Mutations In High-risk Genes Research Articles

High-Throughput Sequencing Identifies 3 Novel Susceptibility Genes for Hereditary Melanoma.

Cutaneous melanoma is one of the most aggressive human cancers due to its high invasiveness. Germline mutations in high-risk melanoma susceptibility genes have been associated with development hereditary melanoma; however, most genetic culprits remain elusive. To unravel novel susceptibility genes for hereditary melanoma, we performed whole exome sequencing (WES) on eight patients with multiple primary melanomas, high number of nevi, and negative for high and intermediate-risk germline mutations. Thirteen new potentially pathogenic variants were identified after bioinformatics analysis and validation. CDH23, ARHGEF40, and BRD9 were identified as the most promising susceptibility genes in hereditary melanoma. In silico analysis of CDH23 and ARHGEF40 variants provided clues for altered protein structure and function associated with the identified mutations. Then, we also evaluated the clinical value of CDH23, ARHGEF40, and BRD9 expression in sporadic melanoma by using the TCGA dataset (n = 461). No differences were observed in BRD9 expression between melanoma and normal skin samples, nor with melanoma stage, whereas ARHGEF40 was found overexpressed, and CDH23 was downregulated and its loss was associated with worse survival. Altogether, these results reveal three novel genes with clinical relevance in hereditary and sporadic melanoma.

Identification of key differentially expressed genes and gene mutations in breast ductal carcinoma in situ using RNA-seq analysis

BackgroundThe aim of this study was to identify the key differentially expressed genes (DEGs) and high-risk gene mutations in breast ductal carcinoma in situ (DCIS).MethodsRaw data (GSE36863) were downloaded from the database of Gene Expression Omnibus (GEO), including three DCIS samples (DCIS cell lines MCF10.DCIS, Sum102, and Sum225) and one normal control sample (normal mammary epithelial cell line MCF10A). The DEGs were analyzed using NOIseq and annotated via DAVID. Motif scanning in the promoter region of DEGs was performed via SeqPos. Additionally, single nucleotide variations (SNVs) were identified via GenomeAnalysisTK and SNV risk was assessed via VarioWatch. Mutant genes with a high frequency and risk were validated by RT-PCR analyses.ResultsFinally, 5391, 7073, and 7944 DEGs were identified in DCIS, Sum102, and Sum22 cell lines, respectively, when compared with MCF10A. VENN analysis of the three cell lines revealed 603 upregulated and 1043 downregulated DEGs, including 16 upregulated and 36 downregulated transcription factor (TF) genes. In addition, six TFs each (e.g., E2F1 and CREB1) were found to regulate the core up- and downregulated DEGs, respectively. Furthermore, SNV detection results revealed 1104 (MCF10.DCIS), 2833 (Sum102), and 1132 (Sum22) mutation sites. Four mutant genes (RWDD4, SDHC, SEPT7, and SFN) with high frequency and risk were identified. The results of RT-PCR analysis as well as bioinformatics analysis consistently demonstrated that the expression of RWDD4, SDHC, SEPT7, and SFN was downregulated in the tumor tissues as compared with that in adjacent non-tumor tissues.ConclusionsThe differentially expressed TFs, TFs regulating DEGs (e.g., E2F1 and CREB1), and high-frequency mutant genes (RWDD4, SDHC, SEPT7, and SFN) might play key roles in the pathogenesis of DCIS.

Abstract P6-08-07: Polygenic breast cancer risk modification in carriers of high and intermediate risk gene mutations

Abstract Background: The incorporation of polygenic scores into breast cancer risk assessment models has led to improved risk management for women of European ancestry. However, few studies have examined the extent to which polygenic scores modify risk for carriers of breast cancer susceptibility gene mutations. Current literature suggests that a 77-SNP polygenic score developed from large, mainly non-carrier general population studies can stratify breast cancer risk for carriers of the CHEK2 founder mutation 1100delC with the same effect size observed for non-carriers. Consequently, several groups have modified risk estimates for carriers of other pathogenic variants by applying published effect estimates from non-carriers. In a recent study, a similar 88-SNP polygenic score showed reduced effectiveness in BRCA1 and BRCA2 carriers compared to non-carriers. This highlights the need for more information on polygenic score performance among women who carry pathogenic variants in ATM or PALB2, or in CHEK2 other than the 1100delC founder mutation. We previously described an 86-SNP polygenic residual risk score (RRS) that characterizes genetic risk which is not due to high- or moderate-penetrance breast cancer gene mutations. Here, we present pre-specified independent validation of the RRS for BRCA1, BRCA2, CHEK2, ATM and PALB2 carriers.Methods: This IRB-approved study included 152,172 women of European ancestry who were tested clinically for hereditary cancer risk with a multi-gene panel. The RRS was evaluated separately for carriers of BRCA1 (N=2,249), BRCA2 (N=2,638), CHEK2 (N=2,564), ATM (N=1,445) and PALB2 (N=906), and for mutation-free women (N=141,160). Clinical information was obtained from test requisition forms. Multivariable logistic regression was used to examine the association of RRS with invasive breast cancer after accounting for age and family cancer history. Effect sizes, expressed as standardized odds ratios (ORs) with 95% confidence intervals (CIs), were assessed for carriers of each gene and for non-carriers. Results: RRS was strongly associated with breast cancer risk in each of the BRCA1, BRCA2, CHEK2, ATM and PALB2 carrier populations (p<10−4). Risk modification in CHEK2 carriers (OR 1.49; CI 1.36-1.64) was consistent with that observed in non-carriers (OR 1.47; CI 1.45-1.49). CHEK2 carriers in the highest RRS quintile had approximately 1.7-fold higher risk than the middle quintile (OR 1.67; CI 1.26 - 2.20), and the lowest quintile had risk lowered by factor of 0.59 (OR 0.59; CI 0.44 - 0.80). We observed reduced modification similar to existing literature for carriers of BRCA1 (OR 1.20; CI 1.10-1.32) and BRCA2 (OR 1.23; CI 1.12-1.34). Odds ratios for ATM (1.37; CI 1.21-1.55) and PALB2 (1.34; CI 1.16-1.55) had wide confidence intervals that overlapped those for the other carrier populations. Discussion: The RRS significantly modifies risk for carriers of BRCA1, BRCA2, CHEK2, ATM and PALB2 mutations albeit with apparently different effect sizes. These results indicate that risk estimates employing polygenic scores may need to be derived separately for each gene. Given the modest effect on BRCA1 and BRCA2 risk and the substantial risks conferred by these genes even with lower RRS, the clinical implications of polygenic modification in this setting are yet to be determined. In CHEK2 carriers, we observed strong polygenic modification similar to that achieved for non-carriers. For ATM and PALB2, larger studies are needed to refine polygenic effect size estimates. Comprehensive risk assessment combining RRS with family cancer history and other risk factors has potential to refine risk estimates and facilitate decision-making for women with mutations in moderate penetrance genes. Citation Format: Shannon Gallagher, Elisha Hughes, Susanne Wagner, Placede Tshiaba, Eric Rosenthal, Benjamin B. Roa, Allison Kurian, Susan Domchek, Judy Garber, Johnathan M. Lancaster, Jeffrey Weitzel, Alexander Gutin, Jerry S. Lanchbury, Mark Robson. Polygenic breast cancer risk modification in carriers of high and intermediate risk gene mutations [abstract]. In: Proceedings of the 2019 San Antonio Breast Cancer Symposium; 2019 Dec 10-14; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2020;80(4 Suppl):Abstract nr P6-08-07.

Excess of singleton loss-of-function variants in Parkinson’s disease contributes to genetic risk

BackgroundParkinson’s disease (PD) is a neurodegenerative disorder with complex genetic architecture. Besides rare mutations in high-risk genes related to monogenic familial forms of PD, multiple variants associated with sporadic PD...

MARS: Mutation-Adjusted Risk Score for Advanced Systemic Mastocytosis.

PURPOSETo develop a risk score for patients with advanced systemic mastocytosis (AdvSM) that integrates clinical and mutation characteristics.PATIENTS AND METHODSThe study included 383 patients with AdvSM from the German Registry on Disorders of Eosinophils and Mast Cells (training set; n = 231) and several centers for mastocytosis in the United States and Europe, all within the European Competence Network on Mastocytosis (validation set; n = 152). A Cox multivariable model was used to select variables that were predictive of overall survival (OS).RESULTSIn multivariable analysis, the following risk factors were identified as being associated with OS: age greater than 60 years, anemia (hemoglobin < 10 g/dL), thrombocytopenia (platelets < 100 × 109/L), presence of one high molecular risk gene mutation (ie, in SRSF2, ASXL1, and/or RUNX1), and presence of two or more high molecular risk gene mutations. By assigning hazard ratio–weighted points to these variables, the following three risk categories were defined: low risk (median OS, not reached), intermediate risk (median OS, 3.9 years; 95% CI, 2.1 to 5.7 years), and high risk (median OS, 1.9 years; 95% CI, 1.3 to 2.6 years; P < .001). The mutation-adjusted risk score (MARS) was independent of the WHO classification and was confirmed in the independent validation set. During a median follow-up time of 2.2 years (range, 0 to 23 years), 63 (16%) of 383 patients experienced a leukemic transformation to secondary mast cell leukemia (32%) or secondary acute myeloid leukemia (68%). The MARS was also predictive for leukemia-free survival (P < .001).CONCLUSIONThe MARS is a validated, five-parameter, WHO-independent prognostic score that defines three risk groups among patients with AdvSM and may improve up-front treatment stratification for these rare hematologic neoplasms.

Contribution of Massive Parallel Sequencing to Diagnosis of Hereditary Ovarian Cancer in the Czech Republic

Ovarian cancer is a disease with high mortality. Approximately 1,000 women are diagnosed with ovarian cancer in the Czech Republic annually. Women harboring a mutation in cancer-predisposing genes face an increased risk of tumor development. Mutations in BRCA1, BRCA2, BRIP1, and Lynch syndrome genes (RAD51C, RAD51D, and STK11) are associated with a high risk of ovarian cancer, and mutations in ATM, CHEK2, NBN, PALB2, and BARD1 appear to increase the risk. Our aim was to examine the frequency of mutations in cancer-predisposing genes in the Czech Republic. We analyzed 1,057 individuals including ovarian cancer patients and 617 non-cancer controls using CZECANCA panel next-generation sequencing on the Illumina platform. Pathogenic mutations in high-risk genes, including CNVs, were detected in 30.6% of patients. The mutation frequency reached 25.0% and 18.2% in subgroups of unselected ovarian cancer patients and patients with a negative family cancer history, respectively. The most frequently mutated genes were BRCA1 and BRCA2. The overall frequency of mutations in non-BRCA genes was comparable to that in BRCA2. The mutation frequency in ovarian cancer patients aged &gt;70 years was three times higher than that in patients diagnosed before the age of 30. Ovarian cancer is a heterogeneous disease with a high proportion of hereditary cases. The lack of efficient screening for early diagnosis emphasizes the importance of identifying carriers of mutations in ovarian cancer-predisposing genes; this is because proper follow-up and prevention strategies can reduce overall ovarian cancer-related mortality. This work was supported by grants AZV 15-27695A, SVV2019/260367, PROGRES Q28/LF1. The authors declare they have no potential conflicts of interest concerning drugs, products, or services used in the study. The Editorial Board declares that the manuscript met the ICMJE recommendation for biomedical papers. Submitted: 7. 3. 2019 Accepted: 24. 4. 2019.

Ability of known susceptibility SNPs to predict colorectal cancer risk for persons with and without a family history.

Before SNP-based risk can be incorporated in colorectal cancer (CRC) screening, the ability of these SNPs to estimate CRC risk for persons with and without a family history of CRC, and the screening implications need to be determined. We estimated the association with CRC of a 45 SNP-based risk using 1181 cases and 999 controls, and its correlation with CRC risk predicted from detailed family history. We estimated the predicted change in the distribution across predefined risk categories, and implications for recommended screening commencement age, from adding SNP-based risk to family history. The inter-quintile risk ratio for colorectal cancer risk of the SNP-based risk was 3.28 (95% CI 2.54-4.22). SNP-based and family history-based risks were not correlated (r = 0.02). For persons with no first-degree relatives with CRC, screening could commence 4years earlier for women (5years for men) in the highest quintile of SNP-based risk. For persons with two first-degree relatives with CRC, screening could commence 16years earlier for men and women in the highest quintile, and 7years earlier for the lowest quintile. This 45 SNP panel in conjunction with family history, can identify people who could benefit from earlier screening. Risk reclassification by 45 SNPs could inform targeted screening for CRC prevention, particularly in clinical genetics settings when mutations in high-risk genes cannot be identified. Yet to be determined is cost-effectiveness, resources requirements, community, patient and clinician acceptance, and feasibility with potentially ethical, legal and insurance implications.

Landscape of multilocus inherited neoplasia alleles syndrome in China.

e13027 Background: Comprehensive gene panels are able to identify patients with more than one pathogenic germline mutations. This phenomenon is known as multilocus inherited neoplasia alleles syndrome (MINAS). The frequency and phenotype of double heterozygous carriers in China are still unknown. Methods: A cohort of 12514 unrelated patients with solid tumor were screened using a validated panel. DNA damage repair-associated genes ( BRCA1, BRCA2, PALB2, ATM) and DNA mismatch repair genes ( MLH1, MSH2, MSH6, PMS2, MLH3, MSH3, PMS1) are taken focused on this study. Results: 10 (2.16%) cases harboring two pathogenic/likely pathogenic mutations were identified in 464 patients with germline variant. All patients had at least one high-risk gene mutation except for G10(LC, 73y), which carried 2 ATM variants in the same allele. All patients developed tumors associated with only one of the mutation identified until now. Among 3 patients had PMS2/MSH6 mutation, G6 &amp; G7 did not translated into recognized Lynch Syndrome due to abnormal BRCA1/2(H-risk for BC), while G8 harboring ATM (M-risk for BC) mutation developed to CRC. All of the five patients developed to breast cancer were TNBC molecular subtype. The median ages of diagnosis for BC were similar to single variation patients (44.3 vs 42, p=0.6190). Conclusions: Two double heterozygotes did not appear to have severe or different manifestations than single heterozygote. With the growing implementation of NGS based panel testing, relevant variants in two (or more) genes will be found more frequently. [Table: see text]

Data Coming out of the Human Inhibitor PUP Study (HIPS) Reveal 4 Subgroups of Patients with Distinct Antibody Signatures

Data Coming out of the Human Inhibitor PUP Study (HIPS) Reveal 4 Subgroups of Patients with Distinct Antibody Signatures

Donor lymphocyte infusion for prevention of relapse after unmanipulated haploidentical PBSCT for very high-risk hematologic malignancies

Unmanipulated haploidentical peripheral blood stem cell transplantation (haplo-PBSCT) has been an established treatment to cure high-risk leukemia/lymphoma. Relapse is the main cause of treatment failure for patients with relapsed/refractory disease or with very high-risk gene mutations such as TP53, TET2, and DNMT3a. In this study, we aimed to establish the tolerance and efficacy of prophylactic donor lymphocyte infusion (DLI) with G-CSF-primed peripheral blood progenitors for prevention of relapse in these very high-risk patients after haplo-PBSCT. The prophylactic DLI was given at a median of 77 days after transplantation in 31 of 45 consecutive patients with very high-risk leukemia/lymphoma. The median dose of CD3+ cells for infusion was 1.8 × 107/kg. The 100-day incidences of acute graft-versus-host disease (GVHD) grades 2–4 and 3–4 after DLI were 55.3% and 10.2%. The 2-year incidences of chronic GVHD and severe chronic GVHD were 52.0% and 18.2%. The 2-year incidences of non-relapse mortality and relapse were 33.1% and 32.5%. The 2-year probabilities of overall survival and relapse-free survival were 40.1% and 31.9%. Poor-risk gene mutations (p = 0.029), disease in non-remission status prior to transplantation (p = 0.005), and donors older than 40 years of age (p = 0.043) were associated with relapse after DLI. In multivariate analysis, disease in non-remission status prior to transplantation was an independent risk factor of relapse (hazard ratio = 4.079; p = 0.035). These data showed the feasibility of the prophylactic DLI in the haplo-PBSCT setting and the anti-leukemic efficacy in very high-risk leukemia/lymphoma.

Abstract B77: Panel testing to evaluate genetic predisposition to breast cancer in African American women

Abstract Background: Although the role of BRCA1 and BRCA2 has been well studied in women of European ancestry, the contribution of these and other genes associated with hereditary cancers remains unknown in other populations. Here, we utilized panel testing to analyze 94 cancer predisposition genes in African American women (AAW) diagnosed with invasive breast cancer. Methods: 145 self-described AAW who enrolled in the Clinical Breast Care Project from 2001-2012 and had genomic DNA available were identified. Targeted sequencing was performed using the TruSight Cancer panel (Illumina). Pathogenic mutations were identified using VariantStudio and classified as pathogenic, uncertain significance (VUS), or benign using ClinVar. Results: Mean age at diagnosis was 52.1 years (range 25-81 years), and 32% of AAW had a family history. The majority of tumors were ER+HER2- (53%) followed by triple-negative breast cancer (TNBC, 34%). Seven percent of AAW had pathogenic mutations in high-risk genes including BRCA1 (n=7), BRCA2 (n=3), and TP53 (n=1); VUS were detected in BRCA1 (n=1) and BRCA2 (n=2); and an additional woman had a private variant (D2965E) in BRCA2. A further 1% of AAW harbored mutations in the moderate-penetrance gene CHEK2. VUS were also detected in ATM (n=9), CDH1 (n=1), CHEK2 (n=2), MSH2 (n=1), MSH6 (n=5), NBN (n=1), PALB2 (n=4), PMS2 (n=3), RAD51C (n=1), SMAD4 (n=1), TP53 (n=1), and TSC2 (n=1). Conclusions: Although 94 cancer predisposition genes were evaluated, pathogenic mutations in AAW were detected only in four well-established breast cancer predisposition genes (BRCA1, BRCA2, CHEK2, and TP53). Overall mutation frequency was 9%; however, an additional 25% of AAW harbored private variants and VUS, underscoring the critical need to establish the pathogenicity of these variants. The opinions or assertions contained herein are the private ones of the author/speaker and are not to be construed as official or reflecting the views of the Department of Defense, the Uniformed Services University of the Health Sciences, or any other agency of the U.S. Government. Citation Format: Heather L. Blackburn, Craig D. Shriver, Rachel E. Ellsworth. Panel testing to evaluate genetic predisposition to breast cancer in African American women [abstract]. In: Proceedings of the Tenth AACR Conference on the Science of Cancer Health Disparities in Racial/Ethnic Minorities and the Medically Underserved; 2017 Sep 25-28; Atlanta, GA. Philadelphia (PA): AACR; Cancer Epidemiol Biomarkers Prev 2018;27(7 Suppl):Abstract nr B77.

Increased single-strand annealing rather than non-homologous end-joining predicts hereditary ovarian carcinoma.

Mutations in genes encoding DNA double-strand break (DSB) repair components, especially homologous recombination (HR) proteins, were found to predispose to breast and ovarian cancer. Beyond high penetrance risk gene mutations underlying monogenic defects, low risk gene mutations generate polygenic defects, enlarging the fraction of individuals with a predisposing phenotype. DSB repair dysfunction opens new options for targeted therapies; poly (ADP-ribose) polymerase (PARP) inhibitors have been approved for BRCA-mutated and platinum-responsive ovarian cancers. In this work, we performed functional analyses in peripheral blood lymphocytes (PBLs) using a case-control design. We examined 38 women with familial history of breast and/or ovarian cancer, 40 women with primary ovarian cancer and 34 healthy controls. Using a GFP-based test we analyzed error-prone DSB repair mechanisms which are known to compensate for HR defects and to generate chromosomal instabilities. While non-homologous end-joining (NHEJ) did not discriminate between cases and controls, we found increases of single-strand annealing (SSA) in women with familial risk vs. controls (P=0.016) and patients with ovarian cancer vs. controls (P=0.002). Consistent with compromised HR we also detected increased sensitivities to carboplatin in PBLs from high-risk individuals (P<0.0001) as well as patients (P=0.0011) compared to controls. Conversely, neither PARP inhibitor responses nor PARP activities were altered in PBLs from the case groups, but PARP activities increased with age in high-risk individuals, providing novel clues for differential drug mode-of-action. Our findings indicate the great potential of detecting SSA activities to deliver an estimate of ovarian cancer susceptibility and therapeutic responsiveness beyond the limitations of genotyping.

A single visit multidisciplinary model for managing patients with mutations in moderate and high-risk genes in a community practice setting.

The introduction of screening for multiple high and moderate risk mutations in genes has resulted in a complex approach to patient care involving multiple disciplines. We sought to describe the feasibility of a single visit multidisciplinary approach to the management of patients with an identified high/moderate risk gene mutation. Patients who presented to our community hospital over a 1-year period who were found to have a high/moderate risk genetic mutation on a screening panel were referred to the High Risk Genetic Clinic. Thirty-five patients were included. The majority were female [34 (97.1%)], Hispanic [22 (62.9%)], with a family history of cancer [21 (60%)]. Mean age was 40.3 years. Most of the participants had a BRCA1 gene mutation [10 (28.6%)]. Patients were seen at the High Risk Genetic Clinic within a mean of 41.9 days from the day of genetic mutation diagnosis. Four patients did not show and were significantly younger (19.3 vs. 39.6 years, p = 0.014). In this community setting, we provided coordinated care within multiple disciplines related to a genetic mutation in a single clinic visit. Increased efforts at coordinating early care should be directed towards patients diagnosed at a younger age.

Abstract PR10: Development of a comprehensive colorectal cancer risk prediction tool (CRiPT) incorporating known and unknown major genes and polygenes

Abstract Aim: We aimed to develop a comprehensive Colorectal cancer Risk Prediction Tool (CRiPT). To achieve this, it is necessary to incorporate germline mutations in the DNA mismatch repair genes and MUTYH to account for a proportion of the familial aggregation of colorectal cancer. Population prevalence of these mutations and the genetic and environmental causes of the remaining familial aggregation, however, are not known. Methods: We studied the families of 5,744 colorectal cancer cases (probands) recruited from population cancer registries in the USA, Canada and Australia, and screened probands for mutations in the mismatch repair genes MLH1, MSH2, MSH6, and PMS2, and MUTYH. We fitted modified segregation analysis models to the cancer history of first-degree relatives, conditional on the age at diagnosis of the proband, using the software MENDEL. We determined the genetic model that best explained the familial aggregation of colorectal cancer by estimating the prevalence of mutations in the known susceptibility genes, the prevalence of and hazard ratio for unmeasured high-risk gene mutations, and the variance of the unmeasured polygenic component, using a χ2 goodness-of-fit test. Results: The best fitting model was a mixed dominant model with the polygenic standard deviation varying by age. Under that model, we estimated 1 in 279 of the population carry mutations in the mismatch repair genes (MLH = 1 in 1946, MSH2 = 1 in 2841, MSH6 = 1 in 758, PMS2 = 1 in 714), 1 in 45 carry mutations in MUTYH, and 1 in 504 carry mutations in unknown major gene(s) which are associated with on average a 31-fold increased risk of colorectal cancer. The estimated variance of the polygenic component decreased from 1.8 for age &amp;lt;40 years to 0.7 for age ≥70 years (equivalent to a sibling relative risk of 5.1 and 1.3, respectively). There was good internal consistency in the best fitting model; i.e., predicted and observed numbers were close. Conclusion: CRiPT is a comprehensive prediction model that incorporates both known and unknown major genes and polygenes. CRiPT can provide the probabilities of having a mutation in a DNA mismatch repair gene or MUTYH as well as estimate future risk (e.g., 5-year risk) of developing colorectal cancer. This model is similar to the Breast and Ovarian Analysis of Disease Incidence and Carrier Estimation Algorithm (BOADICEA) that calculates for women the probabilities of carrying a BRCA1 or BRCA2 mutation and their future risk of developing breast and ovarian cancer based on their family history. Further work will include measured environmental factors and genetic variants to CRiPT, and it will be useful for genetic counselling and targeted colorectal cancer screening in clinical practices. This abstract is also being presented as Poster B04. Citation Format: Aung Ko Win, Mark A. Jenkins, James G. Dowty, Antonis C. Antoniou, Andrew Lee, Yingye Zheng, Noralane M. Lindor, Polly A. Newcomb, John L. Hopper, Robert J. MacInnis. Development of a comprehensive colorectal cancer risk prediction tool (CRiPT) incorporating known and unknown major genes and polygenes. [abstract]. In: Proceedings of the AACR Special Conference: Improving Cancer Risk Prediction for Prevention and Early Detection; Nov 16-19, 2016; Orlando, FL. Philadelphia (PA): AACR; Cancer Epidemiol Biomarkers Prev 2017;26(5 Suppl):Abstract nr PR10.

Abstract A44: The identification of germline mutations in DNA repair genes in Brazilian individuals at-risk for hereditary breast cancer

Abstract Hereditary breast cancer corresponds to 10-15% of all diagnosed cases of breast cancer in the world. The majority germline mutations are identified in BRCA1/2 genes, however the application of multigene panels has increased the number of pathogenic variations detected in DNA repair genes. According to the current version of NCCN Guideline, mutations in BRCA1/2, TP53 and PTEN confers high risk to develop breast cancer, and mutations in CDH1, CHEK2, PALB2, ATM and BRIP can increases over than 20% this risk. We analyzed 157 individuals from Northeastern region of Brazil with personal and/or familial breast cancer history. Genomic DNA was isolated from peripheral blood through saline-based extraction and samples were analyzed using next-generation sequencing (NGS). We identified 15 pathogenic variants and 4 VUS (Variants of Uncertain Significance) in 27 individuals (27/157; 17%), in which three are asymptomatic. Six novel variants in 4 genes were identified: BRCA1_c.3409A&amp;gt;G; BRCA2_c.5800C&amp;gt;T; BRCA2_c.5228G&amp;gt;A; BRCA2_c.5305delG; ATM_c.634delT and ATR_c.3043C&amp;gt;T. Sixty-eight percent (13/19; 68%) of variants was detected in BRCA1/2 genes, while 32% (6/19) were identified in moderate risk genes ATM (2/19); ATR (1/19); CDH1 (1/19); MLH1 (1/19) and MSH6 (1/19). The individuals were separated in two groups for comparative analysis: high-risk genes and moderate risk genes. Among three asymptomatic individuals, two present variants in moderate risk genes ATM and MLH1. Among breast cancer individuals, eighteen patients (18/24; 75%) presents mutations in high-risk genes, while six (6/24; 25%) harbors mutations in moderate risk genes. Both groups had a high incidence of early-onset breast cancer, 83%. The group of individuals harboring variants in high-risk genes presented a greater occurrence of high-grade tumors (83% vs. 67%, P= 0.0090). In the group of individuals harboring mutation in moderate risk genes, tumors presented a more aggressive phenotype with bilateral cancer (33% vs. 11%, P= 0.0002), occurrence of metastasis (33% vs. 5.6%, P&amp;lt;0.0001) and incidence of deaths (33% vs. 5.6%, P&amp;lt;0.0001). Altogether, 1/3 of variants were identified in moderate risk genes in patients presenting a more aggressive phenotype. These results reinforce the importance of applying multigene analysis in individuals at-risk for breast cancer, especially in a heterogeneous population as Brazilian. Citation Format: Ana Rafaela de Souza Timoteo, Jorge Estefano Santana de Souza, Tirzah Braz Petta Lajus. The identification of germline mutations in DNA repair genes in Brazilian individuals at-risk for hereditary breast cancer [abstract]. In: Proceedings of the AACR Special Conference on DNA Repair: Tumor Development and Therapeutic Response; 2016 Nov 2-5; Montreal, QC, Canada. Philadelphia (PA): AACR; Mol Cancer Res 2017;15(4_Suppl):Abstract nr A44.

Clinical Features and Outcome of 22 Leukemia Patients with TLS-ERG Fusion Gene

TLS-ERG fusion gene resulting from translocation changes involving chromosomes 16 and 21 is a rare genetic event mostly observed in acute myeloid leukemia (AML). AML with TLS-ERG has unique clinical and morphological features and showed poor prognosis and a high relapse rate. However, many clinical aspects of this type of leukemia still remain unknown. Here, we report the clinical features and outcome of 22 leukemia patients (20 AML and 2 B-ALL) with TLS-ERG fusion gene. The median age of patients was 6 (2-35) years old. 12 patients were males and 10 were females. The median WBC count at diagnosis was 26.54 (1.3-110.8)X109/L.TLS-ERG is tightly associated with extramedullary disease (EMD), complex chromosome abnormalities, and high risk gene mutations. 9/22 (40.9%) cases had complex chromosome abnormalities, 8/22 (36.4%) cases had EMDs, and a large proportion of cases had hematological malignancies gene mutations such as IKZF1, TET2, WT1, PHF6 and NOTCH2. 9 cases in this study had been examined for congenital inherited diseases (Familial hemophagocytic lymphohistiocytosis, FHLH, Fanconi anemia, FA and Dyskeratosis congenital, DC) gene mutations such as FANCD2, FANCG, FANCA, STXBP2, UNC13D, LAMP1 and LYST, and 7/9 (77.8%) cases had positive results. The details are summarized in Table I.We firstly evaluated the general outcome of these patients. Excluding B-ALL patients, 7/20 (35%) cases achieved complete remission (CR) after induction. The median CR, complete molecular remission (CMR), and overall survival (OS) time of the 20 cases was 7 (0-16), 3 (0-14), and 12 (1-36) months. The 6 months relapse free survival (RFS) of EMD and non-EMD patients was 75% and 83.3% (P=0.017, Figure 1).We evaluated the impact of HCT on the outcome of these patients.11/20 AML received allo-HCT, but 9/20 did not. In non-HCT group, the median CR time was 8 (0-29) months. 7/9 cases achieved CR, 3/9 cases achieved CMR, and all cases had disease progression. The median OS time was 11 (1-76) months. In HCT group, 9/11 cases underwent haploidentical HCT (HID-HCT), and 2/11 underwent HLA-matched unrelated donor HCT (URD-HCT). The median OS time was 19 (9-36) months. 1 year OS in non-HCT and HCT group was 62.5% and 90%, respectively (P=0.026, Figure 2), but 6 month RFS in non-HCT and HCT group was 55.6% and 100% (P=0.192), without statistical significance.We analyzed the effect of diverse clinic factors on the outcome of HCT. At the time of HCT, 1/11 case was NR, 10/11 cases were CR, 7/10 CR cases were not detected blasts by FCM, and 6/10 CR cases were CMR. 6 months RFS of CR and NR case was 67.5% and 0, respectively (P=0.034). 6 months RFS of FCM+ and FCM- cases was 50% and 71.4% (P=0.403). 6 months RFS of CMR and non-CMR cases was 66.7% and 60% (P=0.671). There are 5 EMD cases among the 11 cases that underwent HCT, and 6 months RFS of HCT cases with or without EMDs was 33.3% and 71.4%, respectively (P=0.204). Among the 8 TLS-ERG+ AML patients with EMD, 6/8 cases achieved CR after induction, and 5/8 cases underwent HCT after CR, the 6 months RFS of EMDs with or without HCT was 100% and 33.3% (P=0.203). Among the 12 TLS-ERG+ AML patients without EMD, 10/12 cases achieved CR after induction, and 6/12 cases underwent HCT after CR, the 6 months RFS of them with or without HCT was 100% and 66.7%, respectively (P=0.176).In conclusion, we found TLS-ERG is tightly associated with complex chromosome abnormalities and high risk gene mutations including IKZF1, TET2, WT1, PHF6, FANCD2, FANCG, FANCA, which might partially explain the overall poor prognosis of TLS-ERG patients. The leukemia burden before HCT and EMD has negative impact on the outcome of TLS-ERG patients. HCT could prolong the OS of the patients, but could not overcome the poor prognosis of TLS-ERG. No matter the patients had EMD or not, the RFS could not be improved by HCT. Our study will be valuable for evaluating the therapeutic regimen and prognosis of AML patients with TLS-ERG fusion gene. [Display omitted] [Display omitted] [Display omitted] DisclosuresNo relevant conflicts of interest to declare.

Multiple rare variants in high-risk pancreatic cancer-related genes may increase risk for pancreatic cancer in a subset of patients with and without germline CDKN2A mutations.

The risk of pancreatic cancer (PC) is increased in melanoma-prone families but the causal relationship between germline CDKN2A mutations and PC risk is uncertain, suggesting the existence of non-CDKN2A factors. One genetic possibility involves patients having mutations in multiple high-risk PC-related genes; however, no systematic examination has yet been conducted. We used next-generation sequencing data to examine 24 putative PC-related genes in 43 PC patients with and 23 PC patients without germline CDKN2A mutations and 1001 controls. For each gene and the four pathways in which they occurred, we tested whether PC patients (overall or CDKN2A+ and CDKN2A- cases separately) had an increased number of rare nonsynonymous variants. Overall, we identified 35 missense variants in PC patients, 14 in CDKN2A+ and 21 in CDKN2A- PC cases. We found nominally significant associations for mismatch repair genes (MLH1, MSH2, MSH6, PMS2) in all PC patients and for ATM, CPA1, and PMS2 in CDKN2A- PC patients. Further, nine CDKN2A+ and four CDKN2A- PC patients had rare potentially deleterious variants in multiple PC-related genes. Loss-of-function variants were only observed in CDKN2A- PC patients, with ATM having the most pathogenic variants. Also, ATM variants (n=5) were only observed in CDKN2A- PC patients with a family history that included digestive system tumors. Our results suggest that a subset of PC patients may have increased risk because of germline mutations in multiple PC-related genes.

Genetic Alterations and Their Clinical Implications in Older Patients with Acute Myeloid Leukemia

IntroductionRisk-stratification of patients with acute myeloid leukemia (AML) can not only improve treatment response, but also reduce side effects of the treatment, especially in the elderly. A number of patient-specific and leukemia-associated factors are related to the poor outcome in older patients with AML. However, comprehensive studies regarding the impact of genetic alterations in this group of patients are limited.Methods and MaterialsA total of 500 adult patients with newly diagnosed de novo AML who had enough bone marrow cryopreserved cells for analysis at the National Taiwan University Hospital were enrolled consecutively. We compared the clinico-biological features, cytogenetics and molecular gene mutations between patients aged 60 years or older (n=185) and those younger (<60 years, n=315).ResultAmong older patients, those received standard intensive chemotherapy had a longer overall survival (OS) than those treated with palliative care. Compared with younger patients, the elderly had a higher incidence of poor-risk cytogenetic changes, but a lower frequency of favorable-risk cytogenetics. The median number of molecular gene mutations at diagnosis was higher in the elderly than the younger. Older patients had significantly higher incidences of PTPN11, NPM1, RUNX1, ASXL1, TET2, DNMT3A, and P53 mutations but a lower frequency of WT1 mutations. In multivariate analysis for OS among the elderly who received standard intensive chemotherapy, high WBC >50,000/μL at diagnosis, RUNX1 mutations, DNMT3A mutations, and P53 mutations were independent worse prognostic factors, while the presence of NPM1 mutations in the abcence of FLT3/ITD mutations was an independent good prognostic factor. The frequency of acquiring one or more adverse genetic alterations was much higher in older patients than younger ones. Further, the pattern of gene mutations could divide older patients with intermediate cytogenetics into three groups with significantly different complete remission rates, OS, and disease-free survival.ConclusionOlder AML patients frequently harbored high-risk cytogenetics and gene mutations, and had poorer prognosis. Integration of cytogenetics and molecular alterations could risk-stratify older patients into groups with significant different outcomes. For those patients with poor prognosis under current chemotherapy, novel therapies, such as demethylating agents or other targeted therapies may be indicated. DisclosuresTang:Novartis: Consultancy, Honoraria.

Low-dose alemtuzumab in refractory/relapsed chronic lymphocytic leukemia: Genetic profile and long-term outcome from a single center experience.

Relapsed/refractory chronic lymphocytic leukemia (CLL) represents a clinical challenge, in particular when high risk gene mutations occur. In this setting, alemtuzumab was recognized to be effective. This retrospective study evaluates long-term efficacy and tolerability of low-dose alemtuzumab in relapsed/refractory CLL and correlates clinical outcome with biological feature. Sixty-two consecutive patients (median age 68 years) were evaluated; alemtuzumab was administered 30 mg weekly for up to 18 weeks. Among the patients included in the analysis, 37% were fludarabine-refractory, 33.3% carried a TP53 disruption, 14.8% a NOTCH1 mutation and 9% a SF3B1 mutation. Overall response rate (ORR) was 61.3% (complete remission 25.8%). After a median follow-up of 43 months, overall survival (OS) and progression free survival (PFS) were 43.1 and 15 months, respectively; while ORR was 77.8% for patients carrying TP53 disruptions (OS 33.8 months) and 43.5% for fludarabine-refractory patients (OS 30 months). Noteworthy, long-term survivors (OS ≥ 36 months) were 54.8%. None of the biological poor risk factors negatively impacted on ORR, PFS and OS. Grade ≥3 cytopenia occurred in 24.2% patients, 6.5% experienced a grade ≥3 non-CMV infection and no grade ≥3 CMV-event occurred. In conclusion, low dose-alemtuzumab is safe and effective in relapsed/refractory CLL, also in a long-term follow-up and high-risk genetic subgroups.

Prostate-specific antigen velocity as a predictive biomarker in a prospective prostate cancer screening study (IMPACT study).

16 Background: We retrospectively assessed the clinical application of Prostate Specific Antigen Velocity (PSA V) in the IMPACT study (Identification of Men with a genetic predisposition to ProstAte Cancer: Targeted screening in men at higher genetic risk and controls). This is a case-control prostate cancer (PrCa) screening study for men with a known genetic predisposition to PrCa; participants with a single PSA reading above 3ng/ml are offered diagnostic TRUS prostate biopsies (PB). Methods: We calculated PSA velocity (PSA V) using all three validated methods, including the arithmetic mean, the linear regression and the first and last readings equations. Pearson chi-square test was used to compare PSA V between four genetic groups: BRCA1 carriers and BRCA1 negative controls and BRCA2 carriers and BRCA2 negative controls. Results: PSA V data were evaluated in 191 men who underwent a PB with a total of 57 PrCas diagnosed. PSA V using both a threshold of 0ng/ml/year and 0.75ng/ml/year in any of the three methods was not predictive of PrCa diagnosis in BRCA1/2 controls and BRCA1 carriers. Conversely, BRCA2 carriers with a PSA V over 0.75ng/ml/year (by linear regression) were 5 times more likely to be diagnosed with PrCa [95%CI=1.5-14; p=0.003]. Interestingly PSA V using linear regression was predictive of clinically significant tumours as defined by Gleason Score (GS) &gt;= 7. Regardless of their genetic status, men with a PSA V over 0.75/ng/ml/year were 3 times more likely to have a clinically significant PrCa [95% CI: 1.006-11.107; p=0.045] whereas men with a BRCA2 mutation were 12 times more likely [95%CI: 1.1-98; p=0.039]. Conclusions: PSA V is an important tool for identifying which men with a BRCA2 mutation would benefit from a prostatic biopsy and could be incorporated into a predictive model, along with the total PSA value. PSA V also predicts for tumour aggressiveness regardless of genetic predisposition, but more so for those with a known high risk gene mutation. Clinical trial information: NCT00261456.