bluuebunny/crossref_metadata_2025_split huggingface dataset:
Real-world outcomes of neoadjuvant chemotherapy for breast cancer: Reflections from a community cancer center.
Authors: Bhardwaj Prarthna V , Kaufman Seth , Mason Holly , Visintainer Paul , Makari-Judson Grace 
Published: June 2022

e18690 Background: Neoadjuvant chemotherapy (NAC) has been historically reserved for patients with locally advanced breast cancers. The utilization of NAC remains highly variable in clinical practice based on tumor size and receptor status. The decision to pursue NAC is often based on discussions by a multidisciplinary team (MDT). This study aims to look at real-world data describing the contemporary use of NAC in patients with early-stage operable breast cancer in a community cancer center and evaluate the effectiveness of MDT at our institution. Methods: We conducted a retrospective descriptive study at UMass Chan-Baystate between Oct 2018 and Oct 2020. We included patients receiving NAC for early-stage operable or locally advanced breast cancer. We excluded patients receiving neoadjuvant endocrine therapy. Primary outcomes were rates of pathological complete response (pCR) after surgery. Secondary outcomes were referral timeliness back to the breast surgeon and radiation oncologist, downstaging of cancer in the breast and axilla. Results: Ninety-three patients underwent NAC, of which 84% were white. The mean age was 56.6 yrs. Of these, 86 (93%) had clinical stage II or III cancer, and 80 (86%) had positive lymph nodes. Forty-two patients (46%) were ER positive, 28 (30%) were HER2 positive and 39 (43%) were triple negative. The most common indication for NAC was to downstage axilla (42%) and for HER2 tailoring of treatment (26%). Of the 93 patients, 23 (25%) achieved pCR; 12 (52%) had triple-negative, 7 (30%) had ER-HER2+, 3 (13%) had ER+HER2+ and 1 (4%) had ER+HER2- breast cancer. Eighty-four patients (91%) had downstaging of breast tumor, and 30 (32.3%) had axillary downstaging. Seventy-eight patients (84%) received adjuvant radiation (RT). All patients (N = 93, 100%) followed up with a surgeon prior to completion of NAC, although only 48 (50%) returned to radiation oncology. The mean time from surgery to RT was 64 days, and 6% underwent RT for more than two weeks beyond the expected time. Conclusions: Overall pCR rates were low; however, a third of patients had axillary downstaging, and the majority had breast tumor downstaging. Of the patients in our cohort who achieved pCR, the majority were triple-negative, followed by HER2 positive, consistent with overall trends. All patients were re-referred to the surgeon prior to completion of NAC for surgical planning and the average time from surgery to radiation was within national standards highlighting effective MDT involvement in the care of patients at our institution.[Table: see text]
Accuracy of magnetic localisation device placement and retrieval in breast cancer patients from a single internationally accredited breast center in Johannesburg, South Africa.
Authors: Benn Carol , van Loggerenberg Dominic 
Published: June 2022

e18697 Background: A variety of techniques are used to localise breast cancers prior to breast surgery. One such technique involves the placement of a magnetic device (Magseed). the magnetic device placement data from one radiology unit in a multi-disciplinary unit consisting of 4 radiology units over a 6 month period which sees 450 newly diagnosed breast cancer patients per year and places with over 360 Magseeds in a 6 month period. The aim of the study was to conduct a review of Magseed placement and ease and efficacy of retrieval across varying depths within the breast. Methods: The device used and analyzed in this study is constructed of medical-grade stainless steel magnetized, 1x5mm in size and can be implanted long term. The seeds were placed both under ultrasound guidance and stereotactically, there were no complications at the time of placement. Post-placement ease of localization and retrieval of the Magseed Measurements of distances from the nearest perpendicular skin surface was provided by the radiologist. markers were assessed by confirmation of the presence of the Magseed(s) in the specimen through the use of the Sentimag probe and confirmation visualized by intraoperative radiology and intra-operative pathology. Results: All of the seeds were localised during surgery and retrieved without difficulties reported by surgeons. The use of intraoperative radiology confirmed retrieval of all seeds in all patients. The minimum placement depth was 8.33mm, the maximum placement depth was 87mm and the average placement depth was 47mm. The placement of the seeds were place over a range of times before surgery, from 3 days prior to surgery to up to 249 days. Localisation was 100% successful using the Sentimag probe in theatre, and the retrieval rate was 100% across the full 368 analyzed patient set. . Radiological confirmation of the Magseed placement was confirmed through the use of an intraoperative radiological Biovision machine. Our data shows that Magseeds can be placed across a wide range of breast sizes and at variable depths with no complications or difficulty experienced during intraoperative localization and retrieval of the seeds. Conclusions: The data collected, and the demographic analyzed, shows that magnetic marker placement and retrieval is possible across a wide range of depths in the breast with no complications arising in radiological placement and intraoperative localisation and retrieval. Surgeons reported ease of transcutaneous localisation. A 100% retrieval rate was reported. In all cases, clear margins were achieved with: aid from audio and visual confirmation from the Sentimag probe; intraoperative radiology and intraoperative pathology.
Enabling tandem repeat sequence genotype analysis across capture kits.
Authors: Yip Shun H , Diamreyan Michael , Wong Edmund , Ramamurthy Raghuraman , Tobias Sidney , Cheng Hao , Solovyev Victor , Tang Cheuk Ying 
Published: June 2022

e18700 Background: Previous studies on mutation calling have documented capture kit batch effects in Whole Exome Sequencing (WES) data from The Cancer Genome Atlas (TCGA) database, hindering direct comparison between samples from different capture kits. For example, in classification, a cancer type exclusively sampled by a specific capture kit in the training set would have very low accuracy if the testing set was sampled by another capture kit. To enable cross-capture-kit between-cancer genotype analyses with the TCGA dataset, a novel read count transformation algorithm is developed to remove capture kit batch effects. This algorithm was tested with our Machine Learning model which uses Tandem Repeat Sequence (TRS) mutation markers as training features. Methods: The proposed algorithm transforms TRS read count data to remove low quality samples, read depth differences, and capture kit batch effects from the dataset. Results: 1) TRS read count of WES samples are investigated. Particularly, we show that TRS site read counts do not correlate across capture kits but correlate within capture kits. This suggests that WES read count is largely independent from an exon’s location in the genome and is more strongly correlated with capture kit probes. 2) TRS detection rate for each sample within each capture kit is found to be normally distributed. Outliers with very low TRS detection rate can be used for quality filtering. 3) The transformation algorithm effectively removes capture kit batch effects from the dataset. At the same time, it retains cancer-specific signals in the samples. Before applying the transformation algorithm, cancer type classification accuracy is low (̃0-25%) if the testing data set uses a different capture kit from the training data set. We show that applying the transformation algorithm allows cancer type classification accuracy to improve by over 65%. Conclusions: We demonstrated that direct comparison of WES TRS read count data across capture kits is possible after application of our transformation algorithm. This opens the path to cross-capture-kit between-cancer genotype analyses with the TCGA dataset, which were previously unfeasible due to capture kit batch effects.
COVID-19 vaccine uptake in patients with cancer and Sars-Cov-2 infection in 2020: Results from the ASCO registry.
Authors: Hanley Williams Jen Hanley , Bruinooge Suanna Steeby , Kaltenbaugh Melinda , Gralow Julie R. , Garrett-Mayer Elizabeth 
Published: June 2022

e18713 Background: The availability of safe and effective COVID-19 vaccines has enabled protections against serious outcomes from SARS-CoV-2 infection. The ASCO Registry provides an opportunity to study the rate of vaccine uptake among patients (pts) with cancer who had SARS-CoV-2 infection prior to availability of vaccines. Methods: Participating US medical oncology practices identify pts eligible for inclusion: pts with a positive SARS-CoV-2 test and, at the same time, either (a) or (b) cancer-free less than 12 months (i.e., in complete remission or post-resection) and receiving adjuvant treatment. Registry data were extracted on 2/4/22. Pts in this analysis had a SARS-CoV-2 positive test between 3/1/2020 and 12/31/2020 and at least one clinical encounter on or after 1/1/21, documenting receipt or not of 1st and 2nd vaccine shots. Pts lacking data on vaccination status in their medical records were excluded from analysis. When the exact date of 1st vaccine shot was known, the primary endpoint was number of days from 1/1/21 to 1st shot date. If the exact date of 1st shot was unknown, date was categorized as within 7 days from the clinical encounter, 2-4 weeks, or more than 1 month prior. Summary statistics and 95% confidence intervals (CIs) were calculated using Kaplan-Meier methods. Results: The Registry included 1260 pts with SARS-CoV-2 infection in 2020. Time to vaccination (described using cumulative incidence) across age categories is shown in Table, with 1/1/21 as the baseline. Median time to vaccination ranged from 63 days in the oldest pts (> 80 years of age) to 220 days in the youngest pts (< 45 years of age). Differences in rates of vaccination uptake were most pronounced in the early months (Jan – Mar) and diminished in April and beyond. Conclusions: Older pts with cancer who were infected with SARS-CoV-2 in 2020 received COVID-19 vaccinations in 2021 at higher rates than those of younger ages. Delayed uptake by younger aged pts at outset could be related to lack of clarity on pts with cancer qualifying for early vaccine access and state policies on availability.[Table: see text]
Effectiveness of COVID -19 vaccine on cancer patients in one Latin American country: A follow-up of ACHOC-C19 study.
Authors: Ospina Serrano Aylen Vanessa , Bruges Maya Ricardo Elias , Ramos Pedro , Triana Ivan , Aruachan Sandra , Quiroga Alicia , Rivas Tafurt Giovanna Patricia , Munevar Isabel , Mantilla William , Avendaño Ana Cristina , Gonzalez Florez Hector Alirio , Jimenez Paola , Pacheco Javier orlando , Pinilla Paola , Manneh Kopp Ray , Ortiz Diaz Juan David , Insuasty Jesus , Alcala Marcela , Barrero Angela , Sanchez-Vanegas Guillermo 
Published: June 2022

e18721 Background: In our experience during the first year of development of ACHOC-C19 study, we observed 26% mortality in patients with cancer and COVID 19 infection. The impact of vaccination was not evaluated prior to the implementation of this strategy worldwide in this kind of population. It was proposed to evaluate the effectiveness of immunization during the second phase of our investigation. Methods: Cohort study derived from the National Registry of Patients with Cancer and COVID-19 (ACHOCC-19). Data were collected from June 2021 since vaccine was available. Patients were: older than 18 years, diagnosed with cancer (solid tumors), treated and/or under follow-up, and with COVID-19 infection. The comparative analysis of the vaccinated and non-vaccinated cohort is presented. Outcomes included: all-cause mortality within 30 days of infection diagnosis, hospitalization, and mechanical ventilation. Effect estimation was performed through relative risk (RR) and multivariate analysis for each event, using generalized linear models of the binomial family. Results: 896 patients were included, 470 were older than 60 years (52.4%) and 59% women (n = 530). 172 patients were recruited in the vaccinated cohort and 724 in the non-vaccinated cohort (ratio: 1 to 4.2). The cumulative incidence of hospitalization among the unvaccinated was 42.4% (n = 307), and among the vaccinated, 29% (n = 50); invasive mechanical ventilation requirement was 8.4% (n = 61) in unvaccinated, and 4.6% (n = 8) in vaccinated. The cumulative incidence of mortality from all causes in the unvaccinated was 17% (n = 123) and in the vaccinated 4.65% (n = 8). Table summarizes the multivariate analysis. The adjusted RR for mortality for the unvaccinated is 3.4 (95% CI: 1.7-6.8), for hospitalization 1.36 (95% CI: 1.08-1.72), and for mechanical ventilation 2.1 (95% CI: 1.02-4.2). Conclusions: The incidence of complications and death in patients with cancer and COVID-19 infection is significantly higher in those who have not received a vaccination schedule compared to those who have been vaccinated. Immunization should be promoted and intensified in this population group.[Table: see text]
A single institution cohort of patients with classical Hodgkin lymphoma treated with brentuximab vedotin plus nivolumab.
Authors: Jordan Aryanna , Rose Ashley , Bangash Alizain , Isenalumhe Leidy Lismeri , Gaballa Sameh , Chavez Julio C. , Shah Bijal D. , Sokol Lubomir , Pinilla-Ibarz Javier , Bello Celeste M. , Saeed Hayder 
Published: June 2022

e18738 Background: Classical Hodgkin lymphoma (cHL) is a B-cell neoplasm which affects approximately 8,500 new patients annually. The initial remission rate is greater than 80%; however, 10-30% will have refractory or relapsed disease (R/R). Both Brentuximab vedotin (BV) and nivolumab (Nivo) have recently been approved for the treatment of R/R cHL. Previous studies have shown BV+Nivo to be well tolerated, with high response rates and progression free survival (PFS) in two prospective studies. However, no real-world data is available yet for this combination. Here we present clinical characteristics and outcomes of a single institution cohort of patients with cHL who received BV+Nivo. Methods: A retrospective chart review was completed of all patients with cHL who were treated with BV+Nivo at Moffitt Cancer Center between 2018 and 2021. Baseline characteristics and treatment details were obtained. PFS and overall survival (OS) were evaluated using the Kaplan-Meier curve. Results: A total of 29 patients were included in the cohort. Median follow up time was 3 months (range 1-21). 69% (n = 20) of patients were male. Histology types included unclassifiable 48.3% (n = 14), nodular sclerosis 27.6% (n = 8), lymphocyte depleted 13.8% (n = 4), and lymphocyte rich 10.3% (n = 3). 55.2% (n = 16) of patients had B symptoms at presentation. Initial stage included stage 2 (48.3%, n = 14), stage 3 (20.7%, n = 6), and stage 4 (24.1%, n = 7). 34% of the patients were primary refractory to their first line therapy. Median time from last chemo to BV+Nivo was 4.4 months (range 0.5-50 months). BV+Nivo was most often used as 2nd line therapy (51.7%, n = 15) followed by 3rd line therapy (20.7%, n = 6). One patient received BV+Nivo as first line therapy. Median number of cycles was 4 (range 1-15). The overall response rate was 65.5% (n = 19) (complete response 44.8%), and 17.2% (n = 5) had no response. Of the 15 patients receiving BV+Nivo as 2nd line therapy, 66% proceeded to autologous hematopoietic stem cell transplant. 4 patients did not proceed with transplant per their choice, and one patient could not proceed due to progressive disease. The median PFS was 21 months (95% CI: 9 months-non reached). OS was 100%. Conclusions: Here we describe the first real-world outcomes of BV+Nivo in classical Hodgkin lymphoma. In a high risk and refractory population, BV+Nivo showed excellent responses. Further studies are needed to focus on comparing the outcome to a more traditional chemotherapy based approach.
Real-world outcomes of immunotherapy regimens in first line non small cell lung cancer in lebanese patients.
Authors: Nasr Lewis , Diab Saada , Ghoche Ahmad , Yehia Intissar , Nasr Fadi louis 
Published: June 2022

e18741 Background: Immunotherapy provides improved treatment efficacy and survival in NSCLC patients. This is well established from clinical trials. However, the effectiveness of immunotherapy in real world practice is not well assessed. We aimed to characterize real-world outcomes for patients with NSCLC treated with 1L I-O in Lebanon. Methods: Patients aged ≥18 years with confirmed metastatic NSCLC who received either 1L I-O monotherapy or single-agent I-O combined with chemotherapy on or after January 1, 2014. Primary objectives were to examine overall survival (OS) and real-world progression-free survival. Multivariable analysis were made on correlation of different factors and survival. Results: among 135 patients, Median age at diagnosis was 68 years Most patients received chemotherapy alone as first line(54%), 18.3 % received immunotherapy and 27.8% received the combination treatment of chemotherapy and immunotherapy. Median PFS 1 was 7.7, 14, 11.1 months for chemotherapy, immunotherapy and chemo-immunotherapy respectively (p = 0.062). Median OS was 22.9 months (CI 95%, 17.7-28.1) with no significant correlation with treatment type (p = 0.85) multivariate analysis showed that having PDL levels between 1 and 49 (HRa = 0.15) and ≥50 (HRa = 0.12) compared to < 1 were significantly associated with longer PFS period, whereas having squamous (HRa = 3.45) and other (HRa = 27.36) type of cancer compared to adenocarcinoma was significantly associated with shorter PFS period. (HRa = 3.28) was significantly associated with lower overall survival period (p = 0.10).Concerning adverse effects, rash was the most frequent (14%) followed by pneumonitis (12.2%). Conclusions: In real world practice, IO was well tolerated in lebanese patients. Patients with high (≥50) and intermediate (between 1 and 49) tumor programmed death ligand 1 (PD-L1) expression demonstrated longer median OS vs those with low expression. We hypothesize that bone metastasis impairs immunotherapy efficacy.
Predicting recurrence of venous thromboembolism in anticoagulated cancer patients using real-world data and machine learning.
Authors: Muñoz Martín Andrés J. , Huerga Domínguez Sofía , Souto Juan Carlos , Rogado Revuelta Jacobo , Sanchez Antonio , Garcia-Palomo Andres , Aparicio Jorge , Aguayo Cristina , Gutierrez Abad David , Ortega Laura , Viñuela-Benéitez Maria Carmen , Fanjul Victor , Casadevall David , Arumi Daniel , Hernández-Presa Miguel Ángel 
Published: June 2022

e18742 Background: The clinical predictors of venous thromboembolism (VTE) recurrence in patients with cancer are not well known. Our objective was to develop a predictive model for risk of VTE recurrence in anticoagulant-treated cancer patients within the first 6 months following VTE diagnosis. Methods: Using the EHRead technology, based on Natural Language Processing (NLP) and machine learning (ML), the unstructured clinical data in EHRs from 9 Spanish hospitals between 2014 and 2018 was extracted and analyzed. The study population, comprising all adult anticoagulated cancer patients with VTE, was downsampled to prevent bias and class imbalance. A total of 94 patient characteristics were explored, and Random Forest (RF) feature selection was performed to identify the most relevant predictors for VTE recurrence. Multiple algorithms were used to train different prediction models, which were subsequently validated in a hold-out dataset. The model with the best performance metrics (i.e., ROC-AUC) was selected as the final model. Results: From a source population of 2,893,208 patients, 21,227 anticoagulant-treated patients with VTE and active cancer (53.9% male, median age of 70 years) were identified. Across the study period, yearly incidence of VTE remained relatively stable, ranging from 2.7 to 3.9%. The most common type of VTE was deep vein thrombosis (68.2% of patients), followed by pulmonary embolism (28.4%). Regarding primary cancer locations, the most frequent were colorectal (10.1%) and lung cancer (8.5%). Of all trained and validated models, the RF approach yielded the best performance, with a ROC-AUC = 0.72. The following predictors of VTE recurrence were identified: pulmonary embolism, deep vein thrombosis, metastasis, adenocarcinoma, hemoglobin values, serum creatinine values, platelet count, leukocyte count, family history of VTE, and patients’ age. Conclusions: Using NLP and ML, we were able to use the real-world data in EHRs to build a predictive model of VTE recurrence in cancer patients based on individual clinical features. These results may improve the clinical management of VTE recurrence in this population.
Using Charlson comorbidity index (CCI) to predict outcomes of older patients with acute promyelocytic leukemia (APL).
Authors: Dhakal Prajwal , Lyden Elizabeth , Pyakuryal Avantika , Rai Manoj P. , Bhatt Vijaya Raj 
Published: June 2022

e18751 Background: A large-scale study specifically analyzing an association between comorbidity burden and outcomes is lacking in APL. We hypothesized that a greater comorbidity burden independently predicts worse outcomes in patients ≥60 years with APL. Methods: We utilized the National Cancer Database to identify patients ≥60 years diagnosed with APL between 2004 and 2015. CCI scores were used to evaluate comorbidity burden, and patients were divided into 3 groups with CCI of 0, 1, and ≥2. We used chi-square test to determine association between CCI and different variables. Multiple logistic regression analyses and Cox regression models evaluated the effects of CCI on one-month mortality and overall survival (OS), respectively. Results: Of 2221 patients, 59% had CCI of 0, 27% had CCI 1, and 14% had CCI ≥2. Compared to patients with CCI 1 or CCI ≥2, a higher proportion of patients with CCI 0 had private insurance, and higher education and income status, were treated at academic centers, and received multiagent therapy. One-month mortality was 16%, 24%, and 32% for patients with CCI 0, 1, and ≥2, respectively. After adjusting for other co-variates, patients with CCI 0 had lower one-month mortality compared to CCI 1 (Odds ratio 1.67, 95% confidence interval [CI] 1.29-2.16, p < 0.001) and CCI ≥ 2 (Odds ratio 2.31, 95% CI 1.70-3.13, p < 0.001). Three-year OS was 61%, 53%, and 38% for patients with CCI 0, 1, and ≥2, respectively. After adjusting for other co-variates, OS was worse among patients with CCI 1 (Hazard ratio 1.27, 95% CI 1.10-1.46, p-value < 0.001) and CCI ≥2 (Hazard ratio 1.74, 95% CI 1.48-2.06, p-value < 0.001), compared to patients with CCI 0. Conclusions: Our study is among the first and the largest to examine an association between comorbidity burden and outcomes in older adults with APL. Greater comorbidity burden, indicated by higher CCI, predicted worse one-month mortality and OS, after adjusting for other co-variates. Thus, our study results establish CCI as an important and independent predictor of outcomes in APL. The study results can inform personalized estimates of mortality and OS based on comorbidity burden and facilitate treatment decision-making. Given the significant differences in outcomes of older adults based on comorbidity burden, future trials in APL should present comorbidity data and consider utilizing CCI to risk-stratify patients.