Citations

Abstract Childhood cancers are driven by unique profiles of somatic genetic alterations, with a significant contribution from predisposing germline variants. Understanding the genomic landscape of pediatric cancers is complicated by their rarity, the heterogeneity of variation within a given disease, and the complex forms of structural variation they contain. Variants in childhood disease may differ from those in adult versions of the same cancer type, or may have different clinical significance. Currently, pediatric variants are underrepresented in cancer variant databases, and an urgent need exists for their publicly available expert curation. To address this, the Pediatric Cancer Taskforce (PCT) was formed within the Clinical Genome Resource (ClinGen) Somatic Cancer Clinical Domain Working Group (CDWG) (https://www.clinicalgenome.org/working-groups/somatic/). The PCT is a multi-institutional group of 39 members with broad experience in childhood cancer and variant curation, whose work consists of standardization and classification of genetic variants in pediatric cancers. The CIViC knowledgebase (www.civicdb.org) is a freely available resource for Clinical Interpretation of Variants in Cancer, which leverages public curation and expert moderation to address the problem of annotating the large volume of clinically actionable cancer variants. PCT curators work together with PCT expert members and the CIViC team on variant curation, and have submitted over 230 Evidence Items and over 10 Assertions to CIViC. To further address issues specific to pediatric curation, the PCT is working with CIViC to develop new pediatric-specific CIViC features and modifications of the data model that will aid in pediatric curation. A pediatric user interface, as well as representation of large scale structural and copy number variation are being developed for version two of CIViC, expected to be released in 1-2 years, which will enable curation of a new class of structural variants often encountered in pediatric cancer. A novel standard operating procedure for childhood cancer curation in CIViC is being developed by PCT experts, curators and the CIViC team. This SOP will cover topics including curation of structural variants, as well as pediatric-specific variant tiering guidelines which take into account the sparse nature of evidence in pediatric cases. A companion resource, CIViCmine (http://bionlp.bcgsc.ca/civicmine/), will be further developed to incorporate pediatric data. These and other joint efforts of the PCT and CIViC will significantly enhance pediatric variant representation for public use, to support the care of children with cancer. Citation Format: Arpad Danos, Wan-Hsin Lin, Jason Saliba, Angshumoy Roy, Alanna J. Church, Shruti Rao, Deborah Ritter, Kilannin Krysiak, Alex Wagner, Erica Barnell, Lana Sheta, Adam Coffman, Susanna Kiwala, Joshua F. McMichael, Laura Corson, Kevin Fisher, Heather E. Williams, Matthew Hiemenz, Katherine A. Janeway, Jianling Ji, Kesserwan A. Chimene, Laura Fuqua, Lisa Dyer, Huiling Xu, Jeffrey Jean, Laveniya Satgunaseelan, Liying Zhang, Ted W. Laetsch, Donald W. Parsons, Ryan Schmidt, Lynn M. Schriml, Kristen L. Sund, Shashikant Kulkarni, Subha Madhavan, Xinjie Xu, Rashmi Kanagal-Shamana, Marian Harris, Yasmine Akkari, Nurit Paz Yacov, Panieh Terraf, Malachi Griffith, Obi L. Griffith, Gordana Raca. Advancing knowledgebase representation of pediatric cancer variants through ClinGen/CIViC collaboration [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 210.

Abstract The Clinical Interpretation of Variants in Cancer (CIViC) knowledgebase (civicdb.org) is an open access, centralized hub for structured, community curated and expertly moderated relationships between genomic variants and cancer. Evidence is curated from peer-reviewed, published literature and is classified into one of five Types: Predisposing, Diagnostic, Prognostic, Predictive (therapeutic), or Functional. The robustness of the Evidence is conveyed through the assignment of Levels with the first three derived from patient studies (Validated, Clinical, Case Study), Preclinical, generated from in vivo or in vitro data, and Inferential, which describes indirect associations. Each Evidence Item requires an Evidence Statement written in the curator's own words summarizing the source's results regarding the variant's clinical impact. Collaborations with groups like ClinGen have generated a significant influx of new curators, increasing the demand for detailed principles regarding data prioritization in the Evidence Statement in order to streamline the curation process. The curation community would benefit from simpler, visual guides through the complex decisions needed to appropriately and consistently curate Evidence Items. We are devoting significant effort to continue the development of straightforward Evidence curation algorithms (decision trees) similar to those used in clinical molecular testing labs to aid CIViC curators. Previously published guidelines on development of these statements are the basis of our Evidence algorithms. Obvious inflection points for curators are clearly identified with specific details noted for each to optimize decision efficiency. As the predominant Evidence Type comprising 57% of all CIViC submissions, 58% of referenced patient trials, and 92% of Preclinical submissions, Predictive Evidence is the initial focus of our pilot guidelines with Diagnostic and Prognostic to follow. Within the Predictive Evidence Type, clinical trials, case studies, and preclinical Levels each require vastly different Evidence Statement details and ultimately the creation of three separate, uniquely modeled algorithms. The implementation of these algorithms will assist in streamlining both curation and the expert review process. Notably, a template is not being created, as the preservation of curator style and voice is important to maintain the community feel of the database. To ensure the highest level of clarity, our team is utilizing specific novice and experienced curators to assist with the development process. As these algorithms pass the pilot phase, they are being tested as curator training tools. Ultimately, these guidelines will be used to encourage independence in curators and to enhance the Evidence already contained in CIViC. Citation Format: Jason Saliba, Lana Sheta, Kilannin Krysiak, Arpad Danos, Alex Marr, Erica Barnell, Shahil Pema, Wan-Hsin Lin, Panieh Terraf, Joshua F. McMichael, Cameron J. Grisdale, Shruti Rao, Susanna Kiwala, Adam Coffman, Alex Wagner, Obi L. Griffith, Malachi Griffith. Development of Evidence Statement curation algorithms to aid cancer variant interpretation [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 208.

Abstract Platinum-based DNA cross-linking agents are widely used anti-cancer drugs. Tumor resistance to platinum compounds is a major determinant of patient survival, including in high grade serous ovarian cancer (HGSOC). Remarkably, despite >30 years of literature on platinum responses in human cancer, none of these findings is used clinically as a predictive biomarker to stratify patients for platinum resistance, nor exploited therapeutically to treat platinum-resistant disease. Thus, understanding mechanisms of platinum resistance is an urgent goal, both to identify predictive biomarkers of platinum response (to spare patients with platinum-resistant tumors futile platinum therapy) and to develop efficacious therapies for platinum-resistant disease. To better understand mechanisms underlying platinum resistance in HGSOC, we performed comprehensive, dynamic (+/-carboplatin), multiomic profiling of DNA, RNA, protein and post-translational modifications (phosphorylation, ubiquitination, acetylation) to identify the cellular networks that respond to platinum treatment and associate with platinum resistance in three HGSOC intra-patient cell line pairs (PEA1S/PEA2R, PEO1S/PEO4R, PEO14S/PEO23R). The cell line pairs were derived from ascites or pleural effusions (Langdon et al., 1988) from three patients both before (PEA1S, PEO1S, PEO14S) and after (PEA2R, PEO4R, PEO23R, respectively) their tumors became clinically platinum resistant (i.e., in vivo development of resistance). The molecular profiles revealed extensive responses to carboplatin and differential responses between platinum-sensitive and platinum-resistant cells. Higher oxidative phosphorylation and fatty acid oxidation (FAO) pathway expression were observed in the platinum-resistant cells, which was further validated in patient-derived xenograft (PDX) models. We show that pharmacologic inhibition or CRISPR knockout of CPT1A, which represents a rate limiting step of FAO, sensitize HGSOC cells to platinum. Thus, FAO, and CPT1A in particular, represent a candidate therapeutic target to overcome platinum resistance in HGSOC. Citation Format: Hong Wang, Dongqing Hugang, Shrabanti Chowdhury, Sara Savage, Richard Ivey, Jacob Kennedy, Jeffrey Whiteaker, Chenwei Lin, Xiaonan Hou, Catherine Huntoon, Uliana Voytovich, Zahra Shire, Qing Yu, Steven Gygi, Andrew Hoofnagle, Zachary Herbert, Anna Calinawan, Larry Karnitz, S. John Weroha, Scott Kaufmann, Bing Zhang, Pei Wang, Michael Birrer, Amanda Paulovich. Multiomic analysis identifies CPT1A and fatty acid oxidation as a potential therapeutic target in platinum-refractory high grade serous ovarian cancer [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 1426.

Abstract There is a lack of large comparative study on the outcomes of reduced intensity conditioning (RIC) in acute myeloid leukemia (AML) transplantation using fludarabine/busulfan (FB) and fludarabine/melphalan (FM) regimens. Adult AML patients from Center for International Blood and Marrow Transplant Research who received first RIC allo-transplant between 2001 and 2015 were studied. Patients were excluded if they received cord blood or identical twin transplant, total body irradiation in conditioning, or graft-versus-host disease (GVHD) prophylaxis with in vitro T-cell depletion. Primary outcome was overall survival (OS), secondary end points were leukemia-free survival (LFS), nonrelapse mortality (NRM), relapse, and GVHD. Multivariate survival model was used with adjustment for patient, leukemia, and transplant-related factors. A total of 622 patients received FM and 791 received FB RIC. Compared with FB, the FM group had fewer transplant in complete remission (CR), fewer matched sibling donors, and less usage of anti-thymocyte globulin or alemtuzumab. More patients in the FM group received marrow grafts and had transplantation before 2005. OS was significantly lower within the first 3 months posttransplant in the FM group (hazard ratio [HR] = 1.82, P < .001), but was marginally superior beyond 3 months (HR = 0.87, P = .05). LFS was better with FM compared with FB (HR = 0.89, P = .05). NRM was significantly increased in the FM group during the first 3 months of posttransplant (HR = 3.85, P < .001). Long-term relapse was lower with FM (HR = 0.65, P < .001). Analysis restricted to patients with CR showed comparable results. In conclusion, compared with FB, the FM RIC showed a marginally superior long-term OS and LFS and a lower relapse rate. A lower OS early posttransplant within 3 months was largely the result of a higher early NRM.

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.

AbstractBackgroundAdult medulloblastoma (MB) is rare, and management guidelines are largely based on pediatric clinical trials and retrospective series. Limited data exist with respect to clinical characteristics, prognostic factors, and outcomes based on first-line treatments.MethodsTwo hundred adults with MB seen at a single institution from January 1978 to April 2017 were identified and followed for a median of 8.4 y (7.1, 10.3).ResultsPatient’s median age at diagnosis was 29 y (18, 63). One hundred eleven (55.5%) were standard-risk, 59 (29.5%) were high-risk, and 30 (15.0%) were indeterminate. Most received post-operative radiation (RT) (184 [92.0%]), and 105 (52.5%) received first-line chemotherapy. Median overall survival (OS) was 8.8 y (7.2, 12.2) and median progression-free survival (PFS) was 6.6 y (4.9, 11.2). High-risk patients had inferior OS (Hazard ratio [HR] = 2.5 [1.5, 4.2], P = .0006) and PFS (HR = 2.3 [1.3, 3.9], P = .002) compared to standard-risk patients. Age, sex, and metastatic disease were not associated with survival. After adjusting for risk status, those who received RT plus adjuvant chemotherapy had superior PFS compared to RT plus neoadjuvant chemotherapy [HR = 0.46 (0.22, 0.95), P = .0357]. Within a subgroup for whom detailed clinical data were available, those who received RT plus adjuvant chemotherapy had improved PFS compared to RT only [HR = 0.24 (0.074–0.76), P = .016]. The substitution of cisplatin for carboplatin and the elimination of vincristine did not negatively affect outcomes.ConclusionThis is the largest single-institution retrospective study of adult MB to our knowledge and identifies standard-risk status, first-line RT and adjuvant chemotherapy as factors associated with improved outcomes.

Introduction: Left ventricular assist device (LVAD) is known to extend survival in patients with advanced heart failure but it is associated with intracranial cranial hemorrhage (ICH). In the last decade, the use of LVAD substantially increased along with advances in LVAD technology, but there is limited data regarding the trends of ICH risk and predictors in patients with LVAD. Methods: We included the patients aged≥18 years with primary diagnosis of LVAD hospitalized in the US from 2005 to 2014 using the National Inpatient Sample. We computed the survey weighted percentages with ICH across the 10-year study period and assessed whether the proportions changed over time. Predictors of ICH were evaluated using the multivariable logistic regression model. All analyses were appropriately adjusted for the survey design variables to account for the complex survey design. Results: Of 33,246 hospitalizations, 568 (1.7%) had ICH. The number of LVAD placement has increased from 873 in year 2005 to 5,175 in year 2014. However, the risk of ICH remained largely unchanged from 1.7% to 2.3% (linear trend: p=0.604). The adjusted odds of ICH was increased with the presence one of the following variables: female sex (odds ratio [OR]: 1.58, 95% confidence interval [CI] 1.03-2.43), history of ischemic stroke (OR: 3.13, 95% CI 1.86-5.28), and Charlson Comorbidity Index (CCI) of ≥3 (OR: 77.40, 95% CI 10.03-597.60). Conclusions: Despite advances in LVAD technology and its increased use in patients with advanced heart failure, the risk of ICH has remained relatively unchanged. High CCI and history of ischemic stroke were associated with higher odds of ICH in patients with LVAD. With the advent of magnetically levitated centrifugal-flow LVAD, future trend of ICH may change and further research efforts are needed to prevent ICH in patients with LVAD.

Introduction: Robust leptomeningeal collaterals protect the brain from ischemia, yet the determinants of poor collaterals have not been established. We aimed to identify predictors of poor collaterals in patients with large vessel occlusive stroke. Methods: Consecutive patients with large vessel occlusive stroke who underwent thrombectomy at 2 academic medical centers (derivation cohort/validation cohort) from 2012-2017 were included. Poor collaterals were defined as ≤50% filling on CT angiogram. Pre-specified predictors of poor collaterals were analyzed with adjusted logistic regression models: demographics (age, sex, race), risk factors (hypertension, diabetes, atrial fibrillation, smoking), hemodynamics (blood pressure, cardiac output, troponin), metabolic (hyperglycemia, hyponatremia, uremia), hematologic (anemia, leukocytosis, thrombocytosis) and neuroimaging evidence of chronic cerebral small-vessel disease and chronic steno-occlusive arterial disease. Results: Of the 248 total patients, poor collaterals were detected in 107 (43%). Mean age was 71±14y vs. 63±16y in patients with poor vs good collaterals, respectively (p<.001). There were 136 patients in the derivation cohort; 54 (48%) patients with poor collaterals. Multivariable modeling identified that older age (OR 1.8, p<.001), hyperglycemia (OR 2.4, p=.029) and white matter hyperintensities (WMH) (OR 6.1, p=.003) were independent predictors of poor collaterals in the derivation cohort. The validation cohort consisted of 136 patients; 53 (39%) had poor collaterals, of which older age (OR 1.4, p=.015), thrombocytosis (OR 24.0, p=.012), and WMH (OR 6.7, p=.018) were significant predictors of poor collaterals. Age and WMH were the only significant predictors of poor collaterals across the derivation and validation cohorts. When pooled the cohorts, older age (OR=1.5, p<.001), thrombocytosis (OR=7.6, p=.001) and WMH (OR=6.4, p<.001) were significant predictors of poor collaterals. Conclusions: We have identified that advanced age, WMH, and thrombocytosis are predictors of poor collaterals. Future studies to explore the effect of vascular aging on collateral therapeutics are indicated.

Introduction: Cilostazol has promise as an alternative to aspirin for secondary stroke prevention given its vasodilatory and anti-inflammatory properties in addition to platelet aggregation inhibition. We conducted a systematic review and meta-analysis to estimate the comparative effectiveness and safety of cilostazol compared to aspirin for stroke prevention in patients with previous stroke or TIA. Hypothesis: Cilostazol is more effective than aspirin in preventing recurrent ischemic stroke with lower risk of intracranial hemorrhage and bleeding. Methods: We searched PubMed and the Cochrane Central Register of Controlled Trials from inception to 2019. Randomized clinical trials that compared cilostazol vs aspirin and reported the endpoints of ischemic stroke, intracranial hemorrhage and bleeding were included. A random-effects estimate was computed based on Mantel-Haenszel methods. The pooled estimates with 95% confidence intervals were compared between cilostazol and aspirin and displayed as forest plots (Figure). Results: The search identified 5 randomized clinical trials comparing cilostazol vs aspirin for secondary stroke prevention that enrolled 7,240 patients from primarily Asian countries (3,615 received cilostazol and 3,625 received aspirin). The pooled results from the random-effects model showed that cilostazol was associated with significantly lower risk of recurrent ischemic stroke (Hazard ratio [HR] 0.70; 95%CI, 0.54-0.89), intracranial hemorrhage (HR 0.41; 95%CI, 0.25-0.65) and bleeding (HR 0.71; 95%CI, 0.55-0.91). See forest plots. Conclusion: This meta-analysis suggests cilostazol is more effective than aspirin in the prevention of recurrent ischemic stroke with lower risk of intracranial hemorrhage and bleeding. Confirmatory randomized trials of cilostazol for secondary stroke prevention to be performed in more generalizable populations are needed.

Introduction: Left atrial enlargement (LAE) is associated with atrial fibrillation, a frequent cause of large vessel occlusion (LVO) leading to ischemic stroke. Leptomeningeal collaterals protect tissue from ischemia, but the association between collaterals and structural heart disease is not well described. We aim to investigate the association between LAE and cerebral collaterals during acute LVO when microvasculature, vasodilation, and chronotropic competence are critically important. Hypothesis: Left atrial enlargement is associated with poor collaterals. Methods: We reviewed consecutive patients presenting with middle cerebral and internal carotid LVO who underwent thrombectomy from 2012 to 2017. Patients with CT angiogram of the head and echocardiogram were included. Poor collaterals were defined as ≤ 50% filling on CT angiogram. LAE was defined as left atrial volume index ≥ 35 mL/m 2 . Multivariate logistic regression analysis was performed to evaluate the relationship between LAE and poor collaterals with adjustment for age and hypertension. Results: There were 128 eligible patients. The mean age was 68± 15 years, median NIHSS was 17, and 51 (39.8%) had LAE. Baseline characteristics are described in the table. Poor collaterals were observed in 50 (39%) patients. Patients with LAE were more likely to have poor collaterals compared to those with normal left atrial size (52.9% vs. 29.9%, p=0.009). After adjusting for age and hypertension, a trend towards association remained (OR 2.00, p=0.089). Conclusion: Our results indicate that patients with LVO and LAE were more likely to have poor collaterals. Further research is warranted to determine the cause of the association. One possibility is shared pathophysiology affecting both cardiac and cerebral vasculature such as microvascular disease or endothelial dysfunction. Alternatively, structural heart disease causing chronotropic incompetence may lead to poor collateral filling.