Mutations In Cancer Predisposition Genes Research Articles

Utility of germline multi-gene panel testing in patients with endometrial cancer

ObjectivesPatients with germline mutations in mismatch repair genes (MLH1, MSH2, MSH6, PMS2) associated with Lynch syndrome (LS) have an increased lifetime risk of endometrial cancer (EC). Multi-gene panel testing (MGPT) is a recent hereditary cancer risk tool enabling next-generation sequencing of numerous genes in parallel. We determined the prevalence of actionable cancer predisposition gene mutations identified through MGPT in an EC patient cohort. MethodsA single center retrospective cohort study was conducted of patients with EC who had a clinical indication for genetic testing and who underwent MGPT as part of standard of care treatment between 2012 and 2021. Pathogenic mutations were identified and actionable mutations were defined as those with clinical management implications. Additionally, the number of individuals identified with LS was compared between MGPT and tumor-based screening. ResultsThe study included a total of 224 patients. Thirty-three patients [14.7%, 95% confidence interval (CI) = 10.4–20.1] had actionable mutations. Twenty-one patients (9.4%, 95% CI = 5.9–14.0) had mutations in LS genes (4 MLH1, 5 MSH2, 7 MSH6, 4 PMS2, 1 Epcam-MSH2). MGPT revealed two patients with LS (9.5% of LS cases) not identified through routine tumor-based screening. Thirteen patients (5.8%, 95% CI = 3.1–9.7) had at least one actionable mutation in a non-Lynch syndrome gene (6 CHEK2, 2 BRCA2, 2 ATM, 2 APC, 1 RAD51C, 1 BRCA1). ConclusionsGermline MGPT is both feasible and informative as it identifies LS cases not found on tumor testing as well as additional actionable mutations in patients with EC.

Germline mutations in penetrant cancer predisposition genes are rare in men with prostate cancer selecting active surveillance.

Pathogenic germline mutations in several rare penetrant cancer predisposition genes are associated with an increased risk of aggressive prostate cancer (PC). Our objectives were to determine the prevalence of pathogenic germline mutations in men with low-risk PC on active surveillance, and assess whether pathogenic germline mutations associate with grade reclassification or adverse pathology, recurrence, or metastases, in men treated after initial surveillance. Men prospectively enrolled in the Canary Prostate Active Surveillance Study (PASS) were retrospectively sampled for the study. Germline DNA was sequenced utilizing a hereditary cancer gene panel. Mutations were classified according to the American College of Clinical Genetics and Genomics' guidelines. The association of pathogenic germline mutations with grade reclassification and adverse characteristics was evaluated by weighted Cox proportional hazards modeling and conditional logistic regression, respectively. Overall, 29 of 437 (6.6%) study participants harbored a pathogenic germline mutation of which 19 occurred in a gene involved in DNA repair (4.3%). Eight participants (1.8%) had pathogenic germline mutations in three genes associated with aggressive PC: ATM, BRCA1, and BRCA2. The presence of pathogenic germline mutations in DNA repair genes did not associate with adverse characteristics (univariate analysis HR=0.87, 95% CI: 0.36-2.06, p=0.7). The carrier rates of pathogenic germline mutations in ATM, BRCA1, and BRCA2did not differ in men with or without grade reclassification (1.9% vs. 1.8%). The frequency of pathogenic germline mutations in penetrant cancer predisposition genes is extremely low in men with PC undergoing active surveillance and pathogenic germline mutations had no apparent association with grade reclassification or adverse characteristics.

Concurrent pathogenic variations in patients with hereditary cancer syndromes

Cancer is a multifactorial disorder; however, 5–10% of all cancers show hereditary background. In recent years many targeted next generation sequencing panels comprising cancer predisposition genes have been developed and used for diagnostic purposes in patients with increased cancer risk. Screening multiple genes at a time allows multiple variants in different genes to be detected as well. This study aims to determine the cases with concurrent mutations in different hereditary cancer predisposition genes and how they are clinically affected. Here, we screened 1090 index cases by next generation sequencing based hereditary cancer panels and evaluated the reflection of multiple variations on the phenotype. We detected 11 (1%) cases with pathogenic variants in more than one gene. These concurrent variations occurred mostly in BRCA1/2 (7/11) accompanied with MUTYH, ATM, CHECK2, NBN, and RAD50. In addition, MUTYH&ATM, NBN&MSH6, MUTYH&CHEK2 double heterozygous cases were detected. Moreover, we identified a case with three heterozygous variations in CDH1, MUTYH, and CHEK2. These patients presented malignancies that were mostly related to pathogenic variations they carried. Although they are rare, defining double heterozygous cases is important for managing appropriate therapy and accurate genetic consulting for the patients and family members.

Update Swiss guideline for counselling and testing for predisposition to breast, ovarian, pancreatic and prostate cancer.

This paper presents the Swiss guideline for genetic counselling and testing of individuals with an increased probability for carrying mutations in high risk cancer predisposition genes, particularly BRCA1 and BRCA2. It aims to help providers of genetic counselling to identify valuable candidates for testing and serves as a basis for reimbursement claims to Swiss insurance companies.

Recommendations for a More Organized and Effective Approach to the Early Detection of Pancreatic Cancer From the PRECEDE (Pancreatic Cancer Early Detection) Consortium

Recommendations for a More Organized and Effective Approach to the Early Detection of Pancreatic Cancer From the PRECEDE (Pancreatic Cancer Early Detection) Consortium

Cancer predisposition genes in Japanese children with rhabdomyosarcoma.

Rhabdomyosarcoma (RMS) is one of the most common soft tissue sarcomas in children. Germline mutations in cancer-predisposition genes have been detected in approximately 10% of pediatric cancers. However, the genetic background of RMS is still unclear, especially in Asian children. DNA was extracted from the peripheral blood of children with RMS and cancer-associated genes analyzed using targeted re-sequencing. Twenty patients participated in this study. There were three deaths due to RMS. One patient developed a second neoplasm. Nine patients had long-term co-morbidities. Six pathogenic variants were found in five patients: one nonsense variant of DICER1, one exon deletion of TP53, and three missense variants of BUB1B, LIG4, and MEN1. Two of the five patients had a family history of cancer. Two patients with missense variants of LIG4 had long-term co-morbidities of drug-induced cardiomyopathy. The missense variants of LIG4, essential for DNA double-strand break repair, were detected in two unrelated patients. While this is the first report of the germline genetic analysis of Japanese children with RMS with detailed clinical information, the frequency of the variant was almost equivalent to that of previous reports from western countries. Unbiased exon sequencing may be useful to clarify the pathogenesis of RMS in children and in predicting the clinical course of these patients.

Analysis of Sequence and Copy Number Variants in Canadian Patient Cohort With Familial Cancer Syndromes Using a Unique Next Generation Sequencing Based Approach.

BackgroundHereditary cancer predisposition syndromes account for approximately 10% of cancer cases. Next generation sequencing (NGS) based multi-gene targeted panels is now a frontline approach to identify pathogenic mutations in cancer predisposition genes in high-risk families. Recent evolvement of NGS technologies have allowed simultaneous detection of sequence and copy number variants (CNVs) using a single platform. In this study, we have analyzed frequency and nature of sequence variants and CNVs, in a Canadian cohort of patients, suspected with hereditary cancer syndrome, referred for genetic testing following specific genetic testing guidelines based on patient’s personal and/or family history of cancer.MethodsA 2870 patients were subjected to a single NGS based multi-gene targeted hereditary cancer panel testing algorithm to identify sequence variants and CNVs in cancer predisposition genes at our reference laboratory in Southwestern Ontario. CNVs identified by NGS were confirmed by alternative techniques like Multiplex ligation-dependent probe amplification (MLPA).ResultsA 15% (431/2870) patients had a pathogenic variant and 36% (1032/2870) had a variant of unknown significance (VUS), in a cancer susceptibility gene. A total of 287 unique pathogenic variant were identified, out of which 23 (8%) were novel. CNVs identified by NGS based approach accounted for 9.5% (27/287) of pathogenic variants, confirmed by alternate techniques with high accuracy.ConclusionThis study emphasizes the utility of NGS based targeted testing approach to identify both sequence and CNVs in patients suspected with hereditary cancer syndromes in clinical setting and expands the mutational spectrum of high and moderate penetrance cancer predisposition genes.

Clinically Advanced Pheochromocytomas and Paragangliomas: A Comprehensive Genomic Profiling Study.

Simple SummaryClinically advanced pheochromocytomas and paragangliomas are a rare form of endocrine malignancy which can occur in familial and sporadic clinical settings and feature a variety of genomic alterations. Comprehensive genomic profiling (CGP) was performed to characterize the genomic alterations (GA) in clinically advanced disease to enable the search for potential therapy targets. Although the GA/tumor is relatively low for clinically advanced disease, CGP can reveal important potential targets for therapy in the metastatic setting including RET, NF1 and FGFR1. Based on this data, further study of CGP as a method of developing precision therapies for clinically advanced disease appears warranted.Patients with clinically advanced paragangliomas (CA-Para) and pheochromocytomas (CA-Pheo) have limited surgical or systemic treatments. We used comprehensive genomic profiling (CGP) to compare genomic alterations (GA) in CA-Para and CA-Pheo to identify potential therapeutic targets. Eighty-three CA-Para and 45 CA-Pheo underwent hybrid-capture-based CGP using a targeted panel of 324 genes. Tumor mutational burden (TMB) and microsatellite instability (MSI) were determined. The GA/tumor frequencies were low for both tumor types (1.9 GA/tumor for CA-Para, 2.3 GA/tumor for CA-Pheo). The most frequent potentially targetable GA in CA-Para were in FGFR1 (7%, primarily amplifications), NF1, PTEN, NF2, and CDK4 (all 2%) and for CA-Pheo in RET (9%, primarily fusions), NF1 (11%) and FGFR1 (7%). Germline mutations in known cancer predisposition genes were predicted in 13 (30%) of CA-Pheo and 38 (45%) of CA-Para cases, predominantly involving SDHA/B genes. Both CA-Para and CA-Para had low median TMB, low PD-L1 expression levels and none had MSI high status. While similar GA frequency is seen in both CA-Para and CA-Para, germline GA were seen more frequently in CA-Para. Low PD-L1 expression levels and no MSI high status argue against strong potential for novel immune checkpoint inhibitors. However, several important potential therapeutic targets in both CA-Para and CA-Para are identified using CGP.

Abstract 3030: Heritability of cancer predisposition gene mutations in 556 neuroblastoma patients with paired parental DNA whole genome sequences

Abstract Background: Neuroblastoma is a childhood cancer that arises from the sympathetic nervous system. Approximately 1% of patients have a family history of disease with causal germline mutations in neuroblastoma predisposition genes, ALK or PHOX2B. Recent genome-wide association studies (GWAS) of sporadic cases have identified over two dozen susceptibility loci, and next-generation sequencing studies estimate that 8-10% of children with cancer harbor a rare pathogenic (P) or likely pathogenic (LP) germline variant in a cancer predisposition gene (CPG). To date, the heritability and clinical significance of germline P/LP variants remains unknown due to a lack of parental germline DNA. Methods: Through the Gabriella Miller Kids First program, we performed whole genome sequencing (WGS) at 30x depth on patient-parent triads (n=457) and dyads (n=99), along with WGS and exome sequencing on matched tumor DNA (n=336) and RNA-sequencing on matched tumor RNA (n=207). Rare variants (allele frequency <0.1% in ExAC, 1000 Genomes, and gnomAD) in a predefined set of CPGs (n=197) were annotated, and pathogenicity was assessed using ClinVar, InterVar, and manual review. Gene-based enrichment was performed by comparison to gnomAD WGS data (n=143,068), excluding TCGA samples. Heritability was evaluated using family-based variant calling. Tumor DNA sequencing was analyzed for second hits or somatic enrichment of the germline P/LP variant. Tumor RNA sequencing was interrogated to identify expressed P/LP variants and preferential allelic expression. Ongoing analyses are utilizing polygenic risk scores from our GWAS study to inform tumor penetrance. Results: We observed 78 P/LP germline variants in CPGs in 75 probands (13.5%). Of the 72 probands with trio data, 95% of the P/LP variants were inherited (54% maternal, 46% paternal). Several CPGs showed enrichment of P/LP variants, including BARD1 (p=0.001; OR 16.16; 95% CI 3.21-50.45). We observed one canonical ALK mutation (R1275Q), but no PHOX2B mutations. For patients with corresponding tumor samples, all germline P/LP variants were observed in the tumor DNA. Germline P/LP variants were associated with high-risk disease as defined by risk group (high vs. low/intermediate, p=0.005), INRG stage (stage M vs stage L1/L2/MS, p=0.024), and MYCN amplification status (amplified vs not amplified, p=0.016). Conclusions: Here we show that approximately 13.5% of patients with neuroblastoma harbor a rare P/LP germline variant in a CPG, and the vast majority of these are inherited. Neuroblastoma patients with P/LP germline variants are more likely to have high-risk disease and several variants suggest potential therapeutic opportunities. Work is ongoing to understand the genetic factors that explain why parents harboring the same P/LP variant did not develop neuroblastoma, and to determine the genetic counseling implications of these data. Citation Format: Emily Blauel, Zalman Vaksman, Alex Lee, Rebecca Kaufman, Laura Egolf, Andrew Olshan, John Maris, Diskin Sharon. Heritability of cancer predisposition gene mutations in 556 neuroblastoma patients with paired parental DNA whole genome sequences [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2021; 2021 Apr 10-15 and May 17-21. Philadelphia (PA): AACR; Cancer Res 2021;81(13_Suppl):Abstract nr 3030.

Zebrafish Cancer Predisposition Models.

Cancer predisposition syndromes are rare, typically monogenic disorders that result from germline mutations that increase the likelihood of developing cancer. Although these disorders are individually rare, resulting cancers collectively represent 5–10% of all malignancies. In addition to a greater incidence of cancer, affected individuals have an earlier tumor onset and are frequently subjected to long-term multi-modal cancer screening protocols for earlier detection and initiation of treatment. In vivo models are needed to better understand tumor-driving mechanisms, tailor patient screening approaches and develop targeted therapies to improve patient care and disease prognosis. The zebrafish (Danio rerio) has emerged as a robust model for cancer research due to its high fecundity, time- and cost-efficient genetic manipulation and real-time high-resolution imaging. Tumors developing in zebrafish cancer models are histologically and molecularly similar to their human counterparts, confirming the validity of these models. The zebrafish platform supports both large-scale random mutagenesis screens to identify potential candidate/modifier genes and recently optimized genome editing strategies. These techniques have greatly increased our ability to investigate the impact of certain mutations and how these lesions impact tumorigenesis and disease phenotype. These unique characteristics position the zebrafish as a powerful in vivo tool to model cancer predisposition syndromes and as such, several have already been created, including those recapitulating Li-Fraumeni syndrome, familial adenomatous polyposis, RASopathies, inherited bone marrow failure syndromes, and several other pathogenic mutations in cancer predisposition genes. In addition, the zebrafish platform supports medium- to high-throughput preclinical drug screening to identify compounds that may represent novel treatment paradigms or even prevent cancer evolution. This review will highlight and synthesize the findings from zebrafish cancer predisposition models created to date. We will discuss emerging trends in how these zebrafish cancer models can improve our understanding of the genetic mechanisms driving cancer predisposition and their potential to discover therapeutic and/or preventative compounds that change the natural history of disease for these vulnerable children, youth and adults.

Mutations in BRCA1/2 and Other Panel Genes in Patients With Metastatic Breast Cancer -Association With Patient and Disease Characteristics and Effect on Prognosis.

Among patients with metastatic breast cancer (mBC), the frequency of germline mutations in cancer susceptibility genes and the clinical relevance of these mutations are unclear. In this study, a prospective cohort of patients with mBC was used to determine mutation rates for breast cancer (BC) predisposition genes, to evaluate the clinical characteristics of patients with mutations, and to assess the influence of mutations on patient outcome. Germline DNA from 2,595 patients with mBC enrolled in the prospective PRAEGNANT registry was evaluated for mutations in cancer predisposition genes. The frequencies of mutations in known BC predisposition genes were compared with results from a prospective registry of patients with nonmetastatic BC sequenced using the same QIAseq method and with public reference controls. Associations between mutation status and tumor characteristics, progression-free survival, and overall survival were assessed. Germline mutations in 12 established BC predisposition genes (including BRCA1 and BRCA2) were detected in 271 (10.4%) patients. A mutation in BRCA1 or BRCA2 was seen in 129 patients (5.0%). BRCA1 mutation carriers had a higher proportion of brain metastasis (27.1%) compared with nonmutation carriers (12.8%). Mutations were significantly enriched in PRAEGNANT patients with mBC compared with patients with nonmetastatic BC (10.4% v 6.6%, P < .01). Mutations did not significantly modify progression-free survival or overall survival for patients with mBC. Multigene panel testing may be considered in all patients with mBC because of the high frequency of germline mutations in BRCA1/2 and other BC predisposition genes. Although the prognosis of mutation carriers and nonmutation carriers with mBC was similar, differences observed in tumor characteristics have implications for treatment and for future studies of targeted therapies.

Abstract IA-18: Big pediatric cancer genomic data: Discovery, precision medicine, and data sharing

Abstract High throughput next generation sequencing (NGS) has enabled tremendous advances in our understanding of the genomic landscape of pediatric cancer, leading to discoveries of new mechanisms of tumor initiation and progression, novel targets, and diagnostic and prognostic markers. By focusing on the development of innovative computational analysis tools, we have investigated the genomic variants in pediatric cancer in the following areas: 1) genomic landscapes of &amp;gt;20 subtypes of pediatric cancer; 2) a pan-cancer study of genomes and transcriptomes of pediatric cancer which unveiled that &amp;gt;50% of the driver genes are absent in adult cancer; 3) clonal evolution of relapsed pediatric leukemia driven by therapy-induced variants bearing novel mutational signature; and 4) pathogenic germline mutations in cancer predisposition genes. These insights led to implementation of clinical cancer genomic profiling by three-platform of whole genome, whole exome and transcriptome sequencing for all eligible pediatric cancer patients at St Jude. Use of these data sets improved molecular diagnosis of pediatric cancer. Since 2015, we have analyzed &amp;gt;1,200 pediatric oncology patients providing critical data that may affect patient care. The omics data generated from our research and clinical programs can be accessed on St. Jude Cloud (https://www.stjude.cloud), a cloud-based data sharing ecosystem for accessing, analyzing and visualizing genomic data generated from &amp;gt;10,000 pediatric cancer patients, long-term survivors of pediatric cancer and &amp;gt;800 pediatric sickle cell patients. Access to three interconnected Apps on St. Jude Cloud, i.e. Genomics Platform, Pediatric Cancer (PeCan) Knowledgebase and Visualization Community, provides a unique experience for simultaneously performing advanced data analysis and enhancing the knowledgebase for pediatric cancer. Citation Format: Jinghui Zhang. Big pediatric cancer genomic data: Discovery, precision medicine, and data sharing [abstract]. In: Proceedings of the AACR Virtual Special Conference on Artificial Intelligence, Diagnosis, and Imaging; 2021 Jan 13-14. Philadelphia (PA): AACR; Clin Cancer Res 2021;27(5_Suppl):Abstract nr IA-18.

Characterization and Clinical Outcomes of DNA Mismatch Repair-deficient Small Bowel Adenocarcinoma.

The prevalence and clinical characteristics of small bowel adenocarcinomas (SBA) in the setting of Lynch syndrome have not been well studied. We characterized SBA according to DNA mismatch repair and/or microsatellite instability (MMR/MSI) and germline mutation status and compared clinical outcomes. A single-institution review identified 100 SBAs. Tumors were evaluated for MSI via MSIsensor and/or corresponding MMR protein expression via IHC staining. Germline DNA was analyzed for mutations in known cancer predisposition genes, including MMR (MLH1, MSH2, MSH6, PMS2, and EPCAM). Clinical variables were correlated with MMR/MSI status. Twenty-six percent (26/100; 95% confidence interval, 18.4-35.4) of SBAs exhibited MMR deficiency (MMR-D). Lynch syndrome prevalence was 10% overall and 38.5% among MMR-D SBAs. Median age at SBA diagnosis was similar in non-Lynch syndrome MMR-D versus MMR-proficient (MMR-P) SBAs (65 vs. 61; P = 0.75), but significantly younger in Lynch syndrome (47.5 vs. 61; P = 0.03). The prevalence of synchronous/metachronous cancers was 9% (6/67) in MMR-P versus 34.6% (9/26) in MMR-D SBA, with 66.7% (6/9) of these in Lynch syndrome (P = 0.0002). In the MMR-P group, 52.2% (35/67) of patients presented with metastatic disease, compared with 23.1% (6/26) in the MMR-D group (P = 0.008). In MMR-P stage I/II patients, 88.2% (15/17) recurred, compared with 18.2% (2/11) in the MMR-D group (P = 0.0002). When compared with MMR-P SBA, MMR-D SBA was associated with earlier stage disease and lower recurrence rates, similar to observations in colorectal cancer. With a 38.5% prevalence in MMR-D SBA, germline Lynch syndrome testing in MMR-D SBA is warranted.

Abstract PD7-03: A living biobank of normal mammary organoids derived from patients at low and increased risk of developing breast cancer

Abstract Background: Mutations in BRCA1 and BRCA2 are associated with a high risk of developing breast cancer, but the earliest molecular changes that lead to the transformation of mammary cells in the setting of BRCA1/2 heterozygosity remain unknown. We previously demonstrated that breast organoid cultures derived from histologically normal tissues can preserve all of the major mammary epithelial lineages for further study in vitro1. In addition, organoid culture medium is fully defined, enabling modulation of the medium to enhance the growth of distinct mammary subpopulations. Here, we undertook the development of a large biobank of breast organoids derived from patients with and without increased breast cancer risk, including patients with inherited mutations in BRCA1 and BRCA2. Methods: Breast samples with normal histology (taken from reduction mammoplasties or prophylactic mastectomies), were digested for ~2 hours using collagenase, embedded in basement membrane extract, and grown in a fully-defined organoid medium1. CyTOF profiling was performed using our previously published mammary-specific heavy metal-tagged antibody panel1. Lentiviral transduction was performed to knock-down BRCA1 and/or overexpress mutant p53. Murine engraftment of normal breast organoids was performed by intra-ductal injection of ~1,000 organoids into NCG mice using a modification of protocols for breast cancer cell lines2, with removal of mammary glands after 3 months for detailed immunohistochemistry analysis. Results: A living biobank of &amp;gt; 100 normal breast organoids derived from patients with and without inherited mutations in breast cancer predisposition genes, including BRCA1 and BRCA2, was established. Cultures were generated with high efficiency (&amp;gt;95%) and could be serially passaged with the longest cultures &amp;gt; 16 months. CyTOF profiling of organoids revealed the maintenance of multiple epithelial cell subtypes, with at least one subtype of luminal cells enriched in tissues and organoids from BRCA1/2 mutation carriers. Protein and RNA expression patterns of breast organoids were found to correlate with patient tissues analyzed using a combination of single-cell analyses (CyTOF, single-cell RNA sequencing, and immunohistochemistry). The impact of factors present in the organoid medium on distinct mammary epithelial cell subtypes was assessed by CyTOF, enabling identification of conditions that promote expansion of cell populations that are enriched in tissues from BRCA1/2 mutation carriers. Furthermore, normal breast cell types could be engrafted into the murine mammary gland, and could be modified by lentiviral transduction for gene transfer, enabling future studies of the tumorigenic potential of distinct normal and premalignant epithelial cell subtypes. Conclusion: We have shown that organoid cultures can be used to propagate normal breast tissues with high efficiency, preserve normal as well as potential premalignant breast epithelial cell types, and model methods to inhibit precancerous cells in vitro. Thus, organoids are a useful complement to murine and other models of breast cancer development, and can ultimately be used to identify potential cancer interception strategies for patients at high risk of developing breast cancer.

Influential Factors on Risk-reduction Mastectomy in a High-risk Breast Cancer Population With Genetic Predispositions

BackgroundCarriers of deleterious mutations in breast cancer predisposition genes are presented with critical choices regarding cancer risk management. Risk-reduction mastectomy is a major preventative strategy in this population. Understanding the decision-making process for prophylactic mastectomy is essential in patient-centered care for high-risk carriers and patients with breast cancer. We sought to provide insight into influential factors underlying preventative surgery decisions among individuals with high breast cancer risk. Materials and MethodsWe conducted a retrospective chart review of pathogenic carriers of high-risk breast cancer genes who presented to the Moffitt GeneHome clinic between March 2017 and June 2020. Associations between preventative mastectomy choice and influence variables were analyzed via unadjusted and adjusted logistic regression models. ResultsOf 258 high-risk mutation carriers, 104 (40.3%) underwent risk-reduction mastectomy. A significantly higher proportion of mastectomy patients reported prior history of breast cancer (68.9% vs. 16.5%; P < .001) and history of other risk-reduction or noncancer-related surgeries (61.7% vs. 25.8%; P < .001). Significant predictors affecting surgery decision included previous breast cancer history (adjusted odds ratio [aOR], 10.48; 95% confidence interval [CI], 5.59-19.63; P < .0001), other risk-reduction or noncancer-related surgical history (aOR, 4.65; 95% CI, 2.28-9.47; P < .0001), and age at presentation to the genetics clinic (< 35 years old: aOR, 2.77; 95% CI, 1.04-7.4; P = .042; 35-55 years old: aOR, 2.48; 95% CI, 1.19-5.18; P = .016). ConclusionsPreventive mastectomy decisions are highly personal and complex. In our sample, we observed prior history or concurrent breast cancer, history of other risk-reduction surgery or noncancer-related surgery, and younger age at presentation to the GeneHome clinic to be predictive of mastectomy uptake.

Molecular Changes in Retinoblastoma beyond RB1: Findings from Next-Generation Sequencing

This investigation uses hybridization capture-based next-generation sequencing to deepen our understanding of genetics that underlie retinoblastoma. Eighty-three enucleated retinoblastoma specimens were evaluated using a MSK-IMPACT clinical next-generation sequencing panel to evaluate both somatic and germline alterations. Somatic copy number variations (CNVs) were also identified. Genetic profiles were correlated to clinicopathologic characteristics. RB1 inactivation was found in 79 (97.5%) patients. All specimens had additional molecular alterations. The most common non-RB1 gene alteration was BCOR in 19 (22.9%). Five (11.0%) had pathogenic germline mutations in other non-RB1 cancer predisposition genes. Significant clinicopathologic correlations included: vitreous seeds associated with 1q gains and 16q loss of heterozygosity (BH-corrected p-value = 0.008, 0.004; OR = 12.6, 26.7, respectively). BCOR mutations were associated with poor prognosis, specifically metastases-free survival (MFS) (nominal p-value 0.03). Furthermore, retinoblastoma patients can have non-RB1 germline mutations in other cancer-associated genes. No two specimens had the identical genetic profile, emphasizing the individuality of tumors with the same clinical diagnosis.

Hereditary cancer syndrome-associated pathogenic variants are common in patients with hematologic malignancies subsequent to primary solid cancer.

Background: As the number of long-term survivors of solid cancers keeps increasing, risk assessment of secondary hematologic malignancies is important for the prognosis of the patient. Germline genetic predisposition to secondary hematologic malignancy has been studied widely in myeloid neoplasms and rarely in lymphoid neoplasms. This study aimed to profile the mutational spectrums of patients with subsequent lymphoid tissue neoplasm to shed some light on the understudied area.Methods: In total, 39 patients who had primary solid cancer and subsequent hematologic malignancies were enrolled. We performed two next-generation sequencing (NGS) panel tests encompassing hereditary cancer predisposition genes and genes related to clonal hematopoiesis of indeterminate potential (CHIP). All statistical analyses were performed using R 3.5.1.Results: We found 8 of 39 patients with germline mutations in cancer predisposition genes; 4 of 18 patients had therapy-related myeloid neoplasms (22.2%); and 4 of 15 patients had secondary lymphoid malignancies (26.7%). Notably, of 14 patients who initially suffered from thyroid cancer, 5 patients (35.7%) had germline mutations. Malignancy of lymphoid tissue showed no association with radioactive iodine therapy but was observed to a greater extent in germline mutation-positive thyroid cancer patients regardless of their history of treatment. We observed that 24 of 39 patients (61.5%) were CHIP carriers. Patients who had secondary lymphoid malignancy were less likely to have CHIP than those who had myeloid malignancy.Conclusions: In patients with primary solid cancer who are planning to undergo cytotoxic chemotherapy, radiotherapy, or radioactive iodine therapy, an initial assessment with germline mutation testing using an expanded NGS panel, including low, moderate, and high-risk cancer-associated genes, and somatic CHIP mutation testing can screen the patients who are at risk of developing therapy-related myeloid and lymphoid malignancies. Through careful screening and monitoring throughout the treatment process, patients can benefit from the early detection of secondary malignancies and receive proper treatment.

Cancer Previvors in an Active Duty Service Women Population: An Opportunity for Prevention and Increased Force Readiness.

BackgroundThe majority of active duty service women (ADS) are young, have access to healthcare, and meet fitness standards set by the U.S. military, suggesting that ADS represent a healthy population at low risk of cancer. Breast cancer is, however, the most common cancer in ADS and may have a significant effect on troop readiness with lengthy absence during treatment and inability to return to duty after the treatment. The identification of unaffected ADS who carry germline mutations in cancer predisposition genes (“previvors”) would provide the opportunity to prevent or detect cancer at an early stage, thus minimizing effects on troop readiness. In this study, we determined (1) how many high-risk ADS without cancer pursued genetic testing, (2) how many previvors employed risk-reducing strategies, and (3) the number of undiagnosed previvors within an ADS population.MethodsThe Clinical Breast Care Project (protocol WRNMMC IRB #20704) database of the Murtha Cancer Center/Walter Reed National Military Medical Center was queried to identify all ADS with no current or previous history of cancer. Classification as high genetic risk was calculated using National Comprehensive Cancer Network 2019 guidelines for genetic testing for breast, ovary, colon, and gastric cancer. The history of clinical genetic testing and risk-reducing strategies was extracted from the database. Genomic DNA from ADS with blood specimens available for research purposes were subjected to next-generation sequencing technologies using a cancer predisposition gene panel.ResultsOf the 336 cancer-free ADS enrolled in the Clinical Breast Care Project, 77 had a family history that met National Comprehensive Cancer Network criteria for genetic testing for BRCA1/2 and 2 had a family history of colon cancer meeting the criteria for genetic testing for Lynch syndrome. Of the 28 (35%) high-risk women who underwent clinical genetic testing, 11 had pathogenic mutations in the breast cancer genes BRCA1 (n = 5), BRCA2 (n = 5), or CHEK2 (n = 1). Five of the six ADS who had a relative with a known pathogenic mutation were carriers of the tested mutation. All of the women who had pathogenic mutations detected through clinical genetic testing underwent prophylactic double mastectomy, and three also had risk-reducing salpingo-oophorectomy. Two (6%) of the 33 high-risk ADS tested only in the research setting had a family history of breast/ovarian cancer and carried pathogenic mutations: one carried a BRCA2 mutation, whereas the other carried a mutation in the colon cancer predisposition gene PMS2. No mutations were detected in the 177 low-risk women tested in the research setting.DiscussionWithin this unaffected cohort of ADS, 23% were classified as high risk. Although all of the previvors engaged in risk-reduction strategies, only one-third of the high-risk women sought genetic testing. These data suggest that detailed family histories of cancer should be collected in ADS and genetic testing should be encouraged in those at high risk. The identification of previvors and concomitant use of risk-reduction strategies may improve health in the ADS and optimize military readiness by decreasing cancer incidence.

Germline Variants Associated with Cancer Predisposition and Bone Marrow Failure Are Common in KMT2A-r Infant Acute Lymphoblastic Leukemia Patients

Introduction: Infant acute lymphoblastic leukemia (ALL), is a particularly aggressive subtype of leukemia with an early onset and unfavorable clinical outcome. Most (~70%) cases of infant ALL involve chromosomal rearrangement of KMT2A (KMT2A-r) on chromosome 11q23, the strongest independent predictor of a poor prognosis. To date, genomics studies have consistently demonstrated KMT2A-r infant ALL to have a strikingly silent landscape of DNA mutations, aside from the KMT2A-r itself. Germline mutations in cancer predisposition genes are found in 8.6% of pediatric malignancies and 4.4% of pediatric leukemias, compared to 1.1% in persons in the 1000 Genomes Project (Zhang J et al., N Engl J Med 2015). We hypothesized that germline variants may contribute to the development of KMT2A-r ALL in infants. We examined the germline variants in remission blood samples from a large cohort of infants with KMT2A-r ALL who were enrolled in Children's Oncology Group (COG) trial AALL15P1. Methods: We performed whole genome sequencing (WGS) and whole exome sequencing (WES) on DNA isolated from peripheral blood from 36 KMT2A-r cases at time of remission. Sequencing was performed using an Illumina Hiseq 4000 or 2500 to a minimum depth of 90Gb (WGS) and 15Gb (WES). Alignment and variant calling were performed using the Dragon Bio-IT platform (v 3.2.8, Illumina). Blueprint Genetics clinical panels and the medical literature (Xa M et al., Nature 2018) were used to comprise a list of 346 genes associated with cancer predisposition and bone marrow failure syndromes. From this gene pool, variants were selected for analysis based on a variant allele frequency of ~50% and minor allele frequency &amp;lt;0.1% in control population databases (gnomAD). Variants were analyzed for pathogenicity per the 2015 ACMG/AMP interpretation guidelines for sequence variants. Results: Of 351 variants initially identified, we found 3 likely pathogenic (LP) and 6 pathogenic(P) non-synonymous germline variants (for a total of 9 LP/P variants) and 144 variants of unknown significance (VUS). In total, 19.4% (n=7) of patient samples displayed at least one LP/P variant. Two patient samples contained 2 variants each. Variants classified as VUS, LP, or P were further characterized by possible causative pathway: 37.9% (n=58) of variants were in genes associated with bone marrow failure (BMF), 17.6% (n=27) in driver genes, 13.1% (n=20) in genes associated with inherited leukemias, 11.1% (n=17) in tumor suppressor genes, 7.8% (n=12) in tyrosine kinase genes, and 29.4% (n=45) in other predisposition genes . Many variants were present in more than one pathway and are represented as such. Table 1 demonstrates the genetic characteristics of the 9 P/LP variants found in our cohort. ERCC2 was the only gene with multiple LP/P variants across samples, accounting for 2 (1 LP, 1 P) of the 9 deleterious variants identified (22%). Conclusion: We identified germline variants in cancer predisposition genes in 19.4% of this cohort of infant ALL patients, a higher mutation rate than has previously been reported. Among pathways evaluated, variants in genes associated with bone marrow failure predisposition were the most frequent. Interestingly, variants in ERCC2, which encodes a protein involved with repair of damaged DNA, were recurrent among infants with KMT2A-r ALL. Future directions include comparison to germline variants in cancer predisposition genes in other infant and non-infant ALL cohorts. Disclosures Brown: Novartis: Membership on an entity's Board of Directors or advisory committees; Jazz: Membership on an entity's Board of Directors or advisory committees; Servier: Membership on an entity's Board of Directors or advisory committees; Janssen: Membership on an entity's Board of Directors or advisory committees. Guest:Syndax Pharmaceuticals: Consultancy.

Prevalence of hereditary breast and ovarian cancer predisposition gene mutations among 882 HBOC high-risk Chinese individuals

Objective: Identification of deleterious variants in HBOC susceptible genes allows for increased clinical surveillance and early detection, and could predict the response to PARP inhibitor in patients with advanced ovarian carcinomas.