Citations

Abstract Despite the well-established role of recurrent gene fusions as oncogenic drivers, current practices for characterizing and interpreting gene fusion events in clinical testing and in biomedical literature are inconsistent. From the conceptual definition of gene fusions to the salient elements that characterize these alterations, a lack of community-driven standards for the curation of gene fusions has resulted in a disparate landscape of fusion representations and supporting tools. Consequently, the evidence-based clinical evaluation of gene fusions requires extensive expert review for accurate interpretation of observed gene fusions with respect to putative evidence from biomedical literature. Furthermore, the lack of these standards inhibits the interoperability of tools, resources, and pipelines - impeding data sharing and downstream utility.To address these challenges, a cross-consortia initiative between the Variant Interpretation for Cancer Consortium and ClinGen was formed to develop a standard operating procedure (SOP) for the curation of gene fusions. The SOP is under development by an international and diverse set of experts in the representation, detection, and clinical interpretation of gene fusions. Participating stakeholders across academic, government, and industry sectors showcased challenges and solutions, and participated in community surveys and discussions to define and develop the SOP for this diverse class of alterations.An initial result of this effort was the precise molecular definition of genomic events and features constituting gene fusions. We distinguish these from similar but distinct classes of structural alterations through clinically-relevant examples. Next, we discuss our findings on community practices around the description and evaluation of gene fusions. We provide our recommendations for characterization and representation of gene fusions from these practices, and compare these recommendations to existing variant representation standards and formats (e.g. HGVS variant nomenclature). We also discuss the concurrent application of formats for standardized human- and machine-readable representations of gene fusion events.We conclude with discussion of the salient elements to enable rapid, scalable, and consistent evaluation of fusions curated from the biomedical literature. Recommendations are provided for the standardized capture of these elements to enable both intuitive and precise characterization of this diverse class of alterations in clinical reporting and literature. In summary, we provide a clinical-practice driven framework and nomenclature for gene fusions, including recommendations for human readability, computational precision, and data integrity within the SOP. This work is a substantial advancement towards standardized communication, investigation, and sharing of gene fusion data across clinical and research domains and specialties. Citation Format: Alex H. Wagner, Ioannis S. Vlachos, Dmitriy Sonkin, Panieh Terraf, Chimene Kesserwan, Andrea Sboner, Thomas Coard, Christian Reich, Deborah I. Ritter, Peter Horak, Ying S. Zou, Anna Tanska, Aaron M. Berlin, Anna Lu, Daniel Cameron, Heather E. Williams, Wan-Hsin Lin, Gokce Toruner, Arpad Danos, Jason Saliba, Huiling Xu, Xinjie Xu, Georgina Ryland, Michele Ceccarelli, Liying Zhang, Sarah Rapisardo, Catherine Rehder, Xuelu Liu, Aparna Pallavajjala, Nicole Park, Laveniya Satgunaseelan, Kristy Lee, Jie Liu, Obi Griffith, Robert R. Freimuth, Albrecht Stenzinger, Linda B. Baughn, Michael Baudis, Jennifer Lee, Marilyn Li, Angshumoy Roy, Gordana Raca. A standard operating procedure for the curation of gene fusions [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2021; 2021 Apr 10-15 and May 17-21. Philadelphia (PA): AACR; Cancer Res 2021;81(13_Suppl):Abstract nr 449.

BRASH syndrome is characterized by bradycardia, renal failure, AV nodal blockade, shock, and hyperkalemia. The proposed mechanism involves a vicious cycle between AV nodal blockers, hyperkalemia, and renal failure and was first described in 2016. We present a case of a 52-year-old woman who presented with progressively worsening shortness of breath and hypertensive urgency who subsequently developed profound bradycardia and shock that was refractory to resuscitative measures, she was diagnosed with BRASH syndrome. In this article, we explore the predisposing factors and challenges faced during the management of patients with BRASH syndrome.

Abstract BackgroundCopy number variants (CNVs) are pervasive in the human genome but potential disease associations with rare CNVs have not been comprehensively assessed in large datasets. We analysed rare CNVs in genes and non-coding regions for 86,788 breast cancer cases and 76,122 controls of European ancestry with genome-wide array data.ResultsGene burden tests detected the strongest association for deletions in BRCA1 (P= 3.7E-18). Nine other genes were associated with a p-value < 0.01 including known susceptibility genes CHEK2 (P= 0.0008), ATM (P= 0.002) and BRCA2 (P= 0.008). Outside the known genes we detected associations with p-values < 0.001 for either overall or subtype-specific breast cancer at nine deletion regions and four duplication regions. Three of the deletion regions were in established common susceptibility loci.ConclusionsThis is the first genome-wide analysis of rare CNVs in a large breast cancer case-control dataset. We detected associations with exonic deletions in established breast cancer susceptibility genes. We also detected suggestive associations with non-coding CNVs in known and novel loci with large effects sizes. Larger sample sizes will be required to reach robust levels of statistical significance.

Background: The risk for intracranial (IA) and abdominal aortic aneurysms (AAA) is partially heritable, with evidence mounting in favor of shared genetic risk for both. Methods: The Brain and Aortic Aneurysm Study (BAAS, NCT#17341) at University of Virginia seeks to determine the coprevalence of IA and AAA recruiting patients presenting with an aneurysm at one site and screening for aneurysm at the other. Participants undergo genetic screening and an interview where clinical, demographic, and radiographic data are collected. Recruitment and screening are ongoing, so preliminary demographic data regarding between group differences (IA vs. AAA) are presented. All clinical and demographic data were collected and recorded in REDCap and exported to Excel. We compared a total of 256 participants (IA=164, AAA=92) for demographic factors: age, sex, smoking and past medical history. Results: The AAA cohort was older (70.98 vs. 58.51, p<.001) and more male (79.34% vs. 23.78% p<.001). The AAA cohort had a higher proportion with diabetes mellitus (28.26% vs. 15.24%, p=.012), with hyperlipidemia (67.39% vs. 44.51%, p<.001) and higher smoking pack years (44.07 vs. 17.85, p<.001). The two groups did not differ in proportion with hypertension, coronary artery disease, or peripheral vascular disease (all p>.05). Conclusions: These data suggest that there may be subtle differences in the clinical profile of patients presenting with IA and AAA, especially when considering known aneurysmal risk factors like hypertension, diabetes, and smoking history. Further analyses will consider whether these factors modulate the coprevalence of the two types of aneurysms.

Background: Cardiovascular disease (CVD) remains the leading cause of death for African-American (AA) adults. There is a low prevalence of ideal cardiovascular health (CVH) (as defined by the American Heart Association’s Life’s Simple 7 TM (LS7)), especially diet, physical activity and obesity among AAs placing them at a disproportionately high risk for CVD. The identification of psychosocial stress that may influence ideal CVH could assist in the development of more effective behavior change interventions among AAs. Objectives: The aim of this study is to examine the associations of multidimensional stressors (chronic stress, minor stressors, and major life events - MLEs) with the LS7 components (classified as poor, intermediate and ideal) in AAs. We hypothesize that stress is negatively associated with the likelihood of achievement of intermediate/ideal levels of the LS7 components and LS7 composite score after adjusting for traditional socio-demographic factors. Methods: Using the Jackson Heart Study (JHS), a cohort of AAs based in Jackson, Mississippi (n=4383), we conducted a cross-sectional analysis of the association of stress measures with LS7 components (smoking, diet, physical activity, body mass index, blood pressure, total cholesterol and glucose). This association was measured using logistic regression which assessed the odds ratios (OR, 95% confidence interval (CI)) of the achievement of intermediate/ideal levels of CVH with progressive adjustment for demographic, socioeconomic, behavioral and biomedical factors. A composite LS7 score was calculated [range 0-14; categorized as 0 to 6 (poor), 7 to 8 (intermediate) and 9 to 14 (ideal)]. We also constructed a cumulative stress score as a summation of tertiles of each stress measure (range 3-9). Results: Fewer participants achieved intermediate or ideal CVH for the LS7 components including diet (39%), physical activity (51%) and BMI (47%). Higher chronic stress and minor stressors scores were associated a decreased likelihood of achievement of ideal/intermediate levels for smoking [OR 0.80; 95% CI 0.73-0.88 and OR 0.84; 95% CI 0.75-0.94, respectively). Higher MLE scores were associated decreased likelihood of achievement of ideal/intermediate levels for smoking (OR 0.84; 95% CI 0.76-0.92) and glucose (OR 0.90; 95% CI 0.82-0.98). Those with higher minor stressors and MLE scores were less likely to achieve intermediate or ideal LS7 composite score categories (OR 0.89; 95% CI 0.81-0.97 and OR 0.91; 95% CI 0.84-0.98, respectively). There was no statistically significant association between LS7 composite scores and cumulative stress scores. Conclusions: Our results suggest that key stress measures may contribute adversely to CVH among AAs. These findings provide support for future lifestyle interventions which integrate a focus on alleviating stressors in this high risk population to improve CVH.

Paraganglioma (PGL) is a rare form of neuroendocrine cancer for which the underlying molecular basis is poorly understood. A mysterious hallmark of many PGL tumors is the inactivation of succinate dehydrogenase (SDH), a mitochondrial enzyme of the TCA cycle. Why does SDH loss induce cancer in certain cells? As a result of SDH loss, PGL tumor cells accumulate succinate, which may have epigenetic consequences. For example, certain lysine residues on histone proteins in nucleosomes are subject to succinylation by succinyl‐CoA as a post translational modification (PTM) that converts the lysine cation to an anion. We hypothesize that the structure and stability of the nucleosome core particle (NCP) is affected by succinylation PTMs through weakening of electrostatic histone‐DNA and histone‐histone interactions. Proteomic analysis of an SDH‐loss cell line model of PGL previously demonstrated that the greatest increase in nucleosomal lysine succinylation maps to H4K79 when compared to a control cell line. The mammalian H4K79 residue lies within the nucleosome core near wrapped DNA. We specifically hypothesize that the charge inversion conferred by H4K79 succinylation, destabilizes the NCP. Point mutations at H4K79 have been generated as lysine succinylation mimics at this site. Biophysical and in vitro transcription assays are being utilized to validate the assembly of NCPs incorporating lysine succinylation mimics at this site and to interrogate their resulting stabilities. Analyses of alterations in NCP dynamics in variant NCP will help to elucidate the role of lysine succinylation of histones in the altered chromatin landscape observed during PGL oncogenesis. Support or Funding Information GM75148‐09‐10 PREP This abstract is from the Experimental Biology 2019 Meeting. There is no full text article associated with this abstract published in The FASEB Journal .

Objective To identify novel genes and pathways associated with acute mountain sickness (AMS). Background The uniform, rapid transfer of adults from McMurdo Station (sea level, SL) in Antarctica to the South Pole (SP, 2835m) provides a unique opportunity to study changes in gene expression related to the body's adaptation to hypobaric hypoxia. Methods Venous blood was drawn at SL and after 2 d at SP in 98 subjects (age 37±9 y, 70% male). Peripheral blood mononuclear cells (PBMCs) were isolated and microarray analysis of the mRNA isolated from these cells was performed (Affymetrix HG U133 Plus 2 microarray chip). Analysis and the computation of expression fold changes and phenotypic regression were performed using the Bioconductor package in R. Pathway analysis was performed using MetaCore™. Results ~3200 probe sets with sig. p‐values (p<0.05) and fold changes for each subject were used in a binary logistic regression with the presence or absence of AMS during the 2 d at altitude. Corresponding p‐values and z‐values were entered into MetaCore™ for pathways analysis. Identified pathways included smooth muscle contraction, calcium signaling, and acetylcholine regulation of nerve impulses. Conclusions Probe sets associated with the presence of AMS had a significant representation in pathways involving aspects of the autonomic nervous system including smooth muscle contraction and nerve signaling. NSF B‐179‐M.

Background It is documented that cognitive performance can diminish with altitude, but the sensitivity of specific tests have not been investigated. Our objective was to assess and compare cognitive performance from several tests and relate this to quality of sleep and acute mountain sickness (AMS). Methods During an Everest expedition, 3 cognitive tests (Stroop, Trail Making, and a proprietary motor accuracy test) were used along with a questionnaire to assess sleep and AMS. Six athlete climbers and 9 core team members were assessed pre and post‐expedition and at several time points during the expedition (up to 17,500 ft). Results To normalize for individual differences, scores were assessed as % change from baseline. There was no difference in the variation between repeated attempts in a single testing session (0.19<p<0.87), demonstrating that each test was reproducible. There was no decrement in test scores with altitude, nor was there an association with reported sleep quality. The Stroop performance was associated with AMS (p<0.05) and trending with headache (p< 0.15). The in‐house motor test trended towards an association with AMS and headache (p<0.15). However, the trail making test was not associated with AMS/headache. Conclusion With appropriate acclimatization, cognitive performance is maintained at altitude but is linked to presence of headache and AMS. Mayo Clinic and TNF.