Emily Quinn

Germline Mutations in Predisposition Genes in Pediatric Cancer

BACKGROUND The prevalence and spectrum of predisposing mutations among children and adolescents with cancer are largely unknown. Knowledge of such mutations may improve the understanding of tumorigenesis, direct patient care, and enable genetic counseling of patients and families. METHODS In 1120 patients younger than 20 years of age, we sequenced the whole genomes (in 595 patients), whole exomes (in 456), or both (in 69). We analyzed the DNA sequences of 565 genes, including 60 that have been associated with autosomal dominant cancer-predisposition syndromes, for the presence of germline mutations. The pathogenicity of the mutations was determined by a panel of medical experts with the use of cancer-specific and locus-specific genetic databases, the medical literature, computational predictions, and second hits identified in the tumor genome. The same approach was used to analyze data from 966 persons who did not have known cancer in the 1000 Genomes Project, and a similar approach was used to analyze data from an autism study (from 515 persons with autism and 208 persons without autism). RESULTS Mutations that were deemed to be pathogenic or probably pathogenic were identified in 95 patients with cancer (8.5%), as compared with 1.1% of the persons in the 1000 Genomes Project and 0.6% of the participants in the autism study. The most commonly mutated genes in the affected patients were TP53 (in 50 patients), APC (in 6), BRCA2 (in 6), NF1 (in 4), PMS2 (in 4), RB1 (in 3), and RUNX1 (in 3). A total of 18 additional patients had protein-truncating mutations in tumor-suppressor genes. Of the 58 patients with a predisposing mutation and available information on family history, 23 (40%) had a family history of cancer. CONCLUSIONS Germline mutations in cancer-predisposing genes were identified in 8.5% of the children and adolescents with cancer. Family history did not predict the presence of an underlying predisposition syndrome in most patients. (Funded by the American Lebanese Syrian Associated Charities and the National Cancer Institute.).

Germline ETV6 Mutations Confer Susceptibility to Acute Lymphoblastic Leukemia and Thrombocytopenia

Somatic mutations affecting ETV6 often occur in acute lymphoblastic leukemia (ALL), the most common childhood malignancy. The genetic factors that predispose to ALL remain poorly understood. Here we identify a novel germline ETV6 p. L349P mutation in a kindred affected by thrombocytopenia and ALL. A second ETV6 p. N385fs mutation was identified in an unrelated kindred characterized by thrombocytopenia, ALL and secondary myelodysplasia/acute myeloid leukemia. Leukemic cells from the proband in the second kindred showed deletion of wild type ETV6 with retention of the ETV6 p. N385fs. Enforced expression of the ETV6 mutants revealed normal transcript and protein levels, but impaired nuclear localization. Accordingly, these mutants exhibited significantly reduced ability to regulate the transcription of ETV6 target genes. Our findings highlight a novel role for ETV6 in leukemia predisposition.

Germline genetic variation in ETV6 and risk of childhood acute lymphoblastic leukaemia: a systematic genetic study

Background Hereditary predisposition is rarely suspected for childhood acute lymphoblastic leukemia (ALL). Recent studies identified germline ETV6 variations associated with marked familial clustering of hematologic malignancies, pointing to this gene as a potentially important genetic determinant for ALL susceptibility. The aims of the current study are to comprehensively identify ALL predisposition variants in ETV6 and to determine the extent to which they contribute to the overall risk of childhood ALL. Methods Whole-exome sequencing of an index family with multiple cases of ALL was performed to identify causal variants for ALL predisposition. Targeted sequencing of ETV6 was done in 4,405 children from the Childrens Oncology Group (COG) and St. Jude Childrens Research Hospital frontline ALL trials. Patients were included in this study on the basis of their enrollment in these clinical trials and the availability of germline DNA. ETV6 variant genotypes were compared with non-ALL controls to define ALL-related germline risk variants. ETV6 variant function was characterized bioinformatically and correlated with clinical and demographic features in 2,021 children with ALL. Findings We identified a novel nonsense ETV6 variant (p.R359X) with a high penetrance of familial ALL. Subsequent targeted sequencing of ETV6 in 4,405 childhood ALL cases discovered 31 exonic variants (4 nonsense, 21 missense, 1 splice site, and 5 frame shift variants) that are potentially related to ALL risk in 35 cases (0.79%). Fifteen (48%) of the 31 ALL-related ETV6 variants clustered in the ETS domain and predicted to be highly deleterious. Children with ALL-related ETV6 variants were significantly older at leukemia diagnosis than others (10.2 years [IQR 5.3-13.8] vs 4.7 years [IQR 3.0-8.7], P=0.017). The hyperdiploid leukemia karyotype was strikingly overrepresented in ALL cases harboring germline ETV6 risk variants compared to the wildtype group (9 of 14 cases [64.3%] vs 538 of 2,007 cases [26.8%]; P=0.0050). Interpretation Our findings indicated germline ETV6 variations as the basis of a novel genetic syndrome associated with predisposition to childhood ALL. Funding This study was supported by the National Institutes of Health and by the American Lebanese Syrian Associated Charities.

Andersen–Tawil syndrome: Report of 3 novel mutations and high risk of symptomatic cardiac involvement

Introduction: Andersen–Tawil syndrome (ATS) is a potassium channelopathy affecting cardiac and skeletal muscle. Periodic paralysis is a presenting symptom in some patients, whereas, in others, symptomatic arrhythmias or prolongation of QT in echocardiographic recordings will lead to diagnosis of ATS. Striking intrafamilial variability of expression of KCNJ2 mutations and rarity of the syndrome may lead to misdiagnosis. Methods: We report 15 patients from 8 Polish families with ATS, including 3 with novel KCNJ2 mutations. Results: All patients had dysmorphic features; periodic paralysis affected males more frequently than females (80% vs. 20%), and most attacks were normokalemic. Two patients (with T75M and T309I mutations) had aborted sudden cardiac death. An implantable cardioverter‐defibrillator was utilized in 40% of cases. Conclusions: KCNJ2 mutations cause a variable phenotype, with dysmorphic features seen in all patients studied, a high penetrance of periodic paralysis in males and ventricular arrhythmia with a risk of sudden cardiac death. Muscle Nerve 51: 192–196, 2015

Cancer predisposition syndromes associated with myeloid malignancy

The majority of myeloid malignancies are caused by sporadic somatic events rather than cancer predisposition. Nonetheless, the identification of hereditary cancer predisposition syndromes is critical when caring for patients with myeloid malignancies since detection may direct decisions related to cancer treatment and surveillance. A positive genetic test result also has important implications for other family members who can use this information to undergo their own testing to determine their cancer risk. We review the demographics, genetic mechanisms of disease, diagnostic approach, malignancy risk, and management for the following five cancer predisposition syndromes associated with myeloid malignancies: Li-Fraumeni, constitutional mismatch repair deficiency, Werner, Bloom, and Nijmegen breakage.

Abstract 2033: Germline mutations in ETV6 confer risk of thrombocytopenia and acute lymphocytic leukemia

Germline mutations of transcription factors (e.g. PAX5, CEBPA, GATA2, RUNX1) have been associated with an inherited susceptibility to acute leukemia. Here we report 2 unrelated kindreds harboring germline mutations in ETV6, the gene encoding the transcription factor ETS variants 6. These kindreds were primarily characterized by thrombocytopenia and acute lymphoblastic leukemia (ALL). The first kindred, identified at MSKCC and HMC, includes 9 individuals with thrombocytopenia, and 3 individuals with pre-B ALL. Sequencing a subset of common and somatically altered leukemia genes in this family identified a rare heterozygous non-synonymous missense variation (T>C) in 6 family members with thrombocytopenia and 2 with ALL. Notably, this variant did not segregate in 9 individuals in the kindred without these phenotypes. The amino acid alteration is predicted to lead to an L349P substitution within the DNA binding domain of ETV6 (L349P, NPP_001978). In silico analyses using SIFT and Polyphen assigned pathogenic variant classifications to the L349P variant. The proband of the second family presented to SJCRH with pre-B ALL, a history of thrombocytopenia, and demonstrated hypersensitivity to methotrexate (grade 3 bone marrow suppression). His leukemia transformated to myelodsyplastic syndrome and acute myeloid leukemia, which was treated by unrelated donor transplantation. The proband9s mother, maternal aunt and maternal grandfather had thrombocytopenia, and the maternal great grandfather was diagnosed with chronic myeloid leukemia. The proband and his mother were found to carry a heterozygous 5 bp deletion in ETV6, N385fs (c.1153-5_1153_1delAACAG), which is predicted to produce a truncated protein of 389 amino acids with the last 4 residues different from the canonical ETV6 sequence. This variant has not been described in public sequencing data repositories. Finally, a review of 1,120 cases from the SJCRH/Washington University Pediatric Cancer Genome Project, including 588 cases of leukemia (among which 472 were ALL), revealed 3 rare germline ETV6 variants: L442P (n = 1), R181H (n = 1), and V37M (n = 1), with 2 of these variants L442P and R181H predicted to be pathogenic based on prediction and/or genomic location. Notably, these 2 variants each occurred in patients with ALL. Collectively, these findings suggest that germline ETV6 mutations are associated with a novel syndrome of thrombocytopenia with susceptibility to leukemia. Furthermore, these mutations may account for approximately 0.4% (2/472) of pediatric ALL cases. Further phenotypic characterization of affected patients and functional assessment of ETV6 germline variants, in progress, will be required to reveal the clinical effects of these mutations, their incidence in patients with ALL and their role in leukemogenesis. Citation Format: Vijai Joseph, Michael F. Walsh, Sabine Topka, Gang Wu, Rose B. McGee, Emily Quinn, Hiroto Inaba, Christine Hartford, Ching-Hon Pui, Alberto S. Pappo, Michael Edmonson, Lauren Jacobs, Villano Danylo, Kasmintan Schrader, Pragna Gaddam, Zsofia Stadler, Michael Zhang, Polina Stepensky, Peter Steinherz, James Bussel, M Harit, Michael Weintraub, Akiko Shimamura, Jinghui Zhang, James R. Downing, Kenneth Offit, Kim E. Nichols. Germline mutations in ETV6 confer risk of thrombocytopenia and acute lymphocytic leukemia. [abstract]. In: Proceedings of the 106th Annual Meeting of the American Association for Cancer Research; 2015 Apr 18-22; Philadelphia, PA. Philadelphia (PA): AACR; Cancer Res 2015;75(15 Suppl):Abstract nr 2033. doi:10.1158/1538-7445.AM2015-2033