Moderate-risk Genes Research Articles

Uptake of risk-reduction, surveillance, and therapeutic interventions among patients with breast cancer with pathogenic germline variants.

10579 Background: Management of breast cancer (BC) patients with pathogenic germline variants (PGVs) can include risk-reducing bilateral mastectomy (BLM), PARP inhibitors (PARPi), enhanced breast imaging (MRI/tomosynthesis), risk-reducing salpingo-oophorectomy (RRSO) and pancreatic cancer surveillance (endoscopic ultrasound, EUS/MR cholangiopancreatography, MRCP). We assessed intervention uptake in >1,400 PGV-positive BC patients. Methods: Germline genetic testing (GGT) data (Invitae Corp.) and insurance claims data (Komodo Healthcare Map) were assembled for female patients with BC or DCIS diagnosed 2015-23, GGT <120 days from diagnosis, and >1 year of claims post-GGT. Inclusion/exclusion criteria followed prior work (PMID 32027353). Genes analyzed were those conferring high (>50%; BRCA1, BRCA2, CDH1, PALB2, PTEN, STK11, TP53) or moderate (20-50%; ATM, BARD1, CHEK2, NF1, RAD51C, RAD51D) BC risk. Multivariable logistic regression models of intervention use included PGV risk, race/ethnicity, age, family cancer history, local metastasis, type of insurance, geographic region and time from diagnosis to GGT. Chi-square tests were used to compare intervention uptake rates by PGV risk (Table). Results: 1,432 patients had >1 PGV in a high- (51%) or moderate-risk (49%) gene: 68% White, 32% lymph node involvement, 69% BC family history, 28% Medicare/Medicaid, mean (SD) age at testing: 51 (12) and mean (SD) days from diagnosis to GGT: 40 (26). The intervention with the highest uptake was BLM (60% in all PGV carriers). BLM, RRSO, and PARPi were significantly more frequent in high- vs. moderate-risk PGV carriers. In the multivariable model, patients with BLM uptake were younger (odds ratio, OR 0.9, 95% confidence interval, CI 0.9-1), more often had family cancer history reported (OR 2, 95% CI 1-3) and had high-risk PGV (OR 5, 95% CI 3-7). Patients with RRSO uptake had higher odds of pancreatic (OR 2, 95% CI 1-2) or ovarian (OR 2, 95% CI 1-3) cancer family history and high-risk PGV (OR 6, 95% CI 4-8) and lower odds of Medicare (OR 0.4, 95% CI 0.2-0.8). Conclusions: Overall, the uptake of interventions was higher in patients with high- compared to moderate-risk PGV. More research, however, is needed on the shared decision-making process, as uptake of BLM was relatively high in those with moderate-risk PGV, and uptake of surveillance measures was relatively low.[Table: see text]

Abstract PO1-08-11: The survival rate of hereditary breast cancer in young women of Kazakh population

Abstract Background The study focused on determining survival rates between breast cancer patients with various germinal mutations and those without mutations among Kazakh women. Methods The study included 222 female patients of Kazakh ethnic group diagnosed with stage I-IV stage breast cancer at the age up to 40 years old. DNA samples were tested by next-generation sequencing on the MiSeq Illumina platform using Trusight Cancer kit for the analysis of 94 genes and 287SNPs. Information about dates of diagnosis and death retried from cancer registry system. Survival analyses were performed and compared mutation carriers and non-carriers subgroups. The 5-year survival was calculated using the Kaplan-Meier method. Results Next generation sequencing test identified 11 various pathogenic mutations in 57(25.7%) of overall 222 patients. The 5-year survival analysis for mutation carriers were 72.1%and 82.1% for non-carriers, with no statistically significant difference(P0.232). When stratified by mutational type, the 5-year survival rates were 71.8% for BRCA1 carriers, 81.3% for BRCA2, 53.35% for TP53 and 50% for moderate risk gene PALB2 mutation. These findings suggest that mutations in certain genes may be associated with differences in survival outcomes. Conclusions In breast cancer patients of Kazakh population similar to the world prevalence and predictive value of germline mutations have been found. A subcohort of mutation carriers and non-carriers demonstrated no significant difference in 5-year survival rate which may be associated with an early onset of disease, high-risk predictor of poor prognosis. Long-term survival and detailed PFS will be published according to information of follow-up visits and the cancer register system. Citation Format: Dilyara Kaidarova, Nazgul Omarbayeva, Aliya Abdrakhmanova, Oxana Shatkovskaya, Dilyar Omarov. The survival rate of hereditary breast cancer in young women of Kazakh population [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 PO1-08-11.

Role of Breast Cancer Risk Estimation Models to Identify Women Eligible for Genetic Testing and Risk-Reducing Surgery.

Hereditary breast and ovarian cancer (HBOC) syndrome is responsible for approximately 10% of breast cancers (BCs). The HBOC gene panel includes both high-risk genes, i.e., a four times higher risk of BC (BRCA1, BRCA2, PALB2, CDH1, PTEN, STK11 and TP53), and moderate-risk genes, i.e., a two to four times higher risk of BC (BARD1, CHEK2, RAD51C, RAD51D and ATM). Pathogenic germline variants (PGVs) in HBOC genes confer an absolute risk of BC that changes according to the gene considered. We illustrate and compare different BC risk estimation models, also describing their limitations. These models allow us to identify women eligible for genetic testing and possibly to offer surgical strategies for primary prevention, i.e., risk-reducing mastectomies and salpingo-oophorectomies.

UV-radiation and MC1R germline mutations are risk factors for the development of conventional and spitzoid melanomas in children and adolescents

Genomic characterisation has led to an improved understanding of adult melanoma. However, the aetiology of melanoma in children is still unclear and identifying the correct diagnosis and therapeutic strategies remains challenging. Exome sequencing of matched tumour-normal pairs from 26 paediatric patients was performed to study the mutational spectrum of melanomas. The cohort was grouped into different categories: spitzoid melanoma (SM), conventional melanoma (CM), and other melanomas (OT). In all patients with CM (n=10) germline variants associated with melanoma were found in low to moderate melanoma risk genes: in 8 patients MC1R variants, in 2 patients variants in MITF, PTEN and BRCA2. Somatic BRAF mutations were detected in 60% of CMs, homozygous deletions of CDKN2A in 20%, TERTp mutations in 30%. In the SM group (n=12), 5 patients carried at least one MC1R variant; somatic BRAF mutations were detected in 8.3%, fusions in 25% of the cases. No SM showed a homozygous CDKN2A deletion nor a TERTp mutation. In 81.8% of the CM/SM cases the UV damage signatures SBS7 and/or DBS1 were detected. The patient with melanoma arising in giant congenital nevus (CNM) demonstrated the characteristic NRAS Q61K mutation. UV-radiation and MC1R germline variants are risk factors in the development of conventional and spitzoid paediatric melanomas. Paediatric CMs share genomic similarities with adult CMs while the SMs differ genetically from the CM group. Consistent genetic characterization of all paediatric melanomas will potentially lead to better subtype differentiation, treatment, and prevention in the future. Found in Acknowledgement.

Abstract P6-02-06: Implementation and outcomes of population-based hereditary cancer testing across a diverse multi-location breast imaging center

Abstract Introduction: Up to 10% of all breast cancers (BC) are attributed to inherited pathogenic variants (PV) in BC susceptibility genes, and genetic testing at the time of breast imaging may identify more patients who could benefit from enhanced surveillance and/or risk reduction interventions. Data are limited on the yield of PVs in the setting of a breast imaging center. Hypothesis: Hereditary cancer gene screening at the time of breast imaging may identify patients and families who could benefit from cancer risk management. Methods: This retrospective cohort study included de-identified clinical data and commercial multi-cancer panel (40 genes) test results from sequential patients undergoing breast imaging at 3 centers in Texas over a 17 month period. Patients of providers who elected not to participate were excluded from this cohort. PV prevalence was quantified and stratified based on level of risk for BC and other cancers: high-risk (relative risk >4) for BC, moderate-risk (relative risk 2-4) for BC, high-risk for other cancers, moderate-risk or undefined risk for other cancers. Results: A total of 1,943 patients undergoing breast imaging chose to have genetic testing during the study period. Median age was 66 yrs (range 18-89 yrs). Self-reported race/ethnicity: White (34.5%), Hispanic (27.7%), African American (17.9%), Asian (4.5%), Ashkenazi Jewish (0.6%), Other (3.5%) and unreported (13.0%). A personal history of breast or ovarian-related cancers was reported in 4% (n=78) and a family history of these cancers was reported in 38.9% (n=835) of patients. Among those tested, 44/1,943 (2.3%) had one or more PV in an autosomal dominant clinically actionable gene, further categorized as: high-risk BC gene (36.3%) moderate-risk BC gene (34.1%), high-risk gene for other cancers (13.6%), moderate-risk gene for other cancers (6.8%), or uncertain level of increased risk for other cancers (9.1%). A heterozygous PV in an autosomal recessive gene was present in 31/1943 (1.6%) patients. Overall, 354/1943 (18.2%) patients met current NCCN guidelines for hereditary breast and ovarian cancer (HBOC) gene testing. Only 15/44 (34.1%) patients with an autosomal dominant clinically actionable PV met current NCCN guidelines for HBOC testing. Genetic education was provided to 20/44 (45.5%) patients by lab-based genetic counselors and/or the patient’s healthcare provider. Conclusions: Offering genetic testing in a diverse breast imaging center population was associated with a significant yield (4%) of both dominant and recessive clinically actionable PVs. Of note, almost 2/3 of PVs in hereditary cancer genes were among women who did not meet NCCN testing guidelines. Identification of a PV enables risk stratification, cascade testing of family members and an opportunity to access enhanced surveillance and risk reduction interventions. Citation Format: Darlene Miltenburg, Laura Westbrook, Vivienne Souter, Melissa K. Maisenbacher, Katherine L. Howard, Youbao Sha, Maygol Yavari, Nicholas Kypraios, Sofia Hurtado, Mayra Rodas, Jeffrey N. Weitzel. Implementation and outcomes of population-based hereditary cancer testing across a diverse multi-location breast imaging center [abstract]. In: Proceedings of the 2022 San Antonio Breast Cancer Symposium; 2022 Dec 6-10; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2023;83(5 Suppl):Abstract nr P6-02-06.

Abstract P6-02-07: Uptake of Breast Cancer MRI Screening in Patients After Multiplex Gene Panel Testing

Abstract Purpose: Multiplex gene panel testing (MGPT) is used to identify individuals with an inherited susceptibility to cancer. However, little is known about the uptake of screening and surveillance among patients after MGPT and genetic counseling. The purpose of this study was to measure the uptake of guideline-concordant breast cancer screening after genetic testing and counseling. Patients and Methods: 2,000 patients who met NCCN testing guidelines or had ≥2.5% probability of a pathogenic/likely pathogenic variant (PV) were recruited at three cancer genetics clinics (University of Southern California (USC) Norris Comprehensive Cancer Center, Los Angeles County + USC Medical Center, Stanford Cancer Institute) from July 2014 through November 2016. All patients had 25- or 28-gene MGPT and results were disclosed by a genetic counselor, who provided screening recommendations to patients based on their risk. Post-test surveys were administered at three months, six months, one year, two years, and three years. Results: 1,614/2,000 (80.7%) patients were female and 1,147/1,614 (71.7%) completed at least one survey regarding MRI screening for breast cancer over the three years of longitudinal follow-up. Of these, 94/1,147 (8.2%) patients tested positive for at least one PV in a breast cancer risk gene; 58/94 (61.7%) tested positive for PVs in a high-risk breast cancer gene (BRCA1/2 (n=53), CDH1, PALB2, TP53 (n=5)), and 34/94 (36.2%) of patients tested positive for a PV in a gene characterized as moderate-risk at the time of disclosure (CHEK2, ATM, NBN). MRIs were recommended to 43/58 (74.1%) patients with a high-risk breast cancer gene PV, 20/34 (58.8%) patients with a moderate-risk gene PV, and 171/1,053 (16.2%) patients without a breast cancer risk gene PV. Multivariate logistic regression models revealed that patients with a high-risk gene PV were more likely to undergo MRI screening within 3 months of receiving genetic test results (OR=6.54 95% CI [3.09 - 14.43], p< 0.001), within one year (OR=1.34 95% CI [1.18 - 1.52], p< 0.001), two years (OR=1.43 95% CI [1.24 – 1.65], p< 0.001), and three years (OR=1.44 95% CI [1.25 – 1.66], p< 0.001) when compared to patients without a PV. Patients with a moderate-risk PV were also more likely to have undergone MRI within 3 months of receiving genetic test results (OR=2.89 95% CI [1.05 - 7.81], p=0.036), within one year (OR=1.33 95% CI [1.10 - 1.62], p=0.004), two years (OR=1.31 95% CI [1.09 - 1.59], p=0.004), and three years (OR=1.44 95% CI [1.18 - 1.76], p< 0.001), compared to those without a PV (Table 1). Conclusions: After three years of longitudinal follow up of 2000 patients in this multicenter prospective cohort study, patients with a PV in a breast cancer susceptibility gene were more likely to undergo guideline concordant breast MRI compared to patients without a PV. Carriers of high-risk breast cancer gene PVs were over six times as likely to have undergone MRI compared to patients without PVs within the first three months after genetic results disclosure and counseling. These results demonstrate the effectiveness of MGPT and genetic counseling in guiding patients with PVs in breast cancer susceptibility genes to the appropriate adoption of guideline-concordant screening. Odds ratios of MRI screening in patients carrying PV in breast cancer risk genes. Odds in relation to patients who do not carry a PV High risk gene PV: BRCA1/2, CDH1, PALB2, TP53; Moderate Risk PV: CHEK2, ATM, NBN. Percent of patients having undergone an MRI at the specified time points High risk gene PV: BRCA1/2, CDH1, PALB2, TP53; Moderate Risk PV: CHEK2, ATM, NBN. Citation Format: Leah A. Naghi, Charite N. Ricker, Duveen Sturgeon, Julie Culver, Kerry Kingham, Rachel Hodan, Nicolette M. Chun, John Kidd, Joseph Bonner, Christine Hong, Meredith Mills, Sidney S. Lindsey, Kevin McDonnell, Uri Ladabaum, James M. Ford, Stephen Grube, Allison W. Kurian, Gregory E. Idos. Uptake of Breast Cancer MRI Screening in Patients After Multiplex Gene Panel Testing [abstract]. In: Proceedings of the 2022 San Antonio Breast Cancer Symposium; 2022 Dec 6-10; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2023;83(5 Suppl):Abstract nr P6-02-07.

Abstract P5-03-03: Variant Classification Discordance: A real-world experience of genetic test results in a community-based setting

Abstract BACKGROUND Accurate interpretation of hereditary cancer germline genetic variants is critical to ensuring appropriate care. Myriad Genetics has developed tools that are instrumental in the accurate classification of variants, including a previously described history-weighting algorithm (Pheno), mutation co-occurrence statistical analysis (MCO), and in trans haplotype analysis. Differences in classification are known to occur among commercial testing laboratories, however the rate at which a single provider may observe variants with a different classification has not been reported. Here, we compared genetic test results from multiple laboratories ordered by a single surgical community-based practice with the classifications from Myriad’s testing laboratory. METHODS Variants initially reported as a “variant of uncertain significance” (VUS) on hereditary cancer test results from multiple commercial laboratories ordered by a single surgeon at a community-based, comprehensive breast center from June 2013 to May 2021 were evaluated and compared to the classifications from Myriad. In total, 212 variants were submitted for comparison. After review, 42 variants were excluded because they had not been observed previously in Myriad-tested patients. Therefore, 170 variants were eligible for comparison. Variants were classified as pathogenic/likely pathogenic, VUS, and benign/likely benign for comparison. Descriptive statistics were used for analysis. RESULTS Discordant classification was observed between Myriad and other testing laboratories for 28.2% (48/170) of the variants compared. Initially, all 170 variants were classified and reported by other testing laboratories as VUS, however, 15 variants (8.8%) were subsequently reclassified by other testing laboratories (N=13 were reclassified as benign/likely benign; N=2 were reclassified as pathogenic/likely pathogenic). Among all variants compared, 23.5% (40/170) were definitively classified by Myriad as benign/likely benign. For 90.0% (36/40) of these variants, evidence driving the classification relied upon Pheno (32 variants), MCO (4 variants), and in trans haplotype analysis (8 variants), with some variants having multiple lines of evidence. Other in-house specific rules were used for the remaining classifications (4/40;10%). Fifty-five percent (22/40) of the discordant classifications were seen in high-risk genes including APC, BRCA1/2, MLH1, MSH2, MSH6, PMS2, PALB2 and STK11, and 45% (18/40) were in moderate-risk genes including ATM, BARD1, BRIP1, CHEK2, and RAD51C. Of the 13 variants reclassified by other testing laboratories as benign/likely benign, six were classified as VUS by Myriad. Notably, two variants classified by Myriad as VUS were reclassified by other laboratories as pathogenic/likely pathogenic. CONCLUSIONS These data indicate that even in a single practice, significant discordance in variant classification exists based on the chosen laboratory. Myriad definitively classified nearly one-quarter of variants classified as VUS by other laboratories, likely due to the use of Myriad’s laboratory-developed classification tools. The degree of discordance observed here reflects the need for continuous laboratory investment in variant classification tools and evaluation of genetic variants, enabling physicians and patients to receive accurate results to facilitate appropriate medical management decisions. Citation Format: Shelly Cummings, Erin Mundt, Ann Marie Miller, TinaMarie Bauman, Thomas Slavin, Robert Maganini. Variant Classification Discordance: A real-world experience of genetic test results in a community-based setting [abstract]. In: Proceedings of the 2022 San Antonio Breast Cancer Symposium; 2022 Dec 6-10; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2023;83(5 Suppl):Abstract nr P5-03-03.

Identification of novel exonic variants contributing to hereditary breast and ovarian cancer in west Indian population

Breast and ovarian cancers are the most common cancer types in females worldwide and in India. Patients with these cancers require an early diagnosis which is essential for better prognosis, treatment and improved patient survival. Recently, the utilization of next-generation sequencing (NGS)-based screening has accelerated molecular diagnosis of various cancers. In the present study, we performed whole-exome sequencing (WES) of 30 patients who had a first or second-degree relative with breast or ovarian cancer and are tested negative for BRCA1/2 or other high and moderate-risk genes reported for HBOC. WES data from patients were analyzed and variants were called using bcftools. Functional annotation of variants and variant prioritization was performed by Exomiser. The clinical significance of variants was determined as per ACMG classification using Varsome tool. The functional analysis of genes was determined by STRING analysis and disease association was determined by open target tool. We found novel variants and gene candidates having significant association with HBOC conditions. The genes identified by exomiser (phenotype score > 0.75) are associated with various biological processes such as DNA integrity maintenance, transcription regulation, cell cycle regulation, and apoptosis. Our findings provide novel and prevalent gene variants associated with the HBOC condition in the West Indian population which could be further studied for early diagnosis and better prognosis of HBOC.

Association and performance of polygenic risk scores for breast cancer among French women presenting or not a familial predisposition to the disease

BackgroundThree partially overlapping breast cancer polygenic risk scores (PRS) comprising 77, 179 and 313 SNPs have been proposed for European-ancestry women by the Breast Cancer Association Consortium (BCAC) for improving risk prediction in the general population. However, the effect of these SNPs may vary from one country to another and within a country because of other factors. ObjectiveTo assess their associated risk and predictive performance in French women from (1) the CECILE population-based case-control study, (2) BRCA1 or BRCA2 (BRCA1/2) pathogenic variant (PV) carriers from the GEMO study, and (3) familial breast cancer cases with no BRCA1/2 PV and unrelated controls from the GENESIS study. ResultsAll three PRS were associated with breast cancer in all studies, with odds ratios per standard deviation varying from 1.7 to 2.0 in CECILE and GENESIS, and hazard ratios varying from 1.1 to 1.4 in GEMO. The predictive performance of PRS313 in CECILE was similar to that reported in BCAC but lower than that in GENESIS (area under the receiver operating characteristic curve (AUC) = 0.67 and 0.75, respectively). PRS were less performant in BRCA2 and BRCA1 PV carriers (AUC = 0.58 and 0.54 respectively). ConclusionOur results are in line with previous validation studies in the general population and in BRCA1/2 PV carriers. Additionally, we showed that PRS may be of clinical utility for women with a strong family history of breast cancer and no BRCA1/2 PV, and for those carrying a predicted PV in a moderate-risk gene like ATM, CHEK2 or PALB2.

Moderate-Risk Genes for Hereditary Ovarian Cancers Involved in the Homologous Recombination Repair Pathway.

Approximately 20% of cases of epithelial ovarian cancer (EOC) are hereditary, sharing many causative genes with breast cancer. The lower frequency of EOC compared to breast cancer makes it challenging to estimate absolute or relative risk and verify the efficacy of risk-reducing surgery in individuals harboring germline pathogenic variants (GPV) in EOC predisposition genes, particularly those with relatively low penetrance. Here, we review the molecular features and hereditary tumor risk associated with several moderate-penetrance genes in EOC that are involved in the homologous recombination repair pathway, i.e., ATM, BRIP1, NBN, PALB2, and RAD51C/D. Understanding the molecular mechanisms underlying the expression and function of these genes may elucidate trends in the development and progression of hereditary tumors, including EOC. A fundamental understanding of the genes driving EOC can help us accurately estimate the genetic risk of developing EOC and select appropriate prevention and treatment strategies for hereditary EOC. Therefore, we summarize the functions of the candidate predisposition genes for EOC and discuss the clinical management of individuals carrying GPV in these genes.

A Large Case-Control Study Performed in Spanish Population Suggests That RECQL5 Is the Only RECQ Helicase Involved in Breast Cancer Susceptibility.

Simple SummaryAround 50% of the familial breast cancer (BC) cases are estimated to be caused by variants in low-, moderate-, and high-risk susceptibility genes; however, the other half is of unknown origin. The finding of new susceptibility genes is key to improve diagnosis, take preventive measures, and identify new therapies. In this context, previous studies have discussed whether the genes encoding for the RECQ helicase family could play a role in BC susceptibility, without very conclusive results. To clarify this, in this study, we sequenced the whole coding sequence of the RECQL1, BLM, WRN, RECQL4, and RECQL5 genes in 1993 Spanish BC familial cases and compared it with controls from gnomAD. No association was found for RECQL1, BLM, WRN, and RECQL4; however, we did find an association between RECQL5 and breast cancer as a moderate-risk gene, making it a perfect candidate for further studies.Around 50% of the familial breast cancer (BC) cases are estimated to be caused by germline variants in known low-, moderate-, and high-risk susceptibility genes, while the other half is of unknown genetic origin. In the present study, we wanted to evaluate the role of the RECQ helicases, some of which have been studied in the past as candidates, with unclear results about their role in the disease. Using next-generation sequencing (NGS) technology, we analyzed the whole coding sequence of BLM, RECQL1, RECQL4, RECQL5, and WRN in almost 2000 index cases from BC Spanish families that had previously tested negative for the known BC susceptibility genes (BRCAX) and compared the results with the controls extracted from gnomAD. Our results suggest that BLM, RECQL1, RECQL4, and WRN do not play a major role in BC susceptibility. However, in the combined analysis, joining the present results with those previously reported in a series of 1334 BC Spanish patients and controls, we found a statistically significant association between Loss of Function (LoF) variants in RECQL5 and BC risk, with an OR of 2.56 (p = 0.009; 95% CI, 1.18–4.98). Our findings support our previous work and places the RECQL5 gene as a new moderate-risk BC gene.

Clinical applicability of the Polygenic Risk Score for breast cancer risk prediction in familial cases

BackgroundCommon low-risk variants are presently not used to guide clinical management of familial breast cancer (BC). We explored the additive impact of a 313-variant-based Polygenic Risk Score (PRS313) relative to...

Integrating de novo and inherited variants in 42,607 autism cases identifies mutations in new moderate-risk genes

To capture the full spectrum of genetic risk for autism, we performed a two-stage analysis of rare de novo and inherited coding variants in 42,607 autism cases, including 35,130 new cases recruited online by SPARK. We identified 60 genes with exome-wide significance (P < 2.5 × 10−6), including five new risk genes (NAV3, ITSN1, MARK2, SCAF1 and HNRNPUL2). The association of NAV3 with autism risk is primarily driven by rare inherited loss-of-function (LoF) variants, with an estimated relative risk of 4, consistent with moderate effect. Autistic individuals with LoF variants in the four moderate-risk genes (NAV3, ITSN1, SCAF1 and HNRNPUL2; n = 95) have less cognitive impairment than 129 autistic individuals with LoF variants in highly penetrant genes (CHD8, SCN2A, ADNP, FOXP1 and SHANK3) (59% vs 88%, P = 1.9 × 10−6). Power calculations suggest that much larger numbers of autism cases are needed to identify additional moderate-risk genes.

Germline Testing in a Cohort of Patients at High Risk of Hereditary Cancer Predisposition Syndromes: First Two-Year Results from South Italy.

Germline pathogenic variants (PVs) in oncogenes and tumour suppressor genes are responsible for 5 to 10% of all diagnosed cancers, which are commonly known as hereditary cancer predisposition syndromes (HCPS). A total of 104 individuals at high risk of HCPS were selected by genetic counselling for genetic testing in the past 2 years. Most of them were subjects having a personal and family history of breast cancer (BC) selected according to current established criteria. Genes analysis involved in HCPS was assessed by next-generation sequencing (NGS) using a custom cancer panel with high- and moderate-risk susceptibility genes. Germline PVs were identified in 17 of 104 individuals (16.3%) analysed, while variants of uncertain significance (VUS) were identified in 21/104 (20.2%) cases. Concerning the germline PVs distribution among the 13 BC individuals with positive findings, 8/13 (61.5%) were in the BRCA1/2 genes, whereas 5/13 (38.4%) were in other high- or moderate-risk genes including PALB2, TP53, ATM and CHEK2. NGS genetic testing showed that 6/13 (46.1%) of the PVs observed in BC patients were detected in triple-negative BC. Interestingly, the likelihood of carrying the PVs in the moderate-to-high-risk genes calculated by the cancer risk model BOADICEA was significantly higher in pathogenic variant carriers than in negative subjects. Collectively, this study shows that multigene panel testing can offer an effective diagnostic approach for patients at high risk of hereditary cancers.

Determining the genetic contribution in patients with non-syndromic ascending thoracic aortic aneurysms: Correlation with findings from computational pathology

ObjectivesThis study aims to identify the clinical utility of targeted-genetic sequencing in a cohort of patients with TAA and establish a new method for regional histological characterisation of TAA disease. MethodsFifty-four patients undergoing surgery for proximal TAA were recruited. Exclusions: connective tissue disease, bicuspid aortic valves, redo surgery. All patients underwent next generation sequencing (NGS) using a custom gene panel containing 63 genes previously associated with TAA on Illumina MiSeqor NextSeq550 platforms. Explanted TAA tissue was obtained en-bloc from 34/54 patients, and complete circumferential strips of TAA tissue processed into whole slides which were subsequently digitalised. Computational pathology methods were employed to quantify elastin, cellularity and collagen in six equally divided regions across the whole aneurysm circumference. ResultsOf 54 patients, clearly pathogenic or potentially pathogenic variants were found in 7.4%: namely LOX, PRKG1, TGFBR1 and SMAD3 genes. 55% had at least one variant of unknown significance (VUS) and seven of the VUSs were in genes with a strong disease association (category A) genes, whilst 15 were from moderate risk (category B) genes. Elastin and collagen abundance displayed high regional variation throughout the aneurysm circumference. In patients with <60% total elastin, the loss of elastin was more significant on the outer curve (38.0% vs 47.4%, p = 0.0094). The presence of VUS, higher pulse wave velocity and advancing age were predictors of elastin loss (regression analysis: p < 0.05). ConclusionsThese findings demonstrate the heterogeneity of TAA disease microstructure and the potential link between histological appearance and clinical factors, including genetic variation.

Mainstreaming germline genetic testing for patients with pancreatic cancer increases uptake.

Germline genetic testing is recommended for all patients with pancreatic cancer (PC) but uptake rates are low. We implemented a mainstreaming program in oncology clinics to increase testing for PC patients. Genetic counselors trained oncology providers to offer a standardized multigene panel and obtain informed consent using an educational video. Pre-test genetic counseling was available upon request. Otherwise, patients with identified pathogenic variants, strong family history, or questions regarding their results were referred for post-test genetic counseling. We measured rates of testing and genetic counseling visits. From September 2019 to April 2021, 245 patients with PC underwent genetic testing. This represents a 6.5-fold increase in germline testing volume (95% confidence interval 5.2–8.1) compared to previous years. At least one pathogenic or likely pathogenic variant (PV/LPV) was found in 34 (13.9%) patients, including 17 (6.9%) PV/LPVs in high or moderate risk genes and 18 (7.3%) in low risk or recessive genes. Five (2.0%) PVs had implications on treatment selection. 22 of the positive patients (64.7%) and an additional 8 PC patients (1 negative, 3 VUS, and 4 pre-test) underwent genetic counseling during the study period. Genetic counselors saw 2.0 PC patients/month prior to this project, 1.6 PC patients/month during this project, and would have seen 2.2 PC patients/month if all patients with pathogenic variants attended post-test counseling. Conclusions Mainstreaming genetic testing expands access for PC patients without overwhelming genetic counseling resources.Supplementary InformationThe online version contains supplementary material available at 10.1007/s10689-022-00300-5.

Breast Cancer Risk in Women from Ghana Carrying Rare Germline Pathogenic Mutations.

Risk estimates for women carrying germline mutations in breast cancer susceptibility genes are mainly based on studies of European ancestry women. We investigated associations between pathogenic variants (PV) in 34 genes with breast cancer risk in 871 cases [307 estrogen receptor (ER)-positive, 321 ER-negative, and 243 ER-unknown] and 1,563 controls in the Ghana Breast Health Study (GBHS), and estimated lifetime risk for carriers. We compared results with those for European, Asian, and African American ancestry women. The frequency of PV in GBHS for nine breast cancer genes was 8.38% in cases and 1.22% in controls. Relative risk estimates for overall breast cancer were: (OR, 13.70; 95% confidence interval (CI), 4.03-46.51) for BRCA1, (OR, 7.02; 95% CI, 3.17-15.54) for BRCA2, (OR, 17.25; 95% CI, 2.15-138.13) for PALB2, 5 cases and no controls carried TP53 PVs, and 2.10, (0.72-6.14) for moderate-risk genes combined (ATM, BARD1, CHEK2, RAD51C, RAD52D). These estimates were similar to those previously reported in other populations and were modified by ER status. No other genes evaluated had mutations associated at P &lt; 0.05 with overall risk. The estimated lifetime risks for mutation carriers in BRCA1, BRCA2, and PALB2 and moderate-risk genes were 18.4%, 9.8%, 22.4%, and 3.1%, respectively, markedly lower than in Western populations with higher baseline risks. We confirmed associations between PV and breast cancer risk in Ghanaian women and provide absolute risk estimates that could inform counseling in Ghana and other West African countries. These findings have direct relevance for breast cancer genetic counseling for women in West Africa.

Predictors of use of prevention strategies among women at high-risk for breast cancer.

10554 Background: Uptake of chemoprevention and prophylactic surgery among women at high risk for breast cancer is low, despite proven efficacy. We evaluated breast cancer risk factors as predictors of uptake of prevention treatment (PT) to better understand potential associations with these decisions. Methods: An IRB approved registry established in 2003 at the University of Vermont of high-risk women was used to evaluate the association between both modifiable (obesity, sedentary lifestyle and alcohol use) and non-modifiable (age, history of benign breast disease [BDD], genetic predisposition) risk factors and uptake of PT. Women were eligible for inclusion in this analysis if they had one of the following risk factors (BDD, strong family history, &gt; 20% lifetime modeled risk or genetic predisposition) and completed questionnaires regarding diet and physical activity. Alcohol use was assessed using a health questionnaire and physical activity was assessed using a 7-Day Physical Activity Recall questionnaire. We used logistic regression to estimate odds ratios (OR). Results: 504 women were included and had been followed for median of 13 years. Mean age was 44.5 years (range 19 – 75), 98% were Caucasian, and mean BMI was 26.9 (range 17-57). 78% had a family history of breast cancer, 60% had &gt;20% lifetime modeled risk, 14% had a history of benign breast disease (BBD), and 9% of women had confirmed genetic risk in high or moderate risk genes. Women may have had more than one risk factor. 55% were physically active and 55%. 4.2% were sedentary and 12.3% consumed &gt; 1 alcoholic beverage daily. 20.8% of the cohort participated in PT (8.1% took chemoprevention, 2.0% underwent prophylactic bilateral total mastectomy and 10.7% underwent risk reducing salpingo-oophorectomy). Among non-modifiable risk factors, age, genetic predisposition (ORadj 8.66, 95% CI 2.30–32.33, p &lt; 0.0001), and history of benign breast disease (ORadj 4.09, 95% CI 1.89–8.86, p &lt; 0.001) were associated with uptake of PT. Increasing age was associated with increasing uptake (ptrend was &gt; 0.0001) and highest among women aged 60-69 years (ORadj8.19, 95% CI 2.87-23.37 relative to women aged &lt; 40). Women with a strong family history were significantly less likely to take up PT (p = 0.04). BMI, physical activity status and alcohol use were not associated with uptake of PT. Conclusions: Like other studies, we found a low uptake of PT among women at high risk for developing breast cancer. We found that modifiable risk factors were not associated with uptake of PT, which might suggest that high-risk women with modifiable risk factors could be targeted for interventions designed to modify risk (i.e. chemoprevention, weight reduction, etc). Interestingly, women with a strong family history may be less likely to take up PT, and studies to further examine this relationship may identify opportunities for interventions to improve uptake.

"You Always Have It in the Back of Your Mind"-Feelings, Coping, and Support Needs of Women with Pathogenic Variants in Moderate-Risk Genes for Hereditary Breast Cancer Attending Genetic Counseling in Germany: A Qualitative Interview Study.

Hereditary breast cancer accounts for approximately 30% of newly diagnosed breast cancer (BC) cases. Pathogenic variants in moderate-risk BC genes (MBCG) differ from those in high-risk genes in terms of associated cancer risks, affected organs, and available preventive options. Little is known about how MBCG pathogenic variant carriers who have attended post-test genetic counseling perceive their situation, how they cope with their situation, and which support needs they might have. Problem-centered, guided, individual interviews were conducted with twelve women carrying pathogenic variants in MBCG. The interview analysis was based on Mayring’s qualitative content analysis. The women were between 29 and 59 years old and carried pathogenic variants in the risk genes CHEK2 (n = 8), ATM (n = 1), or PALB2 (n = 3). Women reported a wide range of feelings, both positive (relief, calmness) and negative (overwhelm, fear, grief, guilt). All women applied strategies of emotion-focused coping to deal with this lifelong situation. Appraisal and evaluation of the affected mother’s coping might influence the patient’s own behavior and coping style. These results could be used during and after post-test genetic counseling to provide more needs-oriented counseling, and to help women in adjusting to and coping with being a pathogenic variant carrier.

EP121: Integrating de novo and inherited variants in over 42,607 autism cases identifies variants in new moderate risk genes

We have created a large longitudinal research cohort, SPARK (SPARKForAutism.org) to advance research on the genetic, behavioral, and clinical features associated with ASD. SPARK represents the largest ASD cohort in the world, with over 100,000 individuals with ASD enrolled. Despite the known heritable nature of autism spectrum disorder (ASD), studies have primarily identified risk genes with de novo variants (DNVs).