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Purpose Herein, we report the frequency and distribution of germline pathogenic variants (PVs) among females with breast cancer (BC) and at least one other non-BC who underwent multi-gene panel testing (MGPT). Among females with PVs diagnosed first with BC or ovarian cancer (OC), we sought to enumerate the frequency of subsequent PV-associated cancers. Methods Females with BC and cancer of ≥ 1 other site (multiple primary cancers, MPC) who underwent MGPT through Ambry Genetics from March 2012 to December 2016 were included if they had testing of at least 21 genes of interest (ATM, BARD1, BRCA1, BRCA2, BRIP1, CDH1, CHEK2, EPCAM, MLH1, MSH2, MSH6, MUTYH, NBN, NF1, PALB2, PMS2, PTEN, RAD51C, RAD51D, STK11, and TP53). Phenotypic data were abstracted from test requisition forms and clinical notes. Results Of 6,617 evaluable patients, most were White (70.8%) and median age at first cancer, second cancer, and MGPT was 49 (interquartile range [IQR]: 18), 59 (IQR: 16), and 63 (IQR: 16) years, respectively. PVs were found among 14.1% (932/6617) of the overall cohort and in 16.4% (440/2687) of females who were diagnosed first with BC. Among those, 55.2% (243/440) had an actionable PV associated with a subsequent cancer diagnosis including 150 OCs. Of the 2443 females with breast and ovarian cancer, few (n = 97, 9.5%) were diagnosed first with OC, limiting our analysis. Conclusions Females with MPC, including BC, have a high frequency of germline PVs (14.1%). These data delineate the opportunities for intercepting subsequent cancers associated with genetic risk among females diagnosed first with BC.

PURPOSE With the availability of multigene panel testing (MGPT) for hereditary cancer risk assessment, clinicians need to assess the likelihood of pathogenic germline variants (PGVs) across numerous genes in parallel. This study's aim was to develop and validate a clinical prediction model (PREMMplus) for MGPT risk assessment. MATERIALS AND METHODS PREMMplus was developed in a single-institution cohort of 7,280 individuals who had undergone MGPT. Logistic regression models with Least Absolute Shrinkage and Selection Operator regularization were used to examine candidate predictors (age, sex, ethnicity, and personal/family history of 18 cancers/neoplasms) to estimate one's likelihood of carrying PGVs in 19 genes (broadly categorized by phenotypic overlap and/or relative penetrance: 11 category A [ APC, BRCA1/ 2, CDH1, EPCAM, MLH1, MSH2, MSH6, biallelic MUTYH, PMS2, and TP53] and eight category B genes [ ATM, BRIP1, CDKN2A, CHEK2, PALB2, PTEN, RAD51C, and RAD51D]). Model performance was validated in nonoverlapping data sets of 8,691 and 14,849 individuals with prior MGPT ascertained from clinic- and laboratory-based settings, respectively. RESULTS PREMMplus (score ≥ 2.5%) had 93.9%, 91.7%, and 89.3% sensitivity and 98.3%, 97.5%, and 97.8% negative-predictive value (NPV) for identifying category A gene PGV carriers in the development and validation cohorts, respectively. PREMMplus assessment (score ≥ 2.5%) had 89.9%, 85.6%, and 84.2% sensitivity and 95.0%, 93.5%, and 93.5% NPV, respectively, for identifying category A/B gene PGV carriers. Decision curve analyses support MGPT for individuals predicted to have ≥ 2.5% probability of a PGV. CONCLUSION PREMMplus accurately identifies individuals with PGVs in a diverse spectrum of cancer susceptibility genes with high sensitivity/NPV. Individuals with PREMMplus scores ≥ 2.5% should be considered for MGPT.

Background: Among females with breast cancer, multiple primary cancers (MPCs) are a hallmark of cancer predisposition syndromes. Herein we report the frequency of germline pathogenic/likely pathogenic variants (PVs) among females with breast cancer (BC) and primary cancer of >1 other site who underwent multi-gene panel testing (MGPT) through a single lab. Among females first diagnosed with BC who had a PV in an actionable gene, we quantified the frequency of subsequent breast and non-breast cancers. Among those who later developed a second BC, ovarian, endometrial or colon cancer, we determined the percentage of patients with MPCs who would have been identified as high-risk if all women had had MGPT after a first diagnosis of breast cancer. Methods: Females with breast cancer and MPCs who underwent germline genetic testing with Ambry Genetics from 3/2012 to 12/2016 were included in our cohort. Eligible individuals had multigene panel testing, which included 21 genes at minimum (ATM, BARD1, BRCA1, BRCA2, BRIP1, CDH1, CHEK2, EPCAM, MLH1, MSH2, MSH6, MUTYH, NBN, NF1, PALB2, PMS2, PTEN, RAD51C, RAD51D, STK11, and TP53). Clinical factors including age at diagnosis, age at testing and cancer type were obtained from test requisition forms and clinical notes. Patients with >1 PV were excluded from the analysis. Results: Of the 6617 patients with MPCs including BC tested for the 21 genes in the analytic cohort, most were white (70.8%), with median age at testing 63 years (IQR: 16). The median ages of first and second cancer diagnosis were 49 (IQR: 18) and 59 (IQR: 16) years, respectively. Considering the diagnostic order of BC, PV prevalence was 16.5% (444/2687) with BC as the 1st cancer diagnosis, 11.2% (296/2641) with BC as the 2nd cancer diagnosis, 15.2% (49/323) as 3rd or later diagnosis (p Citation Format: Brittany L. Bychkovsky, Min-Tzu Lo, Amal Yussuf, Carrie Horton, Parichehr Hemyari, Holly LaDuca, Judy E. Garber, Huma Q. Rana. Pathogenic variants among female breast cancer patients with a subsequent cancer demonstrate preventable cancer burden [abstract]. In: Proceedings of the 2021 San Antonio Breast Cancer Symposium; 2021 Dec 7-10; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2022;82(4 Suppl):Abstract nr P2-09-03.

Background: The National Comprehensive Cancer Network guideline on Genetic/Familial High Risk: Breast, Ovarian and Pancreatic Cancer (NCCN) recommends offering increased screening and risk-reduction options to women with a pathogenic/likely pathogenic variant (PV/LPV) in 8 clinically-actionable hereditary breast and ovarian cancer (HBOC) genes: ATM, BRCA1, BRCA2, CDH1, CHEK2, PALB2, PTEN, and TP53. These options range from biannual clinical breast exams and annual breast MRI screening to risk-reducing mastectomy (RRM) and salpingo-oophorectomy (RRSO). Yet health insurance company policies addressing the medical necessity of genetic testing for these genes vary widely. While some payers have adopted the NCCN testing criteria verbatim, others have made specific changes or have developed their own criteria. We sought to quantify the potential impact of this variability on access to enhanced medical management for carriers of PV/LPV in these 8 HBOC genes in a large cohort of patients undergoing genetic testing at a single commercial laboratory. Methods: We reviewed clinical and family histories for patients undergoing multigene panel testing that included testing for the 8 genes of interest and identified 107,344 patients who met NCCN testing criteria (excluding prostate cancer criteria, which were not assessed in this study) for HBOC (v.2.2021). We then compared the histories of these patients to testing criteria for 3 different payer groups: Aetna, Blue Shield of California/Federal Blue Cross-Blue Shield, and eviCore (used by over 30 payers including AmeriHealth, Highmark and Horizon). These are the largest payer groups in our cohort and together represent 19% of patients tested. For each patient we determined whether they met testing criteria for the 3 payer groups. For individuals found to have a PV/LPV we determined the potential missed management opportunities for those who would not have been tested under each payer’s criteria. In addition, we sought to estimate the maximal impact of this missed management for patients with BRCA PV/LPV (not accounting for patient age or medical history). Results: Among patients meeting NCCN testing criteria for HBOC, 10,10,477 (9.8%) were found to have PVs/LPVs in one of the 8 genes. Under the three payer policies 2% to 10.3% of all patients, and up to 4.0% (n=423) of PV/LPV carriers, would not have been eligible for genetic testing. Based on NCCN management guidelines, up to 423 eligible patients would not have been offered annual breast MRI, 208 patients would not have been offered RRM, and 163 eligible patients would not have been offered RRSO. This lack of testing access due to misaligned medical policies also represents missed opportunities for offering potentially life-saving screening and risk reduction measures to these patients as well. Assuming lifetime cancer risks of 85% for breast cancer and 40% for ovarian cancer, and risk-reduction of 95% with RRM and 80% with RRSO. Had all policies matched NCCN testing criteria, up to 132 breast cancers could have potentially been detected earlier or prevented and 52 ovarian cancers could potentially have been prevented in our cohort. Conclusions: In addition to complicating clinical practice, varying testing guidelines have broader implications. Our data show that a significant number of mutation carriers are being missed by payer policies that deviate from NCCN testing criteria. In turn, this represents missed opportunities to offer proactive screening and risk-reduction options that could potentially save lives for those at risk for hereditary cancer. Based on findings from other studies, these actions would likely reduce health insurer costs as well. Citation Format: Robert T Pilarski, Stephanie Noble, Lily Hoang, Randy Hew, Stephanie Gandomi, Holly LaDuca, Jill Dolinsky. Inequitable access to genetic testing leads to missed screening and prevention opportunities for individuals at risk for hereditary breast and ovarian cancer [abstract]. In: Proceedings of the 2021 San Antonio Breast Cancer Symposium; 2021 Dec 7-10; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2022;82(4 Suppl):Abstract nr P2-09-19.

PURPOSE To determine the contribution of germline pathogenic variants (PVs) in hereditary cancer testing panel genes to invasive lobular carcinoma (ILC) of the breast. MATERIALS AND METHODS The study included 2,999 women with ILC from a population-based cohort and 3,796 women with ILC undergoing clinical multigene panel testing (clinical cohort). Frequencies of germline PVs in breast cancer predisposition genes ( ATM, BARD1, BRCA1, BRCA2, BRIP1, CDH1, CHEK2, PALB2, PTEN, RAD51C, RAD51D, and TP53) were compared between women with ILC and unaffected female controls and between women with ILC and infiltrating ductal carcinoma (IDC). RESULTS The frequency of PVs in breast cancer predisposition genes among women with ILC was 6.5% in the clinical cohort and 5.2% in the population-based cohort. In case-control analysis, CDH1 and BRCA2 PVs were associated with high risks of ILC (odds ratio [OR] > 4) and CHEK2, ATM, and PALB2 PVs were associated with moderate (OR = 2-4) risks. BRCA1 PVs and CHEK2 p.Ile157Thr were not associated with clinically relevant risks (OR < 2) of ILC. Compared with IDC, CDH1 PVs were > 10-fold enriched, whereas PVs in BRCA1 were substantially reduced in ILC. CONCLUSION The study establishes that PVs in ATM, BRCA2, CDH1, CHEK2, and PALB2 are associated with an increased risk of ILC, whereas BRCA1 PVs are not. The similar overall PV frequencies for ILC and IDC suggest that cancer histology should not influence the decision to proceed with genetic testing. Similar to IDC, multigene panel testing may be appropriate for women with ILC, but CDH1 should be specifically discussed because of low prevalence and gastric cancer risk.

Multiple primary cancers (MPCs) are a hallmark of cancer predisposition syndromes. Here the frequency of germline pathogenic variants (PVs) among patients with MPCs is reported.Patients with MPCs who underwent multigene panel testing from March 2012 to December 2016 were studied. Eligible patients had an analysis of 21 genes: ATM, BARD1, BRCA1, BRCA2, BRIP1, CDH1, CHEK2, EPCAM, MLH1, MSH2, MSH6, MUTYH, NBN, NF1, PALB2, PMS2, PTEN, RAD51C, RAD51D, STK11, and TP53. The frequencies of PVs by sex, number of cancers, and age at diagnosis were compared with 2-sided χAmong the 9714 patients analyzed, most were female (91.1%) and White (71.0%); the median age at testing was 63 years, and the median ages at first and second cancer diagnoses were 49 and 58 years, respectively. Overall, 1320 (13.6%) had PVs. The prevalence of PVs increased with the number of primary cancers (PCs): 13.1% with 2 PCs, 15.9% with 3 PCs, and 18.0% with ≥4 PCs (P = .00056). Differences in the prevalence of PVs by age at diagnosis were significant: 14.7% with 2 PCs at an age50 years, 15.8% with 1 PC at an age50 years, and 12.0% with all PCs at an age ≥ 50 years (P = 2.07E-05). PVs by the age at second cancer diagnosis were also significant: 14.7% at an age50 years, 13.9% at an age of 50 to 69 years, and 11.4% at an age ≥ 70 years (P for trend = .005).Among patients with MPCs, there is a high frequency of germline PVs, with a higher frequency found among patients with a higher number of PCs. These findings suggest that genetic testing should be considered even among patients who are older at the diagnosis of an additional primary malignancy.

PURPOSE The prevalence of germline pathogenic variants (PVs) in established breast cancer predisposition genes in women in the general population over age 65 years is not well-defined. However, testing guidelines suggest that women diagnosed with breast cancer over age 65 years might have < 2.5% likelihood of a PV in a high-penetrance gene. This study aimed to establish the frequency of PVs and remaining risks of breast cancer for each gene in women over age 65 years. METHODS A total of 26,707 women over age 65 years from population-based studies (51.5% with breast cancer and 48.5% unaffected) were tested for PVs in germline predisposition gene. Frequencies of PVs and associations between PVs in each gene and breast cancer were assessed, and remaining lifetime breast cancer risks were estimated for non-Hispanic White women with PVs. RESULTS The frequency of PVs in predisposition genes was 3.18% for women with breast cancer and 1.48% for unaffected women over age 65 years. PVs in BRCA1, BRCA2, and PALB2 were found in 3.42% of women diagnosed with estrogen receptor (ER)–negative, 1.0% with ER-positive, and 3.01% with triple-negative breast cancer. Frequencies of PVs were lower among women with no first-degree relatives with breast cancer. PVs in CHEK2, PALB2, BRCA2, and BRCA1 were associated with increased risks (odds ratio = 2.9-4.0) of breast cancer. Remaining lifetime risks of breast cancer were ≥ 15% for those with PVs in BRCA1, BRCA2, and PALB2. CONCLUSION This study suggests that all women diagnosed with triple-negative breast cancer or ER-negative breast cancer should receive genetic testing and that women over age 65 years with BRCA1 and BRCA2 PVs and perhaps with PALB2 and CHEK2 PVs should be considered for magnetic resonance imaging screening.

Hereditary endometrial cancer (EC) is most commonly attributed to pathogenic variants in mismatch repair (MMR) genes. Evidence supports existence of additional genetic risk factors in the context of multiple cancer diagnoses and/or family history of EC. EC patients (n=5292) referred for diagnostic multi-gene cancer panel testing were annotated for: presence of a pathogenic gene variant; personal history of prior, concurrent or subsequent cancer of another type; reported family history of Lynch syndrome or endometrial cancer. The Pearson χ2 test was used to assess differences in gene variant prevalence between case sub-groups defined by personal and/or family history of cancer/s, using cases with no family history of Lynch/EC as reference. Another cancer diagnosis was reported for 55% of EC cases. EC cases with prior and reported family history of Lynch cancer were enriched for variants in MLH1 (p=3.5x10-7 ), MSH2 (p=3.1x10-7 ), and PMS2 (p=0.02). Consistent with expectations for a breast cancer (BC) gene also predisposing to EC, variant frequency was increased in EC patients with prior BC and family history of EC for BRCA1 (p=1.7x10-5 ) and PALB2 (p=0.0002). Strategic case-case analyses to address cohort ascertainment bias has provided rationale to direct future studies of candidate hereditary EC genes. This article is protected by copyright. All rights reserved.

Summary Determination of the clinical relevance of rare germline variants of uncertain significance (VUSs) in the BRCA2 cancer predisposition gene remains a challenge as a result of limited availability of data for use in classification models. However, laboratory-based functional data derived from validated functional assays of known sensitivity and specificity may influence the interpretation of VUSs. We evaluated 252 missense VUSs from the BRCA2 DNA-binding domain by using a homology-directed DNA repair (HDR) assay and identified 90 as non-functional and 162 as functional. The functional assay results were integrated with other available data sources into an ACMG/AMP rules-based classification framework used by a hereditary cancer testing laboratory. Of the 186 missense variants observed by the testing laboratory, 154 were classified as VUSs without functional data. However, after applying protein functional data, 86% (132/154) of the VUSs were reclassified as either likely pathogenic/pathogenic (39/132) or likely benign/benign (93/132), which impacted testing results for 1,900 individuals. These results indicate that validated functional assay data can have a substantial impact on VUS classification and associated clinical management for many individuals with inherited alterations in BRCA2.

Background: DNA genetic testing is commonly used to inform treatment decisions for breast cancer patients. In recent years, RNA genetic testing has shown promise for increasing the detection of disease-causing variants and decreasing inconclusive results. Here we describe the impact of concurrent DNA and RNA genetic testing on identifying breast cancer patients with germline cancer predisposition who may have been missed by DNA-only testing. Methods: We performed a retrospective review of breast cancer patients who received concurrent DNA and RNA hereditary cancer panel testing between March 2019 and February 2020 at Ambry Genetics. Patients underwent DNA and RNA genetic testing of up to 18 hereditary cancer genes at the discretion of the ordering healthcare provider (APC, ATM, BRCA1, BRCA2, BRIP1, CDH1, CHEK2, MLH1, MSH2, MSH6, MUTYH, NF1, PALB2, PMS2 exons 1-10, PTEN, RAD51C, RAD51D, and TP53). Breast cancer patients with positive results, defined as the presence of a pathogenic or likely pathogenic variant in any of these 18 genes, were selected for inclusion in this study (n=946). Results: Concurrent DNA and RNA genetic testing led to the identification of 23 breast cancer patients with positive results who would have otherwise received inconclusive or negative results with DNA-only testing. These cases represented 2.4% of all positive results reported in the 18 genes studied (n=23/946). The majority of RNA-related positive results occurred in either ATM (n=14) or BRCA1/2 (n=7). The remaining two cases involved alterations in NF1 and PMS2. Guidelines for risk-reducing breast surgery (BRCA1/2) and breast imaging surveillance (ATM, BRCA1/2, NF1) were relevant for 30.4% and 95.7% of patients with RNA-dependent positive results, respectively. In addition, treatment options such as PARP inhibitors or clinical trial eligibility were potentially implicated for 91.3% of RNA-dependent positives (BRCA1/2, ATM). In 16 of the 23 cases, variants would have been detected by DNA-only testing but would have remained inconclusive without supporting RNA data. In the remaining 7 cases, abnormal RNA results led to the identification of pathogenic/likely pathogenic intronic variants beyond the analytical range of DNA testing. Thus, these seven patients would have received negative results from DNA-only testing. Four of these cases involved pathogenic/likely pathogenic intronic variants in ATM and three involved pathogenic intronic variants in BRCA1. Conclusions: One in 41 breast cancer patients who test positive on concurrent DNA and RNA genetic testing would have received negative or inconclusive results from DNA-only testing. These findings demonstrate the impact of a comprehensive diagnostic testing approach that includes concurrent DNA and RNA analysis and highlights the important implications for the personalized management of these breast cancer patients including potential missed opportunities for early detection and prevention of additional cancer and familial testing in the absence of RGT. Citation Format: Holly LaDuca, Lily Hoang, Carolyn Horton, Jessica Profato, Tameron Harvell, Jill S Dolinsky, Tina Pesaran, Rachid Karam. Rna genetic testing improves detection of patients with hereditary breast cancer [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 PD10-07.

Technology has changed the way we approach medical care: health data is constantly being generated, medical discoveries are progressing more rapidly, and individuals are more connected across the world than ever before. Backpack Health is a global personal health record platform that harnesses the power of technology to connect users to their primary health data sources, the medical community, and researchers. By syncing with existing patient portals, health data can be stored on the Backpack Health platform and easily accessed and controlled by users in one connected interface. Individuals manage and collate their current and past conditions, genetic test results, symptoms, medications, procedures, labs, and other health data. Users are empowered to disseminate their information to clinicians, researchers, foundations, and pharmaceutical and biotechnology companies they connect with through the Backpack Health application. Here, we describe how two rare disease advocacy groups, The Marfan Foundation and Project Alive, utilize Backpack Health to connect with their target populations. Through secure transfer of pseudonymized data, groups can query their members to improve understanding of clinical features and to facilitate meaningful research. Responses to the groups' surveys show strong member engagement with high completion rates and increases in new Backpack Health users when surveys are deployed. Data from these surveys have been published and used to better inform clinical outcomes for treatment trials. By connecting users directly to the foundations, clinicians, researchers, and industry partners working on their condition, Backpack Health is instrumental in fast-tracking medical discoveries and treatment for rare diseases.

To evaluate the racial and ethnic differences in prevalence of germline pathogenic variants (PVs) and the effect of race and ethnicity on breast cancer (BC) risk among carriers, results of multigene testing of 77 900 women with BC (non-Hispanic White [NHW] = 57 003; Ashkenazi-Jewish = 4798; Black = 6722; Hispanic = 5194; and Asian = 4183) were analyzed, and the frequency of PVs in each gene were compared between BC patients (cases) and race- and ethnicity-matched gnomAD reference controls. Compared with NHWs, BRCA1 PVs were enriched in Ashkenazi-Jews and Hispanics, whereas CHEK2 PVs were statistically significantly lower in Blacks, Hispanics, and Asians (all 2-sided P 4.00) of BC in Blacks, Hispanics, and Asians; ATM PVs were associated with increased risk of BC among all races and ethnicities except Asians, whereas CHEK2 and BRIP1 PVs were associated with increased risk of BC among NHWs and Hispanics only. These findings suggest a need for personalized management of BC risk in PV carriers based on race and ethnicity.

Background Genome‐wide association studies have identified over 100 single‐nucleotide polymorphisms (SNPs) associated with prostate cancer (PrCa), and polygenic risk scores (PRS) based on their combined genotypes have been developed for risk stratification. We aimed to assess the contribution of PRS to PrCa risk in a large multisite study. Methods The sample included 1972 PrCa cases and 1919 unaffected controls. Next‐generation sequencing was used to assess pathogenic variants in 14 PrCa‐susceptibility genes and 72 validated PrCa‐associated SNPs. We constructed a population‐standardized PRS and tested its association with PrCa using logistic regression adjusted for age and family history of PrCa. Results The mean age of PrCa cases at diagnosis and age of controls at testing/last clinic visit was 59.5 ± 7.2 and 57.2 ± 13.0 years, respectively. Among 1740 cases with pathology data, 57.4% had Gleason score ≤ 6, while 42.6% had Gleason score ≥ 8. In addition, 39.6% cases and 20.1% controls had a family history of PrCa. The PRS was significantly higher in cases than controls (mean ± SD: 1.42 ± 1.11 vs 1.02 ± 0.76; P

PURPOSE To estimate age-specific relative and absolute cancer risks of breast cancer and to estimate risks of ovarian, pancreatic, male breast, prostate, and colorectal cancers associated with germline PALB2 pathogenic variants (PVs) because these risks have not been extensively characterized. METHODS We analyzed data from 524 families with PALB2 PVs from 21 countries. Complex segregation analysis was used to estimate relative risks (RRs; relative to country-specific population incidences) and absolute risks of cancers. The models allowed for residual familial aggregation of breast and ovarian cancer and were adjusted for the family-specific ascertainment schemes. RESULTS We found associations between PALB2 PVs and risk of female breast cancer (RR, 7.18; 95% CI, 5.82 to 8.85; P = 6.5 × 10−76), ovarian cancer (RR, 2.91; 95% CI, 1.40 to 6.04; P = 4.1 × 10−3), pancreatic cancer (RR, 2.37; 95% CI, 1.24 to 4.50; P = 8.7 × 10−3), and male breast cancer (RR, 7.34; 95% CI, 1.28 to 42.18; P = 2.6 × 10−2). There was no evidence for increased risks of prostate or colorectal cancer. The breast cancer RRs declined with age ( P for trend = 2.0 × 10−3). After adjusting for family ascertainment, breast cancer risk estimates on the basis of multiple case families were similar to the estimates from families ascertained through population-based studies ( P for difference = .41). On the basis of the combined data, the estimated risks to age 80 years were 53% (95% CI, 44% to 63%) for female breast cancer, 5% (95% CI, 2% to 10%) for ovarian cancer, 2%-3% (95% CI females, 1% to 4%; 95% CI males, 2% to 5%) for pancreatic cancer, and 1% (95% CI, 0.2% to 5%) for male breast cancer. CONCLUSION These results confirm PALB2 as a major breast cancer susceptibility gene and establish substantial associations between germline PALB2 PVs and ovarian, pancreatic, and male breast cancers. These findings will facilitate incorporation of PALB2 into risk prediction models and optimize the clinical cancer risk management of PALB2 PV carriers.

Purpose Despite the rapid uptake of multigene panel testing (MGPT) for hereditary cancer predisposition, there is limited guidance surrounding indications for testing and genes to include. Methods To inform the clinical approach to hereditary cancer MGPT, we comprehensively evaluated 32 cancer predisposition genes by assessing phenotype-specific pathogenic variant (PV) frequencies, cancer risk associations, and performance of genetic testing criteria in a cohort of 165,000 patients referred for MGPT. Results We identified extensive genetic heterogeneity surrounding predisposition to cancer types commonly referred for germline testing (breast, ovarian, colorectal, uterine/endometrial, pancreatic, and melanoma). PV frequencies were highest among patients with ovarian cancer (13.8%) and lowest among patients with melanoma (8.1%). Fewer than half of PVs identified in patients meeting testing criteria for only BRCA1/2 or only Lynch syndrome occurred in the respective genes (33.1% and 46.2%). In addition, 5.8% of patients with PVs in BRCA1/2 and 26.9% of patients with PVs in Lynch syndrome genes did not meet respective testing criteria. Conclusion Opportunities to improve upon identification of patients at risk for hereditary cancer predisposition include revising BRCA1/2 and Lynch syndrome testing criteria to include additional clinically actionable genes with overlapping phenotypes and relaxing testing criteria for associated cancers.

Mutations in theThis cross-sectional prevalence study included all patients who underwent MGPT between March 2012 and September 2014 from a commercial laboratory (n = 26,936) and an academic medical center cancer genetics clinic (n = 318) to estimateIn the laboratory cohort, 16 (0.06%) of 26,936 patients were identified as having a pathogenicThe majority of

Background With increased adoption of multi-gene panel testing (MGPT) for hereditary cancer, management guidelines now include a wider range of predisposition genes. Yet little is known about whether MGPT results prompt changes to clinicians’ risk management recommendations and whether those recommendations adhere to guidelines. Methods We assessed cancer risk management recommendations made by clinicians ordering MGPT for hereditary cancer at a diagnostic laboratory using an internet-based survey. We received paired pre- and posttest responses for 2172 patients (response rate = 14.3%). Unpaired posttest responses were received in 168 additional patients with positive results. All tests were 2-sided. Results Clinicians reported a change in risk management recommendations for 76.6% of patients who tested positive for a pathogenic or likely pathogenic variant, with changes to surveillance being most common (71.1%), followed by surgical (33.6%), chemoprevention (15.1%), and clinical trial (9.4%) recommendations. Clinicians recommended risk-reducing interventions more often for patients with pathogenic variants in high-risk than moderate-risk genes (P Conclusions Clinicians report frequent changes to cancer risk management recommendations based on positive results in both high-risk and moderate-risk genes. Reported introduction of interventions in patients with inconclusive and negative results is rare and adherence to practice guidelines is high in patients with positive results, suggesting a low probability of harm resulting from MGPT.

PURPOSE Whether individuals with monoallelic FH pathogenic variants (PVs) associated with autosomal recessive fumarate hydratase (FH) deficiency are also at risk of autosomal dominant FH-associated tumors is of paramount clinical importance. METHODS A retrospective study of individuals with a PV in the FH gene identified via multigene panel testing from 2012 to 2019 through a single testing laboratory was performed. Cancer histories of individuals with PVs in FH ( FH PV) were compared to those with PVs associated only with autosomal recessive FH deficiency (FH-d PV) and to FH-negative controls. Cancer histories of individuals with truncating versus nontruncating FH PV were also compared. RESULTS Individuals with FH PV were more likely to have kidney cancer than those with FH-d PV (odds ratio, 9.0; 95% CI, 4.4 to 20.0; P < .001) or FH-negative controls (odds ratio, 7.6; 95% CI, 5.2 to 11.2; P value < .001). The FH PV cohort had kidney cancer at a significantly younger age (median age: 35.0 years; interquartile range, 26.0-45.0 years) than the FH-d PV cohort (median age: 44.5 years; interquartile range, 43.5-53.5 years; P = .011). Within the FH PV cohort, there were no differences in the frequency or age at kidney cancer between those with truncating versus nontruncating PV. CONCLUSION Unlike FH PV, FH-d PV are not associated with kidney cancers at early ages of onset. The FH-d PV cohort had a cancer phenotype that resembled FH-negative controls. These data may inform genetic counseling and risk assessment of individuals with FH-d PV.

Introduction: The relationship between germline pathogenic variants (PVs) in cancer predisposition genes and ductal carcinoma in situ (DCIS) is not well established. The objective of this study is to determine the risks of DCIS and contralateral breast cancer among women with DCIS associated with germline PVs in cancer predisposition genes. Methods: Associations between pathogenic variants in 11 cancer predisposition genes (ATM, BARD1, BRCA1, BRCA2, BRIP1, CDH1, CHEK2, MSH6, PALB2, RAD51C, and RAD51D) and DCIS were determined in case control analyses of a population-based cohort of 3876 women with DCIS and age-matched unaffected women, and in a clinical cohort of 9887 DCIS cases undergoing clinical genetic testing at Ambry Genetics and unaffected reference controls. The incidence of contralateral breast cancer risk in BRCA1, BRCA2, and PALB2 PV carriers with DCIS was also evaluated in a time-to-event analysis. Results: The mean age at diagnosis of DCIS was 50 years in the clinical testing cohort and 59 years in the population-based cohort. The frequency of PVs in 11 predisposition genes among DCIS cases was 6.9% in the clinical testing cohort and 4.9% in the population-based cohort. PVs in ATM, BRCA1, BRCA2, CHEK2, MSH6, PALB2, and RAD51D were associated with significantly increased risks (Odds Ratio (OR) >2) of DCIS in the clinical testing cohort whereas only PVs in BRCA1, CHEK2, PALB2, and ATM were associated with significantly increased risks of DCIS in the population-based cohort. The cumulative incidence of contralateral breast cancer among BRCA1, BRCA2, and PALB2 PV carriers with DCIS was 11% in 5-years and 20% in 15-years. Conclusions: This study provides new insights into PVs that predispose to DCIS. In addition, it establishes an increased risk of contralateral breast cancer risk among women with DCIS who are carriers of PVs in BRCA1, BRCA2, or PALB2. These findings will guide surveillance and risk reducing strategies in germline PV carriers with DCIS. Citation Format: Huaizhi Huang, Ronan E. Couch, Holly LaDuca, Siddhartha Yadav, Eric C. Polley, Nicholas J. Boddicker, Jie Na, Rohan D. Gnanaolivu, David E. Goldgar, Tina Pesaran, Steven N. Hart, Jill S. Dolinsky, Julie R. Palmer, Lauren Teras, Alpa V. Patel, Kathryn J. Ruddy, Janet E. Olson, Celine M. Vachon, Peter Kraft, Song Yao, Amy Trentham-Dietz, Katherine L. Nathanson, Jeffrey N. Weitzel, Susan M. Domchek, Fergus J. Couch, Chunling Hu. Risks of ductal carcinoma in situ of the breast associated with pathogenic variants in cancer predisposition genes [abstract]. In: Proceedings of the AACR Special Conference on Rethinking DCIS: An Opportunity for Prevention?; 2022 Sep 8-11; Philadelphia, PA. Philadelphia (PA): AACR; Can Prev Res 2022;15(12 Suppl_1): Abstract nr A003.

ImportanceGermline CHEK2 pathogenic variants (PVs) are frequently detected by multigene cancer panel testing (MGPT), but our understanding of PVs beyond c.1100del has been limited.ObjectiveTo compare cancer phenotypes of frequent CHEK2 PVs individually and collectively by variant type.Design, Setting, and ParticipantsThis retrospective cohort study was carried out in a single diagnostic testing laboratory from 2012 to 2019. Overall, 3783 participants with CHEK2 PVs identified via MGPT were included. Medical histories of cancer in participants with frequent PVs, negative MGPT (wild type), loss-of-function (LOF), and missense were compared.Main Outcomes and MeasuresParticipants were stratified by CHEK2 PV type. Descriptive statistics were summarized including median (IQR) for continuous variables and proportions for categorical characteristics. Differences in age and proportions were assessed with Wilcoxon rank sum and Fisher exact tests, respectively. Frequencies, odds ratios (ORs), 95% confidence intervals were calculated, and P values were corrected for multiple comparisons where appropriate.ResultsOf the 3783 participants with CHEK2 PVs, 3473 (92%) were female and most reported White race. Breast cancer was less frequent in participants with p.I157T (OR, 0.66; 95% CI, 0.56-0.78; PPP = .04) PVs compared with other PVs and an association with nonbreast cancers was not found. Following the exclusion of p.I157T, p.S428F, and p.T476M, participants with monoallelic CHEK2 PV had a younger age at first cancer diagnosis (P P P P CHEK2 PV were less likely to have a diagnosis of colorectal cancer (OR, 0.62; 95% CI, 0.51-0.76; P CHEK2 PVs and c.1100del and no differences between CHEK2 missense and LOF PVs.Conclusions and RelevanceCHEK2 PVs, with few exceptions (p.I157T, p.S428F, and p.T476M), were associated with similar cancer phenotypes irrespective of variant type. CHEK2 PVs were not associated with colorectal cancer, but were associated with breast, kidney, and thyroid cancers. Compared with other CHEK2 PVs, the frequent p.I157T, p.S428F, and p.T476M alleles have an attenuated association with breast cancer and were not associated with nonbreast cancers. These data may inform the genetic counseling and care of individuals with CHEK2 PVs.

Background Practice guidelines to identify individuals with hereditary pheochromocytomas and paragangliomas (PPGLs) advocate for sequential gene testing strategy guided by specific clinical features and predate the routine use of multigene panel testing (MGPT). Objective To describe results of MGPT for hereditary PPGL in a clinically and ancestrally diverse cohort. Setting Commercial laboratory based in the United States. Methods Clinical data and test results were retrospectively reviewed in 1727 individuals who had targeted MGPT from August 2013 through December 2019 because of a suspicion of hereditary PPGL. Results Overall, 27.5% of individuals had a pathogenic or likely pathogenic variant (PV), 9.0% had a variant of uncertain significance, and 63.1% had a negative result. Most PVs were identified in SDHB (40.4%), followed by SDHD (21.1%), SDHA (10.1%), VHL (7.8%), SDHC (6.7%), RET (3.7%), and MAX (3.6%). PVs in FH, MEN1, NF1, SDHAF2, and TMEM127 collectively accounted for 6.5% of PVs. Clinical predictors of a PV included extra-adrenal location, early age of onset, multiple tumors, and positive family history of PPGL. Individuals with extra-adrenal PGL and a positive family history were the most likely to have a PV (85.9%). Restricting genetic testing to SDHB/C/D misses one-third (32.8%) of individuals with PVs. Conclusion Our data demonstrate a high diagnostic yield in individuals with and without established risk factors, a low inconclusive result rate, and a substantial contribution to diagnostic yield from rare genes. These findings support universal testing of all individuals with PPGL and the use of concurrent MGPT as the ideal platform.

Background: Polygenic risk scores (PRS) based on a large number of SNPs associated with breast cancer have recently been made available in combination with multigene panel testing for clinical management of breast cancer risk. Breast cancer risk assessment has historically been performed using various non-genetic risk models, which predict lifetime risk of breast cancer in unaffected women based on personal and family history information. While clinical use of PRS in combination with these models continues to increase, the predictive performance of a PRS combined with clinical information in real-world patient populations has not been thoroughly investigated. Methods: We assessed a 100-SNP breast cancer PRS in combination with the Tyrer-Cuzick model-estimated lifetime breast cancer risk in 5,374 Caucasian women from the case-control Mayo Clinic Breast Cancer Study (MCBCS), comprised of 3,373 breast cancer cases and 2,001 unaffected controls seen at Mayo Clinic from 2004 to 2016. Clinical, family history, and demographic information was collected on all MCBCS participants via questionnaires and medical record review. SNPs were selected for the PRS if they exceeded genome-wide significance in ≥2 large-scale breast cancer genome wide association studies (GWAS) in women of European descent. Selected SNPs were then used to construct a population standardized PRS, accounting for per-allele odds ratios reported in the largest GWAS to date and population-specific allele frequencies. PRS and Tyrer-Cuzick model associations with breast cancer and related clinical features were tested using multivariate logistic regression. Results: Among cases and controls, mean±SD age at diagnosis and study enrollment was 56.4±12.4 and 56.2±14.1, respectively. Approximately 36.9% of cases and 16.9% of controls had ≥1 first- or second-degree relative with breast or ovarian cancer, respectively. Among unaffected women, the median (IQR) estimated lifetime risk of breast cancer to age 85 based on Tyrer-Cuzick alone was 8.3% (6.9%), and 2.6% had a clinically actionable lifetime risk of ≥20%. The mean±SD sum of the risk alleles across 100 SNPs was significantly higher for cases vs. controls (94.8±6.3 vs. 92.7±6.2, p Citation Format: Mary Helen Black, Shuwei Li, Holly LaDuca, Sebastian Armasu, Eric C. Polley, Patrick Fitz-Gibbon, Chris G. Scott, Stacey J. Winham, Janet E. Olson, Kathryn J. Ruddy, Celine M. Vachon, Fergus J. Couch. Performance of a polygenic risk score combined with clinical assessment for breast cancer risk [abstract]. In: Proceedings of the 2019 San Antonio Breast Cancer Symposium; 2019 Dec 10-14; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2020;80(4 Suppl):Abstract nr P5-07-06.

Impact of Multigene Panel Testing on Medical Management: Preliminary results of a pre- and post-test clinician survey Identification of individuals with germline variants in cancer predisposition genes has risk management and therapeutic implications. Adoption of multi-gene panel testing (MGPT) has led to the development of management guidelines for numerous high and moderate risk breast/ovarian cancer genes. Limited data exist on the impact of MGPT results as they pertain to these guidelines. Here we describe the results of a survey designed to assess the effect MGPT has on clinical decision making. Clinicians were invited to participate in an IRB-approved study using a web-based survey tool to assess clinical management recommendations before and after MGPT. Pre-test survey invitations were emailed to clinicians upon submission of each order. A post-test survey link was emailed to those who completed a pre-test survey upon results disclosure. For this analysis, we examined responses for cases in which at least one breast cancer susceptibility gene was tested. Genes were grouped into three categories: High Risk breast cancer genes with breast Guidelines (abbreviated HRG: BRCA1, BRCA2, CDH1, TP53), Moderate Risk breast cancer genes with breast Guidelines (MRG: ATM, CHEK2, NBN, NF1, PALB2), and genes often found on breast cancer gene panels but that have No breast Guidelines (NG: BARD1, BRIP1, FANCC, RAD51C, RAD51D). Concordance to National Comprehensive Cancer Network (NCCN) v1.2019 guidelines was calculated with regards to recommendations for mammogram, breast MRI, risk reducing mastectomy (RRM), and bilateral salpingo-oophorectomy (BSO). Pre- and post-test surveys were completed by 160 unique providers for 792 cases. Cases with positive or inconclusive findings in genes outside of the HRG, MRG, or NG groups and those with an elevated polygenic risk score (n=127) were excluded from this study. Of the 665 remaining cases, 90 patients had positive (13.5%), 106 had inconclusive (15.9%), and 469 had negative results (70.5%). At least one management change was recommended in most individuals with positive results in HRG or MRG genes (77.3%), in contrast to those with inconclusive (8.5%) or negative results (8.1%). The proportion of patients with at least one recommended management change did not significantly differ between individuals with positive findings in HRG and MRG genes (82.9% vs. 73.5%, p=0.31). In the HRG group, recommendations were mostly concordant with guidelines for mammogram (85.2%), MRI (74.1%), RRM (82.8%), and BSO (85.7%). Recommendations in the MRG group were also mostly concordant with guidelines for mammogram (93.0%) and MRI (81.4%). No individuals in the NG group received a change in mammogram or MRI recommendations based on test results. Seven of 51 females with positive findings in genes without RRM recommendation were advised to consider RRM (13.7%), and two of 47 females with positive findings in genes without BSO recommendation were advised to consider BSO (4.3%). Recommendations to enroll in a clinical trial were made in 15.5% of all positive cases. The data from this ongoing study demonstrate that positive genetic test results frequently lead to changes in medical management recommendations and in some cases therapeutic options. Our observation that positive results in high risk and moderate risk genes lead to an adjustment in management at similar rates demonstrate the benefit of MGPT. Further, most respondents adhere to NCCN guidelines, even without considering clinical factors and contraindications not captured by this survey that contribute to patient management. While these findings support the clinical utility of MGPT, continued study is essential to guide clinicians and payers on the impact MGPT has on medical management and ultimately health outcomes of high-risk individuals. Citation Format: Carolyn Horton, Holly LaDuca, Mary H Black, Mary Pritzlaff, Jessica Profato, Kyle Allen, Jill S. Dolinsky. Impact of multigene panel testing on medical management: Preliminary pre- and post-test clinician survey results [abstract]. In: Proceedings of the 2019 San Antonio Breast Cancer Symposium; 2019 Dec 10-14; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2020;80(4 Suppl):Abstract nr P6-08-35.

Background: Invasive lobular carcinoma (ILC) of the breast accounts for approximately 10-15% of all histologic subtypes of breast cancer. However, apart from germline mutations in CDH1, the contributions of mutations in other cancer predisposition genes to ILC are largely unknown. Methods: The study population included 3,893 women with ILC of the breast who underwent germline multigene panel testing of cancer predisposition genes at Ambry Genetics from March 2012 to December 2016. The prevalence of predisposition gene mutations in women with ILC was assessed relative to 38,004 women with invasive ductal carcinoma (IDC) who underwent germline multigene panel testing at Ambry Genetics during the same timeframe. Associations between mutations in each gene and risk of ILC were evaluated using reference controls. Results: Of the 3,893 women with ILC included in this study, 70.7% were non-Hispanic white, 65.1% had a family history of breast cancer, and 96.4% had estrogen receptor (ER) positive breast cancer. The overall frequency of germline mutations in cancer predisposition genes (ATM, BARD1, BRCA1, BRCA2, BRIP1, CDH1, CDKN2A, CHEK2, MLH1, MRE11A, MSH2, MSH6, NBN, NF1, PALB2, PTEN, RAD51C, RAD51D and TP53) was 7.8% for women with ILC and 10.7% for women with IDC. Mutations in CDH1 were significantly more frequent (Odds Ratio (OR)=12.1, p2), NBN mutations were associated with ILC (OR=3.4; p Conclusions: In a large cohort of patients with ILC, the frequencies of germline mutations in cancer predisposition genes were similar between ILC and IDC except for ATM, BRCA1, CDH1 and PALB2. Six genes, in addition to CDH1, were found to be germline predisposition genes for ILC. A substantial proportion of patients older than 50 with ILC without a family history of breast or ovarian cancer or a personal history of other cancers were found to be mutation carriers. These findings improve our understanding of germline genetic drivers of ILC and suggest that multigene genetic testing should be considered for all ILC patients. Citation Format: Siddhartha Yadav, Holly LaDuca, Eric C. Polley, Chunling Hu, Steven N. Hart, Jie Na, Rohan Gnanaolivu, Brandon Smith, David E Goldgar, Tina Pesaran, Jill S. Dolinsky, Fergus J. Couch. Germline mutations in cancer predisposition genes in patients with invasive lobular carcinoma of the breast [abstract]. In: Proceedings of the 2019 San Antonio Breast Cancer Symposium; 2019 Dec 10-14; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2020;80(4 Suppl):Abstract nr P6-08-04.

BACKGROUND: Germline genetic testing is routinely incorporated into clinical care for breast cancer patients to inform management decisions and reduce risk for developing subsequent cancers. While the diagnostic yield of cancer genetic testing has increased over the years due to adoption of multigene panels, a substantial portion of breast cancer patients remain without a molecular diagnosis yet are suspected to have a genetic mutation that could not be detected and/or classified with standard DNA testing techniques. We assessed the ability of a novel genetic testing approach involving simultaneous DNA and RNA analysis to increase the diagnostic yield and decrease the number of variants of unknown significance (VUS). METHODS: Women with a personal history of breast cancer were ascertained from a larger cohort of patients referred for concurrent RNA sequencing alongside DNA hereditary cancer panel testing by ordering clinicians from 18 collaborating medical centers across the United States. Test result classifications were evaluated for women whose testing included sixteen clinically-actionable hereditary breast and/or ovarian cancer (HBOC) genes (ATM, BRCA1, BRCA2, BRIP1, CDH1, CHEK2, MLH1, MSH2, MSH6, NF1, PALB2, PMS2, PTEN, RAD51C, RAD51D, and TP53). RESULTS: In this cohort of 746 breast cancer patients, the addition of RNA sequencing increased the pathogenic variant detection rate from 8% to 9% across sixteen HBOC genes. These RNA-related positive results included two pathogenic variants in BRCA1 occurring outside the standard analytical range of DNA testing and three VUS (one each in ATM, BRCA2, and PMS2) that were reclassified as likely pathogenic as a result of additional information provided by RNA sequencing. In addition, two VUS were reclassified to benign/likely benign (one each in MSH2 and BRCA2). Together, these five variant reclassifications contributed to a 3% relative decrease in the number of unique VUS classifications (reduced from 182 to 177 unique VUS). In addition, 31 previously-tested patients received reclassification reports. CONCLUSIONS: Concurrent DNA and RNA genetic testing has shown immediate promise in this pilot study, leading to the identification of five breast cancer patients with mutations in clinically actionable genes that would otherwise have received inconclusive or negative results with DNA testing alone. By increasing the detection of germline pathogenic variants and reducing VUS classifications, concurrent DNA and RNA genetic testing increases the diagnostic yield and clinical impact of hereditary cancer testing for breast cancer patients. Citation Format: Holly LaDuca, Lily Hoang, Jill Dolinsky, Jessica Profato, Amal Yussuf, Carolyn Horton, Cara Dresbold, Cassie Garcia, Catherine Koptiuch, Danielle Dondanville, Danielle McKenna, Danielle Menashe, Deborah Wham, Deepika Nathan, Diane Samad, Elizabeth Hoodfar, Gayle Patel, Jen Moore, Jennifer Geurts, John Lee, Kara Milliron, Khateriaa Pyrtel, Meagan Farmer, Meredith Seidel, Morgan Depas, Nichole Morman, Olivia Tan, Rebekah Krukenberg, Rob Pilarski, Samantha Stachowiak, Sandra Jenkinson, Sara Pirzadeh-Miller, Shraddha Gaonkar, Tiffani Demarco, Brigette Tippin Davis, Elizabeth C Chao, Rachid Karam. Concurrent DNA and RNA genetic testing identifies more patients with hereditary breast cancer than DNA testing alone [abstract]. In: Proceedings of the 2019 San Antonio Breast Cancer Symposium; 2019 Dec 10-14; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2020;80(4 Suppl):Abstract nr P6-08-08.

Panel testing has led to the identification of TP53 pathogenic/likely pathogenic (P/LP) variant carriers (TP53+) who exhibit a broad range of phenotypes. We sought to evaluate and compare genotype–phenotype associations among TP53+ panel-ascertained subjects. Between 2012 and 2017, 317 TP53+ subjects (279 females and 38 males) identified through panel testing at one testing laboratory were found to have evaluable clinical histories and molecular results. Subject cancer histories were obtained from test requisition forms. P/LP variants were categorized by type and were examined in relation to phenotype. Loss-of-function (LOF) variants were associated with the earliest age at first cancer, with a median age of 30.5 years (P = 0.014); increased frequency of a sarcoma diagnosis (P = 0.016); and more often meeting classic LFS testing and Chompret 2015 criteria (P = 0.004 and 0.002 respectively), as compared with dominant-negative missense, other missense, or miscellaneous (splice or in-frame deletion) P/LP variant categories. Loss-of-function variants were more often associated with characteristic LFS cancer histories than other variant categories in TP53+ carriers ascertained through multigene panel testing. These findings require validation in other TP53+ cohorts. Genetic counseling for panel-ascertainedTP53+ individuals should reflect the dynamic expansion of the Li–Fraumeni syndrome phenotype.

BackgroundPathogenic variants in mismatch repair (MMR) genes (MLH1, MSH2,MSH6andPMS2) increase risk for Lynch syndrome and related cancers. We quantified tumour characteristics to assess variant pathogenicity for germline MMR genes.MethodsAmong 4740 patients with cancer with microsatellite instability (MSI) and immunohistochemical (IHC) results, we tested MMR pathogenic variant association with MSI/IHC status, and estimated likelihood ratios which we used to compute a tumour characteristic likelihood ratio (TCLR) for each variant. Predictive performance ofTCLRin combination within silicopredictors, and a multifactorial variant prediction (MVP) model that included allele frequency, co-occurrence, co-segregation, and clinical and family history information was assessed.ResultsCompared with non-carriers, carriers of germline pathogenic/likely pathogenic (P/LP) variants were more likely to have abnormal MSI/IHC status (pTCLRalone. Models leveragingin silicoscores as prior probabilities accurately classified >76.7% variants. AddingTCLRas quantitative evidence in an MVP model (MVP +TCLRPred) increased the proportion of accurately classified variants from 88.0% (MVP alone) to 98.0% and generated optimal performance statistics among all models tested. Importantly, MVP +TCLRPredresulted in the high yield of predicted classifications for missense variants of unknown significance (VUS); among 193 VUS, 62.7% were predicted as P/PL or benign/likely benign (B/LB) when assessed according to American College of Medical Genetics and Genomics/Association for Molecular Pathology guidelines.ConclusionOur study demonstrates that when used separately or in conjunction with other evidence, tumour characteristics provide evidence for germline MMR missense variant assessment, which may have important implications for genetic testing and clinical management.

BackgroundThe clinical phenotype of CDH1 pathogenic variant carriers has mostly been studied in families that fulfil criteria of hereditary diffuse gastric cancer (HDGC). We aimed at determining cancer phenotype and cancer risk estimation among families with CDH1 pathogenic variants not selected by HDGC clinical criteria.MethodsPatients were all consecutively identified CDH1 pathogenic variant carriers from a clinical laboratory tested with multigene panel testing and from an academic cancer genetics programme. Clinical and demographic features, cancer phenotypes and genotype–phenotype correlations were determined among CDH1 families. Age-specific cumulative cancer risks (penetrance) were calculated based on 38 families with available pedigrees.ResultsWithin the 113 CDH1 pathogenic variant probands and 476 relatives, 113 had gastric cancer, 177 breast cancer and 196 other cancers. Mean age at diagnosis was 47 for gastric and 54 for breast cancer. Forty-six per cent fulfilled criteria of HDGC. While 36% of families had both gastric and breast cancers, 36% had breast but no gastric cancers and 16% had gastric but not breast cancers. Cumulative risk of cancer by age 80 was 37.2% for gastric and 42.9% for breast cancer.ConclusionIn unselected CDH1 pathogenic variant carrier families, gastric cancer risks were lower and age at diagnosis higher than previously reported in families pre-selected for HDGC criteria. A substantial proportion of families did not present with any gastric cancers and their cancers were limited to breast. Thus, clinical criteria for CDH1 testing should be widened, including breast cancer families only, and a consideration for delayed prophylactic gastrectomy/surveillance should be evaluated.

PURPOSE The current diagnostic testing algorithm for Lynch syndrome (LS) is complex and often involves multiple follow-up germline and somatic tests. We aimed to describe the results of paired tumor/germline testing performed on a large cohort of patients with colorectal cancer (CRC) and endometrial cancer (EC) to better determine the utility of this novel testing methodology. MATERIALS AND METHODS We retrospectively reviewed a consecutive series of patients with CRC and EC undergoing paired tumor/germline analysis of the LS genes at a clinical diagnostic laboratory (N = 702). Microsatellite instability, MLH1 promoter hypermethylation, and germline testing of additional genes were performed if ordered. Patients were assigned to one of five groups on the basis of prior tumor screening and germline testing outcomes. Results for each group are described. RESULTS Overall results were informative regarding an LS diagnosis for 76.1% and 60.8% of patients with mismatch-repair–deficient (MMRd) CRC and EC without and with prior germline testing, respectively. LS germline mutations were identified in 24.8% of patients in the group without prior germline testing, and interestingly, in 9.5% of patients with previous germline testing; four of these were discordant with prior tumor screening. Upon excluding patients with MLH1 promoter hypermethylation and germline mutations, biallelic somatic inactivation was seen in approximately 50% of patients with MMRd tumors across groups. CONCLUSION Paired testing identified a cause for MMRd tumors in 76% and 61% of patients without and with prior LS germline testing, respectively. Findings support inclusion of tumor sequencing as well as comprehensive LS germline testing in the LS testing algorithm. Paired testing offers a complete, convenient evaluation for LS with high diagnostic resolution.

Background: Women newly diagnosed with primary breast cancer (PBC) often undergo multi-gene panel testing to determine their contralateral breast cancer (BC) risk and whether a contralateral prophylactic mastectomy is warranted. However, with the exception of BRCA1/2, gene-specific associations with contralateral or second PBC (SPBC) have not been established. Methods: The study sample was comprised of 83,278 women with BC referred to a single diagnostic laboratory for multi-gene panel testing. The frequency of pathogenic/likely pathogenic variants in clinically-actionable genes (CAG), including highly penetrant genes (HPG: BRCA1, BRCA2, TP53, PTEN) and moderately penetrant genes (MPG: ATM, CHEK2, PALB2, CDH1, NBN, NF1) was compared between women with a PBC and SPBC. Women with a SPBC 1 first or second degree relative with BC (62.2% vs. 60.8%; p=0.004) than PBC. Among women tested for all CAGs, 4,883 (8.1%) were carriers of pathogenic/likely pathogenic variants (11.1% SPBC vs. 7.8% PBC). CHEK2 was the most frequently mutated gene (3.4% SPBC vs. 2.3% PBC), followed by BRCA1 (2.7% SPBC vs.1.6% PBC), BRCA2 (2.2% SPBC vs. 1.8% PBC), and PALB2 (1.4% SPBC vs. 0.9% PBC). In fully adjusted models, women with SPBC were 1.38 times as likely (p= Citation Format: Yao K, Clifford J, Li S, LaDuca H, Hulick PJ, Xu J, Gutierrez S, Black MH. Prevalence of genetic mutations in patients with second primary breast cancers [abstract]. In: Proceedings of the 2018 San Antonio Breast Cancer Symposium; 2018 Dec 4-8; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2019;79(4 Suppl):Abstract nr P1-09-02.

Purpose Clinical history data reported on test requisition forms (TRFs) for hereditary cancer multigene panel testing (MGPT) are routinely used by genetic testing laboratories. More recently, publications have incorporated TRF-based clinical data into studies exploring yield of testing by phenotype and estimating cancer risks for mutation carriers. We aimed to assess the quality of TRF data for patients undergoing MGPT. Patients and Methods Ten percent of patients who underwent hereditary cancer MGPT between January and June 2015 at a clinical laboratory were randomly selected. TRF-reported cancer diagnoses were evaluated for completeness and accuracy for probands and relatives using clinical documents such as pedigrees and chart notes as the comparison standard in cases where these documents were submitted after the time of test order. Results TRF-reported cancer sites and ages at diagnosis were complete for > 90.0% of proband cancer diagnoses overall, and the completion rate was even higher (> 96.0%) for breast, ovarian, colorectal, and uterine cancers. When reported, these data were accurate on TRFs for > 99.5% of proband cancer sites and > 97.5% of proband ages at diagnosis. Cancer site and age at diagnosis data were also complete on the TRF for the majority of cancers among first- and second-degree relatives. Completeness decreased as relation to the proband became more distant, whereas accuracy remained high across all degrees of relation. Conclusion Data collected as part of cancer genetic risk assessment is completely and accurately reported on TRFs for the majority of probands and their close relatives and is comparable to information directly obtained from clinic notes, particularly for breast and other cancers commonly associated with hereditary cancer syndromes.

Background Few studies have examined gene-specific associations with contralateral and/or second breast cancer (SBC). Methods The frequency of pathogenic and likely pathogenic (P/LP) variants in clinically actionable genes (BRCA1, BRCA2, PTEN, TP53, CHEK2, CDH1, ATM, PALB2, NBN, and NF1) was compared between women with a primary breast cancer (PBC) and SBC who underwent multigene panel testing at a single diagnostic testing laboratory. Race- and ethnicity-specific logistic regression burden tests adjusted for age at diagnosis of first breast cancer, histology, presence of first- or second-degree relatives with breast cancer, and prior testing for BRCA1/2 genes were used to test for associations with SBC. All statistical tests were 2-sided. Results The study was comprised of 75 550 women with PBC and 7728 with SBC. Median time between breast cancers for SBC was 11 (interquartile range = 6–17) years. Restricting to women tested for all actionable genes (n = 60 310), there were 4231 (7.8%) carriers of P/LP variants in actionable genes among the controls (PBC) compared with 652 (11.1%) women with SBC (P< .001). Among Caucasians, exclusive of Ashkenazi Jewish women, those carrying a P/LP variant in a clinically actionable gene were 1.44 (95% confidence interval [CI] = 1.30 to 1.60) times as likely to have SBC than noncarriers, after accounting for potential confounders. Among African American and Hispanic women, a P/LP variant in a clinically actionable gene was 1.88 (95% CI = 1.36 to 2.56) and 1.66 (9% CI = 1.02 to 2.58) times as likely to be associated with SBC, respectively (P < .001 and P = .03). Conclusion Women with P/LP variants in breast cancer predisposition genes are more likely to have SBC than noncarriers. Prospective studies are needed confirm these findings.

Background Genetic testing for cancer predisposition is recommended to women with breast cancer who meet the criteria for such testing. After the FDA approvals of the poly ADP ribose polymerase (PARP) inhibitors, olaparib and talazoparib, for treatment of metastatic breast cancer, carrying germline mutations in BRCA1 and BRCA2 genes, the genetic testing result has become critical in their care. With the recent FDA approval of alpelisib for the treatment of PIK3CA‐mutated hormone‐receptor positive metastatic breast cancer, tumor molecular profiling to identify somatic mutations and potential molecularly targeted agents is increasingly utilized in the treatment of advanced breast cancer. Aim Combining germline and somatic sequencing (paired testing) offers an advantage over a single technique approach. Our study evaluates the role of paired testing on the management of breast cancer patients. Methods and Results Forty‐three breast cancer patients treated at Rush University Medical Center underwent paired germline and somatic variant testing in 2015 to 2017. A retrospective chart review was conducted with the analysis of demographic, clinical, and genomic data. Three actionable germline variants were found in the CHEK2 (2) and ATM (1) genes. 95% of tumors had somatic mutations. Seventy‐seven percent of tumors had genomic alterations targetable with agents approved for breast cancer and 88% had molecular targets for agents approved for other cancers. Clinical examples of such use are described and potential future directions of tumor and paired testing are discussed. Conclusions Germline variants were present in a relatively small patient group not routinely tested for inherited alterations. Potentially targetable somatic alterations were identified in the majority of breast cancers. Paired testing is a feasible and efficient approach that delivers valuable information for the care of breast cancer patients and eliminates serial testing.

Multigene panel testing for cancer predisposition mutations is becoming routine in clinical care. However, the gene content of panels offered by testing laboratories vary significantly, and data on mutation detection rates by gene and by the panel is limited, causing confusion among clinicians on which test to order. Using results from 147,994 multigene panel tests conducted at Ambry Genetics, we built an interactive prevalence tool to explore how differences in ethnicity, age of onset, and personal and family history of different cancers affect the prevalence of pathogenic mutations in 31 cancer predisposition genes, across various clinically available hereditary cancer gene panels. Over 13,000 mutation carriers were identified in this high‐risk population. Most were non‐Hispanic white (74%, n = 109,537), but also Black (n = 10,875), Ashkenazi Jewish (n = 10,464), Hispanic (n = 10,028), and Asian (n = 7,090). The most prevalent cancer types were breast (50%), ovarian (6.6%), and colorectal (4.7%), which is expected based on genetic testing guidelines and clinician referral for testing. The Hereditary Cancer Multi‐Gene Panel Prevalence Tool presented here can be used to provide insight into the prevalence of mutations on a per‐gene and per‐multigene panel basis, while conditioning on multiple custom phenotypic variables to include race and cancer type., Multigene panel testing for cancer predisposition mutations is becoming routine in clinical care; however, data on mutation detection rates by gene and by the panel is limited, causing confusion among clinicians on which test to order. Using results from 147,994 multigene panel tests conducted at Ambry Genetics, we built an interactive prevalence tool to explore how differences in ethnicity, age of onset, and personal and family history of different cancers affect the prevalence of pathogenic mutations in 31 cancer predisposition genes, across various clinically available hereditary cancer gene panels. The Hereditary Cancer Multi‐Gene Panel Prevalence Tool presented here can be used to provide insight into the prevalence of mutations on a per‐gene and per‐multigene panel basis, while conditioning on multiple custom phenotypic variables to include race and cancer type.

Germline variants in tumor suppressor genes (TSGs) can result in RNA mis-splicing and predisposition to cancer. However, identification of variants that impact splicing remains a challenge, contributing to a substantial proportion of patients with suspected hereditary cancer syndromes remaining without a molecular diagnosis. To address this, we used capture RNA-sequencing (RNA-seq) to generate a splicing profile of 18 TSGs (APC, ATM, BRCA1, BRCA2, BRIP1, CDH1, CHEK2, MLH1, MSH2, MSH6, MUTYH, NF1, PALB2, PMS2, PTEN, RAD51C, RAD51D, and TP53) in 345 whole-blood samples from healthy donors. We subsequently demonstrated that this approach can detect mis-splicing by comparing splicing profiles from the control dataset to profiles generated from whole blood of individuals previously identified with pathogenic germline splicing variants in these genes. To assess the utility of our TSG splicing profile to prospectively identify pathogenic splicing variants, we performed concurrent capture DNA and RNA-seq in a cohort of 1000 patients with suspected hereditary cancer syndromes. This approach improved the diagnostic yield in this cohort, resulting in a 9.1% relative increase in the detection of pathogenic variants, demonstrating the utility of performing simultaneous DNA and RNA genetic testing in a clinical context.

Background The germline cancer predisposition genes associated with increased risk of each clinical subtype of breast cancer, defined by estrogen receptor (ER), progesterone receptor (PR), and HER2, are not well defined. Methods A total of 54 555 invasive breast cancer patients with 56 480 breast tumors were subjected to clinical hereditary cancer multigene panel testing. Heterogeneity for predisposition genes across clinical breast cancer subtypes was assessed by comparing mutation frequencies by gene among tumor subtypes and by association studies between each tumor subtype and reference controls. Results Mutations in 15 cancer predisposition genes were detected in 8.6% of patients with ER+/HER2-; 8.9% with ER+/HER2+; 7.7% with ER-/HER2+; and 14.4% of ER-/PR-/HER2- tumors. BRCA1, BRCA2, BARD1, and PALB2 mutations were enriched in ER- and HER2- tumors; RAD51C and RAD51D mutations were enriched in ER- tumors only; TP53 mutations were enriched in HER2+ tumors, and ATM and CHEK2 mutations were enriched in both ER+ and/or HER2+ tumors. All genes were associated with moderate (odds ratio > 2.00) or strong (odds ratio > 5.00) risks of at least one subtype of breast cancer in case-control analyses. Mutations in ATM, BARD1, BRCA1, BRCA2, CHEK2, PALB2, RAD51C, RAD51D, and TP53 had predicted lifetime absolute risks of at least 20.0% for breast cancer. Conclusions Germline mutations in hereditary cancer panel genes confer subtype-specific risks of breast cancer. Combined tumor subtype, age at breast cancer diagnosis, and family history of breast and/or ovarian cancer information provides refined categorical estimates of mutation prevalence for women considering genetic testing.

Background The purpose of this study was to estimate precise age-specific tubo-ovarian carcinoma (TOC) and breast cancer (BC) risks for carriers of pathogenic variants in RAD51C and RAD51D. Methods We analyzed data from 6178 families, 125 with pathogenic variants in RAD51C, and 6690 families, 60 with pathogenic variants in RAD51D. TOC and BC relative and cumulative risks were estimated using complex segregation analysis to model the cancer inheritance patterns in families while adjusting for the mode of ascertainment of each family. All statistical tests were two-sided. Results Pathogenic variants in both RAD51C and RAD51D were associated with TOC (RAD51C: relative risk [RR] = 7.55, 95% confidence interval [CI] = 5.60 to 10.19; P = 5 × 10-40; RAD51D: RR = 7.60, 95% CI = 5.61 to 10.30; P = 5 × 10-39) and BC (RAD51C: RR = 1.99, 95% CI = 1.39 to 2.85; P = 1.55 × 10-4; RAD51D: RR = 1.83, 95% CI = 1.24 to 2.72; P = .002). For both RAD51C and RAD51D, there was a suggestion that the TOC relative risks increased with age until around age 60 years and decreased thereafter. The estimated cumulative risks of developing TOC to age 80 years were 11% (95% CI = 6% to 21%) for RAD51C and 13% (95% CI = 7% to 23%) for RAD51D pathogenic variant carriers. The estimated cumulative risks of developing BC to 80 years were 21% (95% CI = 15% to 29%) for RAD51C and 20% (95% CI = 14% to 28%) for RAD51D pathogenic variant carriers. Both TOC and BC risks for RAD51C and RAD51D pathogenic variant carriers varied by cancer family history and could be as high as 32–36% for TOC, for carriers with two first-degree relatives diagnosed with TOC, or 44–46% for BC, for carriers with two first-degree relatives diagnosed with BC. Conclusions These estimates will facilitate the genetic counseling of RAD51C and RAD51D pathogenic variant carriers and justify the incorporation of RAD51C and RAD51D into cancer risk prediction models.

PURPOSE: To estimate age-specific relative and absolute cancer risks of breast cancer and to estimate risks of ovarian, pancreatic, male breast, prostate, and colorectal cancers associated with germline PALB2 pathogenic variants (PVs) because these risks have not been extensively characterized. METHODS: We analyzed data from 524 families with PALB2 PVs from 21 countries. Complex segregation analysis was used to estimate relative risks (RRs; relative to country-specific population incidences) and absolute risks of cancers. The models allowed for residual familial aggregation of breast and ovarian cancer and were adjusted for the family-specific ascertainment schemes. RESULTS: We found associations between PALB2 PVs and risk of female breast cancer (RR, 7.18; 95% CI, 5.82 to 8.85; P = 6.5 × 10(−76)), ovarian cancer (RR, 2.91; 95% CI, 1.40 to 6.04; P = 4.1 × 10(−3)), pancreatic cancer (RR, 2.37; 95% CI, 1.24 to 4.50; P = 8.7 × 10(−3)), and male breast cancer (RR, 7.34; 95% CI, 1.28 to 42.18; P = 2.6 × 10(−2)). There was no evidence for increased risks of prostate or colorectal cancer. The breast cancer RRs declined with age (P for trend = 2.0 × 10(−3)). After adjusting for family ascertainment, breast cancer risk estimates on the basis of multiple case families were similar to the estimates from families ascertained through population-based studies (P for difference = .41). On the basis of the combined data, the estimated risks to age 80 years were 53% (95% CI, 44% to 63%) for female breast cancer, 5% (95% CI, 2% to 10%) for ovarian cancer, 2%-3% (95% CI females, 1% to 4%; 95% CI males, 2% to 5%) for pancreatic cancer, and 1% (95% CI, 0.2% to 5%) for male breast cancer. CONCLUSION: These results confirm PALB2 as a major breast cancer susceptibility gene and establish substantial associations between germline PALB2 PVs and ovarian, pancreatic, and male breast cancers. These findings will facilitate incorporation of PALB2 into risk prediction models and optimize the clinical cancer risk management of PALB2 PV carriers.

BACKGROUND The objective of this study was to investigate the prevalence of pathogenic germline variants (PGVs) in 32 cancer susceptibility genes in individuals with newly diagnosed pancreatic ductal adenocarcinoma (PDAC). A key secondary objective was to evaluate how often PGVs would have been undetected with existing genetic testing criteria. METHODS From May 2016 through May 2017, this multicenter cohort study enrolled consecutive patients aged 18 to 89 years with histologically confirmed PDAC diagnosed within the previous 12 weeks. Demographics, medical histories, and 3-generation pedigrees were collected from participants who provided samples for germline DNA analysis. RESULTS Four hundred nineteen patients were deemed eligible, 302 were enrolled, and 298 were included in the final cohort. Clinically actionable variants were reported in 29 PDAC patients (9.7%), with 23 (7.7%) having a PGV associated with an increased risk for PDAC. Six of 23 individuals (26%) with PDAC-associated gene mutations did not meet currently established genetic testing criteria. According to guideline-based genetic testing, only 11 of the 23 PGVs (48%) in known PDAC genes would have been detected. Six additional patients (2%) had PGVs associated with an increased risk for other cancers. CONCLUSIONS These findings support the significant prevalence of PGVs associated with PDAC and the limitations of current paradigms for selecting patients for genetic testing, and they thereby lend support for universal germline multigene genetic testing in this population.

Clinical diagnostic exome sequencing (DES) has been effective in diagnosing individuals with suspected genetic conditions; nevertheless little has been described regarding its clinical utility in individuals with a personal and family history of cancer. This study aimed to assess diagnostic yield and clinical characteristics of pediatric and adult patients undergoing germline DES for hereditary cancer. We retrospectively reviewed 2171 patients referred for DES; cases with a personal and/or family history of cancer were further studied. Of 39 cancer patients, relevant alterations were found in eight individuals (21%), including one (3%) positive pathogenic alteration within a characterized gene, two (5%) uncertain findings in characterized genes, and five (13%) alterations in novel candidate genes. Two of the 5 pediatric patients, undergoing testing, (40%) had findings in novel candidate genes, with the remainder being negative. We include brief case studies to illustrate the variety of challenging issues related to these patients. Our observations demonstrate utility of family-based exome sequencing in patients for suspected hereditary cancer, including familial co-segregation analysis, and comprehensive medical review. DES may be particularly useful when traditional approaches do not result in a diagnosis or in families with unique phenotypes. This work also highlights the importance and complexity of analysis of uncharacterized genes in exome sequencing for hereditary cancer.