Genetics, CA, USA). Demographic and clinical parameters, as well as genetic testing results, were retrospectively collected under IRB approval. In the study period, 765 patients were seen over 1370 clinic visits. Of these, 505 patients (66.0%) completed the screening questionnaire. The majority were completed via email (54.5%) with the remainder (45.5%) via text message. Of the patients who completed screening, 125/505 (24.7%) met NCCN criteria for germline testing. 58/125 patients (46.4%) who met criteria underwent germline testing, of whom 5/58 (8.6%) had distinct pathogenic mutations identified. These included actionable mutations in BRCA1, BRCA2, and CHEK2, as well as an additional pathogenic mutation in NBN. Variants of unknown significance were identified in 8/58 patients (13.8%) in 11 total genes. Challenges to implementation of this program included meeting institutional requirements for genetic testing consent, facilitating specimen collection in clinic, and integration of results into the electronic health record. Genetic risk assessment for high-risk individuals is feasible as part of a universal screening program in a community urology practice. Approximately 8% of tested patients were found to have pathogenic germline mutations, which is consistent with contemporary tertiary referral cohorts.

Abstract PO1-08-06: Clinical-molecular correlation in breast cancer with pathogenic variants in CHEK2. Is there a relationship with HER2+ breast cancer?

Abstract 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.

Abstract PO3-08-09: Unique molecular signatures of germline mutations in low expression of human epidermal growth factor receptor 2 (HER2) breast cancer

Abstract Background: Overexpression of human epidermal growth factor receptor 2 (HER2) in breast cancer (BC) is associated with lower survival and higher risk of disease recurrence. A new subtype of HER2-low BC which has been proposed from several studies demonstrates that HER2-low patients have distinct somatically genetic alterations and clinical outcomes. We have previously reported that HER2-low BC had distinct clinical and somatic mutational feature compared with HER2-zero and HER2-high tumors. We have therefore extended studies by comparing germline mutation expression among these HER2 subgroups. Methods: 530 Chinese women with BC were enrolled in a prospective protocol between May 2021 to March 2023 at Guangdong Provincial People's Hospital. Genomics data was generated from a gene panel that surveys 102 tumor mutations. Germline variants were classified into pathogenic (P), likely pathogenic (LP), variant of uncertain significance (VUS), likely benign (LB) and benign (B) groups according to the ACMG/AMP Standards and Guidelines. The cohort was divided into three groups based on HER2 status as HER2-zero (n = 107), HER2-low (n = 259), and HER2-high (n = 127) according to immunohistochemistry and/or fluorescence in situ hybridization results. Results: The most common mutated genes were ATM, FANCD2, ATR, BRACA2, RECQL4 and APC. A total of 71 pathogenic or likely pathogenic (P/LP) mutations were identified in 25 cancer susceptibility genes from 64 patients (12.16%). The most frequent mutated P/LP genes are BRCA2, BRCA1, PALB2, PMS2, MUTYH and PTEN in the HER2-low group; BRCA2, BRCA1 and PALB2 in the HER2-zero cohort; Interestingly, among the nine HER2-high patients, we detected unique P/LP genes in each sample including MRE11, FANCM, ATM, FLCN, NTRK1, TP53, BRCA1, CHEKE2 and FANCA. In addition to P/LP mutations, 751 variants of uncertain significance (VUS) in 95 cancer susceptibility genes were also detected in 361 patients (68.11%). The most frequent mutated VUS mutations occurred genes are FANCD2, ATM, RECQL4, RAD54B and ATR in HER2-low group; ATM, FANCA, POLE, MSH2 and FANCD2 in HER2-zero cohort; and ATM, BRCA2, RECQL4, POLE, FANCI and FANCM for HER2-high patients. Most of mutated genes were homologous recombination repair (HRR) or DNA damage repair (DDR) pathway related genes. Several genes were differentially altered across HER2 subgroups, including the mutation frequency of the BMPR1A (p=0.0344), MSH2 (p=0.0103), and RAD51C (p=0.0336) genes that were significantly higher in HER2-zero group. It’s worth noting that RAD51C was only mutated in HER2-zero subgroup. BMPR1A and MSH2 were also mutated in HER2-low patients. Differentially mutated genes in specific HER2 subgroups may contribute to better research and choice of future therapeutic approaches. In 115 patients who received neoadjuvant therapy and 84 of them were evaluable for pathological response data, HER2-low patients had lower pathological complete response (pCR) rates than HER2-zero and HER2-high subgroups (p=0.0008). In particular, DDR pathway gene ERCC1 have significantly higher mutation frequency in pCR patients (p=0.0115). Conclusion: HER2-low BC patients have distinct germline mutational signatures and differential clinical outcomes under neoadjuvant systemic therapy. These results have provided additional evidence that HER2-low patients comprise a fourth subtype of BC that needs to be accounted for separately in terms of clinical treatment and outcome reporting. Keywords: breast cancer, germline mutations, human epidermal growth factor receptor 2 (HER2), HER2-low, targeted therapy, next-generation sequencing Table 1. List of most frequent mutated genes in HER2-zero, HER2-low and HER2-high groups Citation Format: Ning Liao, Weiqi Zhang, Liangqiu Liu, Wendy Wu, Siqi Wang, Li Cao, Jianguo Lai, Xueying Zhang, Airong Yang, Yulei Wang, Cheukfai Li, Guochun Zhang, Chongyang Ren, Lingzhu Wen. Unique molecular signatures of germline mutations in low expression of human epidermal growth factor receptor 2 (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 PO3-08-09.

Abstract PO1-08-04: Universal Germline Genetic Testing for Breast Cancer: Implementation in a Rural Practice and Impact on Shared Decision Making

Abstract Background: Prior work from our group has shown a high rate of familial breast cancer (BC) among rural BC patients (pts), with 33% reporting > 1 first-degree family members with BC and 55% meeting NCCN germline genetic testing (GGT) criteria (Shelton CH et al. NC Med. J; 2022). In 2018, we increased GGT to include all BC pts and observed: 1) many pts were out-of-criteria per NCCN guidelines but had actionable pathogenic germline variants (PGVs) and 2) knowledge of GGT factored significantly into shared decision making by providers and patients, including for positive and negative results. Beginning in 2019, concurrent with the recommendation from the American Society of Breast Surgeons, we expanded this model of universal GGT to an IRB-approved study to measure the impact of prospective testing on shared decision-making. Herein we report the real-world implementation of universal GGT for patients with BC and genetics-informed treatment decision-making in a rural community practice. Methods: From 2019-2022 all BC pts at a small, rural community hospital were offered GGT. Demographics, clinical features, and GGT results were collected along with clinician-reported clinical recommendations for treatment based on GGT results. Descriptive statistics and two-tailed Fisher’s exact test were employed and significance was set at p< 0.05. Results: 210 BC pts were offered GGT and 192 (91%) underwent testing [97% female, 95% non-Hispanic White, mean age at diagnosis of 62, 75% Stage I], with all but 7 pts completing GGT before primary treatment decisions. 104 (54%) of patients were in-criteria (IC) and 88 (46%) out-of-criteria (OOC) with NCCN GGT guidelines. PGVs were identified in 25 pts (13%) and 15 genes, most commonly BRCA1/2 (5 pts), PALB2 (3), monoallelic MUTYH (3) and ATM, BARD1, CHEK2 (2 pts each). PGV frequencies were 15% in IC and 11% in OOC patients (p=0.495). 46 (24%) pts had only a variant of uncertain significance (VUS) results. 70% of patients had > 1 clinical management change based on their GGT results. Changes in breast surgery, uptake of risk-reducing bilateral salpingo-oophorectomy, surveillance and clinical follow-up were significantly higher in patients with PGV compared to those with VUS/negative results (p < 0.0001). Compared to those with negative results, patients with PGVs in BRCA1 and BRCA2 were significantly more likely to undergo bilateral mastectomy (BLM) while those with PGVs in other genes or with VUS were not significantly more likely to elect for BLM than those with negative results. Clinicians reported that return of GGT reinforced their recommendation for 73/138 (53%) of patients who underwent breast-conserving therapy. GGT results aided in radiation therapy strategy for 54% of pts, most often resulting in dose de-escalation (accelerated fractionation) for negative/VUS pts (Table). Conclusions: Universal GGT for patients with BC was successfully implemented in a rural community practice with >90% uptake. Treatment was enhanced in those with clinically actionable PGVs and de-escalated in those without PGVs. Universal GGT for patients with BC is feasible to implement as the standard of practice within rural populations, enabling optimization of clinical care to patients’ genetic profile and may reduce unnecessary healthcare resource utilization. Universal Germline Genetic Testing for Breast Cancer: Implementation in a Rural Practice and Impact on Shared Decision Making Changes in Radiation Therapy Strategy based on GGT Citation Format: Charles Shelton, Sarah Nielsen, Antonio Ruiz, Lauren Shelton, Karen Freas, Sarah Poll, Brandie Heald, Daniel Pineda-Alvarez, Edward Esplin, Rachel Ellsworth, Hannah Montgomery. Universal Germline Genetic Testing for Breast Cancer: Implementation in a Rural Practice and Impact on Shared Decision Making [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 PO1-08-04.

Abstract PO1-09-03: Clinical Impact of Multigene Panel Testing in Patients with a Personal or Family History of Breast or Ovarian Cancer Previously Negative for BRCA1/2 Genes

Abstract Rapid developments in cancer genetics and hereditary cancer risk assessments have enabled the identification of individuals at elevated risk for hereditary malignancies to guide enhanced cancer screening and prevention efforts. Multigene panel testing has emerged as the standard approach as emphasized in the National Comprehensive Cancer Network (NCCN) guidelines. The purpose of this study was to investigate the frequency of other pathogenic mutations identified through multigene panel testing in individuals who previously tested negative for germline BRCA1/2 and assess the clinical impact of panel testing. Patients either previously diagnosed with breast cancer or with a family history of breast or ovarian cancer that had also been seen by Oncology Genetics at a single institution and tested negative for BRCA1/2 genes but had not undergone prior multigene panel testing were invited via a letter to return for an additional genetic counseling visit to discuss multigene panel testing. Patients were also able to opt-in to a survey component of the study and received an email to fill out the Multidimensional Impact of Cancer Risk Assessment (MICRA) and Cancer Worry Scale (CWS). Surveys were completed prior to the initial genetic counseling appointment and repeated after discussion of the multigene panel test results. A total 24 women met with a genetic counselor of which 22 (92%) had a personal history of breast cancer, 1 (4%) had a family history of breast cancer, and 1 (4%) had a family history of ovarian cancer. The mean age was 52.6 years (range, 42-68) and 100% of women were Caucasian. Of the 24 women, 17 (71%) completed multigene panel testing. Of the women that underwent testing, 7 (41%) had negative results, 6 (35%) had variants of unknown significance (VUS), and 4 (24%) had a pathogenic mutation identified in another gene (CDKN2A, CHEK2, and CFTR). There was no significant change in MICRA or CWS scores after multigene panel results were reviewed in the 9 patients that completed both pre- and post-genetic testing surveys. The mean/median summary MICRA scores pre- and post-counselling were 30 (SD 12.4), median 26 (min 18, max 56), and 21.2 (SD 15.4), median 21 (min 3, max 43), respectively (p=0.19, Wilcoxon signed ranks test). The mean/median summary CWS scores pre- and post-counselling were 14.3 (SD 5), median 15 (min 7, max 24), and 13.6 (SD 2.59), median 14 (min 10, max 17), respectively (p=0.53, Wilcoxon signed ranks test). Of the 4 patients with newly identified pathogenic mutations, 2 started new screening protocols and 1 underwent a prophylactic mastectomy. In conclusion, multigene panel testing identified pathogenic mutations in a subset of individuals who previously tested negative for BRCA1/2 genes leading to changes in clinical management. The completion of multigene panel testing did not lead to a significant increase in MICRA or CWS scores. Key limitations of this study include a small sample size and an all Caucasian population. Citation Format: Devon Miller, Stephanie Pritzl, Angela Tess, Jessica Gooding, Lisa Barroilhet, Lori Dubenske, Kari Wisinski. Clinical Impact of Multigene Panel Testing in Patients with a Personal or Family History of Breast or Ovarian Cancer Previously Negative for BRCA1/2 Genes [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 PO1-09-03.

Abstract PO1-08-10: Impact of Oncologist-Led Genetic Counseling and Testing on Prophylactic Mastectomy Rates Among Multi-Ethnic Women with Operable Breast Cancer

Abstract Introduction: Approximately 5-10% of breast cancers are attributed to an inherited pathogenic variant (PV) in breast cancer predisposition genes, such as BRCA1 and BRCA2. Identifying women with hereditary breast cancer syndromes is critical to inform risk-appropriate screening and prevention strategies. For example, contralateral prophylactic mastectomy (CPM) has been shown to reduce the risk of new breast primaries without a demonstrated survival benefit. In a prior study, we found that women with pathogenic/likely pathogenic (P/LP) variants were over four times more likely to undergo CPM compared to those with benign/likely benign (B/LB) variants. In recent years due to expanded indications for genetic testing and social distancing during the COVID-19 pandemic, oncologist-led genetic testing and telehealth genetic counseling has gradually replaced in-person genetic counseling visits. We aimed to understand how changes in the delivery of genetic counseling and testing services impacted CPM rates among multi-ethnic women with operable breast cancer in the post COVID-19 period. Methods: We conducted a retrospective cohort study among 1,080 women diagnosed with unilateral breast cancer who underwent germline genetic testing between 2013 and 2022 at Columbia University Irving Medical Center (CUIMC) in New York, NY. The pre COVID-19 period was defined as 2013-2019 and the post COVID-19 period as 2020-2022. Demographics, including age, race/ethnicity and marital status, and clinical characteristics, such as year of diagnosis, breast cancer stage, tumor hormone receptor status, family history of breast cancer, and genetic test results, were extracted from the electronic health record (EHR). We used univariable and multivariable logistic regression analyses to estimate the odds ratio (OR) and 95% confidence interval (95% CI) associated with each variable and receipt of CPM. Results: Among 1080 evaluable women, mean age at diagnosis was 51.2 years old (SD, 12.3) with 39.6% non-Hispanic White, 27.8% Hispanic, 11.4% non-Hispanic Black, 9.0% Asian, and 12.2% multi-racial/other. Within the overall study population, 12.1% of women had P/LP variants and 21.4% had variants of unknown significance (VUS) results. Non-Hispanic Whites and Blacks had the highest frequency of P/LP variants, whereas VUS results were more common among Hispanics and Asians (see Table). Twenty-three percent of women in the study population underwent CPM. In multivariable analysis, younger age at diagnosis, more advanced stage breast cancer, family history of breast cancer, Hispanic race and P/LP results on germline genetic testing were associated with increased CPM rates. Hispanic women were over 60% more likely to undergo CPM compared to non-Hispanic White women (adjusted OR=1.63, 95% CI=1.07-2.47). No significant change in CPM rates was observed in the post-COVID era compared to the pre-COVID era. Conclusion: We aimed to understand how the transition to telehealth and oncologist-led genetic testing affected CPM rates. Although we did not observe a change in CPM rates in the post-COVID era, Hispanic women had significantly more VUS results and were over 60% more likely to undergo CPM compared to non-Hispanic White women. In future studies, we hope to improve risk communication of genetic test results and the risks and benefits of CPM, particularly in vulnerable and underserved populations. Table 1 Genetic testing results and rates of contralateral prophylactic mastectomy stratified by race/ethnicity in women diagnosed with operable breast cancer and undergoing germline genetic testing from 2013-2022 at Columbia University Irving Medical Center, New York, NY Citation Format: Alissa Michel, Kelly Luo, Vicky Ro, Matthew Fine, Meghna Trivedi, Wendy Chung, Roshni Rao, Tarsha Jones, Elana Levinson, Carrie Koval-Burt, Donna Russo, Ilana Chilton, Rita Kukafka, Katherine Crew. Impact of Oncologist-Led Genetic Counseling and Testing on Prophylactic Mastectomy Rates Among Multi-Ethnic Women with Operable 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 PO1-08-10.

Abstract PO1-16-10: BRCA mutated Male Breast Cancer, hallmarks of a distinct disease. Data from the Spanish Male Breast Cancer Registry (GEICAM/2016-04)

Abstract Background: Male breast cancer (MBC) accounts for approximately 0.25% of all male cancers and < 1% of all BCs. Its incidence is increasing by 1.1% per year. Most population studies indicate that 10-15% of MBC patients (pts) have a germline BRCA2 mutation (BRCA2 mut). Around 5-10% of BRCA2mut male carriers will develop BC at their lives. Preliminary evidence suggests that BRCA2mut MBC pts tend to have a more aggressive disease. Here we present comparative series of MBC with and without BRCA to gain insight on differences between both groups. Methods: GEICAM/2016-04 (NCT03800355) is a retrospective, observational study which includes data from MBC pts diagnosed between 2000 and 2019 throughout Spain. This analysis includes the 1st unselected 186 pts included in the study, who had BRCA1/2 genes mutational status assessed within clinical practice. BC clinical subtypes are defined: luminal (HR+, HER2-), Triple Negative (TN) (HR-, HER2-), and HER2+ (HR+ or HR-); subtype is unknown in 6% pts. Results: 186 validated pts with BRCA1/2 testing were identified, representing the 24% of pts available in the database at the cut-off date (6-Mar-2023). 36 (19%) pts had germline BRCA1/2 mut (4 pts in BRCA1, 31 pts in BRCA 2 and 1 pt in both BRCA1 and BRCA2), and 150 (81%) pts had BRCA1/2 wild type (wt) or a variant of uncertain significance (VUS)/unknown (UK). Median age at BC diagnosis was 62 (34-87) years, 98% pts were Caucasian, and the median body mass index was 27 (18-46) Kg/m2 (overweight). Prior cancer history was reported in 6% BRCA1/2mut BC pts and 11% BRCA1/2wt or vus/uk, and family history included: 56% BC, 8% ovarian cancer, and 14% prostate cancer (PC). PC as part of prior medical history, cancer family history, and 2nd non-breast primary malignancy, was most frequent in BRCA1/2wt or vus/uk pts, with no statistical differences. At first diagnosis, stages III-IV were higher in BRCA1/2mut pts (28% vs. 17%, p=0.0093). Morphologically, invasive carcinoma of no special type (NST) was the most common pattern (92% in BRCA1/2mut vs. 86% in BRCA1/2wt or vus/uk), and lobular invasive carcinoma was not reported up-to-date. Histological grade 2 was the most frequent (54%), but grade 3 was present in 17/36 BRCA1/2mut pts. 88% pts received adjuvant treatment, 7% (neo-)adjuvant, 2% neoadjuvant and 3% did not receive any systemic therapy. Breast conserving surgery was performed in 4% (5/140) BRCA1/2wt or vus/uk EBC pts, and mastectomy was performed in 55% (n=6/11) de novo metastatic pts. In the advanced setting (n=38), visceral lesions were more frequent in BRCA1/2mut pts. Additionally, 92% BRCA1/2mut pts had ≤ 3 organs involved while one third of BRCA1/2wt or vus/uk pts had ≥ 4 metastatic locations. With a median follow-up of 64 months (mo.), median iDFS and DDFS were higher, but not statistically significant, in BRCA1/2wt or vus/uk pts vs. BRCA1/2mut pts. In advanced setting, median PFS to 1L-3L do not show statistically significant differences between both groups. Regarding OS, no differences were also observed, but the median values were not reached. Further detailed information according to BRCA1/2 mutational status and BC subtypes is included in the table below. Conclusions: In this subset analysis of GEICAM/2016-04, BRCA1/2mut pts had some features of worse prognosis, with a more prevalent de novo metastatic disease. No statistically significant differences were observed in outcomes in both early-stage and advanced setting vs. BRCA1/2wt or vus/uk pts. <graphic> Citation Format: Noelia Martínez-Jáñez, Purificación Martínez, Cristina Hernando, Sabela Recalde, Alfonso Sánchez, David Morales, Marta Santisteban, Isaura Fernández, Sonia Del Barco, Esther Zamora, Vega Iranzo, Tamara Martos, Eduardo Martínez-de Dueñas, Silvia Antolin Novoa, Severina Domínguez, Paula Domínguez, Mª José Echarri, Ana Santaballa Bertrán, Xavier Mira, Andrea Blasco, Susana Bezares, Ander Urriticoechea. BRCA mutated Male Breast Cancer, hallmarks of a distinct disease. Data from the Spanish Male Breast Cancer Registry (GEICAM/2016-04) [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 PO1-16-10.

Abstract PO1-10-01: Racial/Ethnic Disparities in Rates of Pathological Complete Response and Survival in Patients with Inflammatory Breast Cancer

Abstract Radiation Therapy Toxicities and Survival Outcomes in Monoallelic ATM Variant Carriers with Non-Metastatic Breast Cancer: A Retrospective Analysis Rayan Bensenane1 MD, Arnaud Beddok1,2,3 MD, Nadine Andrieu4 PhD, Fabienne Lesueur4 PhD, Eve Cavaciuti 4 MSc, Dorothee Le Gal4 MSc, Eon-Marchais Severine4 PhD, Dominique Stoppa Lyonnet 5MD PhD, Youlia Kirova1 MD 1. Institut Curie, PSL Research University, Radiation Oncology Department, Paris/Saint-Cloud/Orsay, France. 2. Gordon Center for Medical Imaging, Massachusetts General Hospital, Harvard Medical School, 125 Nashua St., Boston, MA, 02114, USA 3. Institut Curie, PSL Research University, University Paris Saclay, Inserm LITO U1288 Orsay, France 4. Inserm, U900, Institut Curie, PSL Research University, Mines ParisTech, Paris, France 5.Department of Genetics, Institut Curie; Inserm U830, Institut Curie; Paris-Cité University Abstract (characters: 2952; max 3400 characters, not include spaces) Background: The Ataxia-Telangiectasia Mutated (ATM) gene, involved in the repair of DNA double-strand breaks, can contribute to radiosensitivity when a bi-allelic variant is present and lead to Ataxia-Telangiectasia syndrome. Moreover, monoallelic ATM pathologic variant (PV) carriers, especially women, has an estimated occurrence rate of 0.5-1% globally and face a 2 to 3-fold increased risk of developing breast cancer. Despite evidence of in vitro radiosensitivity in cells derived from monoallelic variant carriers, there is a dearth of patient studies examining the risk of radiation-induced toxicity. This study aims to explore radiation therapy (RT) toxicities in non-metastatic breast cancer women carrying a germline monoallelic ATM variant, compared to non-carriers. Methods: A retrospective study was conducted on patients treated at Institut Curie, Paris from 1999 to 2014 and participating to CoF-AT (a French national study) and GENESIS database. ATM variant screenings encompassed both PV and non-PV, with toxicities evaluated using CTCAE v.5. Variants were classified as pathogenic, variant of unknown significance (VUS), or benign. Follow-up started from age/date at breast cancer to acute, late toxicities, disease recurrence or last news. Survival and toxicity comparisons were made using Kaplan-Meier survival analysis and Chi-square tests, respectively, with a significance level of α set at 0.05. Results: Among 50 patients, nine were ATM variant carriers (3 PV/5 VUS/1 benign), and 41 were non-carriers. Most patients had no smoking history (68%), and invasive ductal carcinoma was the predominant diagnosis (82%). The majority underwent breast-conservative surgery (80%), and the dominant RT techniques were 3D-Conformational Radiation Therapy (70%) and Isocentric Lateral Decubitus (30%). The median RT dose was 50 Gy over an average period of 36.5 days. With a median follow-up of 12 years post-diagnosis, no significant difference in acute dermatitis, esophagitis, lymphedema, cutaneous fibrosis, telangiectasia, or heart disease was observed between the groups. Analysis of overall survival (OS) showed a 5-year OS of 98%, decreasing to 89% at 10 years. For ATM variant carriers, the OS at 5, 10, and 15 years was 100%, 89%, and 89%, respectively, similar to non-carriers. Kaplan-Meier analysis revealed no significant differences in 5, 10, and 15-year overall survival, progression-free survival, local failure-specific survival, and contralateral breast cancer rates between the groups. Conclusion: In non-metastatic breast cancer patients, monoallelic ATM variant carrier status does not significantly influence acute or late RT toxicities and survival outcomes. These findings, derived from a small cohort, highlight the need for prospective studies for further validation. Table: Acute and Late Toxicities Post-Radiation Therapy in Monoallelic ATM Variant Carriers vs Non-Carriers Citation Format: Rebecca Zasloff, Samantha Thomas, Kendra Parrish, Astrid Botty van de Bruele, Gayle DiLalla, Maggie DiNome, Laura Rosenberger, Hannah Woriax, E Shelley Hwang, Jennifer Plichta, Akiko Chiba. Racial/Ethnic Disparities in Rates of Pathological Complete Response and Survival in Patients with Inflammatory 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 PO1-10-01.

Abstract PO1-22-05: Radiation Therapy Toxicities and Survival Outcomes in Monoallelic ATM Variant Carriers with Non-Metastatic Breast Cancer: A Retrospective Analysis

Abstract Radiation Therapy Toxicities and Survival Outcomes in Monoallelic ATM Variant Carriers with Non-Metastatic Breast Cancer: A Retrospective Analysis Rayan Bensenane1 MD, Arnaud Beddok1,2,3 MD, Nadine Andrieu4 PhD, Fabienne Lesueur4 PhD, Eve Cavaciuti 4 MSc, Dorothee Le Gal4 MSc, Eon-Marchais Severine4 PhD, Dominique Stoppa Lyonnet 5MD PhD, Youlia Kirova1 MD 1. Institut Curie, PSL Research University, Radiation Oncology Department, Paris/Saint-Cloud/Orsay, France. 2. Gordon Center for Medical Imaging, Massachusetts General Hospital, Harvard Medical School, 125 Nashua St., Boston, MA, 02114, USA 3. Institut Curie, PSL Research University, University Paris Saclay, Inserm LITO U1288 Orsay, France 4. Inserm, U900, Institut Curie, PSL Research University, Mines ParisTech, Paris, France Abstract (characters: 2952; max 3400 characters, not include spaces) Background: The Ataxia-Telangiectasia Mutated (ATM) gene, involved in the repair of DNA double-strand breaks, can contribute to radiosensitivity when a bi-allelic variant is present and lead to Ataxia-Telangiectasia syndrome. Moreover, monoallelic ATM pathologic variant (PV) carriers, especially women, has an estimated occurrence rate of 0.5-1% globally and face a 2 to 3-fold increased risk of developing breast cancer. Despite evidence of in vitro radiosensitivity in cells derived from monoallelic variant carriers, there is a dearth of patient studies examining the risk of radiation-induced toxicity. This study aims to explore radiation therapy (RT) toxicities in non-metastatic breast cancer women carrying a germline monoallelic ATM variant, compared to non-carriers. Methods: A retrospective study was conducted on patients treated at Institut Curie, Paris from 1999 to 2014 and participating to CoF-AT (a French national study) and GENESIS database. ATM variant screenings encompassed both PV and non-PV, with toxicities evaluated using CTCAE v.5. Variants were classified as pathogenic, variant of unknown significance (VUS), or benign. Follow-up started from age/date at breast cancer to acute, late toxicities, disease recurrence or last news. Survival and toxicity comparisons were made using Kaplan-Meier survival analysis and Chi-square tests, respectively, with a significance level of α set at 0.05. Results: Among 50 patients, nine were ATM variant carriers (3 PV/5 VUS/1 benign), and 41 were non-carriers. Most patients had no smoking history (68%), and invasive ductal carcinoma was the predominant diagnosis (82%). The majority underwent breast-conservative surgery (80%), and the dominant RT techniques were 3D-Conformational Radiation Therapy (70%) and Isocentric Lateral Decubitus (30%). The median RT dose was 50 Gy over an average period of 36.5 days. With a median follow-up of 12 years post-diagnosis, no significant difference in acute dermatitis, esophagitis, lymphedema, cutaneous fibrosis, telangiectasia, or heart disease was observed between the groups. Analysis of overall survival (OS) showed a 5-year OS of 98%, decreasing to 89% at 10 years. For ATM variant carriers, the OS at 5, 10, and 15 years was 100%, 89%, and 89%, respectively, similar to non-carriers. Kaplan-Meier analysis revealed no significant differences in 5, 10, and 15-year overall survival, progression-free survival, local failure-specific survival, and contralateral breast cancer rates between the groups. Conclusion: In non-metastatic breast cancer patients, monoallelic ATM variant carrier status does not significantly influence acute or late RT toxicities and survival outcomes. These findings, derived from a small cohort, highlight the need for prospective studies for further validation. Table: Acute and Late Toxicities Post-Radiation Therapy in Monoallelic ATM Variant Carriers vs Non-Carriers * Pearson/Chi2 test ; NS: non significant at α=0.05; ATM +/+: wild type for ATM; ATM +/- : ATM monoallelic germline variant carrier Citation Format: Rayan BENSENANE, Youlia Kirova, Arnaud BEDDOK, Andine ANDRIEU, Fabienne Lesueur, Eve CAVACIUTI, Dorothée Le GAL, Severine EON-MARCHAIS, Dominique STOPPA LYONNET. Radiation Therapy Toxicities and Survival Outcomes in Monoallelic ATM Variant Carriers with Non-Metastatic Breast Cancer: A Retrospective Analysis [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 PO1-22-05.

Abstract PS08-03: Sequencing Antibody-Drug Conjugate after Antibody-Drug Conjugate in Metastatic Breast Cancer (A3 study): Multi-Institution Experience and Biomarker Analysis

Abstract Background: Antibody-drug conjugates (ADCs) improve survival in patients with metastatic breast cancer (MBC) and offer the potential for targeted delivery of highly potent therapy. Many patients are now candidates for multiple ADCs, but optimal strategies for sequencing are unknown. We previously reported on a single institution experience of patients receiving multiple ADCs for MBC (Abelman, ASCO 2023). Here we report a multi-institution update with biomarker analysis. Methods: We included all patients treated at three academic medical institutions who received multiple ADCs for MBC. Patients were included if they had hormone receptor positive, HER2-negative (HR+/HER2-) breast cancer or triple-negative breast cancer (TNBC); patients with HER2+ metastatic breast cancer were excluded. Clinical information was determined by chart review. The metric of “cross-resistance” to the second ADC was defined as patients with progressive disease on first restaging assessment or progression within 60 days of treatment initiation. Every subsequent ADC beyond the first was compared against the prior ADC for presence of identical “antibody target” and “payload”. Comparisons across ADCs were performed using Fisher’s exact test. Significance was determined to be a type I error less than 0.05. A subset of patients had available whole exome tissue sequencing through commercially available sequencing platforms (BostonGene and Caris) performed around the time of receipt of ADC. All sequencing reports were examined for presence of pathogenic variants, variants of uncertain significance, and currently undefined variants and fusions as defined by each sequencing platform. Results: 68 patients were identified who received two or more ADCs for metastatic HR+/HER2- breast cancer or TNBC from August 2014-June 2023. 30 patients (44.1%) had HR+/HER2- disease and 38 patients (55.9%) had TNBC; 50 patients (73.5%) had HER2-low disease. Median age at time of second ADC was 59.6 (range 29.9-88.6). Patients had received a median of 4 lines of treatment in the metastatic setting prior to initiation of the second ADC. At time of first restaging, cross-resistance was present in 38/64 evaluable cases (59.4%). When the antibody target of the latter ADC was the same as the prior, cross-resistance was present in 11/14 cases (78.5%) compared to 26/49 cases (53.1%) when the later ADC targeted a different tumor-associated antigen. Relatively similar patterns of cross-resistance were observed regardless of whether the later ADC contained an identical payload to prior (6/10 cases, 60%) versus a different payload (22/42, 52.4%). Sequencing information was available for 20 patients who received multiple ADCs with 15 unique reports performed at the time of resistance to ADC1, prior to initiation of ADC2, or after ADC2 if presence of cross-resistance. Variants in topoisomerase-I associated genes (TOP1, TOP2A, TOP3A, TOP3B) were identified in a subset of patients mediating cross-resistance to the second ADC with a topoisomerase-I inhibitor payload. Conclusions: In this multi-institution study, cross-resistance to the second ADC appears to be driven by the antibody target in some patients versus the payload in others, highlighting the heterogeneity of mechanisms related to ADC resistance. Tumor sequencing revealed candidate resistance mutations that may guide optimal sequencing for patients with MBC. Citation Format: Rachel Occhiogrosso Abelman, Laura Spring, Geoffrey Fell, Andrew Davis, Whitney Hensing, Phoebe Ryan, Neelima Vidula, Seth Wander, Arielle Medford, Jennifer Shin, Elizabeth Abraham, Steven Isakoff, Beverly Moy, Leif Ellisen, Aditya Bardia. Sequencing Antibody-Drug Conjugate after Antibody-Drug Conjugate in Metastatic Breast Cancer (A3 study): Multi-Institution Experience and Biomarker Analysis [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 PS08-03.

Abstract PO4-05-03: Cell-free tumor DNA analysis in advanced or metastatic breast cancer patients enrolled in the German registry study PRAEGNANT

Abstract Background Accurate molecular profiling is crucial for optimal treatment decisions in advanced or metastatic breast cancer. Liquid biopsies, such as circulating cell-free tumor DNA (cfDNA, cftDNA or ctDNA), provide a non-invasive approach to monitor molecular alterations in the tumor. The German PRAEGNANT registry study aims to investigate such molecular biomarkers for precision medicine and their practical integration into clinical practice. In this context, cftDNA testing was performed as part of a PRAEGNANT research subproject, with the objectives of understanding the physician's rationale for initiating cftDNA testing, identifying detected alterations, and assessing the clinical impact of the associated findings Methods Patients with advanced or metastatic breast cancer were prospectively enrolled in the PRAEGNANT registry study (NCT02338167). The decision to undergo cftDNA testing was based on the physician's discretion. Blood samples were collected using Streck cfDNA BCT tubes and sent to the GUARDANT Health central laboratory for cftDNA extraction and subsequent next-generation sequencing analysis, employing the FDA-approved GUARDANT360 CDx test, a 74 gene panel including all guideline-recommended biomarkers, including single nucleotide variants (SNVs), indels, fusions and amplifications. Recruitment of patients occurred at four PRAEGNANT study centers between April 2022 and July 2023. The GUARDANT360 CDx report, along with a questionnaire regarding the testing intent and clinical impact of the results, was provided to the treating physician. Results 46 patients were eligible for analysis as per clinical characteristics. CftDNA analysis was successfully performed for all 46 cases. 38 (83%) harbored at least one somatic alteration in the analyzed genes. Fifteen patients (33%) harbored alterations in TP53, thirteen (28%) in PIK3CA. Five patients (11%) harbored mutations in ESR1. Somatic mutations in BRCA1 or BRCA2 were detected for five (11%) and six (13%) patients, respectively. One BRCA2 mutation was categorized as synonymous and one BRCA2 and three BRCA1 alterations as variants of uncertain significance. Eight patients (17%) harbored mutations in ATM. Most patients included were HR+HER2- (N=27, 58%). In this subgroup, eight (30%) patients had a PIK3CA alteration, five (19%) with an indication for treatment with alpelisib, eight (30%) a mutation in ATM, BRCA1 or BRCA2 and four (15%) in ESR1. Questionnaires regarding intention of testing and clinical impact were completed by 43 treating physicians (93%). Among them, 33% of patients had current indications for PARP inhibitor treatment, and 61% would consider it at the next change of therapy if a BRCA1 or BRCA2 mutation was detected. Additionally, 21% of patients had a current indication for alpelisib treatment if a relevant PIK3CA mutation was found, and 58% would consider it in the next line of treatment. Overall, cfDNA testing influenced the current or future treatment decisions in 35% of patients. Discussion The high prevalence of somatic alterations in TP53, PIK3CA, ESR1, and BRCA1/2 genes, identified through cftDNA testing with GUARDANT360 CDx, highlights their potential as biomarkers for targeted therapies in advanced/metastatic breast cancer. Detection of specific mutations influenced treatment decisions, such as eligibility for alpelisib or PARP inhibitors and might further facilitate treatment with elacestrant in future treatment lines after its approval in Germany. These findings demonstrate the clinical impact of cftDNA testing in guiding personalized treatment selection. Additionally, the identification of such somatic alterations within a registry study like PRAEGNANT presents a unique opportunity to consider enrolling these patients into biomarker-guided clinical trials. Citation Format: Hanna Hübner, Pauline Wimberger, Elena Laakmann, Eugen Ruckhäberle, Matthias Ruebner, Theresa Link, Erik Belleville, Iris Faull, Marcus Hausch, Diethelm Wallwiener, Andreas Schneeweiss, Hans Tesch, Sara Brucker, Peter A. Fasching, Volkmar Müller, Tanja Fehm. Cell-free tumor DNA analysis in advanced or metastatic breast cancer patients enrolled in the German registry study PRAEGNANT [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 PO4-05-03.

Abstract PO4-14-02: Enhancing Informative Outcomes with Liquid Biopsy in a Real-World Population of Patients with Advanced Breast Cancer: Analysis of the SOLTI-1903 HOPE Study

Abstract Background: The integration of next-generation sequencing (NGS) into routine clinical practice is often hindered by financial and logistical challenges, resulting in diagnostic and therapeutic disparities among patients. Addressing these issues, the SOLTI-1903 HOPE study (NCT04497285) seeks to evaluate the feasibility of implementing a molecular screening program that actively involves patients with advanced breast cancer (ABC) in the management of their disease. By empowering patients, this study aims to gain a comprehensive understanding of the genomic landscape of ABC and to facilitate patient access to matched targeted therapies in Spain Methods: In the SOLTI-1903 HOPE study, a patient-centric approach was adopted, allowing patients living anywhere in Spain, and diagnosed with ABC, to actively lead their inclusion, participation, and follow-up using a digital tool (DT). Patients signed an informant consent, and then provided clinical information and underwent a liquid biopsy (LBx) using the Guardant360 panel at a local laboratory. LBx samples could be obtained at the moment of progressive disease (PD), when a new line of treatment was started < 8 weeks before extraction (PT), or during treatment with stable disease o partial response lasting more than 8 weeks (SD/PR). Clinical and molecular findings were evaluated by a Molecular Advisory Board (MAB), which generated a comprehensive report explaining the observed alterations and listing potentially beneficial matched targeted treatments. The primary endpoint of this subanalysis was to compare the genomic outcomes between LBx samples obtained at SD and those obtained at PD or PT. In the study, tissue samples were also collected and analysed by Foundation but this analysis will be reported in other communications. Results: From October 2020 to May 2023, a total of 273 blood samples were obtained from 253 patients diagnosed with ABC, with the majority being HR+/HER2- (81%), followed by HER2-positive (13%) and triple-negative (6%). Mean turnaround time was 10.9 days from blood collection to final result. Despite nearly 40% of patients being SD or PR, in 79.9% of the LBx (n=218), one or more genomic alterations were detected, and among these, 74.0% (n=202) were classified as pathogenic. Among the 74 genes analyzed by the Guardant360 panel, 8 genes were classified as tiers I-III according to the ESCAT levels of clinical relevance. In 150 LBx samples (54.9%), one or more pathogenic alterations were associated with ESCAT levels I-III, while only the remaining 52 LBx samples (19.1%) with pathogenic alterations were not associated with any ESCAT levels I-III. Among the analyzed LBx samples, a total of 928 distinct gene alterations were identified. Of these, 650 alterations (70.1%) were classified as pathogenic, while 278 (29.9%) were categorized as variants of unknown significance or lacked a reported impact. Notably, 25% (n=323) of the pathogenic gene alterations were further classified as ESCAT I-III. Out of the 273 LBx samples, 140 were obtained at PD, 30 at PT, and 103 at SD/PR. Circulating tumor DNA (ctDNA) was detected in 91.4% of PD samples, 86.7% of PT samples, and 62.1% of SD/PR samples (p< 0.001). Alterations classified as ESCAT levels I-III were observed in 70% of PD samples, 60% of PT samples, and 33% of SD/PR samples (p< 0.001). In 20 patients, LBx was repeated, with 16 of them having the first LBx obtained during SD/PR and the second LBx collected during PD or PT. The detection rate of ctDNA increased significantly from 18.7% (n=3) to 87.5% (n=14) (p< 0.001). The number of LBx samples with ESCAT levels I-III alterations also showed a significant increase from 12.5% (n=2) to 68.7% (n=11) (p=0.0032). Conclusions: Our findings highlight the importance of obtaining LBx samples during disease progression -compared to SD/PR- to gain greater genomic informativeness and better guide personalized treatment approaches for patients with advanced breast cancer. Citation Format: Tomás Pascual, Elia Seguí, Ruben Olivera-Salguero, Juan Miguel Cejalvo, Mafalda Oliveira, Pablo Tolosa, Maria Vidal, Marcos Malumbres, Joaquín Gavilá, Cristina Saura, Sonia Pernas, Rafael López, Mireia Margelí, Judith Balmaña, Montserrat Muñoz, Isabel Blancas, Valentina Boni, Eva Ciruelos, Elena Galve, Antonia Perelló, Rodrigo Sánchez-Bayona, Susana De La Cruz, Miguel De La Hoya, Aura Blanch-Torras, Rosana Sposito, Jordi Canes, Helena Masanas, Rosa Olmos, Margarita Forns, Maria José Prieto, Ana Casas, Aleix Prat. Enhancing Informative Outcomes with Liquid Biopsy in a Real-World Population of Patients with Advanced Breast Cancer: Analysis of the SOLTI-1903 HOPE Study [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 PO4-14-02.

Abstract PO2-08-11: The MAGIC study: Universal whole genome tumour and germline sequencing of newly diagnosed breast cancer identifies a high proportion of ER+ BRCA-like tumours

Abstract Background: Identification of germline mutations in hereditary breast cancer (HBC) genes can have profound benefits in the treatment of breast cancer (BC) and manging risk for patient and the family. In addition, sequencing of the tumours can reveal clinically relevant somatic features, such as homologous recombination deficiency (HRD) and mutational signatures, that can guide treatment which are not discernible by germline sequencing alone. We hypothesised that current standard of care where women diagnosed with BC are not routinely offered tumour sequencing is suboptimal as fails to exploit all therapeutic vulnerabilities which can be exploited in the treatment of BC. The MAGIC study is the first prospective trial in Australia of unselected invasive BCs in general oncology practice combining both germline and tumour sequencing. Methods: The MAGIC study included a total of 651 consecutive consented patients presenting with non-metastatic BC between June 2020 to March 2023. It included invasive BC, high-grade DCIS and pleomorphic LCIS. The sequencing was conducted in two phases; for phase one, 157 cases underwent whole genome sequencing (WGS) on both germline and matched BC DNA while for phase two, 494 cases underwent only germline whole exome sequencing. Germline variants were interrogated for pathogenic variants in BRCA1, BRCA2, PALB2, ATM, CHEK2, BARD1, BRIP1, RAD51B, RAD51C, RAD51D, MLH1, MSH2, MSH6, PMS2, CDH1, PTEN, STK11, TP53 and NTHL1. Tumour homologous recombination (HR) repair deficiency was calculated using HRDetect (Nat Med 2017;23:517). For BCs showing a high HRDetect score ( >0.75) all HBC gene promoter CpG islands were assessed for hypermethylation using the Twist NGS Methylation system. Mutational signatures were calculated from somatic mutations identified from whole genome sequenced BCs using the DeconstructSig package in R (Genome Biol. 2016;17:31) and referenced against the COSMIC v2 signature catalogue. Results: Actionable germline variants in any HBC gene were identified in 7.7% of cases (7.8% of invasive and 6.1% of in situ BC) with 5.2% having an actionable mutation in an HR pathway gene (BRCA1, BRCA2, PALB2 and RAD51C). Most cases with pathogenic variants showed bi-allelic inactivation in the tumour. All BRCA1, BRCA2 and PALB2 tumours showed high HRDetect and/or HRD scores consistent with loss of HR repair function, indicating them to be the underlying hereditary driver of the BC. One BC with a pathogenic PMS2 variant showed retention of the wild-type allele with no evidence of a mismatch repair mutational signature suggesting PMS2 was not the driver of this BC. Of the 157 BC in phase one that underwent WGS and did not have a germline pathogenic HBC gene variant, 16% (18/117 invasive and 3/13 DCIS) had an HRDetect score of >0.7 indicative of a homologous recombination repair defect and therefore biologically a “BRCA-like” tumour. Of these 21 BRCA-like cases, only 3 invasive BCs had clear somatic bi-allelic inactivation of an HBC gene that could explain the high HRDetect score (2 BRCA1 and 1 BRCA2). One of the 21 BRCA-like cases had a germline variant of unknown significance (VUS) in an HBC gene (a BRCA2 missense variant in an ER+ tumour. The tumour showed loss of the wild-type allele). Of the BRCA-like cases, 71% were ER positive which included 3 invasive lobular cancers. Conclusion: Tumour sequencing identified three times as many cases that might be eligible for HR repair defect targeted therapy than germline testing alone (16% versus 5.2%). Unlike a previous study (Ann Oncol., 2019 30:1071-1079), the majority of the BRCA-like BCs were ER+ with no evidence of a VUS in a known HBC gene suggesting these are driven by novel germline or somatic mutations in genes involved in DNA HR repair. Citation Format: Ian Campbell, Lisa Devereux, Kirsten Hogg, Luxi Lal, Michelle Sinclair, Lesley Stafford, Magnus Zethoven, Anita Skandarajah, Paul James, Geoffrey Lindeman, Bruce Mann, Dilanka De Silva. The MAGIC study: Universal whole genome tumour and germline sequencing of newly diagnosed breast cancer identifies a high proportion of ER+ BRCA-like tumours [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 PO2-08-11.

Genetic counseling access and service delivery in New York State is variable for parents of infants with complex CFTR genotypes conferring uncertain phenotypes.

New York State (NYS) utilizes a three-tiered cystic fibrosis newborn screening (CFNBS) algorithm that includes cystic fibrosis transmembrane conductance regulator (CFTR) gene sequencing. Infants with >1 CFTR variant of potential clinical relevance, including variants of uncertain significance or varying clinical consequence are referred for diagnostic evaluation at NYS cystic fibrosis(CF) Specialty Care Centers (SCCs). As part of ongoing quality improvement efforts, demographic, screening, diagnostic, and clinical data were evaluated for 289 CFNBS-positive infants identified in NYS between December 2017 and November 2020 who did not meet diagnostic criteria for CF and were classified as either: CFTR-related metabolic syndrome/CF screen positive, inconclusive diagnosis (CRMS/CFSPID) or CF carriers. Overall, 194/289 (67.1%) had CFTR phasing to confirm whether the infant's CFTR variants were in cis or in trans. Eighteen complex alleles were identified in cis; known haplotypes (p.R117H+5T, p.F508del+p.L467F, and p.R74W+p.D1270N) were the most common identified. Thirty-twoinfants (16.5%) with all variants in cis were reclassified as CF carriers rather than CRMS/CFSPID. Among 263 infants evaluated at anNYS SCC, 70.3% were reported as having received genetic counseling about their results by any provider, with 96/263 (36.5%) counseled by a certified genetic counselor. Given the particularly complex genetic interpretation of results generated by CFNBS algorithms including sequencing analysis, additional efforts are needed to ensure families of infants with a positive CFNBS result have CFTR phasing when needed to distinguish carriers from infants with CRMS/CFSPID, and access to genetic counseling to address implications of CFNBS results.

Variants in structural cardiac genes in patients with cancer therapy-related cardiac dysfunction after anthracycline chemotherapy: a case control study

BackgroundVariants in cardiomyopathy genes have been identified in patients with cancer therapy-related cardiac dysfunction (CTRCD), suggesting a genetic predisposition for the development of CTRCD. The diagnostic yield of genetic testing in a CTRCD population compared to a cardiomyopathy patient cohort is not yet known and information on which genes should be assessed in this population is lacking.MethodsWe retrospectively included 46 cancer patients with a history of anthracycline induced CTRCD (defined as a decrease in left ventricular ejection fraction (LVEF) to < 50% and a ≥ 10% reduction from baseline by echocardiography). Genetic testing was performed for 59 established cardiomyopathy genes. Only variants of uncertain significance and (likely) pathogenic variants were included. Diagnostic yield of genetic testing was compared with a matched cohort of patients with dilated cardiomyopathy (DCM, n = 46) and a matched cohort of patients without cardiac disease (n = 111).ResultsAverage LVEF at time of CTRCD diagnosis was 30.1 ± 11.0%. Patients were 52.9 ± 14.6 years old at time of diagnosis and 30 (65.2%) were female. Most patients were treated for breast cancer or lymphoma, with a median doxorubicin equivalent dose of 300 mg/m2 [112.5-540.0]. A genetic variant, either pathogenic, likely pathogenic or of uncertain significance, was identified in 29/46 (63.0%) of patients with CTRCD, which is similar to the DCM cohort (34/46, 73.9%, p = 0.262), but significantly higher than in the negative control cohort (47/111, 39.6%, p = 0.018). Variants in TTN were the most prevalent in the CTRCD cohort (43% of all variants). All (likely) pathogenic variants identified in the CTRCD cohort were truncating variants in TTN.There were no significant differences in severity of CTRCD and in recovery rate in variant-harbouring individuals versus non-variant harbouring individuals.ConclusionsIn this case-control study, cancer patients with anthracycline-induced CTRCD have an increased burden of genetic variants in cardiomyopathy genes, similar to a DCM cohort. If validated in larger prospective studies, integration of genetic data in risk prediction models for CTRCD may guide cancer treatment. Moreover, genetic results have important clinical impact, both for the patient in the setting of precision medicine, as for the family members that will receive genetic counselling.

Investigation of the Frequency and Characteristic Features of De Novo Mutations in Clinical Exome Sequence Trio Samples

Advanced genome sequencing technologies have provided us with the opportunity to deeply understand the mechanisms underlying conditions associated with the genome. There has been significant interest recently in understanding the characteristics of de novo mutations, which are genetic changes that arise in reproductive cells and are not present in parents, as well as the mechanisms involved in their occurrence. These mutations can be transmitted to subsequent generations and have the potential to influence genetic diversity and susceptibility to diseases, making this topic important. Due to limited studies in this area, the formation mechanisms and characteristic features of such mutations have not yet been fully understood. Background/Aims: In this study, we aimed to conduct a comprehensive analysis of de novo mutations in families undergoing trio clinical exome sequencing analysis. The objectives of the study were to investigate the relationship between parental ages and the frequency of de novo mutations, the distribution, prevalence, relationships, and molecular characteristics of de novo mutations. Methods: A total of 69 families who underwent Trio Clinical Exome Sequencing (CES) analysis at the Department of Medical Genetics, Faculty of Medicine, Selçuk University, between January 1, 2017, and December 31, 2023, were included in the study. DNA samples extracted from peripheral venous blood of individuals were sequenced using the Roche CES kit and DNBSEQ-G400™ sequencing device, and a total of 3892 genes were analyzed using the Seq Platform. Results: After analysis, 407 de novo variants were identified, with the majority being variants of unknown significance (55.28%). When examining the base change profile, the most common changes were found to be C -&amp;gt; G, G -&amp;gt; A, A -&amp;gt; G. The most commonly mutated genes were found to be DSPP, HPS4, VCL, and BMP4 genes. Conclusions: Correlation analysis revealed no significant relationship between parental age and the number of de novo mutations, and regression analysis showed that age was not a significant parameter in determining the number of de novo mutations

Exploring genetic variants in congenital monosaccharide-disaccharide metabolism: Carrier ratiosandphenotypic insights.

Adverse food reactions, often underestimated, encompass congenital monosaccharide-disaccharide metabolism disorders, yielding diverse outcomes such as abdominal pain, diarrhea, bleeding disorders, and even death. This study retrospectively scrutinized genetic variants linked to these disorders in a cohort subjected to whole-exome sequence analysis (WES), determining carrier frequencies and genotype-phenotype correlations. Data from 484 patients, were retrospectively analyzed using a gene panel (ALDOB, FBP1, GALE, GALK1, GALM, GALT, LCT, SLC2A2, SLC5A1, SI) for congenital monosaccharide-disaccharide metabolism disorders. WES was performed on patients using the xGen Exome Research Panel v2 kit, utilizing Next Generation Sequence Analysis (NGS). The study encompassed pathogenic, likely pathogenic, and variant of uncertain significance (VUS) variants. Among 484 patients (244 female, 240 male), 17.35% carried 99 variants (67 distinct) in the analyzed genes. Pathogenic/likely pathogenic allele frequency stood at 0.013, while VUS allele frequency was 0.088. Notably, 44% (37/84) of patients harboring mutations manifested at least one relevant phenotype. Carriage frequencies ranged from 1:25 (SI gene) to 1:968 (GALE gene), with the estimated disease frequency spanning from 1:2500 to 1:3748000. Our study underscores clinical manifestations in heterozygous carriers of recessive genetic disorders, addressing gaps in carrier frequencies and phenotypic effects for congenital monosaccharide-disaccharide metabolism disorders. This knowledge can improve these conditions'diagnosis and management, potentially preventing adverse food reactions and their associated complications.

Genetic Screening of Patients with Sporadic Alzheimer’s Disease and Frontotemporal Lobar Degeneration in the Chinese Population

Background: Alzheimer’s disease (AD) and frontotemporal lobar degeneration (FTLD) account for the vast majority of neurodegenerative dementias. AD and FTLD have different clinical phenotypes with a genetic overlap between them and other dementias. Objective: This study aimed to identify the genetic spectrum of sporadic AD and FTLD in the Chinese population. Methods: A total of 74 sporadic AD and 29 sporadic FTLD participants were recruited. All participants underwent whole-exome sequencing (WES) and testing for a hexanucleotide expansion in C9orf72 was additionally performed for participants with negative WES results. Results: Four known pathogenic or likely pathogenic variants, including PSEN1 (p.G206D), MAPT (p.R5H), LRRK2 (p.W1434*), and CFAP43 (p.C934*), were identified in AD participants, and 1 novel pathogenic variant of ANXA11 (p.D40G) and two known likely pathogenic variants of MAPT (p.D177V) and TARDBP (p.I383V) were identified in FTLD participants. Twenty-four variants of uncertain significance as well as rare variants in risk genes for dementia, such as ABCA7, SORL1, TRPM7, NOS3, MPO, and DCTN1, were also found. Interestingly, several variants in participants with semantic variant primary progressive aphasia were detected. However, no participants with C9orf72 gene variants were found in the FTLD cohort. Conclusions: There was a high frequency of genetic variants in Chinese participants with sporadic AD and FTLD and a complex genetic overlap between these two types of dementia and other neurodegenerative diseases.

Exploring the Role of the MUTYH Gene in Breast, Ovarian and Endometrial Cancer

Background: MUTYH germline monoallelic variants have been detected in a number of patients affected by breast/ovarian cancer or endometrial cancer, suggesting a potential susceptibility role, though their significance remains elusive since the disease mechanism is normally recessive. Hence, the aim of this research was to explore the hypothesis that a second hit could have arisen in the other allele in the tumor tissue. Methods: we used Sanger sequencing and immunohistochemistry to search for a second MUTYH variant in the tumoral DNA and to assess protein expression, respectively. Results: we detected one variant of unknown significance, one variant with conflicting interpretation of pathogenicity and three benign/likely benign variants; the MUTYH protein was not detected in the tumor tissue of half of the patients, and in others, its expression was reduced. Conclusions: our results fail to demonstrate that germinal monoallelic MUTYH variants increase cancer risk through a LOH (loss of heterozygosity) mechanism in the somatic tissue; however, the absence or partial loss of the MUTYH protein in many tumors suggests its dysregulation regardless of MUTYH genetic status.

[Efficiency of CNV-seq in detecting fetal DMD gene deletion or duplication in prenatal diagnosis].

Objective: To evaluate the diagnostic efficiency of copy number variation sequencing (CNV-seq) to detect the deletion or duplication of DMD gene in prenatal diagnosis. Methods: A retrospective analysis was carried out on the CNV-seq results of 34 544 fetuses diagnosed in the First People's Hospital of Yunnan Province from January 2018 to July 2023. A total of 156 cases of fetuses were collected, including Group 1:125 cases with family history of Duchenne muscular dystrophy or Becker muscular dystrophy (DMD/BMD), and Group 2:31 cases with no family history but a DMD gene deletion or duplication was detected unexpectedly by CNV-seq. Multiplex ligation-dependent probe amplification (MLPA) was used as a standard method to detect the deletion or duplication. Consistency test was carried out basing on the results of CNV-seq and MLPA of all 156 cases. Results: Comparing to MLPA, CNV-seq had a coincidence rate of 92.3% (144/156) for DMD gene deletion or duplication, with a sensitivity and positive predictive value of 88.2%, with a specificity and negative predictive value of 94.3%, a missed detection rate of 3.8%, and a Kappa value of 0.839. CNV-seq missed 4 cases with deletions and 2 with duplications due to involved fragments less than 100 Kb, among 20 cases of deletions and 6 cases of duplications detected by MLPA in Group 1. In Group 2, the deletions and duplications detected by CNV-seq were 42% (13/31) and 58% (18/31), respectively, in which the percentage of duplication was higher than that in Group 1. Among those 18 cases with duplications, 3 cases with duplication locating in exon 42~67 were likely pathogenic; while 9 cases with duplication covering the 5' or 3' end of the DMD gene, containing exon 1 or 79 and with only one breakpoint within the gene, along with the last 6 cases with duplications locating at chrX: 32650635_32910000 detected only by CNV-seq, which might be judged as variants of uncertain significance. Conclusions: CNV-seq has a good efficiency to detect fetal DMD gene deletion or duplication in prenatal diagnosis, while a further verification test by MLPA is recommended. The duplications on chrX: 32650635_32910000, 5' or 3' end of DMD gene detected by CNV-seq should be carefully verified and assessed because those variants appear to be nonpathogenic polymorphisms.