Mutations In Predisposition Genes Research Articles

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.

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 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.

Germline mutations in RAD51C and RAD51D and hereditary predisposition to ovarian cancer.

Ovarian cancer is one of the most common gynecologic cancers with the highest mortality rate over a long period. Genetic predisposition to ovarian cancer is unusually high. In the Czech Republic, causal mutation in any ovarian cancer predisposition gene is identified in approximately 30% of the ovarian cancer patients. Therefore, according to the current guidelines, all ovarian cancer patients should be provided with genetic testing. The BRCA1 and BRCA2 are the two major ovarian cancer predisposition genes. Nevertheless, mutations in other predisposition genes, including RAD51C and RAD51D, are associated with high ovarian cancer risk. Mutations in RAD51C and RAD51D are found in 1% of ovarian cancer patients in each respective gene. Currently, identification of germline mutation in RAD51C and RAD51D is primarily of preventive importance but it potentially could make a prognostic difference. The aim of this review is to summarize the recent RAD51C and RAD51D knowledge, including the biological function, cancer risks associated with germline mutations, and recommendations for mutation carriers.

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.

The value of a metabolic reprogramming-related gene signature for pancreatic adenocarcinoma prognosis prediction.

Pancreatic ductal adenocarcinoma (PDAC) is one of the most fatal malignancies worldwide. Extensive enhancement of glycolysis and reprogramming of lipid metabolism are both associated with the development and progression of PDAC. Previous studies have suggested that various gene signatures could convey prognostic information about PDAC. However, the use of these signatures has some limitations, perhaps because of a lack of knowledge regarding the genetic and energy supply backgrounds of PDAC. Therefore, we conducted multi-mRNA analysis based on metabolic reprogramming to identify novel signatures for accurate prognosis prediction in PDAC patients. In this study, a three-gene signature comprising MET, ENO3 and CD36 was established to predict the overall survival of PDAC patients. The three-gene signature could divide patients into high- and low-risk groups by disparities in overall survival verified by log-rank test in two independent validation cohorts and could differentiate tumors from normal tissues with excellent accuracy in four Gene Expression Omnibus (GEO) cohorts. We also found a positive correlation between the risk score of the gene signature and inherited germline mutations in PDAC predisposition genes. A glycolysis and lipid metabolism-based gene nomogram and corresponding calibration curves showed significant performance for survival prediction in the TCGA-PDAC dataset. The high-risk designation was closely connected with oncological signatures and multiple aggressiveness-related pathways, as determined by gene set enrichment analysis (GSEA). In summary, our study developed a three-gene signature and established a prognostic nomogram that objectively predicted overall survival in PDAC. The findings could provide a reference for the prediction of overall survival and could aid in individualized management for PDAC patients.

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.

Putative Germline Variants in the Predisposition Genes DDX41, ETV6 and GATA2 investigated in 1,228 Patients with Sporadic AML or MDS

Background: In the latest revision of WHO classification (2017) the new category `myeloid neoplasms with germline predisposition´ was introduced. Pathogenic germline (GL) mutations predisposing to hereditary hematological malignancies (HHMs) have been described in various genes and have largely been identified in families, but may also occur sporadically (Godley, Blood Adv 2019; Rio-Machin et al., Nat Commun 2020). It is estimated that 4-9% of adults with myeloid malignancies have GL predisposition and it is discussed that HHMs could even be more common (Sung and Babushok, Blood 2020). Here, we performed a screening for putative GL variants in the predisposition genes DDX41, ETV6 and GATA2 in a large cohort of 1,228 patients with sporadic AML or MDS. Aim: To determine the frequency of genetic variants in the predisposition genes DDX41, ETV6 and GATA2 in patients with AML or MDS and to characterize the mutational patterns in patients carrying putative GL variants in these genes. Patients and Methods: Between 02/2019 and 01/2020 a total of 1,228 patients were diagnosed with AML or MDS by cytomorphological analysis (475 de novo AML, 647 MDS, 60 s-AML from MDS, 46 MDS/AML; M: 753, F: 475; median age: 74 [20-96]) and analyzed by next-generation sequencing for DDX41, ETV6, GATA2 and additional genes associated with AML or MDS (Figure 1). DNA was isolated from bone marrow or peripheral blood; sequencing was performed on NovaSeq after NextFlex library preparation (Illumina, ILMN, San Diego, CA) and hybrid capture according to manufacturer's protocol (IDT Inc. Coralville, IA). Data was analyzed with Pisces and Pindel (for FLT3-ITD) (available via BaseSpace, ILMN) using a minimum of 3% sensitivity. All changes except for synonymous mutations and known polymorphisms were declared as genetic variants. Results: We identified 73/1,228 patients (5.9%) with genetic variants in DDX41, 28 (2.3%) with variants in ETV6 and 50 (4.1%) with variants in GATA2. Aiming to estimate the proportion of patients carrying a putative GL variant, a variant allele frequency (VAF) higher than 0.3 was considered to be presumptive of a GL origin. We identified 64/1,228 patients (5.2%) with a putative GL variant in DDX41. 37/64 patients harbored DDX41 variants that were previously described as causal GL variants, like for example p.M1I (12/37) or p.D140fs (4/37), and consistent with other studies 43/64 (67.2%) had an additional DDX41 mutation with a lower VAF (&amp;lt;0.3) suggesting somatic acquisition of the second mutation (27/43: p.R525H) (Sébert et al., Blood 2019). 13/1,228 patients (1.1%) were found to have a putative GL variant in ETV6. Two of them carried a p.R353Q mutation which was recently presumed to be a rare GL variant contributing to myeloid malignancy susceptibility (Li et al., Leukemia 2020). 26/1,228 patients (2.1%) carried a putative GL variant in GATA2, including the already in the context of HHMs described mutation p.P41A (3/26) (Holme et al., Br J Haematol 2012). In total, 102/1,228 patients (8.3%) diagnosed with AML or MDS carried a putative GL variant in one of the predisposition genes DDX41, ETV6 or GATA2. Patients with presumed GL variants were about the same age as patients without (mean: 72 vs. 71 years). The mutational patterns for the 102 patients are illustrated in Figure 1. Genes that were most often additionally mutated were ASXL1, DNMT3A, SRSF2 and TET2. For ETV6 and GATA2, all but one of the patients carrying a putative GL variant harbored at least one genetic variant in an additional gene. In contrast, 16/64 patients (25.0%) carrying a presumed GL variant in DDX41 (and in 12 cases a second somatic DDX41 mutation) had no further genetic variants in other well-known AML- or MDS-related genes indicating that DDX41 and especially the gain of a second somatic mutation drives leukemogenesis, while for ETV6 and GATA2 additional hits are required. Conclusions: Our data support the hypothesis that GL mutations in predisposition genes could be more common in sporadic cases of AML or MDS than anticipated highlighting the importance of systematic testing for these variants, irrespective of family history or age. Identifying GL mutations can be important for clinical management, including donor choice for allogeneic stem cell transplantation. Routine workflows should be adapted to improve the identification of variants in predisposition-associated genes and to facilitate confirmation of GL origin, e.g. by analyzing reference material. Figure 1 Disclosures No relevant conflicts of interest to declare.

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.

Adherence to NCCN Guidelines for Genetic Testing in Breast Cancer Patients: Who Are We Missing?

Genetic predisposition accounts for 5-10% of all breast cancers (BC) diagnosed. NCCN guidelines help providers identify appropriate candidates for counseling and testing. Concerns about underutilization of genetic testing have spurred interest in broader peri-diagnostic testing. We evaluated surgeon adherence to NCCN guidelines and studied patterns of testing in newly diagnosed BC patients. A total of 397 patients were identified with newly diagnosed BC treated at our institution between 2016 and 2017 with no prior genetic testing. Eligibility for genetic testing based on NCCN criteria, referral, and patient compliance were recorded. In total, 212 of 397 (53%) met NCCN testing criteria. Fifty-nine of 212 (28%) patients went untested despite meeting one or more criteria. Fourteen of 59 (24%) of these were referred but did not comply. Most common criteria for meeting eligibility for testing both in the overall cohort and among missed patients were family history-based. Age > 45years old and non-Ashkenazi Jewish descent were predictive of missed referral (p < 0.01). We identified pathogenic mutations in 16 of 153 (10%) patients who did undergo testing (11 (7%) BRCA1 or 2 and 5 (3%) with other predisposition gene mutations) or 16 of 397 (4%) among the overall group. Our data highlight the underutilization of genetic testing. Even in the setting of a full-service breast center with readily available genetic counseling, there is a substantial miss rate for identifying eligible patients, related to assessment of family history, patient age, and ethnicity, as well as patient compliance. Broader peri-diagnostic testing should be considered, and higher compliance rates with patients referred should be sought.

Prevalence and clinical implications of germline predisposition gene mutations in patients with acute myeloid leukemia

Acute myeloid leukemia (AML) is one of the most common types of leukemia. With the recent advances in sequencing technology and the growing body of knowledge on the genetics of AML, there is increasing concern about cancer predisposing germline mutations as well as somatic mutations. As familial cases sharing germline mutations are constantly reported, germline predisposition gene mutations in patients with AML are gaining attention. We performed genomic sequencing of Korean patients diagnosed with AML to identify the prevalence and characteristics of germline predisposition mutations. Among 180 patients, germline predisposition mutations were identified in 13 patients (13/180, 7.2%, eight adults and five children). Germline mutations of BLM, BRCA1, BRCA2, CTC1, DDX41, ERCC4, ERCC6, FANCI, FANCM, PALB2, and SBDS were identified. Most of the mutations are in genes involved in DNA repair and genomic stability maintenance. Patients harboring germline mutations tended to have earlier onset of AML (p = 0.005), however, the presence of germline mutations did not showed significant association with other clinical characteristics or treatment outcome. Since each mutation was rare, further study with a larger number of cases would be needed to establish the effect of the mutations.

Abstract 4624: Should genetic testing for cancer predisposition be standard-of-care for women with invasive breast cancer: The Murtha Cancer Center experience

Abstract Background: Currently, genetic testing is recommended to those patients diagnosed with breast cancer at a young age, with triple negative disease, Ashkenazi ancestry and/or a significant family history of breast, ovarian, prostate or pancreatic cancer. This precludes the opportunity to apply precision medicine approaches to women who do not meet these criteria. Timing and uptake of testing in high-risk patients and frequency of mutation detection in low-risk patients was evaluated in a cohort of women with invasive breast cancer treated at the Murtha Cancer Center of the Walter Reed National Military Medical Center (MCC/WRNMMC), the largest hospital of the Department of Defense health-care system. Methods: 1,231 women enrolled in the Clinical Breast Care Project of the MCC/WRNMMC 2001-2018 with invasive breast cancer. Genetic risk status was estimated using NCCN BRCA1/2 Testing Criteria. Panel testing was performed in the research laboratory for 1,043 women who had genomic (blood) DNA available. Genetic variants across 94 cancer predisposition genes were classified as pathogenic, variant of unknown significance (VUS) or benign using the ClinVar database. Results: Using NCCN version 1.2018 criteria, 57.8% of patients were eligible for genetic testing. Uptake of testing within the high-risk group was 40.0%; those who pursued genetic testing were significantly (p&amp;lt;0.001) younger and more likely to be college educated. Time-to-testing ranged from 0 to 15.3 years post-diagnosis and 6.3% of women pursued clinical testing only after a second tumor event. 19.3% of the high-risk women with clinical testing, 7.5% of high-risk women who did not pursue clinical testing and 4.4% of low-risk women carried a pathogenic or likely pathogenic mutation. Conclusions: More than 4% of breast cancer patients who chose not to pursue or were ineligible for genetic testing harbored pathogenic mutations in cancer predisposition genes. These data suggest that inclusion of panel testing at the time of diagnosis would allow for appropriate surveillance and treatment strategies to be employed to reduce the risk of secondary tumors and improve patient outcome. The contents of this publication are the sole responsibility of the author(s) and do not necessarily reflect the views, opinions or policies of Uniformed Services University of the Health Sciences (USUHS), The Henry M. Jackson Foundation for the Advancement of Military Medicine, Inc., the Department of Defense (DoD), the Departments of the Army, Navy, or Air Force. Mention of trade names, commercial products, or organizations does not imply endorsement by the U.S. Government. Citation Format: Seth Rummel, Leann Lovejoy, Clesson Turner, Craig Shriver, Rachel Ellsworth. Should genetic testing for cancer predisposition be standard-of-care for women with invasive breast cancer: The Murtha Cancer Center experience [abstract]. In: Proceedings of the Annual Meeting of the American Association for Cancer Research 2020; 2020 Apr 27-28 and Jun 22-24. Philadelphia (PA): AACR; Cancer Res 2020;80(16 Suppl):Abstract nr 4624.

Abstract 5417: Genomic analysis of infant KMT2A-r acute lymphoblastic leukemia reveals weak association with underlying germline cancer predisposition

Abstract Introduction:KMT2A (MLL) rearranged (KMT2A-r) infant acute lymphoblastic leukemia (ALL) is a distinct leukemia with a poor prognosis, especially when compared to childhood ALL. Previous studies on KMT2A-r leukemia have demonstrated that KMT2A rearrangement can occur in utero with a short latency after birth. Infant ALL with KMT2A-r also demonstrates a low frequency of other somatic mutations. Given that germline mutations in cancer predisposition genes are found in 5-15% of children with cancer, we hypothesized that there might be distinct germline mutations in infants with this type of leukemia that could inform about leukemogenesis and biologic behavior of this entity. Methods: We performed whole genome sequencing (WGS) and whole exome sequencing (WES) on DNA isolated from 43 peripheral blood samples at the time of remission, on 3 cohorts of infants. The cohorts were comprised of infants with KMT2A-r ALL who were known to relapse (n=14) (Cohort A), infants with KMT2A-r ALL who to date have remained in remission (n=14) (Cohort B), and infants with KMT2A germline ALL (n=15) (Cohort C). Sequencing was performed using an Illumina Hiseq 4000 or 2500 to a minimum depth of 90Gb. Alignment and variant calling were performed using the Dragon Bio-IT platform (v 3.2.8, Illumina). We then looked for variants in 347 genes associated with cancer predisposition and bone marrow failure syndromes. Variants present in remission samples at a variant allele frequency of ~50%, and rare (minor allele frequency &amp;lt;0.1%) in control population databases (gnomAD), were considered for analysis and interpreted using ACMG/AMP variant interpretation guidelines.Results:We found 64 germline variants in cohort A (63 variants of unknown significance (VUS) and 1 likely pathogenic (LP) variant), 39 of which are associated with cancer predisposition ( 15 autosomal dominant (AD), 11 autosomal recessive (AR) and 13 others) and 25 other variants associated with bone marrow failure (BMF). In cohort B, we found 67 germline variants (64 VUS and 3 LP), 42 of which are associated with cancer predisposition (12 AD, 14 AR, and 16 others) and 25 other variants associated with bone marrow failure (BMF). Cohort C had 67 germline variants (67 VUS), 50 of which are associated with cancer predisposition (21 AD, 15 AR, and 14 others) and 17 other variants associated with bone marrow failure (BMF).Conclusion:Overall, there were no significant differences across the 3 cohorts in terms of the number and types of variants identified. Although there were germline VUS present in cancer predisposition genes in KMT2A-r infant ALL, there were no distinct recurrent pathogenic variants seen to make a significant association with an underlying cancer predisposition syndrome. Citation Format: Azhar Saeed, Midhat Farooqi, Byunggil Yoo, Rumen Kostadinov, Emily Farrow, Neil Miller, Patrick Brown, Erin Guest. Genomic analysis of infant KMT2A-r acute lymphoblastic leukemia reveals weak association with underlying germline cancer predisposition [abstract]. In: Proceedings of the Annual Meeting of the American Association for Cancer Research 2020; 2020 Apr 27-28 and Jun 22-24. Philadelphia (PA): AACR; Cancer Res 2020;80(16 Suppl):Abstract nr 5417.

Abstract 4600: Germline homologous recombination deficiency pathway defects in a multi-ethnic East Asian, Southeast Asian and South Asian cancer patient cohort

Abstract Introduction There is limited diversity in current hereditary multi-gene testing data-sets, leading to greater challenges in accurate variant classification. To address this, a collaboration between 3 Singapore-based healthcare organizations (Tan Tock Seng Hospital, National Cancer Centre Singapore and Lucence Diagnostics) pooled results from patients of East Asian, Southeast Asian and South Asian ancestry, representing over 60% of the world's population. We hypothesized that a multi-ethnic collaboration would provide deeper understanding of cancer predisposition genes, particularly in terms of novel variants. Methods A total of 704 cancer patients of multi-ethnic Asian (SE Asian, East Asian and South Asian) ethnicity with either a history of breast, ovarian, pancreatic or prostate cancer, were tested with multi-gene panels. All patients were tested by multi-gene testing, including but not limited to BRCA1/2, PALB2 and ATM. In addition to genetic testing, the family histories of the patients were collected. All variants were classified by ACMG criteria. Chi-square testing was used for statistical analysis. Results Three sites (TTSH, NCCS, and Lucence) pooled patients selected for breast (n=458), ovarian (n=176), pancreatic (n=61) and prostate cancer (n=25). The mean and median ages were 44.9 years and 43 years, respectively. Of the 704 patients, 209 had a history of cancer in their first degree relatives, 432 did not and 63 patients did not know of any cancers in their first degree relatives. 122 of 704 patients (17.33%) had pathogenic/likely pathogenic variants in any tested risk-related gene, of which 86 were in BRCA1/2, 11 in PALB2 and 4 in ATM. Some variants were detected in more than one patient. 212 of 704 patients (30.1%) had VUSs detected in any tested risk-related gene, with 32.1% in BRCA1/2. There was a positive association between multiple-cancer status and pathogenic variants (9/22 vs 113/682, p = 0.007). Most notably, among the unique pathogenic/likely pathogenic variants in BRCA1, BRCA2, PALB2 and ATM, 10.64% (5/47), 12.9% (4/31), 30% (3/10) and 25% (1/4) respectively were novel variants, not previously reported in ClinVar (Dec 2019). Conclusion To our knowledge, this is the largest regional multi-ethnic cohort of patients with breast, ovarian, pancreatic and prostate cancer undergoing comprehensive genetic testing. Only one third of patients reported a first-degree family history suggesting that testing ought to be performed if clinical suspicion is high. Notably, 14.1% of BRCA1/BRCA2/PALB2/ATM pathogenic/likely pathogenic variants detected in our cohort were novel variants, not hitherto published in ClinVar. In conclusion, this collaboration demonstrates that testing of Asian patients can enrich global understanding of cancer predisposition gene mutations. This will improve cancer prevention, surveillance, and treatment selection for cancer patients, such as the use of PARP inhibitors for genetic defects of DNA repair. Citation Format: Jens Samol, Wei Lim Chia, Liuh Ling Goh, Matthew Myint, Min-Han Tan, Ru Jin Tay, Hao Chen, Yukti Choudhury, Ann SG Lee. Germline homologous recombination deficiency pathway defects in a multi-ethnic East Asian, Southeast Asian and South Asian cancer patient cohort [abstract]. In: Proceedings of the Annual Meeting of the American Association for Cancer Research 2020; 2020 Apr 27-28 and Jun 22-24. Philadelphia (PA): AACR; Cancer Res 2020;80(16 Suppl):Abstract nr 4600.

The TP53 mutation rate differs in breast cancers that arise in women with high or low mammographic density

Mammographic density (MD) influences breast cancer risk, but how this is mediated is unknown. Molecular differences between breast cancers arising in the context of the lowest and highest quintiles of mammographic density may identify the mechanism through which MD drives breast cancer development. Women diagnosed with invasive or in situ breast cancer where MD measurement was also available (n = 842) were identified from the Lifepool cohort of >54,000 women participating in population-based mammographic screening. This group included 142 carcinomas in the lowest quintile of MD and 119 carcinomas in the highest quintile. Clinico-pathological and family history information were recorded. Tumor DNA was collected where available (n = 56) and sequenced for breast cancer predisposition and driver gene mutations, including copy number alterations. Compared to carcinomas from low-MD breasts, those from high-MD breasts were significantly associated with a younger age at diagnosis and features associated with poor prognosis. Low- and high-MD carcinomas matched for grade, histological subtype, and hormone receptor status were compared for somatic genetic features. Low-MD carcinomas had a significantly increased frequency of TP53 mutations, higher homologous recombination deficiency, higher fraction of the genome altered, and more copy number gains on chromosome 1q and losses on 17p. While high-MD carcinomas showed enrichment of tumor-infiltrating lymphocytes in the stroma. The data demonstrate that when tumors were matched for confounding clinico-pathological features, a proportion in the lowest quintile of MD appear biologically distinct, reflective of microenvironment differences between the lowest and highest quintiles of MD.

Abstract IA04: New approaches to study cancer predisposition syndromes

Abstract The diagnosis of a cancer predisposition syndrome (CPS) in a child diagnosed with cancer influences medical care; however, many open questions remain in the areas of counseling, psychosocial support, cancer prevention, surveillance, and therapy. To address such issues, a CPS-registry was launched: www.cancer-predisposition.org. The CPS-registry (1) provides detailed information for affected families and health care professionals, (2) collects biospecimens for translational research, (3) assembles both retrospective and annual prospective data on cancer diagnoses and surveillance measures in individuals with approximately 60 different CPS, (4) makes mutation data publicly available through accessible databases, (5) shares data internationally, (6) links data with trial groups and cancer registries, and (7) provides expert opinion for individual treatment decisions. Due to hidden clinical signs, CPS are often overlooked; however, various clinical tools have been developed to increase the percentage of families that are being offered counseling and testing. Moreover, CPS diagnosis is dramatically facilitated by the increasing use of agnostic next-generation sequencing in pediatric oncology, supporting the notion that 10% of children with cancer harbor mutations in cancer predisposition genes, often in the absence of clinical signs. CPS diagnosis yet remains a challenge prior to a first cancer diagnosis; however, a more systematic diagnostic approach is required to offer prevention and surveillance measures to these individuals. Strong family support organizations such as LFSA and FARF have dramatically improved collaborative research in the CPS field. In the future, clinical protocols for CPS individuals will pave the way for better prevention, surveillance, and cancer treatment strategies. Citation Format: Christian P. Kratz. New approaches to study cancer predisposition syndromes [abstract]. In: Proceedings of the AACR Special Conference on the Advances in Pediatric Cancer Research; 2019 Sep 17-20; Montreal, QC, Canada. Philadelphia (PA): AACR; Cancer Res 2020;80(14 Suppl):Abstract nr IA04.