ATM Variants Research Articles

Prognostic significance of pathogenic variants in BRCA1, BRCA2, ATM and PALB2 genes in men undergoing hormonal therapy for advanced prostate cancer.

The prognostic significance of germline variants in homologous recombination repair genes in advanced prostate cancer (PCa), especially with regard to hormonal therapy, remains controversial. Germline DNA from 549 Japanese men with metastatic and/or castration-resistant PCa was sequenced for 27 cancer-predisposing genes. The associations between pathogenic variants and clinical outcomes were examined. Further, for comparison, DNA from prostate biopsy tissue samples from 80 independent patients with metastatic PCa were analysed. Forty-four (8%) patients carried germline pathogenic variants in one of the analysed genes. BRCA2 was most frequently altered (n = 19), followed by HOXB13 (n = 9), PALB2 (n = 5) and ATM (n = 5). Further, the BRCA1, BRCA2, PALB2 and ATM variants showed significant association with a short time to castration resistance and overall survival (hazard ratio = 1.99 and 2.36; 95% CI, 1.15-3.44 and 1.23-4.51, respectively), independent of other clinical variables. Based on log-rank tests, the time to castration resistance was also significantly short in patients with BRCA1, BRCA2, PALB2 or ATM somatic mutations and TP53 mutations. Germline variants in BRCA1, BRCA2, PALB2 or ATM are independent prognostic factors of the short duration of response to hormonal therapy in advanced PCa.

Heterozygous BRCA1 and BRCA2 and Mismatch Repair Gene Pathogenic Variants in Children and Adolescents With Cancer.

Genetic predisposition is has been identified as a cause of cancer, yet little is known about the role of adult cancer predisposition syndromes in childhood cancer. We examined the extent to which heterozygous pathogenic germline variants in BRCA1, BRCA2, PALB2, ATM, CHEK2, MSH2, MSH6, MLH1, and PMS2 contribute to cancer risk in children and adolescents. We conducted a meta-analysis of 11 studies that incorporated comprehensive germline testing for children and adolescents with cancer. ClinVar pathogenic or likely pathogenic variants (PVs) in genes of interest were compared with 2 control groups. Results were validated in a cohort of mainly European patients and controls. We employed the Proxy External Controls Association Test to account for different pipelines. Among 3975 children and adolescents with cancer, statistically significant associations with cancer risk were observed for PVs in BRCA1 and 2 (26 PVs vs 63 PVs among 27 501 controls, odds ratio = 2.78, 95% confidence interval = 1.69 to 4.45; P < .001) and mismatch repair genes (19 PVs vs 14 PVs among 27 501 controls, odds ratio = 7.33, 95% confidence interval = 3.64 to 14.82; P<.001). Associations were seen in brain and other solid tumors but not in hematologic neoplasms. We confirmed similar findings in 1664 pediatric cancer patients primarily of European descent. These data suggest that heterozygous PVs in BRCA1 and 2 and mismatch repair genes contribute with reduced penetrance to cancer risk in children and adolescents. No changes to predictive genetic testing and surveillance recommendations are required.

Genetic and Phenotypic Factors Affecting Glycemic Response to Metformin Therapy in Patients with Type 2 Diabetes Mellitus.

Metformin is an oral hypoglycemic agent widely used in clinical practice for treatment of patients with type 2 diabetes mellitus (T2DM). The wide interindividual variability of response to metformin therapy was shown, and recently the impact of several genetic variants was reported. To assess the independent and combined effect of the genetic polymorphism on glycemic response to metformin, we performed an association analysis of the variants in ATM, SLC22A1, SLC47A1, and SLC2A2 genes with metformin response in 299 patients with T2DM. Likewise, the distribution of allele and genotype frequencies of the studied gene variants was analyzed in an extended group of patients with T2DM (n = 464) and a population group (n = 129). According to our results, one variant, rs12208357 in the SLC22A1 gene, had a significant impact on response to metformin in T2DM patients. Carriers of TT genotype and T allele had a lower response to metformin compared to carriers of CC/CT genotypes and C allele (p-value = 0.0246, p-value = 0.0059, respectively). To identify the parameters that had the greatest importance for the prediction of the therapy response to metformin, we next built a set of machine learning models, based on the various combinations of genetic and phenotypic characteristics. The model based on a set of four parameters, including gender, rs12208357 genotype, familial T2DM background, and waist–hip ratio (WHR) showed the highest prediction accuracy for the response to metformin therapy in patients with T2DM (AUC = 0.62 in cross-validation). Further pharmacogenetic studies may aid in the discovery of the fundamental mechanisms of type 2 diabetes, the identification of new drug targets, and finally, it could advance the development of personalized treatment.

Prevalence of Cancer Predisposition Germline Variants in Male Breast Cancer Patients: Results of the German Consortium for Hereditary Breast and Ovarian Cancer.

Simple SummaryMale breast cancer (mBC) is a rare disease associated with a high prevalence of pathogenic germline variants (PVs) in the BRCA2 gene. However, data regarding other breast cancer (BC) predisposition genes are limited or conflicting. We investigated the prevalence of PVs in BRCA1/2 and 23 other cancer predisposition genes using an overall study sample of 614 patients with mBC. A high proportion of patients with mBC carried pathogenic germline variants in BRCA2 (23.0%, 142/614) and BRCA1 (4.6%, 28/614). A BRCA1/2 PV prevalence of 11.0% was identified in patients with mBC without a family history of breast and/or ovarian cancer. Patients with BRCA1/2 PVs did not show an earlier disease onset than those without. Case-control analyses revealed significant associations of protein-truncating variants in BRCA1, BRCA2, CHEK2, PALB2, and ATM with mBC. Our findings support the benefit of multi-gene panel testing in patients with mBC.Male breast cancer (mBC) is associated with a high prevalence of pathogenic variants (PVs) in the BRCA2 gene; however, data regarding other BC predisposition genes are limited. In this retrospective multicenter study, we investigated the prevalence of PVs in BRCA1/2 and 23 non-BRCA1/2 genes using a sample of 614 patients with mBC, recruited through the centers of the German Consortium for Hereditary Breast and Ovarian Cancer. A high proportion of patients with mBC carried PVs in BRCA2 (23.0%, 142/614) and BRCA1 (4.6%, 28/614). The prevalence of BRCA1/2 PVs was 11.0% in patients with mBC without a family history of breast and/or ovarian cancer. Patients with BRCA1/2 PVs did not show an earlier disease onset than those without. The predominant clinical presentation of tumor phenotypes was estrogen receptor (ER)-positive, progesterone receptor (PR)-positive, and HER2-negative (77.7%); further, 10.2% of the tumors were triple-positive, and 1.2% were triple-negative. No association was found between ER/PR/HER2 status and BRCA1/2 PV occurrence. Comparing the prevalence of protein-truncating variants (PTVs) between patients with mBC and control data (ExAC, n = 27,173) revealed significant associations of PTVs in both BRCA1 and BRCA2 with mBC (BRCA1: OR = 17.04, 95% CI = 10.54–26.82, p < 10−5; BRCA2: OR = 77.71, 95% CI = 58.71–102.33, p < 10−5). A case-control investigation of 23 non-BRCA1/2 genes in 340 BRCA1/2-negative patients and ExAC controls revealed significant associations of PTVs in CHEK2, PALB2, and ATM with mBC (CHEK2: OR = 3.78, 95% CI = 1.59–7.71, p = 0.002; PALB2: OR = 14.77, 95% CI = 5.02–36.02, p < 10−5; ATM: OR = 3.36, 95% CI = 0.89–8.96, p = 0.04). Overall, our findings support the benefit of multi-gene panel testing in patients with mBC irrespective of their family history, age at disease onset, and tumor phenotype.

Abstract 5773: A one-stop approach in diagnosing hereditary colorectal cancer: A prospective, proof-of-principle, single-center study

Abstract Background: Colorectal cancer (CRC) remains one of the most commonly diagnosed cancers and a leading cause of cancer-related deaths worldwide. Between 3 and 6% of all CRC cases are attributed to hereditary colorectal cancer (HCRC). It is important to distinguish CRCs that arise hereditarily from those that arise sporadically, because patients with HCRC and their relatives can benefit from intensive clinical management and surveillance. The detection of germline variants using tumor tissue and paired non-cancerous tissue/whole blood cells (WBC) (conventional method) is considered as the gold standard for germline confirmation, but which could introduce high cost and long turnaround time. In this work, we aimed to investigate the feasibility of diagnosing HCRC using only tumor next-generation sequencing data without normal tissue/WBC data. Methods: One-hundred patients with suspected HCRC were prospectively enrolled according to the clinical diagnosis. Both tumor tissue and paired WBC were collected from each patient. Capture-based targeted sequencing using a panel consisting of 41 cancer-related genes was performed on both tumor tissue and WBC sample. The germline variants were identified using conventional and ColonCore method, respectively. The sensitivity and positive predictive value (PPV) of ColonCore method in identifying germline alterations were calculated, when conventional method was used as a reference. Results: A total of 636 alterations were identified using ColonCore method, including 606 somatic alterations and 30 germline alterations. Among the somatic alterations detected from this panel, 599 single-nucleotide variants and 7 copy number variants were observed. The most frequently mutated genes were APC, TP53, and KRAS, occurring in 76%, 66%, and 46% of patients, respectively. For ColonCore analysis, 17, 9, 2, and 2 patients harbored germline pathogenic variants in DNA mismatch repair (MMR) genes, APC, MUTYH, and ATM, respectively. Compared to the conventional method, the sensitivity of ColonCore method in the diagnosis of HCRC achieved 88.5% with a PPV of 82.1%. Next, the diagnostic performance of ColonCore method in Lynch syndrome (LS) and familial adenomatous polyposis (FAP) was subsequently investigated. We found its sensitivity in the diagnosis of LS achieved 100% (with a PPV of 98.8%), which was obviously higher than that in the diagnosis of FAP (70.0% with a PPV of 63.6%). Twenty-three patients identified as having a microsatellite instability (MSI)-high tumor using ColonCore method were also identified as having an MMR-deficient (dMMR) tumor using immunohistochemistry staining analysis. Conclusions: Our study suggests that ColorCore method is a one-stop approach for detecting germline/somatic alterations and MSI/dMMR status for suspected HCRC. Furthermore, ColorCore method is a feasible and valid tool to diagnose HCRC, especially LS. Citation Format: Cong Li, Yun Xu, Fangqi Liu, Ye Xu. A one-stop approach in diagnosing hereditary colorectal cancer: A prospective, proof-of-principle, single-center study [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2022; 2022 Apr 8-13. Philadelphia (PA): AACR; Cancer Res 2022;82(12_Suppl):Abstract nr 5773.

Abstract 57: Patients with germline ATM mutations develop clonal hematopoiesis characterized by co-occurrence of multiple somatic ATM alterations

Abstract BACKGROUND The DNA repair gene ATM is remarkable for its roles across the spectrum of neoplastic biology, including inherited risk of multiple malignancies, somatic tumor biology, and clonal hematopoiesis (CH). We hypothesized that comparison of liquid biopsy (LB) versus tumor tissue (TT) from germline ATM pathogenic mutation carriers (gATM+) might offer additional insights into the role of ATM in CH. METHODS 34,825 LB samples and 384,847 TT specimens were sequenced for up to 324 genes during routine clinical care and analyzed for all classes of genomic alterations (Frampton 2013, Woodhouse 2020). Individual variants were assessed for germline versus somatic origin using the validated somatic-germline zygosity algorithm (Sun 2018). RESULTS Germline ATM mutations were observed in 0.9% (113/12,217) of LB and 0.8% (3,029/384,847) of TT (P&amp;lt;0.001). Up to 27 ATM mutations were identified per gATM+ sample, with a range of 1-27 in LB and 1-8 in TT. Co-occurrence of 3+ ATM mutations in a single sample was 18-fold higher among gATM+ subjects undergoing LB versus TT (23.9% vs. 1.2%, P&amp;lt;0.001). In LB, the incidence of 3+ ATM mutations increased with age for all groups, but the frequency in gATM+ subjects diverged as patient age advanced. In the age 80+ subgroup, 57.1% (28/49) of gATM+ subjects had 3+ ATM mutations, compared to 3.3% (133/4,055) of gATM− subjects (P&amp;lt;0.001). A significant difference was maintained after correcting for the contribution of the germline ATM mutation to the total number of ATM mutations in gATM+ subjects. We hypothesized that multiple ATM variants per sample could be caused by high TMB or positive selection for multiple subclonal hits in the ATM gene. In TT, observation of 3+ ATM mutations was associated with high TMB in 80.5% (513/637) of cases. In contrast, 88.5% (555/627) of LB samples with 3+ ATM mutations had low TMB (Pdiff&amp;lt;0.001), a pattern consistent with positive selection in LB. LB from gATM+ cases with 3+ ATM mutations all had one variant with ~50% variant allele fraction (VAF), while 80.0% (546/682) of the co-mutations had VAF &amp;lt;1%. Co-mutations included 32.0% (793/2,485) truncating alterations and 68.1% (1,692/2,485) missense alterations. Low VAF missense co-mutations were clustered in the FAT and PIKKc domains, which are known pathogenic missense mutation hotspots. This distribution suggests that some missense alterations within these hotspots that are currently classified as VUS are under positive selection and therefore warrant consideration for reclassification. CONCLUSION The finding of numerous ATM mutations under positive selection in gATM+ subjects was specific to LB, increased in incidence with age, and co-mutations tended to have low VAF. All these features are consistent with polyclonal hematopoiesis (polyCH) involving ATM co-mutations in gATM+ subjects. Additional investigation is needed to extend our understanding of this phenomenon. Citation Format: Brennan Decker, Angela A. Kou, Tyler Janovitz, Douglas A. Mata, Ethan S. Sokol, Dexter X. Jin, Hanna Tukachinsky, Jo-Anne Vergilio, Julia A. Elvin, Geoffrey R. Oxnard. Patients with germline ATM mutations develop clonal hematopoiesis characterized by co-occurrence of multiple somatic ATM alterations [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2022; 2022 Apr 8-13. Philadelphia (PA): AACR; Cancer Res 2022;82(12_Suppl):Abstract nr 57.

Deep Sequencing of Early T Stage Colorectal Cancers Reveals Disruption of Homologous Recombination Repair in Microsatellite Stable Tumours with High Mutational Burdens.

Simple SummaryStage IIIA are rare early T stage colorectal cancers that are not widely reported in genome sequencing studies. We aimed to investigate genomics features in common cancer genes associated with lymph node metastasis from these tumours. We discovered that microsatellite stable tumours with high mutational burdens showed different genomic variant frequencies compared to tumours with low mutation burdens. The high burden microsatellite stable tumours showed co-occurrence of mutations in homologous recombination DNA repair genes that where not observed in the microsatellite stable cancers with low mutational burdens. This finding highlights a potential therapeutic approach for high mutation burden microsatellite stable colorectal cancers given the successful clinical implementation of drugs blocking homologous recombination DNA repair in other cancers.Early T stage colorectal cancers (CRC) that invade lymph nodes (Stage IIIA) are rare and greatly under-represented in large-scale genomic mapping projects. We retrieved 10 Stage IIIA CRC cases, matched these to 16 Stage 1 CRC cases (T1 depth without lymph node metastasis) and carried out deep sequencing of 409 genes using the IonTorrent system. Tumour mutational burdens (TMB) ranged from 2.4 to 77.2/Mb sequenced. No stage-related mutational differences were observed, consistent with reanalysis of The Cancer Genome Atlas (TCGA) Stage I and IIIA datasets. We next examined mutational burdens and observed that the top five cancers were microsatellite stable (MSS) genotypes (mean TMB 49.3/Mb), while the other 16 MSS cancers had a mean TMB of 5.9/Mb. To facilitate comparison with TCGA hypermutator CRC, we included four microsatellite instability-high (MSI-H) samples with the high mutation burden MSS cases to form a TMB-High group. Comparison of TMB-High with TMB-Low groups revealed differences in mutational frequency of ATM, ALK, NSD1, UBR5, BCL9, CARD11, KDM5C, MN1, PTPRT and PIK3CA, with ATM and UBR5 validated in reanalysis of TCGA hypermutator Stages I and IIIA samples. Variants in ATM were restricted to the TMB-High group, and in four of five MSS specimens, we observed the co-occurrence of mutations in homologous recombination repair (HRR) genes in either two of ATM, CDK12, PTEN or ATR, with at least one of these being a likely pathogenic truncating mutation. No MSI-H specimens carried nonsense mutations in HRR genes. These findings add to our knowledge of early T stage CRC and highlight a potential therapeutic vulnerability in the HRR pathway of TMB-H MSS CRC.

Germline CHEK2 and ATM Variants in Myeloid and Other Hematopoietic Malignancies

An intact DNA damage response is crucial to preventing cancer development, including in myeloid and lymphoid malignancies. Deficiencies in the homologous recombination (HR) pathway can lead to defective DNA damage responses, and this can occur through inherited germline mutations in HR pathway genes, such as CHEK2 and ATM. We now understand that germline mutations can be identified frequently (~ 5-10%) in patients with myeloid and lymphoid malignancies, and among the most common of these are CHEK2 and ATM. We review the role that deleterious germline CHEK2 and ATM variants play in the development of hematopoietic malignancies, and how this influences clinical practice, including cancer screening, hematopoietic stem cell transplantation, and therapy choice. In recent large cohorts of patients diagnosed with myeloid or lymphoid malignancies, deleterious germline loss of function variants in CHEK2 and ATM are among the most common identified. Germline CHEK2 variants predispose to a range of myeloid malignancies, most prominently myeloproliferative neoplasms and myelodysplastic syndromes (odds ratio range: 2.1-12.3), and chronic lymphocytic leukemia (odds ratio 14.83). Deleterious germline ATM variants have been shown to predispose to chronic lymphocytic leukemia (odds ratio range: 1.7-10.1), although additional studies are needed to demonstrate the risk they confer for myeloid malignancies. Early studies suggest there may also be associations between deleterious germline CHEK2 and ATM variants and development of clonal hematopoiesis. Identifying CHEK2 and ATM variants is crucial for the optimal management of patients and families affected by hematopoietic malignancies. OPENING CLINICAL CASE: "A 45year-old woman presents to your clinic with a history of triple-negative breast cancer diagnosed five years ago, treated with surgery, radiation, and chemotherapy. About six months ago, she developed cervical lymphadenopathy, and a biopsy demonstrated small lymphocytic leukemia. Peripheral blood shows a small population of lymphocytes with a chronic lymphocytic leukemia immunophenotype, and FISH demonstrates a complex karyotype: gain of one to two copies of IGH and FGFR3; gain of two copies of CDKN2C at 1p32.3; gain of two copies of CKS1B at 1q21; tetrasomy for chromosome 3; trisomy and tetrasomy for chromosome 7; tetrasomy for chromosome 9; tetrasomy for chromosome 12; gain of one to twocopies of ATM at 11q22.3; deletion of chromosome 13 deletion positive; gain of one to two copies of TP53 at 17p13.1). Given her history of two cancers, you arrange for germline genetic testing using DNA from cultured skin fibroblasts, which demonstrates pathogenic variants in ATM [c.1898 + 2T > G] and CHEK2 [p.T367Metfs]. Her family history is significant for multiple cancers. (Fig.1)." Fig. 1 Representative pedigree from a patient with germline pathogenic ATM and CHEK2 variants who was affected by early onset breast cancer and chronic lymphocytic leukemia. Arrow indicates proband. Colors indicate cancer type/disease: purple, breast cancer; blue, lymphoma; brown, melanoma; yellow, colon cancer; and green, autoimmune disease.

HGG-35. Radiation Induced High Grade Gliomas: A Single Center Experience

INTRODUCTION: Patients receiving cranial radiotherapy (RT) are at risk for a subsequent radiation-induced glioma (RIG). RIGs are rare, generally develop with a latency of 2 years to several decades, display high-grade histology and an aggressive clinical course with poor prognosis. METHODS: We retrospectively analyzed patients with a diagnosis of RIG seen at our institution from 2001-2021, analyzing clinical, histological, molecular, and genetic characteristics. RESULTS: Twenty-one patients (n=15 male) with a history of ALL (n=6), medulloblastoma (n=5), germ cell tumors (n=4), or other (n=6) diagnosed at a median age of 8.3 years (range 1.6 to 36.4) were identified. Median age at RIG diagnosis was 18 years (range 7.8 to 66.9). Prior RT was focal+craniospinal (n=7), whole brain (n=5), total body (n=3), focal (n=1), or unknown (n=5). Median radiation dose received was 2,340 cGy (range 1,200 to 5,400). The median time from RT to RIG diagnosis was 7.7 years (range 1.6 to 23.8). All RIGs were histologically high grade (WHO Grade III or IV). Immunohistochemistry did not reveal IDH(R132H) (n=9) or H3K27M (n=8) in any tumor. Some tumors demonstrated loss of expression of ATRX (1/9) and/or H3K27me3 (3/6), and/or strong diffuse expression of p53 (0/3). Targeted panel sequencing (n=10) revealed recurrent somatic alterations including CDKN2A/B, PDGFRa/KIT/KDR, TEK, MTAP, ATM and NF1. Germline alterations were detected in 4/12 patients (pathogenetic variants in ATM, CHEK2, HOXB13 and NF1). With median follow-up of 4.5 years, two-year PFS and OS for the cohort (n=20) were 10% and 44% respectively. Two patients (with anaplastic oligodendroglioma and anaplastic astrocytoma) are alive without progression 5.4 and 13.6 years after diagnosis following surgery, RT and chemotherapy. CONCLUSION: Although RIGs are associated with a poor prognosis, they are not always fatal. Our findings suggest aggressive therapy should be considered for these patients.

Germline variants across self-reported racial populations with urothelial carcinoma (UC).

4569 Background: Prior studies of the UC germline landscape centered around White patients with minimal representation of other racial populations. Herein, we examine the frequency of germline pathogenic and likely pathogenic (P/LP) variants in 2,582 patients with UC from various racial populations. Methods: 2,582 patients with UC underwent germline testing of 1 to 126 genes using massively parallel sequencing with customized capture bait-sets to analyze exonic regions, flanking intronic regions, and copy number alterations (CNAs). P/LP variants including single nucleotide variants, indels and CNAs were reported. Fisher’s Exact test and multivariable logistic regression were used after accounting for the number of genes tested, age at diagnosis, site of disease (upper versus lower tract), gender, family history of UC, and personal history of any cancer. Results: Among the 2,582 patients with UC, median age at diagnosis was 63 years (range, 4-90) and 1158 (44.8%) were female. There were 58 Asians (2.2%), 110 Blacks (4.3%), and 2,414 Whites (93.5%). Overall, 1,639/2,582 (63.5%) patients had a personal history of another cancer and 284/2,393 (11.9%) had history of UC in a family member. 465 P/LP variants were identified in 18% of patients, among whom 286 (11.1%) harbored ≥1 clinically actionable variants. P/LP in cancer-associated genes were most frequently reported in MSH2 (72/2,512, 2.9%), monoallelic MUTYH (45/2,136, 2.1%), BRCA2 (44/2,299, 1.9%) and MSH6 (47/2,511, 1.9%). Patients with upper tract UC had significantly more P/LP (72/247, 29.1%) compared to lower tract UC (332/2,076, 16%, p= 1.3x10-5). Age at diagnosis, gender, personal history of other primary cancers, or family history of UC were not significantly associated with the prevalence of P/LP variants. There were no significant differences ( p= 0.33) in P/LP variants across Asians (11/58, 19.0%), Blacks (14/110, 12.7%), and Whites (440/2,414, 18.2%) although a trend towards lower P/LP in Blacks is notable. Compared to Whites, Blacks and Asians harbored significantly more variants of unknown significance (VUS, Whites vs Blacks: 241/2414 vs 25/110, p= 0.0015; Whites vs Asians: 241/2414 vs 17/58, p= 4e-7). Asians with UC harbored significantly more P/LP variants in ATM (2/50, 4%) compared to Whites (30/2122, 1.4%, OR = 1.1 [95% CI, 1.0-1.2]) and Asian controls from the gnomAD Database. There were no significant differences across racial populations for other highly altered genes ( BRCA1/2, CHEK2, FH, MSH2/6, MUTYH) or for actionable variants. Conclusions: Germline P/LP variants were identified in 18% of patients with UC and were enriched in upper tract tumors. Although no significant differences in P/LP prevalence were noted among patients of different racial populations, a trend towards lower P/LP in Blacks and a higher rate of VUS in Asians and Blacks suggest that ongoing analysis by genetic ancestry may provide richer admixture data and insights.

Personalised Risk Prediction in Hereditary Breast and Ovarian Cancer: A Protocol for a Multi-Centre Randomised Controlled Trial.

Simple SummaryWomen with disease-causing gene changes (faults/mutations) in BRCA1, BRCA2, PALB2, CHEK2 and ATM are at an increased risk of developing certain types of cancer—specifically breast (all genes) and epithelial ovarian cancer (only BRCA1, BRCA2, PALB2). At present, the risk estimates given to women by most healthcare professionals are broad (e.g., 35–85% lifetime risk of breast cancer for BRCA1 and BRCA2) and are not personalised. This can make it difficult for women to make informed decisions regarding the risk-management options available to them. By combining information about genetic, lifestyle and hormonal risk factors, we can produce a narrower, more personalised risk estimate (e.g., 44% lifetime risk of breast cancer). In this study, we aim to test whether offering personalised risk estimates to women undergoing predictive testing in genetics centres in the UK and USA better supports women’s mental health and choices about their clinical care, relative to standard care. In addition, we will explore the experiences of both staff and women taking part in the study, to understand whether personalised risk estimates are acceptable, feasible and cost-effective for use in clinical care.Women who test positive for an inherited pathogenic/likely pathogenic gene variant in BRCA1, BRCA2, PALB2, CHEK2 and ATM are at an increased risk of developing certain types of cancer—specifically breast (all) and epithelial ovarian cancer (only BRCA1, BRCA2, PALB2). Women receive broad cancer risk figures that are not personalised (e.g., 44–63% lifetime risk of breast cancer for those with PALB2). Broad, non-personalised risk estimates may be problematic for women when they are considering how to manage their risk. Multifactorial-risk-prediction tools have the potential to deliver personalised risk estimates. These may be useful in the patient’s decision-making process and impact uptake of risk-management options. This randomised control trial (registration number to follow), based in genetic centres in the UK and US, will randomise participants on a 1:1 basis to either receive conventional cancer risk estimates, as per routine clinical practice, or to receive a personalised risk estimate. This personalised risk estimate will be calculated using the CanRisk risk prediction tool, which combines the patient’s genetic result, family history and polygenic risk score (PRS), along with hormonal and lifestyle factors. Women’s decision-making around risk management will be monitored using questionnaires, completed at baseline (pre-appointment) and follow-up (one, three and twelve months after receiving their risk assessment). The primary outcome for this study is the type and timing of risk management options (surveillance, chemoprevention, surgery) taken up over the course of the study (i.e., 12 months). The type of risk-management options planned to be taken up in the future (i.e., beyond the end of the study) and the potential impact of personalised risk estimates on women’s psychosocial health will be collected as secondary-outcome measures. This study will also assess the acceptability, feasibility and cost-effectiveness of using personalised risk estimates in clinical care.

Breast cancer risks associated with missense variants in breast cancer susceptibility genes

BackgroundProtein truncating variants in ATM, BRCA1, BRCA2, CHEK2, and PALB2 are associated with increased breast cancer risk, but risks associated with missense variants in these genes are uncertain.MethodsWe analyzed data on 59,639 breast cancer cases and 53,165 controls from studies participating in the Breast Cancer Association Consortium BRIDGES project. We sampled training (80%) and validation (20%) sets to analyze rare missense variants in ATM (1146 training variants), BRCA1 (644), BRCA2 (1425), CHEK2 (325), and PALB2 (472). We evaluated breast cancer risks according to five in silico prediction-of-deleteriousness algorithms, functional protein domain, and frequency, using logistic regression models and also mixture models in which a subset of variants was assumed to be risk-associated.ResultsThe most predictive in silico algorithms were Helix (BRCA1, BRCA2 and CHEK2) and CADD (ATM). Increased risks appeared restricted to functional protein domains for ATM (FAT and PIK domains) and BRCA1 (RING and BRCT domains). For ATM, BRCA1, and BRCA2, data were compatible with small subsets (approximately 7%, 2%, and 0.6%, respectively) of rare missense variants giving similar risk to those of protein truncating variants in the same gene. For CHEK2, data were more consistent with a large fraction (approximately 60%) of rare missense variants giving a lower risk (OR 1.75, 95% CI (1.47–2.08)) than CHEK2 protein truncating variants. There was little evidence for an association with risk for missense variants in PALB2. The best fitting models were well calibrated in the validation set.ConclusionsThese results will inform risk prediction models and the selection of candidate variants for functional assays and could contribute to the clinical reporting of gene panel testing for breast cancer susceptibility.

Clinical Impact of Pathogenic Variants in DNA Damage Repair Genes beyond BRCA1 and BRCA2 in Breast and Ovarian Cancer Patients.

Simple SummaryThe clinical utility of positive findings in DNA damage-repair (DDR) genes BRCA1 and BRCA2 for the treatment of patients with breast or ovarian cancer is well established. However, multigene panel genetic testing for patients with breast and ovarian cancer now commonly includes DDR genes in addition to BRCA1 and BRCA2, a number of which are considered moderate or low-risk genes. This study aimed to describe the clinical utility of positive results from genetic testing when the findings were in one of these other DDR genes. In a group of 101 women with positive findings in a cancer gene other than BRCA1 or BRCA2 (often in a DDR gene), nearly three-fifths (58%) had a clinical recommendation made based on their positive genetic test result and two-thirds (65%) had the clinician make recommendations for family members that may be at risk. This real-world data provides evidence that positive findings from genetic testing for moderate and low-risk genes, including DDR genes, can have clinical utility and can impact a patient’s clinical management.Consensus guidelines for hereditary breast and ovarian cancer include management recommendations for pathogenic/likely pathogenic (P/LP) variants in ATM, CHEK2, PALB2, and other DNA damage repair (DDR) genes beyond BRCA1 or BRCA2. We report on clinical management decisions across three academic medical centers resulting from P/LP findings in DDR genes in breast/ovarian cancer patients. Among 2184 patients, 156 (7.1%) carried a P/LP variant in a DDR gene. Clinical follow-up information was available for 101/156 (64.7%) patients. Genetic test result-based management recommendations were made for 57.8% (n = 59) of patients and for 64.7% (n = 66) of patients’ family members. Most recommendations were made for moderate-to-high risk genes and were consistent with guidelines. Sixty-six percent of patients (n = 39/59) implemented recommendations. This study suggests that P/LP variants in DDR genes beyond BRCA1 and BRCA2 can change clinical management recommendations for patients and their family members, facilitate identification of new at-risk carriers, and impact treatment decisions. Additional efforts are needed to improve the implementation rates of genetic-testing-based management recommendations for patients and their family members.

Evaluating breast cancer predisposition genes in women of African ancestry

PurposeStudies conducted primarily among European ancestry women reported 12 breast cancer predisposition genes. However, etiologic roles of these genes in breast cancer among African ancestry women have been less well-investigated. MethodsWe conducted a case-control study in African American women, which included 1117 breast cancer cases and 2169 cancer-free controls, and a pooled analysis, which included 7096 cases and 8040 controls of African descent. Odds ratios of associations with breast cancer risk were estimated. ResultsUsing sequence data, we identified 61 pathogenic variants in 12 breast cancer predisposition genes, including 11 pathogenic variants not yet reported in previous studies. Pooled analysis showed statistically significant associations of breast cancer risk with pathogenic variants in BRCA1, BRCA2, PALB2, ATM, CHEK2, TP53, NF1, RAD51C, and RAD51D (all P < .05). The associations with BRCA1, PALB2, and RAD51D were stronger for estrogen receptor (ER)-negative than for ER-positive breast cancer (P heterogeneity < .05), whereas the association with CHEK2 was stronger for ER-positive than for ER-negative breast cancer. ConclusionOur study confirmed previously identified associations of breast cancer risk with BRCA1, BRCA2, PALB2, ATM, TP53, NF1, and CHEK2 and provided new evidence to extend the associations of breast cancer risk with RAD51C and RAD51D, which was identified previously in European ancestry populations, to African ancestry women.

Population-based estimates of age-specific cumulative risk of breast cancer for pathogenic variants in ATM

BackgroundMultigene panel tests for breast cancer predisposition routinely include ATM as it is now a well-established breast cancer predisposition gene.MethodsWe included ATM in a multigene panel test applied to the Australian Breast Cancer Family Registry (ABCFR), a population-based case–control–family study of breast cancer, with the purpose of estimating the prevalence and penetrance of heterozygous ATM pathogenic variants from the family data, using segregation analysis.ResultsThe estimated breast cancer hazard ratio for carriers of pathogenic ATM variants in the ABCFR was 1.32 (95% confidence interval 0.45–3.87; P = 0.6). The estimated cumulative risk of breast cancer to age 80 years for heterozygous ATM pathogenic variant carriers was estimated to be 13% (95% CI 4.6–30).ConclusionsAlthough ATM has been definitively identified as a breast cancer predisposition gene, further evidence, such as variant-specific penetrance estimates, are needed to inform risk management strategies for carriers of pathogenic variants to increase the clinical utility of population testing of this gene.

Functional analysis of ATM variants in a high risk cohort provides insight into missing heritability

Variants of unknown significance (VUS) remain a constant challenge in the diagnosis of hereditary cancer and the counseling of patients with pedigrees suggestive of such a syndrome. In order to assess some of this limitation, several variants in the DNA repair gene ATM were selected from a cohort of high risk individuals with negative genetic diagnoses. ATM has proven a challenge in the counseling of patients due to its nature as a moderate penetrance gene. In this study, six ATM missense mutations with a high likelihood for pathogenicity were assessed through a battery of experiments to yield high fidelity information on their biochemical effect on ATM activity. We report that several of these variants show signs of reduced ATM function indicative of likely pathogenicity. With further study, this data may be used in clinic, improving diagnosis, surveillance, and outcome for patients carrying these mutations.

OP008: Implementation of a universal somatic tumor screening program for hereditary cancer in patients with advanced cancer in a large HMO

Somatic variants in hereditary cancer (hCa) risk genes are frequently identified in tumors and represent an opportunity to diagnose hCa. We implemented a universal hCa somatic screening program in a large HMO to identify patients with hCa and determine if this approach augmented existing genetic counseling approaches. An automated “somatic safety net” process offered germline testing (gDNAt) to patients with advanced cancer harboring somatic variants in ATM, BRCA1, BRCA2, MLH1, MSH2, MSH6, PALB2, and/or PMS2 who had not previously undergone gDNAt. Patients previously completing gDNAt via “traditional genetic counseling” and “somatic safety net” were compared for demographics, tumor type, presence of germline pathogenic/likely pathogenic (gP/LP) variant, and whether NCCN criteria were met for hCa genetic testing. A total of 584 unique somatic variants were identified in the gene list of interest (ATM, BRCA1, BRCA2, MLH1, MSH1, MSH6, PALB2 and PMS2) from 503 unique tumor samples/patients during the study period. 111 patients had previously undergone gDNAt prior to completing their somatic tumor DNA test and were considered part of the “traditional genetic counseling” group (where a patient was referred for genetic counseling and gDNAt due to personal/family history criteria and/or cascade testing). Among the 392 patients who had not undergone gDNAt at the time of their somatic tumor testing: 1) 52.6% (206/392) patients never completed gDNAt (they were deceased, declined gDNAt or could not be contacted), 2) 14.0% (55/392) patients completed gDNAt concurrently/after their somatic tumor test for a personal/family history indication unrelated to the somatic tumor testing results (this group also comprised part of the “traditional genetic counseling” group), and 3) 131/392 (33.4%) patients completed gDNAt specifically due to their somatic result or “somatic safety net” searches of the somatic tumor database resulting in direct outreach by the genetics department and gDNAt. In the “traditional genetic counseling” group that completed gDNAt, 54% (89/166) of patients harbored a pathogenic or likely pathogenic (P/LP) germline variant in at least one of the genes of interest, while 46% (77/166) had a germline test that was negative/normal or contained one or more variants of uncertain clinical significance (negative/VUS). In the “somatic safety net” group that completed gDNAt, 29% (38/131) of patients had at least one germline P/LP variant, while 71% (93/131) of patients had a normal/VUS result on gDNAt. Among patients with a germline P/LP variant, significantly more patients met criteria under NCCN breast/colon guidelines for gDNAt in the “traditional genetic counseling” group (99%; 88/89) compared to the “somatic safety net” group (34%; 13/38) with p < 0.001 (Fisher’s exact test). For all patients who completed gDNAt, we also determined the percentage of P/LP somatic variants that were germline for each of the 8 genes. For genes where at least 20 somatic variants were identified in the tumor data set (ATM, BRCA1/2, MSH2, MSH6) between 20-50% of these somatic variants were also germline. Genes with fewer than 10 somatic variants identified (MLH1, PALB2, PMS2) had more variable frequencies of being germline (likely due to low n value for each of these genes), but collectively they had a similar percentage of being germline when combined as a single group (40%). Across all genes, 36% (127/357) of the P/LP somatic variants identified were present in the patient’s germline. We also determined the primary tumor type for all patients who underwent gDNAt and the likelihood for a germline variant to be present in different primary tumors with a somatic variant. Collectively, 43% (127/297) of all tumors with a somatic variant in the gene list of interest also harbored a germline variant. The most frequent primary tumors containing a somatic variant (in decreasing order) were breast, pancreatic, ovarian, colorectal, lung, and prostate. Other tumor types (eg, melanoma, bladder, hepatobiliary, sarcoma) represented a smaller proportion of the overall tumor group, but these tumors contained a collectively similar frequency of germline variants to more common tumors analyzed. Patients who received gDNAt through the “traditional genetic counseling” were more likely to have cardinal hereditary tumors than the “somatic safety net” group. A universal “somatic safety net” screen is a successful strategy to diagnose hCa and augments traditional strategies based on personal/family history. We argue that this approach should be more widely applied and will complement existing universal tumor screening strategies such as MMR-immunohistochemistry for HNPCC.

EP054: Real-world clinical characteristics and management of breast cancer in patients with germline pathogenic variants in ATM, CHEK2 and PALB2

Breast cancer is the most common type of cancer in women. While breast cancer risk associated with BRCA1 and BRCA2 variants are well-defined, the characteristics associated with germline pathogenic variants (PVs) in the moderate penetrant genes, ATM, CHEK2 and PALB2, are less clear. We describe the clinical characteristics, management, and treatment outcomes associated with germline moderate penetrant PVs in a large real-world clinical cohort.

EP061: Genetic risk for breast and ovarian cancer in a diverse and unselected population

eP061: Genetic risk for breast and ovarian cancer in a diverse and unselected population

EP059: Breast cancer characteristics among women with hereditary breast cancer

Women with pathogenic/likely pathogenic (P/LP) variants in inherited breast cancer genes are more likely to develop breast cancer in their lifetime. We sought to explore and compare clinical and family history characteristics among women with a breast cancer diagnosis and a confirmed P/LP variant in BRCA1, BRCA2, PALB2, CHEK2, or ATM.