Cancer Susceptibility Genes In Patients Research Articles

Landscape of potential germline pathogenic variants in select cancer susceptibility genes in patients with adult-type ovarian granulosa cell tumors.

The objective of this study was to assess the frequency of potential germline pathogenic variants that may contribute to risk of development of adult granulosa cell tumors (AGCT) given the paucity of germline testing guidelines for these patients. This was a retrospective cross-sectional study analyzing comprehensive genomic profiling (CGP) results of AGCT with the FOXL2 p.C134W mutation submitted to Foundation Medicine between 2012 and 2022. Cases with a potential germline pathogenic variant were identified by filtering single nucleotide variants and short indels by variant allele frequency (VAF) and presence in ClinVar for select cancer susceptibility genes. Odds ratios for AGCT risk were calculated compared to a healthy population. Prior to analysis, 595 patients were screened and 516 with a somatic FOXL2 p.C134W mutation were included. Potential germline pathogenic variants in a DNA repair-related gene (ATM, BRCA1, BRCA2, CHEK2, PALB2, PMS2, RAD51C, or RAD51D) were found in 6.6% of FOXL2-mutated AGCT. Potential germline pathogenic CHEK2 variants were found in 3.5% (18/516) of AGCT patients, a rate that was 2.8-fold higher than Genome Aggregation Database non-cancer subjects (95% CI 1.8-4.6, p < 0.001). The founder variants p.I157T (38.9%, 7/18) and p.T367fs*15 (c.1100delC; 27.8%, 5/18) were most commonly observed. CHEK2 VAF indicated frequent loss of the wildtype copy of the gene. These results support ongoing utilization of genomic tumor profiling and confirmatory germline testing for potential germline pathogenic variants. Further prospective investigation into the biology of germline variants in this population is warranted.

Abstract 7334: Germline mutations in cancer susceptibility genes in patients with mucosal melanoma

Abstract Background: Mucosal melanoma (MM) is the rarest subtype of melanoma with markedly worse outcomes compared to cutaneous melanoma (CM). Unlike CM which is driven by somatic mutations due to UV exposure, risk factors for MM are less defined. While germline mutations in cancer susceptibility genes are well-studied in CM, they are less understood in MM. Herein, we aimed to identify the prevalence of germline mutations in cancer susceptibility genes in a large MM cohort. Methods: A cohort of 247 MM patients (pts) from MD Anderson Cancer Center with available blood for germline sequencing was identified. Pt characteristics were reflective of U.S. MM population with median age of 63, 60% females and 84.6% white. Clinicodemographic features of pts including tumor site, key somatic mutations (BRAF, NRAS, KIT) and personal history of other malignancies were abstracted, and their frequencies were compared in pts with and w/o germline mutation. Frequency of MITF and CHEK2 alleles were compared to expected population control rate based on TOPMED by Fisher’s exact test. Results: Among 247 pts, 10.9% had germline mutations, primarily in MITF (c.G952A:p.E318K) (2.4%) and CHEK2 (c.1100delC:p.T367fs) (1.6%) at OR of 13.9 (95%CI 5.0, 30.9) and 16.4 (4.4, 42.9) compared to population control rate (Table 1). MM sites of origin were gastrointestinal (36%), genitourinary (34%) and head &amp; neck (30%). In terms of somatic mutations, KIT (26%) was most common, followed by NRAS (15%), non-V600E BRAF (6.5%) and BRAF V600E (2.4%). These variables did not differ between those with and w/o germline mutation. Pts with germline mutation had a higher incidence of non-melanoma malignancies (48% vs 29%; p=0.044). Table 1. Summary of identified germline mutations in the mucosal melanoma cohort. Germline mutation Protein MITF (N= 6) p.E318K CHEK2 (N=4) p.T367fs MUYTH p.G368D ATM splice ATM p.L263fs ATM p.R1875X ATM p.L1327X ATM p.A2067D ATM p.R2034X BRCA2 p.A1689fs CHEK2 p.S400T ERCC3 p.R109X MITF p.C29Y NF1 p.L1183R PALB2 p.V221X POLE p.D287E TP53 p.R306X TP53 p.V73Wfs*50 TSC1 p.Q844X Conclusions: This study reports a high prevalence of germline cancer susceptibility mutations in the largest cohort of MM to date, including mutations which are actionable. There is overlap with known MITF risk alleles for CM. We are currently performing a GWAS to comprehensively understand the genetic architecture of risk in MM. Citation Format: Afsaneh Amouzegar, Xiaogang Wu, James Long, Sabitha Prabhakaran, Latasha Little, Curtis Gumbs, Jared Malke, Julie Simon, Jianhua Zhang, Jennifer Wargo, Paul Scheet, Justin W. Wong, Priyadharsini Nagarajan, Jennifer L. McQuade, Andrew Futreal. Germline mutations in cancer susceptibility genes in patients with mucosal melanoma [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 7334.

Germline mutations of 4567 patients with hereditary breast-ovarian cancer spectrum in Thailand

Multi-gene panel testing has led to the detection of pathogenic/likely pathogenic (P/LP) variants in many cancer susceptibility genes in patients with breast-ovarian cancer spectrum. However, the clinical and genomic data of Asian populations, including Thai cancer patients, was underrepresented, and the clinical significance of multi-gene panel testing in Thailand remains undetermined. In this study, we collected the clinical and genetic data from 4567 Thai patients with cancer in the hereditary breast-ovarian cancer (HBOC) spectrum who underwent multi-gene panel testing. Six hundred and ten individuals (13.4%) had germline P/LP variants. Detection rates of germline P/LP variants in breast, ovarian, pancreatic, and prostate cancer were 11.8%, 19.8%, 14.0%, and 7.1%, respectively. Non-BRCA gene mutations accounted for 35% of patients with germline P/LP variants. ATM was the most common non-BRCA gene mutation. Four hundred and thirty-two breast cancer patients with germline P/LP variants (80.4%) met the current NCCN genetic testing criteria. The most common indication was early-onset breast cancer. Ten patients harbored double pathogenic variants in this cohort. Our result showed that a significant proportion of non-BRCA P/LP variants were identified in patients with HBOC-related cancers. These findings support the benefit of multi-gene panel testing for inherited cancer susceptibility among Thai HBOC patients. Some modifications of the testing policy may be appropriate for implementation in diverse populations.

B-210 Spectrum of Germline Mutation with Characteristic MLH1 Hotspots and High Concordance with MMR Deficiency Phenotype in Lynch Syndrome Patients in Taiwan

Abstract Background Patients carried defects on cancer susceptibility genes or had cancer family history have at least twice the risk of developing cancer than the general population, with both early onset and multiple cancers features. For elucidating the carrier rate of cancer susceptibility genes in patients with inherited colorectal cancer (CRC) and endometrial cancer (EnCa) in Taiwan, we established a NCCN guided 30-gene panel which included four DNA Mismatch Repair (MMR) genes to detect the germline mutation of patients with Lynch Syndrome. Correlation of genotype and phenotype of MMR enzymes are under investigation as well. Methods Sixty-eight blood samples were collected from unrelated cancer patients, 42 of them were from patients with inherited colon cancer, 13 from patients with diagnosis of both CRC and endometrial cancer and 13 from patients with early onset EnCa. 30-gene panel was performed by next generation sequencing (NGS) platform and variants were annotated following ACMG guideline. MMR protein expression in tumor tissue sections were identified by conventional immunohistochemistry (IHC) stain. Loss of nuclear staining were classified as MMR deficiency. Results Average age of first tumor onset of 68 patients were 49.2 years old. 54% (37/68) of the subjects had at least one germline mutations with pathogenic effect or deleterious variant predicted by in silico protein function software. Five of them carried two heterozygous mutations. Total 42 mutations appeared majority on three MMR genes, MLH1 (17/42, 40%), MSH2 (10/42, 24%) and MSH6 (6/42, 11%) with notified three hotspots on MLH1 p.R265C (7/17, 41%); p.T117M (2/17, 12%) and p.K618del(2/17, 12%). The rest mutations spread sporadically on nine genes (PMS2, TP53, CHEK2, POLE, POLD1, ATM, EPCAM, MLH3 and RNF43). For exploring the effect of germline mutation on MMR protein expression status on tissue, we compared the MMR IHC results and the germline mutation pattern. As high as 57% concordance between phenotype and genotype were found. We also collected six blood samples from relatives of our CRC cohort to demonstrate the inheritance and pathogenesis of the germline mutation. Exactly the same germline mutations can be found in diseased relatives among different generation or siblings. Conclusion In spite of having founder mutations on MLH1 gene in Taiwanese Lynch syndrome, most of the germline mutations randomly occurred in MMR-related genes. Comprehensive cancer susceptible gene screening panel by NGS is a cost-effective way to identify the inherited status of individuals with family cancer history and serves as a surrogate tool to predict MMR protein expression. Genetic counseling and prophylactic therapeutic information can be provided for positive cases for better cancer prevention.

PD58-01 PREVALENCE AND SPECTRUM OF GERMLINE MUTATIONS IN PATIENTS WITH UPPER TRACT UROTHELIAL CARCINOMA

You have accessJournal of UrologyCME1 May 2022PD58-01 PREVALENCE AND SPECTRUM OF GERMLINE MUTATIONS IN PATIENTS WITH UPPER TRACT UROTHELIAL CARCINOMA Hong Truong, Rania Sheikh, Yelena Kemel, Manuel Jesus Escano, Andrew Lenis, Peter Reisz, Alvin Goh, Eugene Cha, Bernard Bochner, Maria Carlo, Hikmat Al-Ahmadie, and Jonathan Coleman Hong TruongHong Truong More articles by this author , Rania SheikhRania Sheikh More articles by this author , Yelena KemelYelena Kemel More articles by this author , Manuel Jesus EscanoManuel Jesus Escano More articles by this author , Andrew LenisAndrew Lenis More articles by this author , Peter ReiszPeter Reisz More articles by this author , Alvin GohAlvin Goh More articles by this author , Eugene ChaEugene Cha More articles by this author , Bernard BochnerBernard Bochner More articles by this author , Maria CarloMaria Carlo More articles by this author , Hikmat Al-AhmadieHikmat Al-Ahmadie More articles by this author , and Jonathan ColemanJonathan Coleman More articles by this author View All Author Informationhttps://doi.org/10.1097/JU.0000000000002643.01AboutPDF ToolsAdd to favoritesDownload CitationsTrack CitationsPermissionsReprints ShareFacebookLinked InTwitterEmail Abstract INTRODUCTION AND OBJECTIVE: Deleterious germline mutations confer high cancer risks and require enhanced cancer screening, yet the prevalence and spectrum of germline mutations among patients with upper tract urothelial carcinoma (UTUC) are unknown. We sought to determine the frequency of germline mutations in cancer susceptibility genes in patients with UTUC and identify clinical and pathologic factors associated with the presence of germline mutations in DNA mismatch repair (MMR) genes. METHODS: We retrospectively reviewed patients with UTUC who underwent germline sequencing with a targeted panel of >75 cancer-associated genes as part of an institutional protocol of matched tumor-germline sequencing initiative from 04/2015 to 04/2021. Prevalence and spectrum of pathogenic/likely pathogenic variants were determined. Clinicopathologic characteristics were assessed by mutation status. All statistical computations were performed using STATA version 12.1. RESULTS: Of 232 patients, 70% were male, 85% had high grade UTUC, 12% had bilateral tumors, and 11% had metastasis at diagnosis. Germline mutations were identified in 37 (16%) patients. 21 (9%) had mutations in Lynch syndrome (LS) associated MMR genes (13 MSH2, 4 MSH6, 4 MLH1) and 11 (5%) had mutations in moderate/high penetrance non-MMR genes (3 BRCA1, 3 BRCA2, 2 ATM, 1 BARD, 1 BRIP1, and 1 CHEK2). In 21 patients with MMR mutations, 3 (14%) had bilateral UTUC, 10 (48%) and 15 (71%) had personal and family history of LS-associated cancers, respectively. Only 10 (48%) of patients with MMR mutations met current NCCN guideline for genetic testing. UTUC tumor analyses of patients with MMR mutations revealed 15/16 (94%) had MMR-deficiency, and 12/18 (67%) had microsatellite instability. CONCLUSIONS: In our cohort of patients with UTUC identified to have pathogenic germline variants in MMR gene, half did not qualify for germline testing based on current genetic guideline for Lynch syndrome. Importantly, most patients with MMR mutations had microsatellite unstable or MMR-deficient UTUC tumors which would qualify patients for immunotherapy. Our findings support germline testing, especially for MMR genes, for all patients with UTUC. Source of Funding: NIH T32 Ruth L. Kirschstein National Research Service Award 2020 - 2022 © 2022 by American Urological Association Education and Research, Inc.FiguresReferencesRelatedDetails Volume 207Issue Supplement 5May 2022Page: e1011 Advertisement Copyright & Permissions© 2022 by American Urological Association Education and Research, Inc.MetricsAuthor Information Hong Truong More articles by this author Rania Sheikh More articles by this author Yelena Kemel More articles by this author Manuel Jesus Escano More articles by this author Andrew Lenis More articles by this author Peter Reisz More articles by this author Alvin Goh More articles by this author Eugene Cha More articles by this author Bernard Bochner More articles by this author Maria Carlo More articles by this author Hikmat Al-Ahmadie More articles by this author Jonathan Coleman More articles by this author Expand All Advertisement PDF DownloadLoading ...

OP013: Landscape of germline pathogenic variants in cancer susceptibility genes in patients with sarcoma

Sarcomas are heterogenous mesenchymal tumors that mostly arise in bone or soft tissue. Sarcomas comprise only 1% of adult-onset cancers and over 20% of all pediatrics solid malignant cancers. The majority of sarcomas are soft tissue sarcoma and >40% of cases happen above age 65. Sarcoma is usually sporadic. Several rare cancer predisposition syndromes are associated with sarcoma such as Li-Fraumeni syndrome (LFS), Hereditary Retinoblastoma and Neurofibromatosis Type 1. These syndromes account for a small fraction of sarcomas.

Clinical Contribution of Next-Generation Sequencing Multigene Panel Testing for BRCA Negative High-Risk Patients With Breast Cancer

BackgroundBreast cancer is the most common malignancy in women and thought to be hereditary in 10% of patients. Recent next-generation sequencing studies have increased the detection of pathogenic or likely pathogenic (P/LP) variants in genes other than BRCA1/2 in patients with breast cancer. This study evaluated pathogenic variants, likely pathogenic variants, and variants of unknown significance in 18 hereditary cancer susceptibility genes in patients with BRCA1/2-negative breast cancer. Patients and MethodsThis retrospective study included 188 high-risk BRCA1/2-negative patients with breast cancer tested with a multigene cancer panel using next-generation sequencing. ResultsAmong 188 proband cases, 18 variants in 21 patients (11.1%) were classified as P/LP in PALB2 (n = 6), CHEK2 (n = 5), MUTYH (n = 4), ATM (n = 3), TP53 (n = 2), BRIP1 (n = 1), and MSH2 (n = 1). Three novel P/LP variants were identified. An additional 28 variants were classified as variants of unknown significance and detected in 30 different patients (15.9%). ConclusionThis is one of the largest study from Turkey to investigate the mutation spectrum in non-BRCA hereditary breast cancer susceptibility genes. A multigene panel test increased the likelihood of identifying a molecular diagnosis in patients with BRCA 1/2-negative breast cancer at risk for a hereditary breast cancer syndrome. More studies are needed to enable the clinical interpretation of these P/LP variants in hereditary patients with breast cancer.

Mutation Rates in Cancer Susceptibility Genes in Patients With Breast Cancer With Multiple Primary Cancers.

Women with breast cancer have a 4%-16% lifetime risk of a second primary cancer. Whether mutations in genes other than BRCA1/2 are enriched in patients with breast and another primary cancer over those with a single breast cancer (S-BC) is unknown. We identified pathogenic germline mutations in 17 cancer susceptibility genes in patients with BRCA1/2-negative breast cancer in 2 different cohorts: cohort 1, high-risk breast cancer program (multiple primary breast cancer [MP-BC], n = 551; S-BC, n = 449) and cohort 2, familial breast cancer research study (MP-BC, n = 340; S-BC, n = 1,464). Mutation rates in these 2 cohorts were compared with a control data set (Exome Aggregation Consortium [ExAC]). Overall, pathogenic mutation rates for autosomal, dominantly inherited genes were higher in patients with MP-BC versus S-BC in both cohorts (8.5% v 4.9% [P = .02] and 7.1% v 4.2% [P = .03]). There were differences in individual gene mutation rates between cohorts. In both cohorts, younger age at first breast cancer was associated with higher mutation rates; the age of non-breast cancers was unrelated to mutation rate. TP53 and MSH6 mutations were significantly enriched in patients with MP-BC but not S-BC, whereas ATM and PALB2 mutations were significantly enriched in both groups compared with ExAC. Mutation rates are at least 7% in all patients with BRCA1/2 mutation-negative MP-BC, regardless of age at diagnosis of breast cancer, with mutation rates up to 25% in patients with a first breast cancer diagnosed at age < 30 years. Our results suggest that all patients with breast cancer with a second primary cancer, regardless of age of onset, should undergo multigene panel testing.

Frequency of Pathogenic Germline Variants in Cancer-Susceptibility Genes in Patients With Osteosarcoma

Osteosarcoma, the most common malignant bone tumor in children and adolescents, occurs in a high number of cancer predisposition syndromes that are defined by highly penetrant germline mutations. The germline genetic susceptibility to osteosarcoma outside of familial cancer syndromes remains unclear. To investigate the germline genetic architecture of 1244 patients with osteosarcoma. Whole-exome sequencing (n = 1104) or targeted sequencing (n = 140) of the DNA of 1244 patients with osteosarcoma from 10 participating international centers or studies was conducted from April 21, 2014, to September 1, 2017. The results were compared with the DNA of 1062 individuals without cancer assembled internally from 4 participating studies who underwent comparable whole-exome sequencing and 27 173 individuals of non-Finnish European ancestry who were identified through the Exome Aggregation Consortium (ExAC) database. In the analysis, 238 high-interest cancer-susceptibility genes were assessed followed by testing of the mutational burden across 736 additional candidate genes. Principal component analyses were used to identify 732 European patients with osteosarcoma and 994 European individuals without cancer, with outliers removed for patient-control group comparisons. Patients were subsequently compared with individuals in the ExAC group. All data were analyzed from June 1, 2017, to July 1, 2019. The frequency of rare pathogenic or likely pathogenic genetic variants. Among 1244 patients with osteosarcoma (mean [SD] age at diagnosis, 16 [8.9] years [range, 2-80 years]; 684 patients [55.0%] were male), an analysis restricted to individuals with European ancestry indicated a significantly higher pathogenic or likely pathogenic variant burden in 238 high-interest cancer-susceptibility genes among patients with osteosarcoma compared with the control group (732 vs 994, respectively; P = 1.3 × 10-18). A pathogenic or likely pathogenic cancer-susceptibility gene variant was identified in 281 of 1004 patients with osteosarcoma (28.0%), of which nearly three-quarters had a variant that mapped to an autosomal-dominant gene or a known osteosarcoma-associated cancer predisposition syndrome gene. The frequency of a pathogenic or likely pathogenic cancer-susceptibility gene variant was 128 of 1062 individuals (12.1%) in the control group and 2527 of 27 173 individuals (9.3%) in the ExAC group. A higher than expected frequency of pathogenic or likely pathogenic variants was observed in genes not previously linked to osteosarcoma (eg, CDKN2A, MEN1, VHL, POT1, APC, MSH2, and ATRX) and in the Li-Fraumeni syndrome-associated gene, TP53. In this study, approximately one-fourth of patients with osteosarcoma unselected for family history had a highly penetrant germline mutation requiring additional follow-up analysis and possible genetic counseling with cascade testing.

Characteristics of cancer susceptibility genes mutations in 282 patients with gastric adenocarcinoma.

ObjectiveTo reveal the distribution signature of cancer susceptibility genes in patients with gastric adenocarcinoma, offering a diagnostic and prognostic surrogate for disease risk management and therapeutic decisions.MethodsA total of 282 patients with gastric adenocarcinoma (182 males and 100 females) were enrolled in this study, with peripheral blood genomic DNA extracted. Mutations of 69 canonical cancer susceptibility genes or presumably tumor-related genes were analyzed by targeted capture-based high-throughput sequencing. Candidate mutations were particularly selected for discussion on tumor pathogenesis according to the American College of Medical Genetics and Genomics (ACMG) guidelines.ResultsIn this study, 7.1% (20/282) of patients with gastric adenocarcinoma were found to harbor mutations of canonical or presumable cancer susceptibility genes. The detection rate in male patients (3.8%, 7/182) was significantly lower than that in female patients (13%, 13/100) (P=0.004). The most recurrent mutations were in A-T mutated (ATM) (1.1%, 3/282), followed by BRCA1, BRIP1 and RAD51D, all showed a detection rate of 0.7% (2/282). Mutations in three genes associated with hereditary gastric cancer syndromes were detected, namely, PMS2 and EPCAM associated with Lynch syndrome and CDH1 associated with hereditary diffuse gastric cancer. The detection frequencies were all 0.4% (1/282). Notwithstanding no significant difference observed, the age of patients with pathogenic mutations or likely pathogenic mutations is slightly younger than that of non-carriers (median age: 58.5 vs. 60.5 years old), while the age of patients with ATM mutations was the youngest overall (median age: 49.3 years old). ConclusionsOur study shed more light on the distribution signature and pathogenesis of mutations in gastric cancer susceptibility genes, and found the detection rate of pathogenic and likely pathogenic mutations in male patients was significantly lower than that in female patients. Some known and unidentified mutations were found in gastric cancer, which allowed us to gain more insight into the hereditary gastric cancer syndromes from the molecular perspective.

Prevalence of pathogenic variants and variants of unknown significance in patients at high risk of breast cancer: A systematic review and meta-analysis of gene-panel data.

Gene-panels are used to assess predisposition to breast cancer by simultaneous testing of multiple susceptibility genes. This approach increases the identification of variants of unknown significance (VUS) that cannot be used in clinical decision-making. We performed a systematic review of published studies to calculate the prevalence of VUS and pathogenic variants (PV) in routinely tested breast cancer susceptibility genes in patients at high risk of breast cancer. We comprehensively searched the literature using Medline through May 23, 2017 for studies conducting gene-panel testing on germline DNA of women with familial breast cancer and reporting on both PVs and VUSs. A meta-analysis of the collected data was carried out to obtain pooled VUS and PV prevalence estimates per gene using a generalized linear mixed model with logit link for binomial distribution. Of 602 publications, 4 were eligible and included 1870 patients. The panels encompassed 4-27 considered genes. Overall, the estimated probability per gene of a PV and VUS was 55% (95% confidence interval (CI) 26%-81%) and 91% (95% CI 78%-97%), respectively (p = 0.0066). The estimated probability per patient of a PV and VUS was 8% (95% CI 1%-34%) and 23% (95% CI 7%-52%), respectively (p = 0.0052). The ratio of VUS to PV was highest in the mismatch repair genes MLH1, MSH2, MSH6, PMS2 (18.7), CDH1 (13.4) and ATM (9.5). Amongst the 1468 patients tested for BRCA1 and BRCA2, only these two genes had a VUS to PV ratio of less than one (0.2 and 0.6, respectively). With the current panels, the probability of detecting a VUS is significantly higher than the probability of detecting a PV. Better classification of VUSs is therefore critical and requires gene-specific VUS-assessment in every future study of gene-panel testing in patients at high risk of breast cancer.

Prevalence of Germline Mutations in Cancer Susceptibility Genes in Patients With Advanced Renal Cell Carcinoma

Identification of patients with hereditary renal cell carcinoma (RCC) is important for cancer screening and, in patients with advanced disease, for guiding treatment. The prevalence of cancer-related germline mutations in patients with advanced RCC and the phenotypes associated with some rare mutations are unknown. To examine the prevalence of germline mutations in both known RCC predisposition genes and other cancer-associated genes and to identify clinical and pathologic factors associated with germline mutations. In this cohort study conducted from October 1, 2015, to July 31, 2017, 254 of 267 patients with advanced (American Joint Committee on Cancer stage III or IV) RCC who were seen in medical oncology or urology clinics agreed to germline sequencing and disclosure of results under an institutional protocol of matched tumor-germline DNA sequencing. Mutation prevalence and spectrum in patients with advanced RCC were determined. Clinical characteristics were assessed by mutation status. Of the 254 patients (median age [range], 56 [13-79] years; 179 [70.5%] male; 211 [83.1%] non-Hispanic white), germline mutations were identified in 41 (16.1%); 14 (5.5%) had mutations in syndromic RCC-associated genes (7 in FH, 3 in BAP1, and 1 each in VHL, MET, SDHA, and SDHB). The most frequent mutations were CHEK2 (n = 9) and FH (n = 7). Of genes not previously associated with RCC risk, CHEK2 was overrepresented in patients compared with the general population, with an odds ratio of RCC of 3.0 (95% CI, 1.3-5.8; P = .003). Patients with non-clear cell RCC were significantly more likely to have an RCC-associated gene mutation (9 [11.7%] of 74 vs 3 [1.7%] of 177; P = .001), and 8 (10.0%) had a mutation in a gene that could guide therapy. Of patients with mutations in RCC-associated genes, 5 (35.7%) failed to meet current clinical guidelines for genetic testing. Of patients with non-clear cell RCC, more than 20% had a germline mutation, of which half had the potential to direct systemic therapy. Current referral criteria for genetic testing did not identify a substantial portion of patients with mutations, supporting the role of a more inclusive sequencing approach.

Abstract 1245: Identification of germline variants in cancer susceptibility genes in patients with hereditary breast and ovarian cancer syndrome by massive parallel sequencing in Argentinean population

Abstract Breast cancer is the most frequent cancer and ovarian cancer the seventh most frequent cancer among females worldwide, representing approximately 25% and 4% of all cancers. In Argentina, breast cancer and Ovarian cancer cause 6163 and 1332 deaths per year, respectively. Both breast and ovarian cancers are heterogeneous diseases composed of different tumor types with distinctive features and behaviors. The main risk factors for breast and ovarian cancer include age, family history, and genetics.The genetic components of both of the diseases have been well established, contributing to up to 10% of all breast cancer cases and 15% of all ovarian cancer cases.The two major susceptibility genes for both diseases are BRCA1 and BRCA2, and several other susceptibility genes have been identified. However, in the majority of high-risk breast and/or ovarian cancer (HBOC) families, the genetic predisposition factors remain unidentified, making the genetic counseling of these families challenging. The aim of the current study is to utilize an NGS approach to identify genetic factors that predispose individuals to hereditary breast and/or ovarian cancer (HBOC) in the high-risk Argentinian BRCA1/2 mutation-negative HBOC patients.16 patients were analyzed, the DNA was extracted from a blood samples and was subjected to a targeted massively parallel sequencing platform comprising 141 cancer predisposition genes. We detected in these patient 6 pathogenic variants in SBDS, FANCA, MC1R, WRN, MSR1 and SDHD genes. The effect of these variants are of type: non-synonymous (67%) and stop codon gains (33%). We also found 6 variants of uncertain significance (VUS) in APC, RAD50, SDHB, FANCD2, MLH1 and CDH1 genes.In conclusion, the identification of new variants could help to discover new genes associated to HBOC in the population of Argentina.These findings provide an excellent premise for further studies and could be utilized in the design of more efficient clinical management strategies for HBOC. Citation Format: Alejandra Franco, Fernando Orti, Sandra Perdomo, Cecilia Riggi, Cecilia Frecha, Javier Oliver. Identification of germline variants in cancer susceptibility genes in patients with hereditary breast and ovarian cancer syndrome by massive parallel sequencing in Argentinean population [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2018; 2018 Apr 14-18; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2018;78(13 Suppl):Abstract nr 1245.

High frequency of pathogenic non-founder germline mutations in BRCA1 and BRCA2 in families with breast and ovarian cancer in a founder population

BackgroundPathogenic BRCA1 founder mutations (c.4035delA, c.5266dupC) contribute to 3.77% of all consecutive primary breast cancers and 9.9% of all consecutive primary ovarian cancers. Identifying germline pathogenic gene variants in patients with primary breast and ovarian cancer could significantly impact the medical management of patients. The aim of the study was to evaluate the rate of pathogenic mutations in the 26 breast and ovarian cancer susceptibility genes in patients who meet the criteria for BRCA1/2 testing and to compare the accuracy of different selection criteria for second-line testing in a founder population.MethodsFifteen female probands and 1 male proband that met National Comprehensive Cancer Network (NCCN) criteria for BRCA1/2 testing were included in the study and underwent 26-gene panel testing. Fourteen probands had breast cancer, one proband had ovarian cancer, and one proband had both breast and ovarian cancer. In a 26-gene panel, the following breast and/or ovarian cancer susceptibility genes were included: ATM, BARD1, BLM, BRCA1, BRCA2, BRIP1, CDH1, CHEK2, EPCAM, FAM175A, MEN1, MLH1, MRE11A, MSH2, MSH6, MUTYH, NBN, PALB2, PMS2, PTEN, RAD50, RAD51C, RAD51D, STK11, TP53, and XRCC2. All patients previously tested negative for BRCA1 founder mutations.ResultsIn 44% (7 out of 16) of tested probands, pathogenic mutations were identified. Six probands carried pathogenic mutations in BRCA1, and one proband carried pathogenic mutations in BRCA2. In patients, a variant of uncertain significance was found in BRCA2, RAD50, MRE11A and CDH1. The Manchester scoring system showed a high accuracy (87.5%), high sensitivity (85.7%) and high specificity (88.9%) for the prediction of pathogenic non-founder BRCA1/2 mutations.ConclusionA relatively high incidence of pathogenic non-founder BRCA1/2 mutations was observed in a founder population. The Manchester scoring system predicted the probability of non-founder pathogenic mutations with high accuracy.

Abstract 4663: Identification of germline variants in cancer susceptibility genes in patients with multiple primary cancers

Abstract The occurrence of multiple primary (MP) cancers in a patient suggests a genetic predisposition to tumor formation. Multiplex panel testing may be an efficient way of evaluating MP patients for the presence of germline mutations in cancer susceptibility genes. However the spectrum of mutations in many cancer susceptibility genes in the MP patient population is largely unknown. We performed massively parallel sequencing using targeted capture of 15 genes with well-established risks of breast and/or other cancers, specifically TP53, CDH1, PTEN, STK11, ATM, CHEK2, MRE11A, NBN, RAD50, PALB2, MLH1, MSH2, MSH6, PMS2, and MUTYH. Our patient cohort consisted of 221 BRCA1/2 negative patients diagnosed with breast cancer and at least one other primary cancer, excluding non-melanoma skin cancer. Patients diagnosed with contralateral breast cancer were included. Thirty patients (14%) were found to have at least one deleterious variant in these 15 genes. Deleterious variants were found in CHEK2 (16 patients, 7.2%), TP53 (4, 1.8%), MSH6 (3, 1.4%), ATM (2, 0.9%) and one patient each had deleterious variants in CDKN2A, PTEN, PMS2, PALB2, BRIP1 and NBN. In addition, six patients (2.7%) were found to be heterozygous carriers of a MUTYH mutation. In comparison, deleterious variants were identified in 9% of 341 patients with breast cancer only, indicating a small but nonsignificant increase in the rate of deleterious variants in MP patients. The rate of MUTYH heterozygous mutations was also non-significantly different in patients with breast cancer only (1.2%). There was a significant increase in the rate of CHEK2 and MSH6 mutations in the MP versus breast-only patients (7.2% vs 3.5%, p = 0.04 for CHEK2 and 1.4% vs 0%, p = 0.05 for MSH6). As a corollary study, a subset of MP patients (n = 165) were assayed on a panel including TET2. Deleterious TET2 mutations were identified in 2 of 165 patients (1.2%) at allele frequencies of 0.17 and 0.36. These patients blood samples were ascertained at ages 77 and 72, respectively. These preliminary data show that in our cohort of patients with multiple primary cancers, over 16% of patients were found to have deleterious variants in 15 cancer susceptibility genes. In addition, approximately 1% of MP patients have deleterious variants in TET2 that may be due to age-related clonal hematopoiesis, although it is unknown if these mutations are related to the development of the tumors in these individuals. Further analysis of variants in less well-characterized cancer susceptibility genes and unclassified variants is ongoing. Discovery of clinically relevant mutations can potentially guide future treatment practices for those with similar diagnoses to our patients. Citation Format: Brandon Wenz, Kara N. Maxwell, Bradley Wubbenhorst, Kurt D'Andrea, Bradley Garman, Jessica M. Long, Jacquelyn Powers, Jill E. Stopfer, Angela R. Bradbury, Angela DeMichele, Susan M. Domchek, Katherine L. Nathanson. Identification of germline variants in cancer susceptibility genes in patients with multiple primary cancers. [abstract]. In: Proceedings of the 106th Annual Meeting of the American Association for Cancer Research; 2015 Apr 18-22; Philadelphia, PA. Philadelphia (PA): AACR; Cancer Res 2015;75(15 Suppl):Abstract nr 4663. doi:10.1158/1538-7445.AM2015-4663

Prevalence of mutations in a panel of breast cancer susceptibility genes in patients with early onset breast cancer.

1510 Background: Approximately 5-10% of breast cancers are attributable to inherited single gene mutations. Clinical testing for germline variation in multiple cancer susceptibility genes is availa...

Abstract 2280: Targeted massively parallel sequencing identifies a limited number of clinically actionable variants in women with early onset breast cancer.

Abstract Approximately 5-10% of breast cancers are likely attributable to single gene mutations. Multiple breast cancer susceptibility genes have been identified; however, there is insufficient information on the clinical benefit of testing for variants in many of these genes outside of BRCA1, BRCA2, TP53 and PTEN. To obtain further information on the spectrum of variants in breast cancer susceptibility genes, we performed massively parallel sequencing using targeted capture of 28 known or proposed breast cancer susceptibility genes in over 250 patients with breast cancer diagnosed under age 40, negative clinical BRCA1 and BRCA2 testing and no personal or family history of ovarian cancer. Sixty-five percent of the patients had a family history of breast cancer. Breast cancers were triple negative in 26% of the patients; 70% of the patients presented with Stage II or greater disease. Positive control mutations in BRCA1, BRCA2, PALB2, CHEK2, MSH2 and BRCC3 were identified using the targeted panel. In analysis of the first 98 study patients, 46+/8 total variants were identified on average per patient with a median read depth of 131. Of the 4,483 total variants identified in the 98 patients, ten variants that are known to be or are likely functionally significant were identified in ten patients (10%). One patient had the CHEK2 1100delC mutation, and another the known deleterious TP53 mutation, P151T. Four of the functionally significant variants are novel frameshift or nonsense mutations in ATM, BRIP1, BARD1 and MRE11A. Four variants predicted to affect splicing, located within the first two nucleotides within the intron, were identified in CHEK2 (3) and MUTYH (1) and are therefore likely to be functionally significant. In addition, 29 patients (29%) were found to carry 27 variants predicted to be deleterious missense variants by multiple variant calling software programs and found at less than 1% frequency in the control population, but are of unclear functional significance as they are either novel or functionally untested. These potentially deleterious variants were identified in ATM (4), RAD50 (3), BRCA2 (3), BARD1 (2), BRCA1 (2), MLH1 (2), NBS (2), BRIP1 (1), CHEK2 (1), MCPH1 (1), MRE11A (1), MSH6 (1), PMS1 (1), and PMS2 (1). These data show that massively parallel sequencing has the ability to identify multiple potentially causative variants in known breast cancer susceptibility genes in patients who present with early onset breast cancer. However, only rare patients, 1% in our initial sample, which will be reported in full, have actionable mutations given current clinical management guidelines. Given the difficulty in determining the functional significance of novel variants, outside of truncating mutations, there is a great deal of uncertainty about how these findings can be translated into improvements in patient care. Citation Format: Kara N. Maxwell, Bradley Wubbenhorst, Richard Letrero, Kurt D'Andrea, Jacqueline Powers, Jill E. Stopfer, Susan M. Domchek, Katherine L. Nathanson. Targeted massively parallel sequencing identifies a limited number of clinically actionable variants in women with early onset breast cancer. [abstract]. In: Proceedings of the 104th Annual Meeting of the American Association for Cancer Research; 2013 Apr 6-10; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2013;73(8 Suppl):Abstract nr 2280. doi:10.1158/1538-7445.AM2013-2280