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Article ; Online: Demographic disparities in receipt of care at a comprehensive cancer center.

Kirtane, Kedar / Zhao, Yayi / Amorrortu, Rossybelle P / Fuzzell, Lindsay N / Vadaparampil, Susan T / Rollison, Dana E

2023 Volume 12, Issue 12, Page(s) 13687–13700

Abstract: Background: National Cancer Institute cancer centers (NCICCs) provide specialized cancer care including precision oncology and clinical treatment trials. While these centers can offer novel therapeutic options, less is known about when patients access ... ...

Abstract	Background: National Cancer Institute cancer centers (NCICCs) provide specialized cancer care including precision oncology and clinical treatment trials. While these centers can offer novel therapeutic options, less is known about when patients access these centers or at what timepoint in their disease course they receive specialized care. This is especially important since precision diagnostics and receipt of the optimal therapy upfront can impact patient outcomes and previous research suggests that access to these centers may vary by demographic characteristics. Here, we examine the timing of patients' presentation at Moffitt Cancer Center (MCC) relative to their initial diagnosis across several demographic characteristics. Methods: A retrospective cohort study was conducted among patients who presented to MCC with breast, colon, lung, melanoma, and prostate cancers between December 2008 and April 2020. Patient demographic and clinical characteristics were obtained from the Moffitt Cancer Registry. The association between patient characteristics and the timing of patient presentation to MCC relative to the patient's cancer diagnosis was examined using logistic regression. Results: Black patients (median days = 510) had a longer time between diagnosis and presentation to MCC compared to Whites (median days = 368). Black patients were also more likely to have received their initial cancer care outside of MCC compared to White patients (odds ratio [OR] and 95% confidence interval [CI] = 1.45 [1.32-1.60]). Furthermore, Hispanics were more likely to present to MCC at an advanced stage compared to non-Hispanic patients (OR [95% CI] = 1.28 [1.05-1.55]). Conclusions: We observed racial and ethnic differences in timing of receipt of care at MCC. Future studies should aim to identify contributing factors for the development of novel mitigation strategies and assess whether timing differences in referral to an NCICC correlate with long-term patient outcomes.
MeSH term(s)	Humans ; Demography ; Healthcare Disparities/ethnology ; Healthcare Disparities/statistics & numerical data ; Hispanic or Latino/statistics & numerical data ; Precision Medicine/statistics & numerical data ; Prostatic Neoplasms/epidemiology ; Prostatic Neoplasms/therapy ; Retrospective Studies ; United States/epidemiology ; Cancer Care Facilities/statistics & numerical data ; White/statistics & numerical data ; Black or African American/statistics & numerical data ; Time-to-Treatment/statistics & numerical data ; National Cancer Institute (U.S.)/statistics & numerical data
Language	English
Publishing date	2023-04-28
Publishing country	United States
Document type	Comparative Study ; Journal Article ; Research Support, N.I.H., Extramural ; Research Support, Non-U.S. Gov't
ZDB-ID	2659751-2
ISSN	2045-7634 ; 2045-7634
ISSN (online)	2045-7634
ISSN	2045-7634
DOI	10.1002/cam4.5992
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Article ; Online: Factors Associated with Self-reported COVID-19 Infection and Hospitalization among Patients Seeking Care at a Comprehensive Cancer Center.

Amorrortu, Rossybelle P / Zhao, Yayi / Keenan, Robert J / Gilbert, Scott M / Rollison, Dana E

Journal of racial and ethnic health disparities

2023

Abstract: Background: COVID-19 infection severity differs by race and ethnicity, but its long-term effect on cancer-related outcomes is unknown. Therefore, information on COVID-19 history is critical to ascertain among new cancer patients in order to advance ... ...

Abstract	Background: COVID-19 infection severity differs by race and ethnicity, but its long-term effect on cancer-related outcomes is unknown. Therefore, information on COVID-19 history is critical to ascertain among new cancer patients in order to advance research on its impact on cancer outcomes and potentially related health disparities. Methods: A cross-sectional study was conducted among 16,025 new patients seeking care at Moffitt Cancer Center (MCC) between 2021 and 2022. Patient self-reported histories of COVID-19 infection and other pre-existing health conditions were obtained from electronic questionnaires administered to all new MCC patients. Associations between demographics and COVID-19 infection and hospitalization were examined. Results: A total of 1,971 patients (12.3%) reported ever having COVID-19. Self-reported COVID-19 history was significantly more prevalent in Hispanic vs. non-Hispanic patients (OR = 1.24, 1.05-1.45) and less prevalent in Asian versus White patients (OR = 0.49, 95% 0.33-0.70). Among patients who ever had COVID-19, 10.6% reported a COVID-19-related hospitalization. Males had higher odds of a COVID-19 related hospitalization than females (OR = 1.50, 95% CI = 1.09-2.05), as did Black/African American patients (OR = 2.11, 95% CI = 1.18-3.60) and patients of races other than Black/African American and Asian (OR = 2.61, 95% CI = 1.43-4.54) compared to White patients. Hispanic patients also experienced higher odds of hospitalization (OR = 2.06, 95% CI-1.29- 3.23) compared with non-Hispanic patients of all races in a sensitivity analysis that combined race/ethnicity. Pre-existing lung and breathing problems were associated with higher odds of being hospitalized with COVID-19 (OR = 2.38, 95% CI = 1.61-3.48), but these and other health conditions did not explain the observed associations between race and COVID-19 hospitalization. Conclusions: Higher rates of COVID-19 hospitalization were observed among patients identifying as Black/African American or Hispanic independent of pre-existing health conditions. Future studies evaluating long-term effects of COVID-19 should carefully examine potential racial/ethnic disparities in cancer outcomes.
Language	English
Publishing date	2023-11-02
Publishing country	Switzerland
Document type	Journal Article
ZDB-ID	2760524-3
ISSN	2196-8837 ; 2197-3792
ISSN (online)	2196-8837
ISSN	2197-3792
DOI	10.1007/s40615-023-01855-4
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Article ; Online: Assessing the Contribution of Scanned Outside Documents to the Completeness of Real-World Data Abstraction.

Zhao, Yayi / Howard, Rachel / Amorrortu, Rossybelle P / Stewart, Sandra C / Wang, Xiaoliang / Calip, Gregory S / Rollison, Dana E

JCO clinical cancer informatics

2023 Volume 7, Page(s) e2200118

Abstract: Purpose: Electronic health record (EHR) data are widely used in precision medicine, quality improvement, disease surveillance, and population health management. However, a significant amount of EHR data are stored in unstructured formats including ... ...

Abstract	Purpose: Electronic health record (EHR) data are widely used in precision medicine, quality improvement, disease surveillance, and population health management. However, a significant amount of EHR data are stored in unstructured formats including scanned documents external to the treatment facility presenting an informatics challenge for secondary use. Studies are needed to characterize the clinical information uniquely available in scanned outside documents (SODs) to understand to what extent the availability of such information affects the use of these real-world data for cancer research. Materials and methods: Two independent EHR data abstractions capturing 30 variables commonly used in oncology research were conducted for 125 patients treated for advanced non-small-cell lung cancer at a comprehensive cancer center, with and without consideration of SODs. Completeness and concordance were compared between the two abstractions, overall, and by patient groups and variable types. Results: The overall completeness of the data with SODs was 77.6% as compared with 54.3% for the abstraction without SODs. The differences in completeness were driven by data related to biomarker tests, which were more likely to be uniquely available in SODs. Such data were prone to missingness among patients who were diagnosed externally. Conclusion: There were no major differences in completeness between the two abstractions by demographics, diagnosis, disease progression, performance status, or oral therapy use. However, biomarker data were more likely to be uniquely contained in the SODs. Our findings may help cancer centers prioritize the types of SOD data being abstracted for research or other secondary purposes.
MeSH term(s)	Humans ; Carcinoma, Non-Small-Cell Lung/diagnosis ; Carcinoma, Non-Small-Cell Lung/epidemiology ; Electronic Health Records ; Lung Neoplasms/diagnosis ; Lung Neoplasms/epidemiology ; Medical Oncology ; Disease Progression
Language	English
Publishing date	2023-02-15
Publishing country	United States
Document type	Journal Article
ISSN	2473-4276
ISSN (online)	2473-4276
DOI	10.1200/CCI.22.00118
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Article ; Online: The Alpha, Beta, Gammas of Oral Human Papillomavirus Infection and Head and Neck Cancer Risk.

Rollison, Dana E / Gillison, Maura L

JAMA oncology

2016 Volume 2, Issue 5, Page(s) 606–607

Language	English
Publishing date	2016-01-21
Publishing country	United States
Document type	Journal Article
ISSN	2374-2445
ISSN (online)	2374-2445
DOI	10.1001/jamaoncol.2015.5686
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Article ; Online: MinION nanopore sequencing and assembly of a complete human papillomavirus genome.

Brancaccio, Rosario N / Robitaille, Alexis / Dutta, Sankhadeep / Rollison, Dana E / Tommasino, Massimo / Gheit, Tarik

Journal of virological methods

2021 Volume 294, Page(s) 114180

Abstract: Background: The MinION sequencer belongs to the third generation of sequencing technology that allows for the generation of ultra-long reads, representing a potentially more effective approach to characterize entire viral genome sequences than other ... ...

Abstract	Background: The MinION sequencer belongs to the third generation of sequencing technology that allows for the generation of ultra-long reads, representing a potentially more effective approach to characterize entire viral genome sequences than other time-consuming and low-throughput methodologies. Methods: We report the use of the MinION nanopore sequencer to sequence the full-length genome of human papillomavirus (HPV)-ICB2 (7441 bp), which was previously characterized in our laboratory. Three independent MinION libraries were prepared and sequenced using either three consecutive 12 -h runs (Protocol A) or a single run of 48 h starting from a pool of three barcoded DNA libraries (Protocol B). A fully automated bioinformatics pipeline was developed for the reconstruction of the viral genome. Results: Protocols A and B generated 9,354,933 and 3,255,879 reads, respectively. Read length N50 values ranged between 6976 and 7360 nucleotides over the four sequencing runs. Bioinformatics analysis showed that both protocols allowed for the reconstruction of the whole viral genome, with pairwise percentages of identity to HPV-ICB2 of 100 % for protocol A and 99.98 % for protocol B. Conclusion: Our results show that the use of the MinION nanopore sequencer represents an effective strategy for whole-genome sequencing of HPVs with a minimal error rate.
MeSH term(s)	Alphapapillomavirus ; High-Throughput Nucleotide Sequencing ; Humans ; Nanopore Sequencing ; Papillomaviridae/genetics ; Sequence Analysis, DNA
Language	English
Publishing date	2021-05-07
Publishing country	Netherlands
Document type	Journal Article ; Research Support, N.I.H., Extramural ; Research Support, Non-U.S. Gov't
ZDB-ID	8013-5
ISSN	1879-0984 ; 0166-0934
ISSN (online)	1879-0984
ISSN	0166-0934
DOI	10.1016/j.jviromet.2021.114180
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Article ; Online: JC virus infection: a cause of colorectal cancer?

Rollison, Dana E

Journal of clinical gastroenterology

2010 Volume 44, Issue 7, Page(s) 466–468

MeSH term(s)	Animals ; Colorectal Neoplasms/virology ; DNA, Viral ; Humans ; JC Virus/genetics ; JC Virus/isolation & purification ; Polyomavirus Infections/complications ; Polyomavirus Infections/virology ; Risk Factors
Chemical Substances	DNA, Viral
Language	English
Publishing date	2010-07-01
Publishing country	United States
Document type	Comment ; Editorial
ZDB-ID	448460-5
ISSN	1539-2031 ; 0192-0790
ISSN (online)	1539-2031
ISSN	0192-0790
DOI	10.1097/MCG.0b013e3181e0084b
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Zs.A 1523: Show issues

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Article ; Online: Advancing Digital Health Innovation in Oncology: Priorities for High-Value Digital Transformation in Cancer Care.

Patel, Smit / Goldsack, Jennifer C / Cordovano, Grace / Downing, Andrea / Fields, Karen K / Geoghegan, Cindy / Grewal, Upinder / Nieva, Jorge / Patel, Nikunj / Rollison, Dana E / Sah, Archana / Said, Maya / Van De Keere, Isabel / Way, Amanda / Wolff-Hughes, Dana L / Wood, William A / Robinson, Edmondo J

Journal of medical Internet research

2023 Volume 25, Page(s) e43404

Abstract: Although health care delivery is becoming increasingly digitized, driven by the pursuit of improved access, equity, efficiency, and effectiveness, progress does not appear to be equally distributed across therapeutic areas. Oncology is renowned for ... ...

Abstract	Although health care delivery is becoming increasingly digitized, driven by the pursuit of improved access, equity, efficiency, and effectiveness, progress does not appear to be equally distributed across therapeutic areas. Oncology is renowned for leading innovation in research and in care; digital pathology, digital radiology, real-world data, next-generation sequencing, patient-reported outcomes, and precision approaches driven by complex data and biomarkers are hallmarks of the field. However, remote patient monitoring, decentralized approaches to care and research, "hospital at home," and machine learning techniques have yet to be broadly deployed to improve cancer care. In response, the Digital Medicine Society and Moffitt Cancer Center convened a multistakeholder roundtable discussion to bring together leading experts in cancer care and digital innovation. This viewpoint highlights the findings from these discussions, in which experts agreed that digital innovation is lagging in oncology relative to other therapeutic areas. It reports that this lag is most likely attributed to poor articulation of the challenges in cancer care and research best suited to digital solutions, lack of incentives and support, and missing standardized infrastructure to implement digital innovations. It concludes with suggestions for actions needed to bring the promise of digitization to cancer care to improve lives.
MeSH term(s)	Humans ; Delivery of Health Care/methods ; Neoplasms/therapy ; Patient Reported Outcome Measures
Language	English
Publishing date	2023-01-04
Publishing country	Canada
Document type	Journal Article
ZDB-ID	2028830-X
ISSN	1438-8871 ; 1438-8871
ISSN (online)	1438-8871
ISSN	1438-8871
DOI	10.2196/43404
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Article ; Online: U2AF1 and EZH2 mutations are associated with nonimmune hemolytic anemia in myelodysplastic syndromes.

Komrokji, Rami / Aguirre, Luis E / Al Ali, Najla / Hussaini, Mohamad / Sallman, David / Rollison, Dana / Padron, Eric

Blood advances

2022 Volume 7, Issue 1, Page(s) 1–8

Abstract: Hemolysis is a well-recognized but poorly characterized phenomenon in a subset of patients with myelodysplastic syndromes (MDS). Its pathobiological basis seems to underpin a nonimmune etiology whose clinical significance has not been adequately ... ...

Abstract	Hemolysis is a well-recognized but poorly characterized phenomenon in a subset of patients with myelodysplastic syndromes (MDS). Its pathobiological basis seems to underpin a nonimmune etiology whose clinical significance has not been adequately characterized. Hemolysis in MDS is often attributed to either ineffective intramedullary erythropoiesis or acquired hemoglobinopathies and red blood cell (RBC) membrane defects. These heterogeneous processes have not been associated with specific genetic subsets of the disease. We aimed to describe the prevalence of hemolysis among patients with MDS, their baseline characteristics, molecular features, and resulting impact on outcomes. We considered baseline serum haptoglobin <10 mg/dL a surrogate marker for intravascular hemolysis. Among 519 patients, 10% had hemolysis. The baseline characteristics were similar among both groups. Only 13% of patients with hemolysis were Coombs-positive, suggesting that hemolysis in MDS is largely not immune-mediated. Inferior survival trends were observed among lower-risk patients with MDS undergoing hemolysis. Decreased response rates to erythropoiesis-stimulating agents (ESA) and higher responses to hypomethylating agents (HMA) were also observed in the hemolysis group. U2AF1 and EZH2 hotspot mutations were more prevalent among those undergoing hemolysis (P < .05). U2AF1 mutations were observed in 30% of patients with hemolysis and occurred almost exclusively at the S34 hotspot. Somatic mutations encoding splicing factors may affect erythrocyte membrane components, biochemical properties, and RBC metabolic function, which underpin the development of atypical clones from erythroid precursors in MDS presenting with hemolysis. Future studies will explore the contribution of altered splicing to the development of acquired hemoglobinopathies.
MeSH term(s)	Humans ; Splicing Factor U2AF/genetics ; Hemolysis ; Mutation ; Myelodysplastic Syndromes ; Anemia, Hemolytic ; Enhancer of Zeste Homolog 2 Protein/genetics ; Enhancer of Zeste Homolog 2 Protein/metabolism
Chemical Substances	Splicing Factor U2AF ; U2AF1 protein, human ; EZH2 protein, human (EC 2.1.1.43) ; Enhancer of Zeste Homolog 2 Protein (EC 2.1.1.43)
Language	English
Publishing date	2022-10-04
Publishing country	United States
Document type	Journal Article
ZDB-ID	2915908-8
ISSN	2473-9537 ; 2473-9529
ISSN (online)	2473-9537
ISSN	2473-9529
DOI	10.1182/bloodadvances.2022007504
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Zs.A 7153: Show issues

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Article ; Online: A Question-and-Answer System to Extract Data From Free-Text Oncological Pathology Reports (CancerBERT Network): Development Study.

Mitchell, Joseph Ross / Szepietowski, Phillip / Howard, Rachel / Reisman, Phillip / Jones, Jennie D / Lewis, Patricia / Fridley, Brooke L / Rollison, Dana E

Journal of medical Internet research

2022 Volume 24, Issue 3, Page(s) e27210

Abstract: Background: Information in pathology reports is critical for cancer care. Natural language processing (NLP) systems used to extract information from pathology reports are often narrow in scope or require extensive tuning. Consequently, there is growing ... ...

Abstract	Background: Information in pathology reports is critical for cancer care. Natural language processing (NLP) systems used to extract information from pathology reports are often narrow in scope or require extensive tuning. Consequently, there is growing interest in automated deep learning approaches. A powerful new NLP algorithm, bidirectional encoder representations from transformers (BERT), was published in late 2018. BERT set new performance standards on tasks as diverse as question answering, named entity recognition, speech recognition, and more. Objective: The aim of this study is to develop a BERT-based system to automatically extract detailed tumor site and histology information from free-text oncological pathology reports. Methods: We pursued three specific aims: extract accurate tumor site and histology descriptions from free-text pathology reports, accommodate the diverse terminology used to indicate the same pathology, and provide accurate standardized tumor site and histology codes for use by downstream applications. We first trained a base language model to comprehend the technical language in pathology reports. This involved unsupervised learning on a training corpus of 275,605 electronic pathology reports from 164,531 unique patients that included 121 million words. Next, we trained a question-and-answer (Q&A) model that connects a Q&A layer to the base pathology language model to answer pathology questions. Our Q&A system was designed to search for the answers to two predefined questions in each pathology report: What organ contains the tumor? and What is the kind of tumor or carcinoma? This involved supervised training on 8197 pathology reports, each with ground truth answers to these 2 questions determined by certified tumor registrars. The data set included 214 tumor sites and 193 histologies. The tumor site and histology phrases extracted by the Q&A model were used to predict International Classification of Diseases for Oncology, Third Edition (ICD-O-3), site and histology codes. This involved fine-tuning two additional BERT models: one to predict site codes and another to predict histology codes. Our final system includes a network of 3 BERT-based models. We call this CancerBERT network (caBERTnet). We evaluated caBERTnet using a sequestered test data set of 2050 pathology reports with ground truth answers determined by certified tumor registrars. Results: caBERTnet's accuracies for predicting group-level site and histology codes were 93.53% (1895/2026) and 97.6% (1993/2042), respectively. The top 5 accuracies for predicting fine-grained ICD-O-3 site and histology codes with 5 or more samples each in the training data set were 92.95% (1794/1930) and 96.01% (1853/1930), respectively. Conclusions: We have developed an NLP system that outperforms existing algorithms at predicting ICD-O-3 codes across an extensive range of tumor sites and histologies. Our new system could help reduce treatment delays, increase enrollment in clinical trials of new therapies, and improve patient outcomes.
MeSH term(s)	Algorithms ; Humans ; Language ; Medical Oncology ; Natural Language Processing ; Neoplasms
Language	English
Publishing date	2022-03-23
Publishing country	Canada
Document type	Journal Article
ZDB-ID	2028830-X
ISSN	1438-8871 ; 1439-4456
ISSN (online)	1438-8871
ISSN	1439-4456
DOI	10.2196/27210
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Article ; Online: Effect of prior antibiotic or chemotherapy treatment on immunotherapy response in non-small cell lung cancer.

Nyein, Andrew F / Bari, Shahla / Hogue, Stephanie / Zhao, Yayi / Maller, Bradley / Sha, Sybil / Gomez, Maria F / Rollison, Dana E / Robinson, Lary A

BMC cancer

2022 Volume 22, Issue 1, Page(s) 101

Abstract: Background: Treatment outcomes of advanced non-small cell lung cancer (NSCLC) have substantially improved with immune checkpoint inhibitors (ICI), although only approximately 19% of patients respond to immunotherapy alone, increasing to 58% with the ... ...

Abstract	Background: Treatment outcomes of advanced non-small cell lung cancer (NSCLC) have substantially improved with immune checkpoint inhibitors (ICI), although only approximately 19% of patients respond to immunotherapy alone, increasing to 58% with the addition of chemotherapy. The gut microbiome has been recognized as a modulator of ICI response via its priming effect on the host immune response. Antibiotics as well as chemotherapy reduce gut microbial diversity, hence altering composition and function of the gut microbiome. Since the gut microbiome may modify ICI efficacy, we conducted a retrospective study evaluating the effects of prior antibiotic or chemotherapy use on NSCLC patient response to ICI. Methods: We retrospectively evaluated 256 NSCLC patients treated between 2011-2017 at Moffitt Cancer Center with ICI ± chemotherapy, examining the associations between prior antibiotic or chemotherapy use, overall response rate and survival. Relative risk regression using a log-link with combinatorial expectation maximization algorithm was performed to analyze differences in response between patients treated with antibiotics or chemotherapy versus patients who didn't receive antibiotics or chemotherapy. Cox proportional hazards models were constructed to evaluate associations between risk factors and overall survival. Results: Only 46 (18% of 256) patients used antibiotics prior to and/or during ICI treatment, and 146 (57%) had prior chemotherapy. Antibiotic users were 8% more likely to have worse overall response rate (RR:1.08; CI:0.93-1.26; p = 0.321), as well as a 35% worse overall survival (HR:1.35; CI:0.91-2.02; p = 0.145), although results were not statistically significant. However, prior use of chemotherapy was significantly associated with poor ICI response (RR:1.24; CI:1.05-1.47; p = 0.013) and worse overall survival (HR:1.47; CI:1.07-2.03; p = 0.018). Conclusions: Patients receiving antibiotics prior to and/or during ICI therapy might experience worse treatment outcomes and survival than unexposed patients, although these associations were not statistically significant and hence warrant further prospective study. Prior chemotherapy significantly reduced ICI response and overall survival. Antibiotic or chemotherapy exposure may negatively impact ICI response, perhaps through disruption of the eubiotic gut microbiome.
MeSH term(s)	Aged ; Anti-Bacterial Agents/adverse effects ; Antineoplastic Agents/administration & dosage ; Carcinoma, Non-Small-Cell Lung/drug therapy ; Carcinoma, Non-Small-Cell Lung/immunology ; Carcinoma, Non-Small-Cell Lung/mortality ; Female ; Gastrointestinal Microbiome/drug effects ; Gastrointestinal Microbiome/immunology ; Humans ; Immune Checkpoint Inhibitors/immunology ; Immune Checkpoint Inhibitors/therapeutic use ; Immunotherapy/mortality ; Lung Neoplasms/drug therapy ; Lung Neoplasms/immunology ; Lung Neoplasms/mortality ; Male ; Middle Aged ; Retrospective Studies ; Survival Rate ; Treatment Outcome
Chemical Substances	Anti-Bacterial Agents ; Antineoplastic Agents ; Immune Checkpoint Inhibitors
Language	English
Publishing date	2022-01-24
Publishing country	England
Document type	Evaluation Study ; Journal Article
ZDB-ID	2041352-X
ISSN	1471-2407 ; 1471-2407
ISSN (online)	1471-2407
ISSN	1471-2407
DOI	10.1186/s12885-022-09210-2
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