Actionable Pathogenic Variants Research Articles

Abstract PO1-09-06: Patient Barriers to Genetic Counseling

Abstract Patient Barriers to Genetic Counseling Background: Access to genetic counseling is becoming more important as new targeted drugs are developed and as recommendations for testing for hereditary cancer syndromes expands. Yet, significant barriers hinder patients’ access to these services leading to a certain percentage of patients declining a genetic counseling referral (Ochoa, O’Neill). Among one of the more often cited reasons for declining genetic counseling is the cost of the consultation when it is not covered by insurance or a patient is uninsured. This potentially limits patient treatment options and can result in a missed opportunity to identify at-risk relatives. There is scant data documenting why women do not accept genetic counseling referrals and our study sought to better identify these potential barriers. In doing so we hope to enable healthcare providers and policymakers to develop strategies to ensure equitable access to these crucial services. Methods: Breast cancer patients for whom a genetic counseling referral was placed and who self-declared the inability to pay our Cancer Center’s genetic counseling fee ($126) were approached about filling out an anonymous survey regarding their reasons for declining. The survey queried, in addition to cost, other patient-related barriers to genetic testing. The survey also captured the number of first-degree relatives who might be affected by an actionable pathogenic variant. After patients were consented and completed the survey, genetic testing, paid for by the study, was offered. Results: To date, 13 patients were approached about the study and 10 patients (77%) agreed to participate, were consented and filled out surveys. Women could choose more than one reason for declining a genetic counseling referral but the most prevalent reasons cited were cost (10), worried there is nothing to be done about inherited cancers (3), concern about genetic material being taken and/or results being used against them (2), too many appointments (2). Of these 10, all (100%) elected to proceed with genetic counseling and all 10 (100%) elected to proceed with genetic testing. Two of the 10 patients (20%) tested were found to have actionable pathogenic variants (one in BRCA2 and one in CHEK2) potentially impacting 13 adult first-degree relatives. Conclusion: These preliminary findings underscore the importance of access to genetic counseling in order to facilitate appropriate genetic testing. The identification of actionable genetic mutations allows for early detection, timely interventions, and tailored management plans, ultimately leading to improved patient outcomes. By identifying cost as the most often cited reason for declining genetic counseling, healthcare providers and policymakers can develop strategies such as the implementation of financial assistance programs and universal insurance coverage for genetic counseling services in order to alleviate the financial burden and ensure equitable access to these crucial services.

Abstract 7506: Comprehensive mutational profile of true single circulating tumor cells compared with CtDNA in advanced pancreatic adenocarcinoma

Abstract Introduction: Pancreatic ductal adenocarcinoma (PDAC) is aggressive malignancy characterized by 5-year survival rate of <10%. Comprehending PDAC's mutational landscape through NGS-based assays, acquiring representative tumor tissue biopsies remains arduous. Single circulating tumor cell (sCTC) genomics could provide clinically relevant personalized diagnostics. Here we demonstrate comparative analysis of sCTCs genomics and ctDNA outcomes in paired advanced PDAC patients. Methods: Retrospectively, 25 live sCTCs and sCTC clusters were isolated from 10 advanced PDAC patients' blood using OncoRadar platform consisting glass beads conjugated with antiEPCam antibodies, tuned for releasing CTCs, without cell fixing, an assay in 96 well plate. Whole genomes from sCTCs were amplified using random degenerate primer-based PCR. Amplified genomes and paired ctDNA were subjected to CGP using clinical assay OncoIndx® to identify patient-specific genomic alterations in sCTC and paired ctDNA samples. The raw sequence alignment and variant calling was performed using iCare software®. Results: Live 25 sCTCs and 8 CTC clusters were isolated (≥2 CTCs). Mutational profiling revealed multiple pathogenic (P) and likely pathogenic (LP) variants. sCTCs exhibited at least twice as many P variants compared to paired ctDNA samples, with CHD4, FGFR2, and HNF1α being the most common. The mutational profile of sCTCs showed concordance with at least one variant in paired ctDNA, and was enriched in dysregulated cytoskeleton and cell migration machinery. Specifically, COL7A, KIF5B, and RHOA mutations were prevalent in almost all sCTCs, with exclusive mutations (KIF5B and RHOA) in some cases. KRAS P variants were exclusive to 50% of ctDNA samples, paired sCTCs exhibited NRAS P variants. RAS isoforms were observed in 70% of sCTCs. Gene amplification occurred in CCND1/2, FGFR2, and ERBB2 in 90% of sCTCs, with CCND1 amplification more prevalent in sCTC clusters. Mutations in epigenetic repressors (HDAC1, KDM2B) were ubiquitous in sCTCs, co-occurring with DDR pathway mutations (F test, P 0.003, OR 11). Loss-of-function BRCA mutations were detected in 60% of sCTCs, and were absent in paired ctDNA. Additionally, 70% of sCTCs exhibited therapy-resistant variants (NF1, STK11, ARID1A, and PIK3CA), contrasting with a 10% frequency in paired ctDNA. Conclusions: Genomic profile of sCTCs in advanced PDAC patients revealed a complex mutational landscape, providing additional clinically relevant insights that complemented ctDNA findings. sCTCs exhibited greater tumor mutational heterogeneity compared to paired ctDNA samples, and detected additional actionable pathogenic variants. Results suggest that sCTCs may offer therapeutically relevant molecular information for advanced PDAC patients for whom tissue is unavailable and ctDNA fails to provide actionable therapy options. Citation Format: Jayant Khandare, Atul Bharde, Ganesh Khutale, Saloni Andhari, Richa Deshpande, Kanchan Hariramani, Madhura Basavalingegowda, Vikas Jadhav, Mohan Uttarwar, Gowhar Shafi. Comprehensive mutational profile of true single circulating tumor cells compared with CtDNA in advanced pancreatic adenocarcinoma [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2024; Part 1 (Regular Abstracts); 2024 Apr 5-10; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2024;84(6_Suppl):Abstract nr 7506.

Recontact to return new or updated PALB2 genetic results in the clinical laboratory setting.

The purpose of this study was to recontact individuals with clinically actionable test results identified through a retrospective research study and to provide a framework for laboratories to recontact patients. Genetic testing was conducted on 2977 individuals originally referred for BRCA1 and BRCA2 hereditary breast and ovarian cancer testing that had a negative genetic test result. A gene panel was used to identify pathogenic variants in known or newly discovered genes that could explain the underlying cause of disease; however, analysis was restricted to PALB2 for the purposes of this study. A patient recontact decision tree was developed to assist in the returning of updated genetic test results to clinics and patients. Novel clinically actionable pathogenic variants were identified in the PALB2 gene in 18 participants (0.6%), the majority of whom were recontacted with their new or updated genetic test results. Eight individuals were unable to be recontacted; five individuals had already learnt about their new or updated findings from genetic testing outside the context of this study; three individuals prompted cascade testing in family members; two individuals were deceased. Novel pathogenic variants in PALB2 were identified in 18 individuals through retrospective gene panel testing. Recontacting these individuals regarding these new or updated findings had a range of outcomes. The process of conveying genomic results within this framework can be effectively accomplished while upholding patient autonomy, potentially leading to advantageous outcomes for patients and their families.

Determination of Carrier Frequency of Actionable Pathogenic Variants in Autosomal Recessive Genetic Diseases in the Turkish Cypriot Population.

Whole-exome DNA sequencing is a rich source of clinically useful information for specialists, patients, and their families, as well as elucidating the genetic basis of monogenic and complex diseases in clinical diagnosis. However, interpreting and reporting variants encompassing exome and genome sequence analysis outcome data are one of the greatest challenges of the genomic era. In this study, we aimed to investigate the frequency and allele frequency spectrum of single nucleotide variants accepted as recessive disease carrier status in Turkish Cypriot exomes. The same sequencing platform and data processing line were used for the analysis of data from 100 Turkish Cypriot whole-exome sequence analysis. Identified variants were classified according to ACMG guidelines, and pathogenic variants were confirmed in other databases such as ClinVar, HGMD, Varsome, etc. Pathogenic variants were detected in 68 genes out of 100 whole-exome sequence data. The carriage rate was the highest in the CYP21A2 gene, causing 21-hydroxylase deficiency (14.70%), 11.76% in the HBB gene causing β-thalassemia, 10.29% in the BTD gene causing biotinidase deficiency, 8.82% in the CFTR gene causing cystic fibrosis, 8.82% in the RBM8A gene causing thrombocytopenia-absent radius syndrome, which is an ultra-rare disease, and 5.88% in the GAA gene causing glycogen storage disease II. The carriage of pathogenic variants in other genes causing the disease (GJB2, PAH, GALC, CYP11B2, COL4A3, HBA1, etc.) was determined as less than 5.00%. Also, the identified variations in the mentioned gene within the examined population were reported. The most prevalent mutation in North Cyprus was a missense variant (c.1360 C>T, p.Pro454Ser) detected in the CYP21A2 gene (rs6445), and the most frequently seen variant in the HBB gene was c.93-21G>A (rs35004220). We investigated reported pathogenic variants by estimating the lower and upper limits of carrier and population frequencies for autosomal recessive diseases, for which exome sequencing may reveal additional medically relevant information. Determining the lower and upper limits of these frequencies will shed light on preventive medicine practices and governmental actions.

Male breast cancer risk associated with pathogenic variants in genes other than BRCA1/2: an Italian case-control study

BackgroundGermline pathogenic variants (PVs) in BRCA1/2 genes are associated with breast cancer (BC) risk in both women and men. Multigene panel testing is being increasingly used for BC risk assessment, allowing the identification of PVs in genes other than BRCA1/2. While data on actionable PVs in other cancer susceptibility genes are now available in female BC, reliable data are still lacking in male BC (MBC). This study aimed to provide the patterns, prevalence and risk estimates associated with PVs in non-BRCA1/2 genes for MBC in order to improve BC prevention for male patients. MethodsWe performed a large case-control study in the Italian population, including 767 BRCA1/2-negative MBCs and 1349 male controls, all screened using a custom 50 cancer gene panel. ResultsPVs in genes other than BRCA1/2 were significantly more frequent in MBCs compared with controls (4.8% vs 1.8%, respectively) and associated with a threefold increased MBC risk (OR: 3.48, 95% CI: 1.88–6.44; p < 0.0001). PV carriers were more likely to have personal (p = 0.03) and family (p = 0.02) history of cancers, not limited to BC. PALB2 PVs were associated with a sevenfold increased MBC risk (OR: 7.28, 95% CI: 1.17–45.52; p = 0.034), and ATM PVs with a fivefold increased MBC risk (OR: 4.79, 95% CI: 1.12–20.56; p = 0.035). ConclusionsThis study highlights the role of PALB2 and ATM PVs in MBC susceptibility and provides risk estimates at population level. These data may help in the implementation of multigene panel testing in MBC patients and inform gender-specific BC risk management and decision making for patients and their families.

Health Disparities in Presentation, Treatment, Genomic Testing, and Outcomes of Pancreatic Cancer in Hispanic and Non-Hispanic Patients

BackgroundThere are few conflicting results regarding the treatment and outcomes of Hispanic patients with pancreatic cancer. This study comprehensively evaluated the differences in baseline characteristics, treatments, genomic testing, and outcomes among Hispanic (H) and Non-Hispanic (NH) patients with early-stage (ES) and late-stage (LS) pancreatic cancer (PC).MethodsThis is a retrospective analysis from 2013 to 2020 of 294 patients with pancreatic ductal adenocarcinoma; data collected included patient demographics, clinical characteristics, treatment regimens, response, germline and somatic genetic testing, and survival outcomes. Excluded those with insufficient data. Univariate comparisons used parametric and nonparametric tests as appropriate to evaluate for differences between H and NH groups. Fisher’s exact tests were performed to evaluate the difference in frequency. Kaplan–Meier and Cox regression analysis assessed the survival.ResultsThe analysis included 198 patients who had a late-stage disease and 96 patients with early-stage disease at the time of diagnosis. Among the early-stage patients, the median age at diagnosis was 60.7 years in the H versus 66.7 years in the NH (p = 0.03). No other differences were observed in baseline characteristics, treatments offered, and median overall survival (NH 25 vs. H 17.7 months, p = 0.28). Performance status, negative surgical margins, and adjuvant therapy were clinically significant and univariable with improved OS (p < 0.05), regardless of ethnicity. Hispanic patients with early pancreatic cancer were noted to be at a greater risk of death with a statistically significant hazard ratio of 3.1 (p = 0.005, 95% CI, 1.39–6.90). Among the late-stage patients, Hispanic patients with ≥ 3 predisposing risk factors for pancreatic cancer were 44% vs. 25% of NH (p = 0.006). No significant differences were noted in baseline characteristic treatments, progression-free, and median overall survivals (NH 10.0 vs. 9.2 months, p = 0.4577). In the late-stage genomic testing, germline testing performed in NH 69.4% vs. H 43.9% (p = 0.003) revealed no difference among groups. For the somatic testing, the pathogenic variants with actionable mutations were 2.5% of NH and 17.6% of H patients (p = 0.03).ConclusionHispanic patients with early-stage pancreatic adenocarcinoma present at a younger age and with more risk factors in the late stage. These patients have significantly lower overall survival compared to their non-Hispanic counterparts. Hispanic patients in our study were 2.9 less likely to receive germline screening and more like to have somatic genetic actionable pathogenic variants. Overall, only a minority of all patients were enrolled in a pancreatic cancer clinical trial or offered genomic testing, highlighting a critical need and missed opportunity in advancing progress and improving outcomes for this disease, mainly in the underrepresented Hispanic population.

Disparities in late-stage pancreatic cancer: Retrospective analysis of genomic testing and outcomes between Hispanics and non-Hispanics.

663 Background: Late-Stage Pancreatic Cancer (LS-PC) represents the 7th leading cause of cancer-related deaths worldwide. Hispanic (H) ethnicity is underrepresented in genomic studies and disparities have been demonstrated in overall treatment and outcomes. Germline, somatic tissue, and somatic liquid testing are effective tools that aid in identifying targeted genetic alterations. We comprehensively evaluated the differences in genomic testing among H and Non-Hispanic (NH) patients with LS-PC. Methods: This is a retrospective analysis of LS-PC with ductal adenocarcinoma from the University of Arizona Cancer Center from 2013 to 2021. Data collected included: patient demographics, clinical characteristics, treatment regimens, germline, somatic tissue, and somatic liquid genetic testing, and outcomes. LS was defined as unresectable and/or metastatic de novo or recurrence. Univariate comparisons used parametric and nonparametric tests as appropriate to evaluate for differences between H and NH groups. Fisher's exact tests were performed to evaluate the difference in frequency. Kaplan Meier and Cox regression analysis assessed progression-free and overall survival. Results: The analysis included 198 patients who had LS-PC with 20.7% H. 64.1%, 48.9%, and 48.9% of the patients had germline, somatic tissue, and somatic liquid testing, respectively. No significant differences were noted in baseline characteristics, treatments, and outcomes [PFS (HR 1.1, 95% CI 0.7-1.6, p=0.70) / OS (HR 1.2, 95% CI 0.7-1.9, p= 0.54)]. There was no statistically significant difference in common mutations or variants among groups. Conclusions: To our knowledge, this is the first and largest study to report LS-PC genomic and therapeutic implications in H patients. H were significantly less likely to receive germline screening and more likely to have potentially actionable pathogenic variants via somatic tissue and liquid biopsy testing. This highlights the importance of genetic testing to reveal mutations that can be targeted by clinical trials for LS-PC on minorities. Although our review revealed increased germline, somatic tissue, and somatic liquid biopsy genetic testing over time, there remains a critical need towards advancing genomic sequencing efforts to improve outcomes for LS-PC in the underrepresented H population.[Table: see text]

Ethnic-specificity, evolution origin and deleteriousness of Asian BRCA variation revealed by over 7500 BRCA variants derived from Asian population.

Pathogenic variation in BRCA1 and BRCA2 (BRCA) causes high risk of breast and ovarian cancer, and BRCA variation data are important markers for BRCA-related clinical cancer applications. However, comprehensive BRCA variation data are lacking from the Asian population despite its large population size, heterogenous genetic background and diversified living environment across the Asia continent. We performed a systematic study on BRCA variation in Asian population including extensive data mining, standardization, annotation and characterization. We identified 7587 BRCA variants from 685 592 Asian individuals in 40 Asia countries and regions, including 1762 clinically actionable pathogenic variants and 4915 functionally unknown variants (https://genemutation.fhs.um.edu.mo/Asian-BRCA/). We observed the highly ethnic-specific nature of Asian BRCA variants between Asian and non-Asian populations and within Asian populations, highlighting that the current European descendant population-based BRCA data is inadequate to reflect BRCA variation in the Asian population. We also provided archeological evidence for the evolutionary origin and arising time of Asian BRCA variation. We further provided structural-based evidence for the deleterious variants enriched within the functionally unknown Asian BRCA variants. The data from our study provide a current view of BRCA variation in the Asian population and a rich resource to guide clinical applications of BRCA-related cancer for the Asian population.

Uptake in genetic testing in patients with pancreatic cancer with oncologist-driven testing protocol.

33 Background: The objective was to compare the uptake of genetic testing in patients with pancreatic adenocarcinoma (PDAC) seen at a single center (1) before the 2019 NCCN recommendation of universal screening for genetic mutations in all new PDAC diagnoses, (2) after this change in guideline, and (3) after transitioning to an oncologist-driven genetic testing protocol. Methods: A retrospective review of patient records seen for a new PDAC diagnosis at BIDMC between May 2018-May 2022 was performed. Patients were categorized into three groups by date of visit: pre-guideline change (5/2018-4/2019), post-guideline change (5/2019-12/ 2020), and after implementation of an oncologist-driven testing protocol (12/ 2020-5/2022). The primary outcome was the differences in rates of testing between each time period. Results: An increase in rates of genetic testing occurred between each successive time period. Pre-guideline change, 22% of patients had testing sent, and this increased to 32% post-guideline. With the oncologist-driven testing, this increased to 73%. There was an increase in referrals for genetic testing from the pre- to post-guideline change time periods (42% to 61%). However, in both groups, the number of patients who completed testing was approximately half of those who were referred (23% and 34%, respectively). Conclusions: Our cancer center moved to oncologist-driven testing to increase uptake in the wake of a guideline change recommending universal testing of all PDAC patients. By this protocol, germ-line testing is sent by the medical oncologist at the initial multidisciplinary clinic visit, rather than following a consultation with our genetic counseling team. With this change, there was a dramatic increase in genetic testing (32% to 73%), thereby capturing approximately 10 additional patients with actionable pathogenic variants. However, this change necessitated additional resources in the multidisciplinary clinic and time from the oncologist to consent for testing. In addition, the expertise of cancer genetics counselors was not provided to all patients. We attempted to address the latter via selective referral after positive results. Despite these trade-offs, oncologist-driven testing successfully met the goal of increasing our adherence with guideline-based genetic testing of all PDAC patients.[Table: see text]

S244 An Appraisal of the Referral, Uptake and Outcomes of Genetic Counseling and Testing in Patients With Young Onset Colorectal Cancer

Introduction: The incidence of young-onset colorectal cancer (YOCRC) defined as CRC in individuals < 50 years of age is rapidly rising. Germline genetic testing is currently recommended for all patients with CRC< 50 years. Germline pathogenic variants (PV) are detected in 16-20% of patients with YOCRC and many are diagnosed with an actionable PV not typically associated with CRC, highlighting a need for genetic counseling and multi-panel gene testing (MGPT) in these patients. We aimed to determine the rate of referral to genetic counseling, and uptake and outcomes of germline testing in YOCRC patients seen at a tertiary referral center. Methods: Patients diagnosed with YOCRC from 2010-2019 were included. Patients with appendiceal cancer, known family history of a hereditary cancer syndrome and inflammatory bowel disease were excluded. Demographic data including age, sex, race and family history of CRC were extracted from the electronic medical record (EMR).Genetic counseling referral was confirmed through an order in the EMR, clinical documentation in office visits with colorectal surgery, oncology or gastroenterology, or a completed visit with the genetic counselor. Data was analyzed using STATA, Chi-square and t-test and descriptive analyses were included. Results: 793 YOCRC patients (457 male and 336 female) were included. 56% (445) were referred for genetic counseling and 88% of referred patients completed genetic testing. 20.5% had a PV detected; 83% were in CRC associated genes and 18% were in other actionable genes (Table). Referral to genetic counseling was higher in younger patients (mean age= 40 years in those referred vs. mean age= 43 years in those not referred, p < 0.05) and those with a family history of CRC (70% of patients with family history of CRC vs. 53% of patients without family history were referred, p< 0.05) There was no significant association between referral rate and sex or race. Conclusion: Even in a large academic center, the rates of referrals for genetic counseling in patients with YOCRC were documented in only about half the patients. 1 in 5 YOCRC patients had a PV detected. If the 348 patients not referred to genetic counseling underwent testing, an additional 71 patients may be detected with a germline PV. Our findings highlight the need to raise awareness of the importance of genetic counseling and testing in YOCRC patients, and suggest that health systems should consider implementing care pathways to mitigate the potential impact of under-referral. Table 1. - Demographics, Referral to and Uptake of Genetic Counseling and Testing and Outcome of Genetic Testing Number of patients with YOCRC 793 Demographics N (%) Mean (SD) Age 41.9 (6.8) Sex Male 457 (57.6) Female 336 (42.4) Race White 684 (86.3) Black 72 (9.1) Other 37 (4.7) Family History of CRC Yes 280 (40.2) No 417 (59.8) Referral for Genetic Counseling 445 (56.1) Attended Genetic Counseling 390 (87.6) Underwent Genetic Testing 376 (96.4) • Pathogenic Variant Detected 77 (20.5) • Variant of Uncertain Significance Detected 88 (23.4) • No Variant Detected 211 (56.1) Genetic Testing Outcomes Genetic Syndrome Pathogenic Variant Number of Patients Total (%) CRC and polyposis genes N=64 (83%) Lynch syndrome N=37 (48%) MLH1 11 37 (48) MSH2 13 MSH6 8 PMS2 5 FAP N= 15 (19.4%) APC 15 15 (19.4) MYH- Associated polyposis N =10 (12.9%) MUTYH (Biallelic) 6 10 (12.9) MUTYH (Monoallelic) 4 Juvenile polyposis syndrome N = 1 (1.2%) SMAD4 1 1 (1.2) MSH3 (monoallelic) 1 1 (1.2) Other genes N=13 (17%) ATM 4 13 (17) BRCA1/2 4 BLM (monoallelic) 1 CHEK2 2 FLCN 1 CDKN2A 1

19P Deciphering the role of precision oncology in the treatment of biliary tract cancer in daily routine practice: Retrospective analysis from the cancer center Upper Austria

BackgroundThe routine therapeutic landscape of metastatic CCC is still largely based on cytotoxic chemotherapy. This standard gets increasingly challenged with the advent of next generation sequencing (NGS) in routine practice and evolving trials of targeted therapies in CCC. However the value of comprehensive genetic profiling of CCC in actual routine clinical practice remains poorly characterized.MethodsWe performed a retrospective study at the clinical cancer center of Upper Austria (Tumorzentrum Oberösterreich) in 2018-2021. Tumor samples from 56 patients with advanced CCC underwent comprehensive genetic profiling. TruSight Tumor 170 Assay (Illumina), Archer FusionPlex Panel (ArcherDX), Oncomine Focus Assay (Thermo Fisher Scientific) were used for NGS analysis. Furthermore MSI status was determined by custom made Multiplex PCR-Based Methods. Immunhistochemistry (IHC) collected data on Her2neu and PDL-1expression.ResultsA potentially actionable pathogenic variant was identified in 32 patients (57%). Pathogenic variants were ranked according ESMO Scale for Clinical Actionability of molecular Targets (ESCAT). In 15 patients with ESCAT I-III criteria a molecular informed therapy was established targeting 8 FGFR alterations, 2 MSI high status, 1 Pi3kinase mutation, 2 BRCA1/2 mutations, 2 BRAF V600Emutations. In 13 of the 15 treated patients we could observe a favorable PFS2 (targeted therapy)/PFS1 (previous standard therapy) ratio >1,3, suggesting clinical benefit. Overall survival in patients receiving molecular matched therapy showed a positive trend compared to patients remaining on standard treatment protocol.ConclusionsWe could show that comprehensive molecular characterization of advanced CCC during routine clinical care leads to favorable PFS2/PFS1 ratios and probable positive overall survival. This underscores the recent ESMO recommendations for NGS reflex testing in advanced CCC.Legal entity responsible for the studyThe authors.FundingHas not received any funding.DisclosureAll authors have declared no conflicts of interest. BackgroundThe routine therapeutic landscape of metastatic CCC is still largely based on cytotoxic chemotherapy. This standard gets increasingly challenged with the advent of next generation sequencing (NGS) in routine practice and evolving trials of targeted therapies in CCC. However the value of comprehensive genetic profiling of CCC in actual routine clinical practice remains poorly characterized. The routine therapeutic landscape of metastatic CCC is still largely based on cytotoxic chemotherapy. This standard gets increasingly challenged with the advent of next generation sequencing (NGS) in routine practice and evolving trials of targeted therapies in CCC. However the value of comprehensive genetic profiling of CCC in actual routine clinical practice remains poorly characterized. MethodsWe performed a retrospective study at the clinical cancer center of Upper Austria (Tumorzentrum Oberösterreich) in 2018-2021. Tumor samples from 56 patients with advanced CCC underwent comprehensive genetic profiling. TruSight Tumor 170 Assay (Illumina), Archer FusionPlex Panel (ArcherDX), Oncomine Focus Assay (Thermo Fisher Scientific) were used for NGS analysis. Furthermore MSI status was determined by custom made Multiplex PCR-Based Methods. Immunhistochemistry (IHC) collected data on Her2neu and PDL-1expression. We performed a retrospective study at the clinical cancer center of Upper Austria (Tumorzentrum Oberösterreich) in 2018-2021. Tumor samples from 56 patients with advanced CCC underwent comprehensive genetic profiling. TruSight Tumor 170 Assay (Illumina), Archer FusionPlex Panel (ArcherDX), Oncomine Focus Assay (Thermo Fisher Scientific) were used for NGS analysis. Furthermore MSI status was determined by custom made Multiplex PCR-Based Methods. Immunhistochemistry (IHC) collected data on Her2neu and PDL-1expression. ResultsA potentially actionable pathogenic variant was identified in 32 patients (57%). Pathogenic variants were ranked according ESMO Scale for Clinical Actionability of molecular Targets (ESCAT). In 15 patients with ESCAT I-III criteria a molecular informed therapy was established targeting 8 FGFR alterations, 2 MSI high status, 1 Pi3kinase mutation, 2 BRCA1/2 mutations, 2 BRAF V600Emutations. In 13 of the 15 treated patients we could observe a favorable PFS2 (targeted therapy)/PFS1 (previous standard therapy) ratio >1,3, suggesting clinical benefit. Overall survival in patients receiving molecular matched therapy showed a positive trend compared to patients remaining on standard treatment protocol. A potentially actionable pathogenic variant was identified in 32 patients (57%). Pathogenic variants were ranked according ESMO Scale for Clinical Actionability of molecular Targets (ESCAT). In 15 patients with ESCAT I-III criteria a molecular informed therapy was established targeting 8 FGFR alterations, 2 MSI high status, 1 Pi3kinase mutation, 2 BRCA1/2 mutations, 2 BRAF V600Emutations. In 13 of the 15 treated patients we could observe a favorable PFS2 (targeted therapy)/PFS1 (previous standard therapy) ratio >1,3, suggesting clinical benefit. Overall survival in patients receiving molecular matched therapy showed a positive trend compared to patients remaining on standard treatment protocol. ConclusionsWe could show that comprehensive molecular characterization of advanced CCC during routine clinical care leads to favorable PFS2/PFS1 ratios and probable positive overall survival. This underscores the recent ESMO recommendations for NGS reflex testing in advanced CCC. We could show that comprehensive molecular characterization of advanced CCC during routine clinical care leads to favorable PFS2/PFS1 ratios and probable positive overall survival. This underscores the recent ESMO recommendations for NGS reflex testing in advanced CCC.

Clinical and genetic findings of incidental serous tubal intraepithelial carcinoma (145)

<b>Objectives:</b> Serous tubal intraepithelial carcinoma (STIC) is thought to represent the precursor lesion to the high-grade serous fallopian tube or ovarian carcinoma. STIC lesions are found 0.6-6% of the time in women undergoing risk-reducing salpingo-oophorectomy (RRSO) in the setting of a known hereditary predisposition. = However, due to the rarity of incidentally identified STIC lesions, there is limited data to guide management. NCCN guidelines suggest consideration of surgical staging and referral for genetic evaluation. In the absence of a known pathogenic variant as the indication for surgery, there is no data on rates of genetic testing or long-term outcomes. The objective of this study was to describe both clinical outcomes as well as genetic information collected for patients with incidentally noted STIC lesions. <b>Methods:</b> Following IRB approval, pathology records were used to identify all patients diagnosed with a STIC lesion on final pathology from 2007-2021 at a single institution. STIC lesions were characterized utilizing immunohistochemistry. Only patients with STIC lesions undergoing surgery for benign indications were included. Demographic, clinical-pathologic, and genetic data were collected. <b>Results:</b> A total of 16 patients were identified. The median age at diagnosis was 65.5 years (39-80). Fifteen patients (93.8%) had unilateral STIC lesions with one patient having bilateral STIC lesions. Most lesions were positive for p53 (94.1%) and had increased Ki67 proliferation, defined as >10% (94.1%). Two patients (12.5%) had a personal history of malignancy prior to their STIC lesion diagnosis. Patients had a wide variety of presentations, including pelvic mass (37.5%), prolapse (31.3%), abnormal uterine bleeding (25%), and pelvic pain (6.3%). Nine patients had additional surgical procedures performed (56.3%), and no cancer diagnosis was identified for any patient. Additional procedures included contralateral salpingo-oophorectomy, omentectomy, pelvic and paraaortic lymph node dissection, and peritoneal biopsies. No patients received adjuvant treatment. Eleven patients were offered a genetic counseling referral (68.8%), with seven patients completing a counseling appointment (63.6%). Five of the seven patients who completed their visit met criteria for testing based on additional personal and/or family history (71.4%), with one patient testing positive for a PALB2 pathogenic variant (20% of tested patients). Three patients, none of whom underwent genetic testing, were subsequently diagnosed with breast cancer during the follow-up period. <b>Conclusions:</b> Incidental STIC lesions are rare. In this cohort, there were no ovarian, fallopian tube, or primary peritoneal cancer diagnoses after additional surgical staging or during follow-up. More data is needed to guide treatment recommendations. However, compared to STIC lesions in patients undergoing RRSO for a known predisposition, it is not clear whether additional surgical procedures are warranted in patients with incidentally noted STIC lesions. Our data support NCCN recommendations for referral for genetic evaluation as 71% qualified for testing. One patient (20% of those who qualified for testing) had a clinically actionable pathogenic variant. Notably, three patients later developed breast cancer; however, without genetic testing, we cannot determine if there may be a genetic link. Further studies of these lesions are warranted.

Frequency of actionable Exomic secondary findings in 160 Colombian patients: Impact in the healthcare system

IntroductionBy 2021, the American College of Medical Genetics and Genomics (ACMG) published the last version of their secondary findings (SF) reporting recommendations for cases in which a person receives a genetic test. ObjectiveTo determine in a sample of the Colombian population the prevalence of SF for the 59 genes on the ACMG SF v2.0 list associated with 27 genetic diseases. Materials and methodsAn analytical cross-sectional study was developed by examining the sequences of 160 exomes. Based on the ACMG guidelines, a variant classification algorithm was designed to filter and select reportable SF. ResultsEleven pathogenic variants were identified in 13/160 (8.13%) patients in genes APOB, BRCA2, CACNA1S, COL3A1, LDLR, MYBPC3, PCSK9, PKP2, PMS2 and RYR2. No association was found between the sociodemographic variables and the SF to report (P > 0,05). ConclusionWe reported the first approach of actionable pathogenic variants spectrum in the Colombian population. Given the frequency found in this study and the clinical impact of genomic variants on health, it is essential to actively search for SF having the opportunity to receive genetic counselling, prevention and clinical management.

Abstract CT225: A randomized trial of integrated genomics, organoids and avatar mouse models for personalized treatment of pancreatic cancer

Abstract Background: Pancreatic adenocarcinoma (PDAC) remains one of the most lethal cancers. This study aimed to compare the efficacy of a comprehensive approach to precision medicine, including genomic and bio-informatic analysis of tumor biopsies, as well as modeling of the disease in Avatar Mouse Models and Patient Derived Organoids (PDO) to conventional treatment. Method: We conducted a prospective, randomized, multicenter clinical trial in which, patients with newly diagnosed advanced PDAC were randomized to either a personalized medicine approach or to a conventional treatment in a 2:1 ratio. Patients randomized to the conventional arm were treated with standard of care therapy. Patients randomized to the experimental arm underwent a tumor biopsy to determine their genetic status through whole exome sequencing (WES) and to generate an Avatar and PDO model. Personalized treatment was based on the targets identified by genetic and bioinformatic analysis, as well as by phenotypic screening of 40 anticancer agents in the patient derived models after discussion in a molecular committee. Results: A total 129 PDAC patients with a median age of 62 years old, were enrolled and 122 were included in the analysis. Seventy-eight patients were randomized to the experimental arm and 44 to the conventional one. WES has been performed in 66 patients and in 56 of them potentially actionable pathogenic variants were detected. Experimental models were successfully generated in 28 patients and screened. However, only 4 patients were treated with selected agents. The remaining 52 patients could not be treated according to the results of the study: 73% of them because of premature clinical deterioration, 8% because of delaying in obtaining results due to technical matters and 19% because the recommended treatment was not felt to have adequate data support by the molecular committee. The median overall survival (from the date of randomization until the date of death) was 8,7 months for patients from conventional arm and 8,8 months for patients from experimental arm (not statistically different). The median overall survival (from the date of randomization until the date of death) for the four patients treated according to the results of the study was 19,5 months. Conclusions: In our study, a full personalized medicine approach did not improve the overall survival of patients with PDAC. Failure to obtain genomic data and models, lack of actionable genetic alterations and targeted agents in living models, and the rapid course of PDAC limited the implementation of precision medicine treatments. Outcome was improved in the 6% of patients in whom a personalized treatment was administered. Citation Format: Manuel Hidalgo, Francesca Sarno, Laura Medina, Roberto Pazo, Ignacio Juez, Rocío García-Carbonero, Carmen Guillén-Ponce, Jaime Feliú, Carolina Alonso, Jair Tenorio_Castano, Pablo Lapunzina. A randomized trial of integrated genomics, organoids and avatar mouse models for personalized treatment of pancreatic cancer [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 CT225.

Breast cancer risk stratification in women of screening age: Incremental effects of adding mammographic density, polygenic risk, and a gene panel

There is great promise in breast cancer risk stratification to target screening and prevention. It is unclear whether adding gene panels to other risk tools improves breast cancer risk stratification and adds discriminatory benefit on a population basis. In total, 10,025 of 57,902 women aged 46 to 73 years in the Predicting Risk of Cancer at Screening study provided DNA samples. A case-control study was used to evaluate breast cancer risk assessment using polygenic risk scores (PRSs), cancer gene panel (n= 33), mammographic density (density residual [DR]), and risk factorscollected using a self-completed 2-page questionnaire (Tyrer-Cuzick [TC] model version 8). In total, 525 cases and 1410 controls underwent gene panel testing and PRS calculation (18, 143, and/or 313 single-nucleotide polymorphisms [SNPs]). Actionable pathogenic variants (PGVs) in BRCA1/2 were found in 1.7% of cases and 0.55% of controls, and overall PGVs were found in 6.1% of cases and 1.3% of controls. A combined assessment of TC8-DR-SNP313 and gene panel provided the best risk stratification with 26.1% of controls and 9.7% of cases identified at <1.4% 10-year risk and 9.01% of controls and 23.3% of cases at ≥8% 10-year risk. Because actionable PGVs were uncommon, discrimination was identical with/without gene panel (with/without: area under the curve= 0.67, 95% CI= 0.64-0.70). Only 7 of 17 PGVs in cases resulted in actionable risk category change. Extended case (n= 644)-control (n= 1779) series with TC8-DR-SNP143 identified 18.9% of controls and only 6.4% of stage 2+ cases at <1.4% 10-year risk and 20.7% of controls and 47.9% of stage 2+ cases at ≥5% 10-year risk. Further studies and economic analysis will determine whether adding panels to PRS is a cost-effective strategy for risk stratification.

Unselected Women's Experiences of Receiving Genetic Research Results for Hereditary Breast and Ovarian Cancer: A Qualitative Study.

Background: Although there is growing consensus that clinically actionable genetic research results should be returned to participants, research on recipients' experiences and best practices for return of research results is scarce. Objective: This study explored how women in a population-based study (lifepool) experience receiving research results about actionable pathogenic variants (PVs) for hereditary breast and ovarian cancer (HBOC) using a two-step notification process with telephone genetic counseling (TGC) support. Methods: We conducted qualitative interviews with lifepool participants with an HBOC PV. We used team-based codebook thematic analysis to develop findings. Findings: Thirty-one women participated (mean age 62.5 years) on average 2.3 years (range 0.3-5.1 years) after result notification. Notification was unexpected but not traumatic and TGC support helped meet women's information and support needs. Notification with referral to a local genetics service empowered women to make informed decisions about personal and familial health. Adaptation to results over time was facilitated by three main processes: seeking information, family communication, and undertaking risk management and/or risk-reducing strategies. Conclusion: Using a two-step notification process to return clinically actionable HBOC PVs from research was well received by women in a population-based study of breast and ovarian cancer susceptibility. Having genetic counseling support with referral to local genetics services in the notification process facilitated women's feelings of empowerment and adaptation to their genetic information over time. These findings build the basis for future methods for the return of actionable genetic research results and population screening.

Homologous Recombination Deficiency: Cancer Predispositions and Treatment Implications.

Homologous recombination (HR) is a highly accurate DNA repair mechanism. Several HR genes are established cancer susceptibility genes with clinically actionable pathogenic variants (PVs). Classically, BRCA1 and BRCA2 germline PVs are associated with significant breast and ovarian cancer risks. Patients with BRCA1 or BRCA2 PVs display worse clinical outcomes but respond better to platinum-based chemotherapies and poly-ADP ribose polymerase inhibitors, a trait termed "BRCAness." With the advent of whole-exome sequencing and multigene panels, PVs in other HR genes are increasingly identified among familial cancers. As such, several genes such as PALB2 are reclassified as cancer predisposition genes. But evidence for cancer risks remains unclear for many others. In this review, we will discuss cancer predispositions and treatment implications beyond BRCA1 and BRCA2, with a focus on 24 HR genes: 53BP1, ATM, ATR, ATRIP, BARD1, BLM, BRIP1, DMC1, MRE11A, NBN, PALB2, RAD50, RAD51, RAD51B, RAD51C, RAD51D, RIF1, RMI1, RMI2, RPA1, TOP3A, TOPBP1, XRCC2, and XRCC3. IMPLICATIONS FOR PRACTICE: This review provides a comprehensive reference for readers to quickly identify potential cancer predisposing homologous recombination (HR) genes, and to generate research questions for genes with inconclusive evidence. This review also evaluates the "BRCAness" of each HR member. Clinicians can refer to these discussions to identify potential candidates for future clinical trials.

High likelihood of actionable pathogenic variant detection in breast cancer genes in women with very early onset breast cancer

BackgroundWhile the likelihood of identifying constitutional breast cancer-associated BRCA1, BRCA2 and TP53 pathogenic variants (PVs) increases with earlier diagnosis age, little is known about the correlation with age at diagnosis...

Stakeholder views on opportunistic genomic screening in the Netherlands: a qualitative study.

Genome sequencing can be used to actively search for genetic variants unrelated to the initial clinical question. While such 'opportunistic genomic screening' (OGS) has been proposed in the USA, a European discussion on the ethics of OGS is only starting. Should testing for selected 'secondary findings' be offered to patients who need genetic sequencing? Using focus groups and interviews, we explored views on OGS in adults and minors from three perspectives: policy experts (n = 9), health professionals (n = 8) and patient representatives (n = 7). A thematic approach was used to analyze the data. There was consensus that OGS should be evaluated in terms of the classical 'screening' framework, rather than as a form of 'good patient care'. Accordingly, stakeholders agreed that professionals do not have a 'fiduciary duty' to look for secondary findings. Adding screening to clinical care was only conceivable with the patient's informed consent. In general, stakeholders were reluctant towards OGS. Arguments for regarding OGS being premature included lack of evidence regarding its clinical utility, also in view of uncertainties regarding general population penetrance, and concerns about both its psychosocial impact and respect for autonomy. All groups agreed that OGS means unequal access, which was seen as problematic. Yet, despite their concerns, stakeholders felt that offering screening for certain actionable pathogenic variants with known high penetrance could potentially be valuable in certain contexts for both adults and minors. Pharmacogenetic variants were regarded as a category by itself, for which OGS could potentially be beneficial.

Abstract PS8-14: Pathogenic variants in hereditary cancer syndrome genes are prevalent among breast cancer patients not meeting various ex-U.S. genetic testing guidelines

Abstract Background:Therapeutic and risk management options have expanded for patients harboring pathogenic variants (PVs) in cancer predisposition genes. Historically, testing costs and clinical implementation challenges led to restrictive testing guidelines in many countries. Increasing evidence demonstrates that narrow criteria will miss patients with potentially actionable PVs and broader testing is a cost-effective way to identify patients (and their family members) with PVs. Here we assess the efficacy of multiple international testing guidelines in identifying breast cancer patients with clinically actionable PVs. Methods:We reanalyzed a prospective cohort of breast cancer (BC) patients referred by their providers for multigene germline genetic testing (PMID: 30526229) 50% of which met U.S. testing criteria, by design. The is a cohort of U.S.-based patients, primarily Caucasian of Northern European ancestry. We applied testing guidelines from Australia, U.K. and 2 Canadian provinces (Ontario, British Columbia) to this cohort to determine their efficacy in selecting patients with PVs. These countries were chosen because of their single-payer healthcare model and their similar ethnic distribution to the U.S. Analysis focused on yield of PVs in high risk (&amp;gt;4x risk compared to general population) breast/ovarian (BC/OV) cancer genes. Results:Table 1 displays the distribution of in criteria (IC) vs. out of criteria (OOC) patients by country/testing criteria. Over 75% of patients in each country/province analyzed were OOC. Rates of PVs were similar between IC and OOC patients across countries. Existing Canadian, Australian and U.K. criteria missed up to 30% of patients with high risk PVs (Table 1). The majority (&amp;gt;80%) of PVs in OOC patients were in genes with published management guidelines. Conclusions:In our cohort, select ex-U.S. testing criteria identified &amp;lt;30% of patients with PVs, while almost half of OOC patients harbored clinically relevant, potentially actionable mutations. These data suggest expanding certain international testing criteria would allow better identification and improved management for many patients diagnosed with breast cancer across the globe, and their families via cascade testing. This study also suggests additional research is needed to evaluate the efficacy of additional provincial and international criteria, including cost-effectiveness analyses, to inform future guideline updates. Table 1. Findings in IC vs. OOC patientsOverallIn criteria Out of criteriaCountry/providenceGuidelineTotal n of cohortIC (% of total cohort)OOC (% of total cohort)Total PV IC (% of IC cohort)Total PV OOC (% of OOC cohort)High risk^ PVs (% of total PVs)High risk^ PVs (% of total PVs)U.S.NCCN953473 (49.6)480 (50.4)43 (9.1)40 (8.3)22 (26.5)8 (9.6)OntarioMOHLTC953210 (22.0)743 (78.0)18 (8.6)65 (8.7)5 (6.0)25 (30.1)B.C.BCHCP953203 (21.3)750 (78.7)24 (11.8)59 (7.9)9 (10.8)19 (22.9)AustraliaeviQ953180 (18.9)773 (81.1)19 (10.6)64 (8.3)12 (14.5)18 (21.7)U.K.NICE*826**127 (14.7)736 (85.3)11 (8.7)64 (8.7)6 (7.2)22 (26.5)US, United States; B.C., British Columbia; UK, United KingdomNCCN, National Comprehensive Cancer Network v. 2017MOHLTC, Ministry of Health and Long Term Care BCHCP, BC Provincial Health Services Authority Hereditary Cancer Program NICE, National Institute for Health Care Excellence*testing eligibility requires &amp;gt;10% BRCA mutation detection rate, typically assessed by BOADICEA model in the UK but for this cohort risk estimates were only available via BRCAPro ** BRCAPro scores were not available for the full cohort ^Includes BRCA1, BRCA2, PALB2, TP53, RAD51C, RAD51D, MSH6 Citation Format: Sarah M Nielsen, Peter Beitsch, Pat Whitworth, Emily Decker, Natalie Rickers, Hana Sroka, Alekhya Narravula, Ed D Esplin, Robert L. Nussbaum. Pathogenic variants in hereditary cancer syndrome genes are prevalent among breast cancer patients not meeting various ex-U.S. genetic testing guidelines [abstract]. In: Proceedings of the 2020 San Antonio Breast Cancer Virtual Symposium; 2020 Dec 8-11; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2021;81(4 Suppl):Abstract nr PS8-14.