Genetic Risk Stratification Research Articles

Measurable Residual Disease (MRD) Monitoring in Acute Myeloid Leukemia (AML) with t(8;21)(q22;q22.1) RUNX1-RUNX1T1 Identifies Patients at High Risk of Relapse: Results of the AML Study Group (AMLSG)

Measurable Residual Disease (MRD) Monitoring in Acute Myeloid Leukemia (AML) with t(8;21)(q22;q22.1) RUNX1-RUNX1T1 Identifies Patients at High Risk of Relapse: Results of the AML Study Group (AMLSG)

The 2017 European Leukemianet Genetic Risk Classification Performs Poorly in Older Patients with Acute Myeloid Leukemia (AML) and Should be Refined to Identify Patients Requiring Additional or Alternative Treatment

The 2017 European Leukemianet Genetic Risk Classification Performs Poorly in Older Patients with Acute Myeloid Leukemia (AML) and Should be Refined to Identify Patients Requiring Additional or Alternative Treatment

Impact of Somatic Mutations on Outcome in Patients > 60 Years Old with Newly Diagnosed AML Treated with Response-Adapted Sequential Azacitidine and Induction Chemotherapy within the DRKS00004519 Trial (RAS-AZIC) of the East German Study Group of Hematology and Oncology (OSHO)

Introduction: Old age and unfavorable cytogenetics are well-established adverse prognostic factors for outcome in patients (pts) with AML. Recently, high-throughput sequencing techniques have identified multiple somatically acquired driver mutations (muts) with a strong prognostic impact in AML. We explored the relative contribution of baseline molecular genetics versus a response-based sequential treatment approach on response and overall survival (OS) at two years in pts >60 years (y) with newly diagnosed AML treated within the multicenter RAS-AZIC study of the OSHO. Patients and methods: In the RAS-AZIC trial, 112 pts received priming with Azacitidine (AZA) followed by a day (d) 15 bone marrow (BM) blast count-adapted sequential treatment with AZA or intensive chemotherapy (IC). Pts with d15 blasts ≥45% received IC. If the count was <45%, AZA was continued at d28. The second treatment adaptation was based on d56 response. If no complete remission (CR) or CR with incomplete recovery (CRi) were documented, IC was applied followed by AZA maintenance or allogeneic hematopoietic stem cell transplantation if a remission was achieved on d90. Conventional cytogenetics, NPM1, and FLT3 mutational screening were used for genetic risk stratification following the 2010 ELN recommendations. Response [CR/CRi/Partial remission (PR)] and treatment-related mortality on d90, the two-year OS, event-free survival (EFS), and relapse-free survival (RFS) were previously presented (Jaekel N, et al; ASH 2018). Baseline BMs of 77 pts who signed the translational informed consent were analyzed by NGS using the NEOmyeloid panel of NEO New Oncology (Siemens Healthineers Company, Germany). This hybrid capture-based assay comprises 43 genes and detects point muts, small insertions and deletions in 30 genes as well as gene fusions in 18 genes. Molecular results were correlated to outcome data. Results: Median age was 70y. Secondary AML was present in 39%. Genetic risk was int-II and adverse in 25% and 27% respectively. Response on d90 was 67% (CR/CRi 58%, PR 9%). A median of 3 muts per pt were found. Mutations in DNA methylation-related-, spliceosome complex-, and chromatin-modifying-genes were 62%, 39%, and 30% respectively. Overall, muts in DNMT3A (34%), ASXL1 (25%), RUNX1 (24%), SRSF2 (23%), and TET2 (23%) were the most frequently detected (fig. 1). As expected, 72% of SRSF2 muts were associated with ASXL1 and/or RUNX1 muts. CR/CRi in the favorable and int-I 2010 ELN genetic risk groups was 81% and 57.5% in int-II and adverse risk pts. With the exception of muts in spliceosome complex-related genes, the mutational status (including the FLT3 status) seemed to have no impact on response in this cohort (table 1). In the presence of splicing factor gene muts a trend towards an inferior response of 53% compared to 77% in pts without such a mut was observed. High risk muts such as ASXL1, RUNX1, and TP53 muts which were included in the 2017 ELN adverse risk stratification were present in 20/32 (63%) of pts with favorable and int-I genetic risk. Yet, only 5/32 (16%) did not achieve a response. Similarly, CR/CRi was achieved in 7/9 (78%) pts with TP53 mut which was associated with an adverse karyotype in 8 pts. Likewise, OS tended to be similar across all molecular classes with the exception of KMT2A gene fusions with their well-known negative impact on outcome. The presence of such a fusion (n=4) was associated with a median survival time of only 8 compared to 16 months in pts without a detectable KMT2A fusion. These KMT2A gene fusions also correlated with a shorter EFS and RFS. The presence of myeloid transcription factor gene muts such as in RUNX1 (24%) and BCOR (13%) tended to be associated with an inferior EFS, while cohesin complex- (STAG2 8%), tumour suppressor-, and DNA-methylation-related gene muts with a negative RFS (table 1). Conclusions: This explorative analysis with a limited number of patients describes the pattern of genetic mutations in elderly AML treated with a response-based sequential approach that integrates epigenetic and chemotherapeutic treatments and their association with outcome. Whether such a response-based treatment mitigates the negative impact of (some) high risk mutations on outcome needs to be addressed in a much larger trial. Disclosures Jaekel: Celgene: Other: travel grant. Siebolts:Merck: Honoraria; Boehringer Ingelheim: Honoraria; MSD: Honoraria; Pfizer: Honoraria; AstraZeneca: Honoraria; Roche: Honoraria; Novartis: Honoraria; BMS: Honoraria. Pazaitis:Novartis: Consultancy. Niederwieser:Daichii: Speakers Bureau; Cellectis: Consultancy. Hänel:Amgen: Honoraria; Roche: Honoraria; Novartis: Honoraria; Takeda: Other: advisory board; Celgene: Other: advisory board. Maschmeyer:Gilead, Janssen Cilag, Astra Zeneca; BMS, Merk-Serono: Honoraria. Heukamp:NEO New Oncology GmbH: Employment. Menon:NEO New Oncology GmbH: Employment. Bertrand:NEO New Oncology GmbH: Employment. Wickenhauser:BMS: Honoraria; Merck-Serono: Honoraria; MSD: Honoraria; Böhringer: Honoraria; Novartis: Honoraria; Takeda: Honoraria; Roche: Honoraria. Brosteanu:University Leipzig: Employment. Al-Ali:Celgene: Research Funding; Novartis: Consultancy, Honoraria, Research Funding; CTI: Honoraria.

Genetic Characterization and Prognostic Relevance of Acquired Uniparental Disomies in Cytogenetically Normal Acute Myeloid Leukemia.

Uniparental disomy (UPD) is a way cancer cells duplicate a mutated gene, causing loss of heterozygosity (LOH). Patients with cytogenetically normal acute myeloid leukemia (CN-AML) do not have microscopically detectable chromosome abnormalities, but can harbor UPDs. We examined the prognostic significance of UPDs and frequency of LOH in patients with CN-AML.Experimental Design: We examined the frequency and prognostic significance of UPDs in a set of 425 adult patients with de novo CN-AML who were previously sequenced for 81 genes typically mutated in cancer. Associations of UPDs with outcome were analyzed in the 315 patients with CN-AML younger than 60 years. We detected 127 UPDs in 109 patients. Most UPDs were large and typically encompassed all or most of the affected chromosome arm. The most common UPDs occurred on chromosome arms 13q (7.5% of patients), 6p (2.8%), and 11p (2.8%). Many UPDs significantly cooccurred with mutations in genes they encompassed, including 13q UPD with FLT3-internal tandem duplication (FLT3-ITD; P < 0.001), and 11p UPD with WT1 mutations (P = 0.02). Among patients younger than 60 years, UPD of 11p was associated with longer overall survival (OS) and 13q UPD with shorter disease-free survival (DFS) and OS. In multivariable models that accounted for known prognostic markers, including FLT3-ITD and WT1 mutations, UPD of 13q maintained association with shorter DFS, and UPD of 11p maintained association with longer OS. LOH mediated by UPD is a recurrent feature of CN-AML. Detection of UPDs of 13q and 11p might be useful for genetic risk stratification of patients with CN-AML.

Machine Learning by Ultrasonography for Genetic Risk Stratification of Thyroid Nodules

Thyroid nodules are common incidental findings. Ultrasonography and molecular testing can be used to assess risk of malignant neoplasm. To examine whether a model developed through automated machine learning can stratify thyroid nodules as high or low genetic risk by ultrasonography imaging alone compared with stratification by molecular testing for high- and low-risk mutations. This diagnostic study was conducted at a single tertiary care urban academic institution and included patients (n = 121) who underwent ultrasonography and molecular testing for thyroid nodules from January 1, 2017, through August 1, 2018. Nodules were classified as high risk or low risk on the basis of results of an institutional molecular testing panel for thyroid risk genes. All thyroid nodules that underwent genetic sequencing for cytological results with Bethesda System categories III and IV were reviewed. Patients without diagnostic ultrasonographic images within 6 months of fine-needle aspiration or who received definitive treatment at an outside medical center were excluded. Thyroid nodules were categorized by the model as high risk or low risk using ultrasonographic images. Results were compared using genetic testing. Among the 134 lesions identified in 121 patients (mean [SD] age, 55.7 [14.2] years; 102 women [84.3%]), 683 diagnostic ultrasonographic images were selected. Of the 683 images, 556 (81.4%) were used for training the model, 74 (10.8%) for validation, and 53 (7.8%) for testing. Most nodules had no mutation (75 [56.0%]), whereas 43 nodules (32.1%) had a high-risk mutation and 16 (11.9%) had an unknown or a low-risk mutation (χ2 = 39.060; P < .001). In total, 228 images (33.4%) were of nodules classified as genetically high risk (n = 43), and 455 (66.6%) were of low-risk nodules (n = 91). The model performed with a sensitivity of 45% (95% CI, 23.1%-68.5%), a specificity of 97% (95% CI, 84.2%-99.9%), a positive predictive value of 90% (95% CI, 55.2%-98.5%), a negative predictive value of 74.4% (95% CI, 66.1%-81.3%), and an overall accuracy of 77.4% (95% CI, 63.8%-97.7%). The study found that the model developed through automated machine learning could produce high specificity for identifying nodules with high-risk mutations on molecular testing. This finding shows promise for the diagnostic applications of machine learning interpretation of sonographic imaging of indeterminate thyroid nodules.

Cost-Effectiveness Analysis of a HMGA2 Prognostic Test for Acute Myeloid Leukemia in a Canadian Setting.

BackgroundCurrent strategies for risk stratification of patients with acute myeloid leukemia assign approximately 40% of patients to the intermediate-risk group, where uncertainty about optimal therapy still persists.ObjectiveThe objective of this study was to assess the cost effectiveness of a HMGA2 prognostic test based on HMGA2+/HMGA2− expression, which improves genetic risk stratification in acute myeloid leukemia, and compare this test with the current standard of care in Canada.MethodsA cost-effectiveness model was developed from the Canadian National Healthcare Service and societal perspective using data from the Quebec Leukemia Cell Bank, published literature, and physician surveys. The model includes a lifetime horizon assessing the HMGA2 test vs. standard of care.ResultsThe HMGA2 test outperformed the standard of care at all time horizons culminating with estimated improvements of 1.92 and 3.12 months in leukemia-free survival and overall survival, respectively. Costs associated with the HMGA2 test were consistently lower, except diagnostic costs, routine medical costs, and costs related to infections and false positives. From a societal perspective, total lifetime costs were $161,358 CAD and $151,908 CAD with the standard of care and the HMGA2 test, respectively. The incremental quality-adjusted life-year gain was 0.138, which led to dominance over the standard of care. Deterministic sensitivity analyses confirmed the results of the base-case scenario. Probabilistic sensitivity analyses revealed that for a willingness-to-pay threshold of $100,000 CAD, the probability of cost effectiveness was 87.19%.ConclusionsThe HMGA2 test is estimated to improve leukemia-free survival and overall survival outcomes, and yield costs savings from a healthcare system and societal perspective.Electronic supplementary materialThe online version of this article (10.1007/s40258-019-00503-5) contains supplementary material, which is available to authorized users.

Genome-wide association study of medication-use and associated disease in the UK Biobank

Genome-wide association studies (GWASs) of medication use may contribute to understanding of disease etiology, could generate new leads relevant for drug discovery and can be used to quantify future risk of medication taking. Here, we conduct GWASs of self-reported medication use from 23 medication categories in approximately 320,000 individuals from the UK Biobank. A total of 505 independent genetic loci that meet stringent criteria (P < 10−8/23) for statistical significance are identified. We investigate the implications of these GWAS findings in relation to biological mechanism, potential drug target identification and genetic risk stratification of disease. Amongst the medication-associated genes are 16 known therapeutic-effect target genes for medications from 9 categories. Two of the medication classes studied are for disorders that have not previously been subject to large GWAS (hypothyroidism and gastro-oesophageal reflux disease).

A genetic risk score to personalize prostate cancer screening, applied to population data.

181 Background: Genetic risk stratification may inform the decision of whether—and at what age—a man should undergo prostate cancer (PCa) screening. We previously validated a polygenic hazard score (PHS) for accurate prediction of age of onset of aggressive PCa and for improved screening PSA performance. The PHS is a weighted sum of 54 SNP genotypes. Here, we applied the PHS to population data to assess its potential impact on individualized screening. Methods: Age-specific PCa incidence data were obtained for men aged 40-70 years from the United Kingdom (Cancer Research UK, 2013-2015) and fit to an exponential curve as a continuous model of age-specific PCa incidence. Using hazard ratios estimated from ProtecT study data, annualized incidence rate curves were calculated for the following percentiles of genetic risk: 1, 5, 20, 50, 80, 95, and 99. The proportion of incidence classified as aggressive (Gleason score ≥7) was estimated as 59.7%, the reported result from the CAP trial. PHS was combined with incidence data to give a risk-equivalent age, when a man with given PHS percentile will have the same risk of aggressive PCa as that of a typical man at age 50 years. Results: The age-specific incidence rate of PCa for the UK population was modeled as: 0.004 e0.203(age-40) ( R2 = 0.957, p = 0.001). Table shows risk-equivalent age for each genetic risk percentile. For example, a man with a PHS in the 95th percentile reached PCa risk equivalent to a typical 50-year-old man at age 44 years; conversely, a man with a PHS in the first percentile does not reach this risk level until age 60 years. Initiation of screening discussions could be adjusted accordingly. Conclusions: PHS may inform PCa screening with individualized estimates of risk-equivalent age for aggressive PCa. Risk-equivalent age for aggressive prostate cancer, by PHS percentile. [Table: see text]

Molecular characterization of Portuguese patients with dilated cardiomyopathy

IntroductionDilated cardiomyopathy (DCM) is a disease of the heart muscle characterized by ventricular dilatation and impaired systolic function. Familial forms account for 30-50% of cases. Autosomal dominant inheritance is the predominant pattern of transmission. Causal genetic variants have been identified in several genes and molecular diagnosis has implications for genetic counseling and risk stratification. ObjectiveWe aimed to estimate the frequency of genetic variants and the molecular basis of DCM in Portugal. MethodsWe performed a multicenter study of unrelated patients, recruited between 2013 and 2014. Variants in 15 genes were screened using PCR with direct sequencing (next-generation sequencing with at least 30-fold coverage combined with Sanger sequencing). ResultsA total of 107 patients were included, 64 (60%) men, mean age at diagnosis 38±13 years, with 48 (45%) familial cases. In total, 31 rare variants in eight genes (mainly in MYBPC3, TNNT2 and LMNA) were identified, in 28 patients (26%). Only four variants had been previously described in association with DCM, 11 with hypertrophic cardiomyopathy, and nine variants were novel. Four variants were likely pathogenic and the remainder were of uncertain significance. We found no major differences in the main clinical and imaging characteristics between patients with or without rare variants and patients with likely pathogenic variants. ConclusionsOur results reflect the complexity and diversity of DCM genetics. For better interpretation of the pathogenicity of the variants found and their causative roles in DCM, molecular cascade screening of families is imperative. Further insight into genotype-phenotype correlations and risk stratification is desirable.

A 17-Gene Leukemia Stem Cell (LSC) Score in Adult Patients (Pts) with Acute Myeloid Leukemia (AML) Reveals a Distinct Mutational Landscape and Refines Current European Leukemianet (ELN) Genetic Risk Stratification

Introduction: Prognosis of AML pts is still poor mainly because of refractoriness to or relapse after intensive chemotherapy. High rates of relapse are also attributed to LSCs, which are a small subset of cells with acquired abnormal self-renewal capacity and increased resistance to chemotherapy. A better understanding of LSCs is critical to improve outcomes of pts with AML. Ng et al. (Nature 2016;540:433) defined a 17 stemness-associated gene score that was highly prognostic.Aims: The aim of this study was to validate the prognostic relevance of the 17-gene LSC score and explore its utility in the context of the ELN classification. We also examined gene mutations associated with the 17-gene LSC score.Methods: We analyzed a total of 934 pts [729 aged <60 years (y) and 205 aged ≥60 y] with de novo AML. We used whole transcriptome expression data (RNAseq) to calculate the aforementioned 17-gene LSC score for each pt in our cohort. Similar to Ng et al., we used the median of the whole cohort to discriminate between pts with LSChigh and LSClow scores. The mutational status of 80 cancer- and leukemia-associated genes (Eisfeld et al. Leukemia 2017;31:2211) were determined using a targeted next-generation sequencing panel, CEBPA mutations using Sanger sequencing, and an internal tandem duplication (ITD) of the FLT3 gene using fragment analysis in pretreatment bone marrow or blood samples. All pts were treated on frontline Cancer and Leukemia Group B/Alliance protocols.Results: A comparison of pretreatment clinical and genetic features revealed that LSChigh pts were older (P<.001; median age, 53 vs 46 y) and had higher platelet counts (P<.001; median, 63 vs 50x109/L) than LSClow pts. Pts with a LSChigh score more frequently had FLT3-ITD (P<.001) and mutations in the ASXL1 (P=.001), DNMT3A (P<.001), RUNX1 (P=.002), SRSF2 (P=.02), STAG2 (P=.009), TET2 (P=.008) and TP53 (P<.001) genes. Conversely, these pts had a lower frequency of biallelic CEBPA (P<.001), GATA2 (P=.008) and KIT (P<.001) mutations.Because of differences in treatment intensity, we analyzed outcomes of younger and older pts separately. Younger pts with a LSChigh score had a lower complete remission (CR) rate (P<.001; 63% vs 87%), shorter disease-free survival (DFS; P<.001; 3-y rates, 26% vs 48%; Figure 1A) and overall survival (OS; P<.001; 3-y rates, 27% vs 59%; Figure 1B) compared to those of LSClow pts. In multivariable analyses including clinical and genetic factors that impact on outcome, a LSChigh score associated with lower remission rates (P<.001; HR: 0.36), shorter DFS (P<.001; HR: 1.67) and OS (P<.001; HR: 1.88) after adjusting for other co-variates. We also analyzed the prognostic impact of the LSC score with respect to the 2017 ELN classification. We found that LSC score associated with different ELN groups (P<.001), with LSChigh pts being more often classified in the Adverse or Intermediate group and less often in the Favorable group. Within the ELN Favorable and Adverse groups, LSChigh score retained its prognostic impact and identified pts with a lower CR rate and shorter DFS and OS (Table1).In older pts, a LSChigh score also associated with lower CR rate (P=.004; 50% vs 72%), shorter DFS (P=.04; 3-y rates, 6% vs 17%; Figure 1C) and OS (P<.001; 3-y rates, 9% vs 27%; Figure 1D). In multivariable analyses, LSC score remained significant only for OS (P<.003; HR: 1.70) after adjusting for other co-variates. Regarding the ELN classification, pts with LSChigh score in the Favorable group had shorter OS (P=.05; 3-y rates, 17% vs 50%) and, by trend, shorter DFS (P=.09; 3-y rates, 17% vs 39%); no significant differences were found in Intermediate or Adverse groups.Conclusions: We used RNAseq expression data and applied the previously established 17-gene LSC signature to score 934 de novo AML pts. We detected distinct mutational differences between LSChigh and LSClow pts, with LSChigh pts more often carrying gene mutations associated with age-related clonal hematopoiesis (i.e., ASXL1, DNMT3A, TET2, SRSF2 and TP53 mutations). Moreover, this score, derived from the expression of stemness-associated genes, has not only a prognostic impact on its own but also in the context of the current 2017 ELN classification. [Display omitted] DisclosuresKolitz:Magellan Health: Consultancy, Honoraria. Powell:Rafael Pharmaceuticals: Membership on an entity's Board of Directors or advisory committees.

Clinical Utility of Multiple-Gene Mutation Testing By Next-Generation Sequencing in Acute Myeloid Leukemia in Community Hospital Setting

Clinical Utility of Multiple-Gene Mutation Testing by Next-Generation Sequencing in Acute Myeloid Leukemia in Community Hospital SettingIntroductionThe WHO 2016 classification system and the 2017 European LeukemiaNet (ELN) genetic risk stratification system incorporate cytogenetic aberrations and mutations of specific genes to classify acute myeloid leukemia (AML) and stratify prognosis of AML patients. Next-generation sequencing (NGS) of multiple genes associated with AML has been shown to be an important tool in studying AML in research and academic center settings. Our goal is to evaluate the clinical application of NGS in a community hospital setting which has not been well documented leading to rejection of coverage by some insurers.MethodologyThis retrospective study included 109 patients (52 females and 57 males with mean age of 58.7) from November, 2016 to June, 2018 with various races/ethnicities background and confirmed diagnosis of AML at Florida Hospital (FH). DNA was extracted from the peripheral blood/bone marrow for NGS analysis. A total of 54 hematopoietic tumor associated genes were studied: ABL1, ASXL1, ATM, BCOR, BIRC3, BRAF, CALR, CBL, CEBPA, CREBBP, CSF1R, CSF3R, DNMT3A, EP300, ETV6, EZH2, FBXW7, FGFR4, FLT3, GATA1, GATA2, GATA3, IDH1, IDH2, IL7R, JAK2, JAK3, KDM6A, KIT, KMT2A, KRAS, MPL, NF1, NOTCH1, NOTCH2, NPM1, NRAS, NSD1, PAX5, PDGFRA, PDGFRB, PTPN11, RUNX1, SETBP1, SF3B1, SRSF2, STAG2, TERT, TET1, TET2, TP53, TSLP,U2AF1 and ZRSR2. The sequencing was performed at Genomics and Pathology Services laboratory at Washington University in St. Louis and initial informatics analysis was performed by PierianDX using Clinical Genome Working platform. The initial analysis results were delivered to the pathologists at FH to do final interpretation with integration of the results of morphology/flow cytometry/karyotyping studies.The clinical utility of NGS was evaluated by: 1) comparing the AML classification and ELN genetic risk stratification of each patient with and without NGS data, 2) identifying gene mutations for targeted therapy and 3) other clinical impacts.ResultsNGS results changed ELN risk stratification in 45 cases (41.3%) and WHO AML classification in 37 cases (33.9%) out of 109 cases after considering the mutation status of NPM1, FLT3, RUNX1, ASXL1 and TP53. Among the 45 cases that had changes of ELN risk, 25 cases (55%) were downgraded to favorable risk group all because of mutations in NPM1 gene. While, the rest 20 cases (45%) were upgraded to adverse risk group due to the following mutations (RUNX1 in 7, TP53 in 5, ASXL1 in 4, RUNX1 and ASXL1 in 4). The change of WHO classification was caused by mutations in NPM1 (n=26) or RUNX1 (n=11). Additionally, NGS identified 8 cases with either GATA2 or CEBPA gene mutation, which are considered to increase the risk of myeloid neoplasms with germline predisposition based on WHO classification. Finally, NGS identified 42 patients (38.5%) carrying FLT3-ITD (n=17), FLT3-TKD (n=8) and/or IDH1/IDH2 (n=16) mutations. These mutations are known to have approved targeted therapies (FLT3 inhibitors and IDH2 inhibitors) or ongoing clinical trials (IDH1 inhibitors). Overall, NGS results led to clinically significant impacts in 62/109 (56.9%) patients by changing the AML classification/risk stratification, finding potential germline mutation and/or targeted therapies.DiscussionOur results indicate that NGS findings provide important information for classification, risk stratification, genetic predisposition, and treatment options in the majority (62/109, 56.9%) of AML patients in a community hospital setting. How the information exactly changes the clinical management by community practicing hematologists is currently ongoing and will provide further insights in regards to the clinical utilities of NGS. In addition, NGS of multiple genes is more cost- and labor-effective than single gene sequencing. Taken together, the insurers should accept NGS testing as a standard of care for AML patients. DisclosuresNo relevant conflicts of interest to declare.

ELN Genetic Risk Stratification Not Affect the Mid-Term Survival in Childhood AML: Report from Southern China Childhood AML Group

OBJECTIVETo evaluate the survival of children with acute myeloid leukemia (AML) in the ELN genetic risk stratification. To explore the precise treatment and efficacy in childhood AML. MethodsThe information of genetics of 151 newly diagnosed AML children enrolled in the Southern China Childhood AML Collaboration Group from December 2014 to June 2017 were retrospectively analyzed. These patients was divided into low-risk, intermediate-risk and high-risk groups according to the ELN genetic risk stratification. All cases were treated with the Southern China Childhood AML Collaborative Group protocol. The induction of remission was not randomized using FLAG-IDA and DAE regimens for 2 courses of treatment. The consolidation therapy was performed using HAE and MidAC regimens. 20 cases underwent hematopoietic stem cell transplantation. The mediate follow-up time was 18 months. Survival analysis and Log-Rank test were investigated by Graphpad Prism software. RESULTSOf 151 children with AML, AML1/ETO positive in 46(30.5%) cases, CBFβ/MYH11 positive in 12(7.9%) cases, MLL gene in 18(11.9%) cases (including MLLT3-KMT2A in 7 cases). There were mutation gene FTL3/ITD in 24(15.9%) cases, ASXL1 mutation In 10(6.6%) cases, NPM1 mutation in 3(2.0%) cases and CEBPA double mutation in 4(2.6%) cases. Chromosome -7 or 7q- was found in 5(3.3%) cases. According to the ELN genetic risk stratification, 60/151(39.7%), 52/151(34.4%) and 39/151(25.8%) of patients were classified as low-risk, intermediate-risk and high-risk respectively. In the cohort of DAE induction, the CR+CRi rate was 95%, 69% and 80% in the low-risk, intermediate-risk and high-risk group. In the cohort of FLAG-IDA induction, the CR+CRi rate was 100%, 95% and 100% in the low-risk, intermediate-risk and high-risk group. The significance of CR+CRi rate only were be seen in the intermediate-risk group( P=0.02). The 2 year overall OS and DFS were 82.56% and 75.74% respectively. The 2-year DFS of the FLAG-IDA and DAE groups were 85.38% and 53.72% respectively (P=0.0004). The 2-year DFS of the LR, IR, and HR groups in the FLAG-IDA group were 89.23%, 92.29%, and 91.67% respectively, and no statistical difference was found among the groups (P=0.909). The 2-year DFS of the chemotherapy group and the hematopoietic stem cell transplantation group were 82.24% and 63.38%. There were no statistical differences between the groups. DiscussionThe FLAG-IDA induction group significantly improved DFS compared with the DAE group. Hematopoietic stem cell transplantation failed to improve the survival of children with AML in the short period in our multicentre study. Our mid-term results show that the ELN genetic risk stratification had not a significant impact on the prognosis of newly diagnosed childhood AML with high-intensity therapy. DisclosuresNo relevant conflicts of interest to declare.

Uniparental Disomies (UPD) of Chromosome 13q Is Associated with Shorter Disease-Free Survival in Adult Patients (Pts) with De Novo Cytogenetically Normal Acute Myeloid Leukemia (CN-AML)

Approximately 45% of adult AML pts do not have cytogenetic abnormalities visible by microscopic karyotype analysis and are classified as CN-AML. However, these pts can still have one or more UPD (the loss of a chromosome or its segment and duplication of the remaining chromosome or segment), since UPDs are not detectable by typical karyotyping methods. Because UPDs have been shown to contribute to malignant transformation and outgrowth in various cancers and leukemias, we sought to identify recurrent UPDs in CN-AML pts and explore their associations with disease presentation, gene mutations and outcome. We used Infinium OmniExpress SNP arrays to detect UPDs in a cohort of 425 pts, who were similarly treated with intensive chemotherapy on Alliance for Clinical Trials in Oncology therapeutic trials. Pts having early death (<30 days) were excluded. The mutation status of 80 genes were previously assessed by targeted sequencing (Leukemia, 2017;31(10):2211-8).UPDs of 10 different chromosome arms were detected in >1% of pts (Figure A). The most commonly occurring UPDs were UPD of 13q (present in 7.5% of pts), UPD of 6p (in 2.4% of pts) and UPD of 11p (in 2.4% of pts). We examined associations between UPDs of 13q, 6p and 11p with demographic and clinical diagnostic characteristics. UPD of 6p was associated with higher peripheral blood (PB) blast percentage (median 86% vs 70%, P=.02); UPD of 11p was associated with lower platelet counts (41 vs. 60 x 109/L, P=.03) and higher PB blast percentage (85% vs 60%, P=.002); and UPD of 13q was associated with higher white blood cell count (53 vs 29 x 109/L, P=.02), higher PB blast percentage (77% vs 58%, P=.004) and higher bone marrow blast percentage (80% vs 69%, P=.005). We also examined the associations between UPDs and gene mutations present in >2% of CN-AML pts in our sample series. 13q UPD significantly co-occurred with FLT3-internal tandem duplication (ITD) (P<.001), and UPD of 11p significantly co-occurred with bi-allelic CEBPA mutations (P<.001). The co-occurrence of FLT3-ITD with 13q UPD likely has biologic relevance since FLT3 is located on 13q, whereas the association between 11p UPD with CEBPA mutation is less clear, as CEBPA is on 19q.Assessment of the association between UPDs and outcome was performed. Because of differences in induction therapies between pts younger and older than 60 years (y), outcome analyses must be performed separately in these two age groups. Based on sample size limitations we were only able to assess the impact of 11p UPD and 13q UPD on achievement of complete remission (CR), disease-free survival (DFS) and overall survival (OS) in the 315 pts younger than 60 y. UPD of 11p was associated with longer OS (3 y rates, 83% vs 45%, P=.02), and UPD of 13q was associated with shorter DFS and OS (3 y rates, 0% vs 38%, P<.001; 17% vs 49%, P<.001) (Figure B). To examine the combined effect of mutations and UPDs on outcome we performed multivariable analyses (MVAs). We found that UPD of 13q was significantly associated with shorter DFS (P=.009) after adjusting for hemoglobin levels (P=.02), FLT3-ITD status (P <.001), and mutation of DNMT3A (P<.001), RUNX1 (P=.002) and WT1 (P=.03) (Table). UPD of 13q did not impact on CR or OS when considered in a MVA, and UPD of 11p did not remain significant in MVA.Finally, since FLT3-ITD and UPD of 13q often co-occurred and were both found to be associated with shorter DFS in the MVA of adult younger pts, we examined younger pts who harbored FLT3-ITD for differences in DFS associated with UPD of 13q. We found those pts with 13q UPD had significantly shorter DFS (P=.003) compared to those without (Figure C), which further demonstrates 13q UPD status is useful for prognostic stratification independent from its association with the known prognostic marker FLT3-ITD.These data show the incorporation of 13q UPD might improve current genetic risk stratification models. Follow-up studies investigating the mechanistic roles of these recurrent UPDs, especially the relationship between UPD of 11p and bi-allelic CEBPA mutation, could shed light on novel pathways underlying leukemic transformation and proliferation in CN-AML. [Display omitted] DisclosuresPowell:Rafael Pharmaceuticals: Membership on an entity's Board of Directors or advisory committees. Kolitz:Magellan Health: Consultancy, Honoraria.

Postnatally Acquired Mutations Underlie the Progression of Transient Leukemia to Myeloid Leukemia of Down Syndrome

INTRODUCTION. Transient Leukemia (TL; also termed Transient Myeloproliferative disorder, TMD, and Transient Abnormal Myelopoiesis, TAM) occurs in 10-30% of newborns with Down syndrome (DS). Approx. 20% of infants with TL go on to develop acute myeloid leukemia of DS (ML-DS), typically within the first four years of life. Somatic, clone-specific mutations of GATA1 are found both in the blasts of TL and ML-DS, are concordant within the same individual and thought to function as initiating event in the development of ML-DS. In contrast, additional mutations of cohesin complex and related genes (e.g. RAD21, STAG2, CTCF), epigenetic regulators (e. g. EZH2) and signal transducers (e.g. within RAS, JAK signaling pathways) have been identified only in ML-DS blasts and are thought to cooperate with mutant GATA1 in the progression from TL to ML-DS. It is not known whether these cooperating mutations already mark a minor subclone of TL blasts at birth - allowing, at least in principle, a genetic risk stratification of TL - or are acquired postnatally during the first four years of life.OBJECTIVES. We tested the functional impact of impaired function of cohesin complex genes, CTCF and EZH2 on the progression of TL to ML-DS. We asked if mutations representing putative genetic progression events were already detectable at birth in a minor clone of TL blasts or were acquired postnatally (during the first four years of life).METHODS. The spectrum of GATA1 and cooperating mutations was determined by whole exome sequencing in fractions of TL and ML-DS blasts sorted from blood and bone marrow samples of five patients who had successively developed both disorders including one with a relapse of ML-DS. Corresponding normal T lymphocyte fractions of each patient at the stage of TL and ML-DS served as controls. Numbers of blasts harboring specific mutations were quantified by digital droplet PCR (BioRad, Inc.). Primary TL cells were transduced with lentivirus encoding shRNA (pLVX-shRNA, Clontech, Inc.) to suppress expression of cohesin complex genes, CTCF and EZH2 and intrafemurally injected into 8 week old NSG recipient mice. Engraftment in the bone marrow was assessed 8 weeks later by flow cytometry and GATA1 mutational analysis and compared to TL cells transduced with control vector.RESULTS. TL blasts harbored fewer mutations than those of ML-DS. GATA1 mutations were concordant in TL and ML-DS blasts in the same patient, consistent with development of ML-DS from subclone of TL. Knockdown of RAD21 expression in primary TL blasts, mimicking loss of function mutation of a cohesin complex gene, resulted in significantly increased engraftment of transduced cells in xenograft recipients compared to controls. This finding is consistent with RAD21 loss of function mutations playing the role of a progression event. Mutations of cohesin complex genes (SMC1A, STAG2, RAD21), NRAS and other putative cooperating mutations (with mutant GATA1) were not detectable in any sample of primary TL blasts by either whole exome sequencing or digital droplet PCR. The same result was obtained with control T lymphocytes sorted from TL samples. ML-DS blasts in one case were oligo-clonal with regard to cohesin complex gene mutations. Relapse in this patient arose from a minor clone as defined by cohesin complex gene mutations; mutations of NRAS, KNASL1 and SMC1A were present in ML-DS blasts but absent at relapse.CONCLUSIONS. Increased engraftment of TL cells with suppressed RAD21 expression is consistent with a model in which RAD21 loss of function mutations function as a progression event in the development of ML-DS. Absence of detectable cohesin complex gene mutations and other putative cooperating events in TL blasts suggests these mutations are acquired during the first four years of life and do not mark a minor clone of TL blasts present at birth. Genomic screening of TL blasts at birth therefore is unlikely to predict the risk for development of ML-DS. DisclosuresNo relevant conflicts of interest to declare.

Additional Gene Mutations Refine the 2017 European Leukemianet (ELN) Classification of Adult Patients (Pts) with De Novo Acute Myeloid Leukemia (AML) Aged

The ELN recommendations for diagnosis and management of AML in adults, authored by a panel of international experts, have become an important tool to assess pts' prognosis and guide treatment decisions. Following advances in our understanding of the molecular landscape of AML, several gene mutations were added as criteria for assigning pts to genetic risk categories in the 2017 ELN classification.The aim of our study was to apply the 2017 ELN risk groups to a large cohort of 864 AML pts aged <60 years who were similarly treated with intensive cytarabine/daunorubicin based chemotherapy on Cancer and Leukemia Group B/Alliance protocols. In addition, we sought to identify novel gene markers that could refine the ELN classification.Using the 2017 ELN genetic risk-stratification criteria, we assigned 49% of pts to the Favorable-risk group, whereas 22% and 29% of pts belonged to the Intermediate- and Adverse-risk groups, respectively. The complete remission (CR) rate of Favorable-risk pts was 92%, compared with 77% and 48% CR rates of Intermediate-risk and Adverse-risk pts. Fifty-two percent of Favorable-risk pts were disease-free and 63% were alive 3 years after diagnosis, compared with the respective 3-year rates of 22% and 32% for pts belonging to the Intermediate-risk group, and only 10% and 19%, respectively, for pts classified in the Adverse-risk group. Using a targeted 80-gene sequencing panel, we detected 2,354 mutations, with a median of 3 per pt. The frequencies of specific mutations differed between the ELN risk groups. We performed multivariable outcome analyses for the achievement of CR, disease-free (DFS) and overall (OS) survival within each of the ELN groups. Within the Favorable-risk group MVA analyses, the presence of WT1 mutations associated with lower CR rates (P=0.02). Mutations in BCOR (P=0.02), IDH1 (P=0.04), KIT (P<0.001), PTPN11 (P=0.01) and SETBP1 (P=0.02) associated with a shorter DFS; mutated BCOR (P=0.02), IDH1 (P=0.006), SETBP1 (P=0.004), WT1 (P<0.001) and ZRSR2 (P=0.002) associated with a shorter OS. In the Intermediate-risk group MVA analyses, mutations in WT1 associated with lower CR rates (P=0.02). Mutations in DNMT3A and WT1 associated with shorter DFS (DNMT3A, P<0.001; WT1, P=0.01) and OS (DNMT3A, P<0.001; WT1, P=0.005). In the Adverse-risk group MVA analyses, IDH2 mutations associated with lower CR rates (P=0.05). NRAS mutations associated with shorter DFS (P<0.001) and OS (P=0.008). In addition, IDH2- (P=0.03) and TET2-mutated pts (P=0.009) had shorter OS than pts without these mutations. Among FLT3-ITDlow pts, those harboring NPM1 mutation had higher CR rates (P<0.001) and longer OS (P=0.001), but not DFS (P=0.16), than pts with wild-type (wt) NPM1. Within the FLT3-ITDhigh cohort, pts with an NPM1 mutation had higher CR rates than those without (P<0.001). However, there was no difference in either DFS or OS between NPM1 mutated and NPM1 wt pts, indicating that the negative prognostic impact of FLT3-ITDhigh may outweigh the positive prognostic impact of NPM1 mutations with respect to those survival endpoints. We also noted that the negative prognostic impact of WT1 mutations was worsened by co-occurring NPM1 mutations. Similarly, the impact of IDH1 mutations within the Favorable group was influenced by NPM1 mutations, with IDH1/NPM1 co-mutated patients having inferior survival. Based on the results of our multivariable analyses, as well as co-occurring mutations, we provide a possible refinement of the ELN genetic risk stratification in Table 1. DFS and OS of the re-classified pts were comparable to DFS and OS of the original ELN groups (Figure 1). Importantly, the re-classification also changed the percentages of AML patients assigned to specific risk groups, reducing the Favorable-risk group from 49% to 39% and increasing the Adverse-risk group from 29% to 38%, with the Intermediate-risk group remaining almost the same (23% vs 22%). In summary, our study provides a comprehensive analysis of genetic prognostic markers in younger AML pts treated with standard chemotherapy within the framework of the ELN risk classification. Furthermore, we identified several combinations of co-occurring mutations with prognostic significance. Our results provide a refinement of the 2017 ELN risk classification, and identify additional pts that may need more intensive treatment early on.Support: U10CA180821, U10CA180882, U10CA180861, U24CA196171; ClinicalTrials.gov [Display omitted] DisclosuresMims:Abbvie Pharmaceuticals: Membership on an entity's Board of Directors or advisory committees; Agios Pharmaceuticals: Consultancy, Membership on an entity's Board of Directors or advisory committees; Novartis: Consultancy. Kolitz:Magellan Health: Consultancy, Honoraria. Powell:Rafael Pharmaceuticals: Membership on an entity's Board of Directors or advisory committees.

Allotransplants for Patients 65 Years or Older with High-Risk Acute Myeloid Leukemia

Abstract Outcome of persons &gt;65 years with acute myeloid leukemia (AML) is poor. Allogeneic transplant can cure some of these patients but is associated with substantial transplant-related mortality (TRM) and high relapse risk. We analyzed 185 consecutive patients &gt;65 years with high-risk AML between 2010 and 2015 who had measurable residual disease (MRD) and molecular risk assessments and who received myeloablative conditioning (MAC, n=42) or reduced-intensity conditioning (RIC, n=143) and a transplant from an HLA-identical sibling (n=66) or a 10/10 loci HLA-matched unrelated donor (MUD, n=119) in order to identify patients who would benefit from allotransplant. MRD was assessed by flow cytometry in bone marrow samples. AML cytogenetic and molecular risk were defined using the 2017 European Leukemia Net genetic risk stratification. The patients who were MRD-negative at time of transplant had a better 2-year cumulative incidence of relapse (CIR 17.6%) and a 2-year overall survival (OS, 69.4%) as compared to the patients in remission but MRD-positive (55.6% CIR, 21.5% OS) or the patients who had morphological evidence of leukemia prior to transplant (48.7% CIR, 19.9% OS), (p&lt;0.0001). Multivariate analysis for 2-year CIR showed that having detectable leukemia at time of SCT (defined as MRD-positive or morphological evidence of leukemia) (HR=14.5, CI=3.4-61.4, p&lt;0.0001), having received &lt;3 cycles of chemotherapy prior to SCT (HR=1.8, CI=1.1-2.8 p=0.01), and high-risk genetics were independent predictors of relapse. However, high-risk genetics only had a deleterious effect on outcomes for MRD-negative patients (HR=9.4, CI=2.0-43.6, p=0.004), and did not affect the outcome of patients with detectable leukemia (HR=1.1, CI=0.7-1.9, p=0.61). Patients who received RIC (Flu-Mel-RIC or Bu-Flu-RIC) or MAC (Bu-Flu-MAC) had similar proportion of MRD-negative patients (p=1.0). However, MRD-negative patients who received Flu-Mel-RIC had a superior OS than patients who received Bu-Flu-RIC (adjusted HR=1 vs 5.3, p=0.02) or patients who received Bu-Flu-MAC (HR=1 vs 5.093, p=0.04), which is explained by a significantly lower relapse rate in patients receiving Flu-Mel-RIC (adjusted HR=1 vs 4.8, p=0.03) and a significantly lower TRM as compared to patients receiving Bu-Flu-MAC (adjusted HR= 5.1, p=0.01). Patients who had major medical complications (MMC), defined as a medical event requiring admission to the intensive care unit for ventilatory or inotropic support or a medical event that prolonged the patient hospitalization for more than 2 weeks, during induction or consolidation chemotherapy preceding the transplant, had a higher day +100 mortality (30.6% vs 6.0%, p&lt;0.0001), 2-year TRM (55.6% vs 16.8%, p&lt;0.0001) and lower 2-year OS (8.3% vs 44.6%, p&lt;0.0001). Multivariate analysis for 2-year OS showed that history of delayed hematological recovery during induction or consolidation chemotherapy prior to transplantation (HR=1.5, CI=1.0-2.3, p=0.04), high risk genetics (HR=1.8 CI:1.2-2.6, p=0.006), donor-recipient HLA-DRβ3/4/5-DP mismatch (HR=2.2, CI=1.3-3.6, p=0.001), history of cardiovascular disease (HR=1.7, CI=1.1-2.6, p=0.02) were independent predictors for OS. Other variables such as secondary leukemia, CMV sero-status, FEV1 or creatinine clearance prior to SCT, sex mismatch, ABO group mismatch, donor type, or stem cell source did not have a significant impact on OS or TRM. Outcomes were also similar between patients transplanted in CR1 or in ≥ CR2 or in CR or CRi. We sought to identify those patients who may clearly benefit from a SCT. To that end, we classified patients according to the MRD status prior to transplantation and the presence or absence of the other prognostic factors identified in the multivariate analysis. As seen in the Figure, the High risk group which includes patients with detectable leukemia and &gt;1 additional adverse prognostic factors (or a MMC), had a 2-year OS of 7.7% (CI=3.1-17.8). In comparison, the Low risk group which includes MRD-negative patients with ≤3 other prognostic factors (and no MMC), had a 2-year OS of 76.2% (CI=63.3-85.6). Finally, the Intermediate risk group which constituted the remaining patients, had a 2-year OS of 32.2% (CI=22.1-44.3, p&lt;0.00001). These data indicate the possibility to identify persons &gt;65 years with high-risk AML likely to benefit from an allotransplant. Figure. Figure. Disclosures Rezvani: Affirmed GmbH: Research Funding. Oran:ASTEX: Research Funding; Celgene: Consultancy, Research Funding; AROG pharmaceuticals: Research Funding. Shpall:Affirmed GmbH: Research Funding. Champlin:Otsuka: Research Funding; Sanofi: Research Funding.

Differential Burden of Rare and Common Variants on Tumor Characteristics, Survival, and Mode of Detection in Breast Cancer.

Genetic variants that increase breast cancer risk can be rare or common. This study tests whether the genetic risk stratification of breast cancer by rare and common variants in established loci can discriminate tumors with different biology, patient survival, and mode of detection. Multinomial logistic regression tested associations between genetic risk load [protein-truncating variant (PTV) carriership in 31 breast cancer predisposition genes-or polygenic risk score (PRS) using 162 single-nucleotide polymorphisms], tumor characteristics, and mode of detection (OR). Ten-year breast cancer-specific survival (HR) was estimated using Cox regression models. In this unselected cohort of 5,099 patients with breast cancer diagnosed in Sweden between 2001 and 2008, PTV carriers (n = 597) were younger and associated with more aggressive tumor phenotypes (ER-negative, large size, high grade, high proliferation, luminal B, and basal-like subtype) and worse outcome (HR, 1.65; 1.16-2.36) than noncarriers. After excluding 92 BRCA1/2 carriers, PTV carriership remained associated with high grade and worse survival (HR, 1.76; 1.21-2.56). In 5,007 BRCA1/2 noncarriers, higher PRS was associated with less aggressive tumor characteristics (ER-positive, PR-positive, small size, low grade, low proliferation, and luminal A subtype). Among patients with low mammographic density (<25%), non-BRCA1/2 PTV carriers were more often interval than screen-detected breast cancer (OR, 1.89; 1.12-3.21) than noncarriers. In contrast, higher PRS was associated with lower risk of interval compared with screen-detected cancer (OR, 0.77; 0.64-0.93) in women with low mammographic density. These findings suggest that rare and common breast cancer susceptibility loci are differentially associated with tumor characteristics, survival, and mode of detection.Significance: These findings offer the potential to improve screening practices for breast cancer by providing a deeper understanding of how risk variants affect disease progression and mode of detection. Cancer Res; 78(21); 6329-38. ©2018 AACR.

Genetic Risk Stratification: Tipping Point for Global Primary Prevention of Coronary Artery Disease.

In 2003, Wald and Law1 predicted that coronary artery disease (CAD) would be markedly attenuated if not eliminated. CAD is a preventable disease based on randomized, placebo-controlled clinical trials that consistently showed 30% to 40% reduction in cardiac events with decreased plasma cholesterol.1 Epidemiologists claimed for decades that 40% to 50% of predisposition for CAD is genetic. Discovery of the first genetic risk variant in 2007 has led to an avalanche of >90 genetic risk variants predisposing to CAD, each of genome-wide significance and replicated in independent populations,2 but each with relatively low individual effect sizes. The total individual genetic risk burden for CAD is proportional to the number of genetic risk variants inherited. These variants account for ≈25% of genetic predisposition to CAD, which is less than the predicted 40%, signaling that more genetic risk variants are yet to be discovered. It is interesting to note that only one third of the genetic risk variants for CAD mediate their risk through known conventional risk factors. Exploration of the unknown pathways mediating the risk conferred by these genetic variants is already enabling new insights into the pathogenesis of coronary atherosclerosis (eg, inflammation, lack of protection of high-density lipoprotein cholesterol) and novel targets for the development of specific drugs. A major impetus for our pursuit of genetic risk variants was to better predict those at higher risk for CAD who would benefit most from preventive measures, particularly primary prevention. The genetic …

Genetic risk stratification in cardiac arrhythmias.

The current article provides a concise summary of the possibilities and limitations of genotype-based risk stratification of cardiac arrhythmias. We will outline the most important findings of the recent years in the light of their chronological and conceptual development. Genotype-phenotype association studies in families with single-gene disorders as well as in the general population led to the discovery of several DNA variants significantly associated with the risk of sudden death or life-threatening arrhythmias. In genetic (monogenic) diseases, the disease-causing mutations modulate the risk of events and response to antiarrhythmic therapy according to the specific gene involved, to their position of the mutation and to their functional effects. These causal relationships have been quite well characterized in the case of long QT syndrome but are still less defined in the case of other inherited conditions. Quantitatively, the risk associated with a single genetic variant is large for DNA variants that cause monogenic inherited arrhythmias. Much different is the case of more common variants associated with the risk of arrhythmias in the general population as they are generally associated with a small effect size. Genetic profiling identifies arrhythmogenic risk even if a complete picture allowing high-granularity risk stratification is yet to come.

Paternal lineage early onset hereditary ovarian cancers: A Familial Ovarian Cancer Registry study

Given prior evidence that an affected woman conveys a higher risk of ovarian cancer to her sister than to her mother, we hypothesized that there exists an X-linked variant evidenced by transmission to a woman from her paternal grandmother via her father. We ascertained 3,499 grandmother/granddaughter pairs from the Familial Ovarian Cancer Registry at the Roswell Park Cancer Institute observing 892 informative pairs with 157 affected granddaughters. We performed germline X-chromosome exome sequencing on 186 women with ovarian cancer from the registry. The rate of cancers was 28.4% in paternal grandmother/granddaughter pairs and 13.9% in maternal pairs consistent with an X-linked dominant model (Chi-square test X2 = 0.02, p = 0.89) and inconsistent with an autosomal dominant model (X2 = 20.4, p<0.001). Paternal grandmother cases had an earlier age-of-onset versus maternal cases (hazard ratio HR = 1.59, 95%CI: 1.12–2.25) independent of BRCA1/2 status. Reinforcing the X-linked hypothesis, we observed an association between prostate cancer in men and ovarian cancer in his mother and daughters (odds ratio, OR = 2.34, p = 0.034). Unaffected mothers with affected daughters produced significantly more daughters than sons (ratio = 1.96, p<0.005). We performed exome sequencing in reported BRCA negative cases from the registry. Considering age-of-onset, one missense variant (rs176026 in MAGEC3) reached chromosome-wide significance (Hazard ratio HR = 2.85, 95%CI: 1.75–4.65) advancing the age of onset by 6.7 years. In addition to the well-known contribution of BRCA, we demonstrate that a genetic locus on the X-chromosome contributes to ovarian cancer risk. An X-linked pattern of inheritance has implications for genetic risk stratification. Women with an affected paternal grandmother and sisters of affected women are at increased risk for ovarian cancer. Further work is required to validate this variant and to characterize carrier families.