bluuebunny/crossref_metadata_2025_split huggingface dataset:
Assessment of a highly curated somatic oncology mutation database to facilitate identification of clinically important variants in NGS results.
Authors: Ma Xiaoju Max , Yaung Stephanie J. , Xi Liu , Ju Christine , Palma John F. , Schmid Maximilian 
Published: May 2019

e18086 Background: The increasing adoption of Next Generation Sequencing (NGS) in molecular profiling of cancer presents a growing need for streamlined interpretation of NGS results in clinical labs. This can be achieved through bioinformatics tools equipped with a highly-curated database on clinically important variants. Methods: We performed an initial assessment of an NGS result interpretation tool called NAVIFY Mutation Profiler (NMP), which enabled us to process a Variant Call Format (VCF) file and generate a report with consensus recommendations of NCCN, ASCO, CAP and ACMG. This annotation tool identifies pathogenic variants and variants of unknown clinical significance (VUS), and groups variants by AMP Tiers. At the time of this assessment, NMP contained curation for ~4,000 variants. In this study, we used NGS results from 38 anonymized clinical cases with known treatment regimens to retrospectively assess NMP as the variant interpretation tool. Our cohort contained lung cancer subjects treated with EGFR tyrosine kinase inhibitor (TKI) (5 cases), as well as subjects relapsed against EGFR TKI (1 case) or ALK TKI crizotinib (22 cases). We also included 10 control cases where standard of care chemo was used because initial diagnostic methods did not reveal any actionable targets. Results: NMP annotated NGS VCF data and generated a report within 10 minutes per case although some cases contained > 100 variants. NMP correctly associated EGFR TKI therapies options with the corresponding 5 cases. As expected, NMP did not recommend targeted therapies for the 10 chemo-treated control cases. For the subject relapsed against EGFR TKI, NMP correctly interpreted the complex EGFR mutation profile containing both activating (L858R) and drug-resistance (T790M) variants. In addition, out of 22 cases relapsed against ALK TKI crizotinib, NMP correctly marked 14 with crizotinib resistance when a known ALK variant conferring crizotinib resistance was detected. There was limited or no published clinical evidence to interpret the remaining 8 cases of ALK TKI resistance. Conclusions: NMP correctly interpreted cases containing EGFR and ALK variants in this study. With a highly-curated knowledge base, this tool simplifies NGS clinical reporting by identifying clinically actionable mutations and associating treatment options qualified by supporting clinical evidence.
A novel approach to support community oncology practices in building a clinical research program.
Authors: Miller Jeremy , Kientop Debra A. , Andrews Linda , Edenfield William Jeffery , Hadley David 
Published: May 2019

e18087 Background: Starting a clinical research program in a community oncology setting has a myriad of challenges. While ASCO provides guidance through its “Basic Requirements for Starting a Research Practice”, building a research program requires significant time and effort. We present an example of how a technology-enabled solution supports a consortium of community oncology practices to rapidly grow their clinical research program, as they strive to meet the Commission on Cancer goal of > 4% clinical trial enrollment. Methods: Four key pillars that support a successful research program include: building program infrastructure, establishing standard operating procedures, engaging patients and accessing clinical trials. The consortium receives support for each of these components through a combination of software tools and professional services. Results: The practices in the consortium currently have clinical trial enrollment that is less than desired, but the number of patients on clinical trials in the consortium for coming year is expected to grow between two and ten-fold. The table below shows the enrollment by site in 2018 for the 7 practices that have been engaged for the full year. Candidates are patients who have found to be eligible for at least one clinical trial, but have not yet been enrolled or declined. Conclusions: The practices have been engaged in the consortium for approximately one year. While some practices are well below their eventual target of 4% enrollement, the increasing number of patients screened, and their growing clinical trial portfolio of well-matched clinical trials has them well on their way to that target over the next two years.[Table: see text]
Artificial Intelligence (AI) and machine learning (ML) in risk prediction of hospital acquired pressure injuries (HAPIs) among oncology inpatients.
Authors: Ravi Vinod , Zheng Jing , Subramaniam Aparna , Thomas Lavonia G , Showalter John , Frownfelter John , Miller Kelly 
Published: May 2019

e18095 Background: Utilizing AI and ML is an emerging method to improve risk identification, characterization and stratification for clinical outcomes such as HAPIs. The Jvion Cognitive Clinical Success Machine (CCSM) utilizes the Eigen Sphere technique to factor in clinical, socioeconomic, and behavioral covariates at the individual patient level to maximize accuracy of risk prediction and provide insights on prevention of HAPIs. Methods: A retrospective analysis was performed utilizing claims and EHR data on 63,476 inpatient admissions between June 2016 and June 2018 at M D Anderson Cancer Center, a 660-bed oncology facility (Table). All risk assessment indicators in the data were removed prior to analysis by the CCSM to compute unbiased risk probabilities for HAPIs. The performance of the CCSM risk prediction for all new stage 2 and above HAPIs ( > = Stage 2 HAPIs) was compared with the Braden scale using AUC. Results: The Jvion CCSM had an AUC of 0.84 compared to the AUC of 0.72 for the Braden scale in the prediction of > = Stage 2 HAPIs. Conclusions: The AUC value indicates that the Jvion CCSM has better predictive accuracy than the Braden scale. It also has better discrimination in risk identification. Thus, Jvion CCSM can be a valuable tool in risk screening for HAPIs which can lead to early preventative interventions. [Table: see text]
Searching for lymphoma: An analysis of internet and social network activity and engagement.
Authors: Galvin John Patrick , Meier Anne Catherine , Peace David J. 
Published: May 2019

e18102 Background: Online search engines, forums and social networks can offer an important space to ask questions and share experiences. Online searches, forums and social networks have become one of the most common ways patients learn about their lymphoma. However, not much is known about which sites and online sources engage people on the topic of lymphoma and which social networks are used to learn and/or share experiences. Methods: Our objective was to analyze the sites with the most engagement online on the topic of lymphoma. We used an online analytical research program (BuzzSumo), which can assess specific content and identify sites that generate the greatest frequency of engagement across social platforms. Our analysis covered activity from 2/2014-2/2019. Results: From the analysis of 9,141 online articles on the topic of lymphoma and 662,690 engagements, we found that the social network that was used the most was Facebook and to a much lesser extent Twitter. The Pinterest and Reddit platforms were not engaged on this topic. Most engagements were with “List” and “What you should know” articles on lymphoma for both Facebook and Twitter with a significantly lesser amount of engagement for video content. Articles on lymphoma less than 2000 words had the most engagement. A number of different types of sites generated the most engagements -- ranging from media outlets, lymphoma foundations and large medical centers. An analysis of 28,863 Facebook posts on lymphoma with 4,765,956 total engagements revealed that video posts generated the most engagements and that posts that were > 300 characters generated more engagement. An analysis of questions asked online mentioning lymphoma revealed that the most common topics were that of “diagnosis” and associated emotions – “worried” or “scared.” Conclusions: Online articles and social networks have become integrated into our daily lives. It is important that we start to understand how these information sources are being used by patients, caregivers and health care providers. Our analysis of online engagement on the topic of lymphoma is an example of how analytical programs can be used to help understand where and how people are engaging to learn and share their experiences with lymphoma.
Experience and challenges of setting up a new lung cancer chemotherapy clinic in resource limited setting in Nepal.
Authors: Mishra Deebya Raj , Bhatta Narendra , Shah Niharika 
Published: May 2019

e18104 Background: Nepal is a developing country with a Gross Domestic Product per capita of 2400 US dollars. There are only two specialized cancer centers in whole of Nepal. They are at best, understaffed, overburdened and limited by logistics. Cancer diagnosis is easily accepted as a death sentence in the society and treatment rarely done due to the lack of universal coverage or health insurance. The nearest Cancer hospital is 400km away. In this background, in an academic institute serving as the referral center for Eastern Nepal, lung cancer chemotherapy clinic has started in last one year duration. Methods: A prospective Observational Study was done from May 2017 to May 2018 by the newly set up Lung Cancer treatment unit in an academic medical institute in Eastern Nepal. Readiness to undergo biopsy after suspicion of lung cancer as well as readiness for chemotherapy was looked at along with Clinico-radiologic characteristics, demographics, presumptive stage of disease and treatment outcome were recorded. Results: 53 patients were suspected of lung cancer based on imaging. Of these 14 did not agree for biopsy. Of the 39 who underwent biopsy, lung cancer was the diagnosis in 31 cases. In 4 cases the lung biopsy was not definitive for a diagnosis. Histology samples were obtained by USG guided Trans-thoracic needle biopsy in 25 cases and by bronchoscopic biopsy in 14 cases. The predominant histology was Adenocarcinoma (42%, 13/31) followed by Squamous Cell Carcinoma (29%, 9/31). There were 3 cases of Small Cell Carcinoma. Of the cases diagnosed as lung cancer, 45% (14/31) refused treatment. Immunohistochemistry and/or molecular testing for EGFR and ALK are not available routinely in our country. Only 3 patients opted for molecular testing abroad and of these 3, 2 were EGFR positive. Conclusions: Due to perception of poor prognosis, cancer diagnosis is taken as a death sentence and only 50% patients opt for treatment. Treatment is limited by lack of adequately trained surgeons, availability of radiotherapy facilities, lack of Molecular testing and especially by the high cost of treatment. There is an urgent need to train manpower, increase awareness and subsidize the treatment of lung cancer in some form in our country.
Survey of medical student knowledge in oncology and survivorship care in Nigeria: A pilot study.
Authors: Leng Jim , Ibraheem Abiola Falilat , Ntekim Atara Isaiah , Popoola Abiodun , Agaga Luther , Ukoh Emmanuel , Golden Daniel William , Olopade Olufunmilayo I. 
Published: May 2019

e18106 Background: In low middle-income countries (LMICs), cancer patients present in later stages of disease for many reasons, including missed diagnoses. Due to high patient: physician ratios, generalists are taught broadly and prepared to treat diseases outside the scope of their interest in training. The delivery of high-quality cancer care requires an interdisciplinary team of physicians with excellent medical school training in oncology. To date, there has been no formal assessment of medical education for oncology in Nigeria. This study aims to assess the ability of the curriculum in Nigeria to prepare future doctors tasked with treating a growing number of patients with cancer. Methods: An anonymous survey was administered to final year medical students at Lagos State University and University of Ibadan, Nigeria. The survey assessed demographics, reports of experience during medical school with oncology, comfort ratings with different aspects of oncologic care (Likert scale, 1 = not at all, 5 = extremely), and included five clinical vignettes. Results: 146 graduating students in two medical schools responded (response rate = 36.6%). Twelve percent of students indicated that they planned to pursue a career in oncology. The majority of students reported exposure through lectures to medical oncology (85%), radiation oncology (82%), and surgical oncology (85%), but fewer reported exposure to lectures in hospice care (75%) and cancer survivorship care (52%). Most students (87%) have not attended a tumor board during medical school. In clinical vignettes, students performed worst on long-term chemotherapy toxicities, and best on surgical oncology risk. Overall, students indicated being “moderately comfortable” with topics in medical, radiation, surgical, and palliative care on a Likert scale, and “somewhat comfortable” with survivorship care. Conclusions: Although students in Nigeria report learning about disciplines in oncology care, they report varying comfort levels with specific oncology topics by the end of medical school. The results of this pilot study support the need to develop an interdisciplinary oncology curriculum in Nigeria.
Clinical responses and survival in Hispanic patients with non-small cell lung cancer treated with immunotherapy compared with non-Hispanic whites.
Authors: Raez Luis E. , Saravia Diana , Ruiz Rossana , Sumarriva Daniel , Munoz-Antonia Teresita , Hunis Brian , Cress W. Douglas , Mas Luis , Izquierdo Paola , Kaen Diego , Lopes Gilberto , Antonia Scott Joseph 
Published: May 2019

e18109 Background: The main immunotherapy (IMMUNO) trials that led to the approval of these agents for non-small cell lung cancer (NSCLC) accrued a minimum number of Hispanic (HISP) patients (pts) or, in some studies, no HISP pts at all. Additional data is thus needed to validate outcomes in HISP pts with NSCLC treated with IMMUNO. While it is known that genomic profiles and cancer survivals are different between HISP, Non-Hispanic Whites (NHW), and African-Americans; no study has yet looked at differences in IMMUNO outcomes between these populations. Methods: We present data in 436 NSCLC pts treated with IMMUNO at 5 large institutions (3 in the US, 2 in Latin America). The agents evaluated include: nivolumab, pembrolizumab and atezolizumab. 256 pts were HISP and 180 pts were NHW. Most of the pts were treated with single agent therapy as second line (or beyond) while a small group of pts were treated as first line. The primary endpoints of the study were: response rate (ORR), progression free survival (PFS) and overall survival (OS). Results: Among NHW pts, disease control rate (DCR) was 67% for Adenocarcinomas (Adeno) and 46% for squamous cell carcinomas (SQCC). In HISP pts there were no differences in DCR rates between both histologies: 68% for Adeno and 67% SQCC. There were no statistical significant differences among HISP and NHW pts regarding ORR, PFS, OS, and responses according to PD-L1 status. Conclusions: This is the largest publication and comparison of NSCLC immunotherapy outcomes in HISP vs NHW pts. No significant differences were found in the clinical outcomes between these 2 ethnic groups despite expected genomic differences. Pts with actionable mutations were excluded as they usually do not get IMMUNO as first or second line; an approach that might change after IMPOWER 150. These results are comparable to the ones seen in Checkmate and Keynote studies. As expected, higher response rates were seen in first line therapy and pts with PD-L1 (+) status. Further comparisons will be better addressed by a larger prospective study.[Table: see text]
Enrollment disparities in cancer clinical trials: A single institution experience.
Authors: Perez Perez Ariel , Sarwari Nawid Mohammad , Warner Terra , Ni Liqiang , Landau Danny 
Published: May 2019

e18128 Background: The importance of population heterogeneity in clinical cancer research is universally recognized. This study aims to identify possible disparities in trial participation at UF Health Cancer Center at Orlando Health. Methods: Data on patients’ enrollment, during the period from 01/01/2016 to 12/31/2016, was obtained from our research C-base. We utilized descriptive statistics to characterize the main demographic variables. Pearson's Chi-squared and Z-tests were utilized to compare percentages of enrolled versus not enrolled patients by ethnicity, race and gender. Results: A total of 3704 cases were established as new patients during the study period, of which 369 (10%) were enrolled in cancer research studies (Table). Our analysis showed statistically significant differences in enrollment by racial category (χ2= 95.09, df = 3, p < 0.0000). American Indian (n = 6) and Native Hawaiian (n = 4), were excluded from the analysis due to small sample sizes and no enrollments. In addition we tested with the Z-stat whether the enrollment in each group was different from the population average (p = 0.10). The Caucasian group did not differ from the average (z = 0.3944; p < 0.6933), whereas both the African American (z = -4.2286; p < 0.0001) and the Asian group (z = -2.3102; p < 0.0209) were under enrolled. The Others group was above the average (z = 8.4632; p < 0.0001). There were also differences in enrollment by gender and ethnicity. Females were under enrolled as compared to Males (z = -7.0716; p < 0.0001). The Hispanic group enrollment was significantly below the population average (z = -4.17; p < 0.0001). Conclusions: We found significant differences in the enrollment of minorities in cancer trials in our institution. African Americans, Asians, Hispanics and Females were all under represented. The group labeled as Others requires further attention. [Table: see text]
Barriers to clinical trial enrollment of older adults with cancer: A systematic review.
Authors: Sedrak Mina S. , Hurria Arti , Li Daneng , George Kevin , Padam Simran , Liu Jennifer , Wong Andrew R. , Vargas Noel , Eskandar Joy , Katheria Vani , Mortimer Joanne E. , Mohile Supriya Gupta , Dale William 
Published: May 2019

e18130 Background: Despite the disproportionate impact of cancer on older adults, older patients are vastly underrepresented in clinical trials that set the standards for cancer treatment. To better understand the reasons for this disparity, we conducted a systematic review of studies that have specifically examined barriers and interventions to improve clinical trial enrollment of older adults with cancer. Methods: We conducted a comprehensive two-step search strategy. First, we consulted an information specialist to develop an electronic search for the following databases from inception to January 15, 2019: PubMed, Ovid/Medline, Embase, Scopus, PsycINFO, and Cochrane library. Second, references of retrieved key articles were screened for relevant studies. Two authors then independently reviewed all titles and abstracts (N = 10,985) and examined studies for full text eligibility (N = 221). Inclusion criteria were: 1) original research; 2) study assessed barriers and/or interventions to enrollment in oncology clinical trials; 3) included patients ≥ 60 years with cancer. Narrative reviews and abstracts without full text were excluded. Data was extracted by independent raters and summarized using a qualitative analysis software, NVivo v12. Results: 12 observational studies examining barriers and 1 randomized intervention were included. Barriers were assessed at the patient level (N = 5 studies), healthcare professional (HCP) level (N = 5), and both patient and HCP levels (N = 2). Stringent eligibility criteria (N = 7) and oncologists’ concerns for toxicity (N = 7) were the most common barriers cited. Patient barriers included transportation (N = 6), time/burden (N = 6), and awareness (N = 6). Although caregiver barriers (N = 4) were identified, none of the studies examined caregiver perceptions. One study evaluated a physician-directed educational intervention and found no significant impact on accrual of older adults. Conclusions: Although several studies have examined the barriers to accrual of older adults with cancer, only one intervention study has attempted to address these barriers. Given the aging of the cancer population, new strategies for including older adults in cancer clinical trials are critically needed.
Barriers and facilitators to oncology clinical trial accrual: Comparing perceptions of community and academic oncologists.
Authors: Wong Andrew R. , Hurria Arti , Sun Virginia , Li Daneng , George Kevin , Liu Jennifer , Padam Simran , Katheria Vani , Waisman James Ross , Mortimer Joanne E. , Mohile Supriya Gupta , Dale William , Sedrak Mina S. 
Published: May 2019

e18131 Background: Multiple studies have described the barriers and facilitators to oncology clinical trial accrual in academic practices. However, few studies have been done in community settings, even though the majority of patients with cancer receive their care in the community. We examined and compared community and academic oncologists’ perceptions of the barriers and facilitators to cancer clinical trial accrual. Methods: Semi-structured interviews were conducted from March to June 2018 with 44 medical oncologists at City of Hope (24 in academia; 20 in community sites). Purposive sampling was used to ensure participant diversity. Primary measures were oncologists’ self-reported perceptions of the barriers and facilitators to clinical trial accrual. Responses were recorded digitally, transcribed, and de-identified. Data was managed using NVivo v12. Two analysts coded the interview data using thematic content analysis (kappa = 0.74). A third analyst adjudicated discrepancies. Results: Of the 44 participants, 36% were women, and 68% had > 10 years of experience. Compared to academic oncologists, community oncologists more often cited barriers due to the lack of protocols suitable for community patients’ histology and stage (13% vs. 6%) and insufficient trial personnel support (13% vs. 9%). Compared to community oncologists, academic oncologists more often cited barriers due to limited time (14% vs. 8%) and overly stringent eligibility criteria (14% vs. 9%). Community oncologists more commonly reported extrinsic facilitators (e.g. reminders of available protocols from trial support staff) (91% vs. 76%) while academic oncologists more commonly reported intrinsic facilitators for offering clinical trials (e.g. self-motivation to prioritize clinical trials) (24% vs. 9%). Conclusions: Community oncologists more often reported facing barriers to accrual due to limited suitable trials and insufficient personnel support compared to academic oncologists. Additionally, community oncologists cite the need for more infrastructure to support accrual. Interventions to increase trial accrual must be tailored to address the unique needs of both community and academic practices.