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Bonilla H, Peluso MJ, Rodgers K, Aberg JA, Patterson TF, Tamburro R, Baizer L, Goldman JD, Rouphael N, Deitchman A, Fine J, Fontelo P, Kim AY, Shaw G, Stratford J, Ceger P, Costantine MM, Fisher L, O’Brien L, Maughan C, Quigley JG, Gabbay V, Mohandas S, Williams D, McComsey GA. Therapeutic trials for long COVID-19: A call to action from the interventions taskforce of the RECOVER initiative. Front Immunol 2023; 14:1129459. [PMID: 36969241 PMCID: PMC10034329 DOI: 10.3389/fimmu.2023.1129459] [Citation(s) in RCA: 22] [Impact Index Per Article: 22.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2022] [Accepted: 02/06/2023] [Indexed: 03/11/2023] Open
Abstract
Although most individuals recover from acute SARS-CoV-2 infection, a significant number continue to suffer from Post-Acute Sequelae of SARS-CoV-2 (PASC), including the unexplained symptoms that are frequently referred to as long COVID, which could last for weeks, months, or even years after the acute phase of illness. The National Institutes of Health is currently funding large multi-center research programs as part of its Researching COVID to Enhance Recover (RECOVER) initiative to understand why some individuals do not recover fully from COVID-19. Several ongoing pathobiology studies have provided clues to potential mechanisms contributing to this condition. These include persistence of SARS-CoV-2 antigen and/or genetic material, immune dysregulation, reactivation of other latent viral infections, microvascular dysfunction, and gut dysbiosis, among others. Although our understanding of the causes of long COVID remains incomplete, these early pathophysiologic studies suggest biological pathways that could be targeted in therapeutic trials that aim to ameliorate symptoms. Repurposed medicines and novel therapeutics deserve formal testing in clinical trial settings prior to adoption. While we endorse clinical trials, especially those that prioritize inclusion of the diverse populations most affected by COVID-19 and long COVID, we discourage off-label experimentation in uncontrolled and/or unsupervised settings. Here, we review ongoing, planned, and potential future therapeutic interventions for long COVID based on the current understanding of the pathobiological processes underlying this condition. We focus on clinical, pharmacological, and feasibility data, with the goal of informing future interventional research studies.
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Pan H, Ives C, Mandal M, Qin Y, Hendershot T, Popovic J, Brambilla D, Stratford J, Treadwell M, Wu X, Kroner B. CureSCi Metadata Catalog-Making sickle cell studies findable. PLoS One 2022; 17:e0256248. [PMID: 36508412 PMCID: PMC9744304 DOI: 10.1371/journal.pone.0256248] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2021] [Accepted: 10/27/2022] [Indexed: 12/14/2022] Open
Abstract
OBJECTIVES To adopt the FAIR principles (Findable, Accessible, Interoperable, Reusable) to enhance data sharing, the Cure Sickle Cell Initiative (CureSCi) MetaData Catalog (MDC) was developed to make Sickle Cell Disease (SCD) study datasets more Findable by curating study metadata and making them available through an open-access web portal. METHODS Study metadata, including study protocol, data collection forms, and data dictionaries, describe information about study patient-level data. We curated key metadata of 16 SCD studies in a three-tiered conceptual framework of category, subcategory, and data element using ontologies and controlled vocabularies to organize the study variables. We developed the CureSCi MDC by indexing study metadata to enable effective browse and search capabilities at three levels: study, Patient-Reported Outcome (PRO) Measures, and data element levels. RESULTS The CureSCi MDC offers several browse and search tools to discover studies by study level, PRO Measures, and data elements. The "Browse Studies," "Browse Studies by PRO Measures," and "Browse Studies by Data Elements" tools allow users to identify studies through pre-defined conceptual categories. "Search by Keyword" and "Search Data Element by Concept Category" can be used separately or in combination to provide more granularity to refine the search results. This resource helps investigators find information about specific data elements across studies using public browsing/search tools, before going through data request procedures to access controlled datasets. The MDC makes SCD studies more Findable through browsing/searching study information, PRO Measures, and data elements, aiding in the reuse of existing SCD data.
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Bridgewater J, Jiao X, Parimi M, Flach C, Stratford J, Kamburov A, Schmitz AA, Zong J, Reeves JA, Keating K, Bruno A, Fellous M, Pereira MB, Bazhenova L. Prognosis and oncogenomic profiling of patients with tropomyosin receptor kinase fusion cancer in the 100,000 genomes project. Cancer Treat Res Commun 2022; 33:100623. [PMID: 36041373 DOI: 10.1016/j.ctarc.2022.100623] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2022] [Revised: 08/02/2022] [Accepted: 08/12/2022] [Indexed: 06/15/2023]
Abstract
INTRODUCTION Neurotrophic tyrosine receptor kinase (NTRK) gene fusions are oncogenic drivers in various tumor types. Limited data exist on the overall survival (OS) of patients with tumors with NTRK gene fusions and on the co-occurrence of NTRK fusions with other oncogenic drivers. MATERIALS AND METHODS This retrospective study included patients enrolled in the Genomics England 100,000 Genomes Project who had linked clinical data from UK databases. Patients who had undergone tumor whole genome sequencing between March 2016 and July 2019 were included. Patients with and without NTRK fusions were matched. OS was analyzed along with oncogenic alterations in ALK, BRAF, EGFR, ERBB2, KRAS, and ROS1, and tumor mutation burden (TMB) and microsatellite instability (MSI). RESULTS Of 15,223 patients analyzed, 38 (0.25%) had NTRK gene fusions in 11 tumor types, the most common were breast cancer, colorectal cancer (CRC), and sarcoma. Median OS was not reached in both the NTRK gene fusion-positive and -negative groups (hazard ratio 1.47, 95% CI 0.39-5.57, P = 0.572). A KRAS mutation was identified in two (5%) patients with NTRK gene fusions, and both had hepatobiliary cancer. High TMB and MSI were both more common in patients with NTRK gene fusions, due to the CRC subset. While there was a higher risk of death in patients with NTRK gene fusions compared to those without, the difference was not statistically significant. CONCLUSION This study supports the hypothesis that NTRK gene fusions are primary oncogenic drivers and the co-occurrence of NTRK gene fusions with other oncogenic alterations is rare.
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Bridgewater J, Jiao X, Parimi M, Flach C, Stratford J, Kamburov A, Schmitz A, Zong J, Reeves JA, Keating K, Bruno A, Fellous M, Bazhenova L. Abstract 394: Prognosis and molecular characteristics of patients with TRK fusion cancer in the 100,000 Genomes Project. Cancer Res 2021. [DOI: 10.1158/1538-7445.am2021-394] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Abstract
Background: NTRK gene fusions are oncogenic drivers in various tumor types. Overall survival (OS) of patients (pts) with tumors harboring NTRK fusions compared to pts without is unknown, and data on co-occurrence of NTRK fusions with other oncogenic drivers are limited.1
Methods: This retrospective study used genomic data generated by the 100,000 Genomes Project with linked clinical data from UK cancer databases. Pts with cancer who had undergone tumor whole genome sequencing between Mar 2016 and Jul 2019 were included. OS of pts with and without NTRK fusions, matched by exact and distance matching with a 1:4 NTRK+:NTRK− ratio, was analyzed by Kaplan-Meier method and Cox regression. Key alterations in ALK, BRAF, EGFR, HER2, KRAS and ROS1, and tumor mutation burden (TMB) and microsatellite instability (MSI), were evaluated along with NTRK gene fusions.
Results: Of 15,223 pts analyzed, 38 (0.2%) had NTRK fusions, identified in 11 cancers (Genomics England classification), the most common being breast cancer (n=9), colorectal cancer (CRC; n=9), and sarcoma (n=7). While there was no significant OS difference in pts with and without NTRK fusions, the HR was 1.47 (95% CI 0.39-5.57; Table). Of the tested oncogenic drivers, only KRAS mutation was identified in 2 (5%) pts with an NTRK fusion (both hepatobiliary cancer), while oncogenic driver frequency in pts without NTRK fusions ranged from 0.1-11.6%. High TMB was more common in pts with NTRK fusions than in those without (21% vs 6%), as was high MSI (18% vs 6%); all pts with NTRK fusions and high TMB and/or MSI had CRC.
Conclusions: While no statistical difference in OS was observed, there was a trend to higher risk of death in pts with NTRK fusions compared to those without, consistent with a recent US study.1 Co-occurrence of NTRK fusions and other biomarkers was rare, except for high TMB and high MSI in CRC. These results highlight NTRK fusions as actionable biomarkers and emphasize the need for NTRK gene fusion testing.
NTRK− (n=72†)NTRK+ (n=18†)Median follow-up (IQR), years2.28 (1.57-2.98)2.01 (1.40-2.97)Median OS (IQR), yearsNE (NE-NE)NE (NE-NE)Landmark OS, % (95% CI)1 year96 (91-100)94 (84-100)2 years94 (89-100)87 (71-100)3 years88 (78-99)87 (71-100)HR (95% CI)1.47 (0.39-5.57)†Only patients with linked clinical data and who were matched were included in the OS analysis.1CI, confidence interval; HR, hazard ratio; IQR, interquartile range; NE, not estimable; NTRK; neurotrophic tyrosine receptor kinase; OS, overall survival.1. Bazhenova L, et al. Clin Cancer Res. 2020;26(12 Suppl 1):09-09.
Citation Format: John Bridgewater, Xiaolong Jiao, Mounika Parimi, Clare Flach, Jeran Stratford, Atanas Kamburov, Arndt Schmitz, Jihong Zong, John A. Reeves, Karen Keating, Amanda Bruno, Marc Fellous, Lyudmila Bazhenova. Prognosis and molecular characteristics of patients with TRK fusion cancer in the 100,000 Genomes Project [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 394.
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Grobman WA, Sandoval G, Reddy UM, Tita AT, Silver RM, Mallett G, Hill K, Rice MM, El-Sayed YY, Wapner RJ, Rouse DJ, Saade GR, Thorp JM, Chauhan SP, Iams JD, Chien EK, Casey BM, Gibbs RS, Srinivas SK, Swamy GK, Simhan HN, Macones GA, Peaceman A, Plunkett B, Paycheck K, Dinsmoor M, Harris S, Sheppard J, Biggio J, Harper L, Longo S, Servay C, Varner M, Sowles A, Coleman K, Atkinson D, Stratford J, Dellermann S, Meadows C, Esplin S, Martin C, Peterson K, Stradling S, Willson C, Lyell D, Girsen A, Knapp R, Gyamfi C, Bousleiman S, Perez-Delboy A, Talucci M, Carmona V, Plante L, Tocci C, Leopanto B, Hoffman M, Dill-Grant L, Palomares K, Otarola S, Skupski D, Chan R, Allard D, Gelsomino T, Rousseau J, Beati L, Milano J, Werner E, Salazar A, Costantine M, Chiossi G, Pacheco L, Saad A, Munn M, Jain S, Clark S, Clark K, Boggess K, Timlin S, Eichelberger K, Moore A, Beamon C, Byers H, Ortiz F, Garcia L, Sibai B, Bartholomew A, Buhimschi C, Landon M, Johnson F, Webb L, McKenna D, Fennig K, Snow K, Habli M, McClellan M, Lindeman C, Dalton W, Hackney D, Cozart H, Mayle A, Mercer B, Moseley L, Gerald J, Fay-Randall L, Garcia M, Sias A, Price J, Hale K, Phipers J, Heyborne K, Craig J, Parry S, Sehdev H, Bishop T, Ferrara J, Bickus M, Caritis S, Thom E, Doherty L, de Voest J. Health resource utilization of labor induction versus expectant management. Am J Obstet Gynecol 2020; 222:369.e1-369.e11. [PMID: 31930993 DOI: 10.1016/j.ajog.2020.01.002] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2019] [Revised: 11/26/2019] [Accepted: 01/06/2020] [Indexed: 11/25/2022]
Abstract
BACKGROUND Although induction of labor of low-risk nulliparous women at 39 weeks reduces the risk of cesarean delivery compared with expectant management, concern regarding more frequent use of labor induction remains, given that this intervention historically has been thought to incur greater resource utilization. OBJECTIVE The objective of the study was to determine whether planned elective labor induction at 39 weeks among low-risk nulliparous women, compared with expectant management, was associated with differences in health care resource utilization from the time of randomization through 8 weeks postpartum. STUDY DESIGN This is a planned secondary analysis of a multicenter randomized trial in which low-risk nulliparous women were assigned to induction of labor at 39 weeks or expectant management. We assessed resource utilization after randomization in 3 time periods: antepartum, delivery admission, and discharge through 8 weeks postpartum. RESULTS Of 6096 women with data available, those in the induction of labor group (n = 3059) were significantly less likely in the antepartum period after randomization to have at least 1 ambulatory visit for routine prenatal care (32.4% vs 68.4%), unanticipated care (0.5% vs 2.6%), or urgent care (16.2% vs 44.3%), or at least 1 antepartum hospitalization (0.8% vs 2.2%, P < .001 for all). They also had fewer tests (eg, sonograms, blood tests) and treatments (eg, antibiotics, intravenous hydration) prior to delivery. During the delivery admission, women in the induction of labor group spent a longer time in labor and delivery (median, 0.83 vs 0.57 days), but both women (P = .002) and their neonates (P < .001) had shorter postpartum stays. Women and neonates in both groups had similar frequencies of postpartum urgent care and hospital readmissions (P > .05 for all). CONCLUSION Women randomized to induction of labor had longer durations in labor and delivery but significantly fewer antepartum visits, tests, and treatments and shorter maternal and neonatal hospital durations after delivery. These results demonstrate that the health outcome advantages associated with induction of labor are gained without incurring uniformly greater health care resource use.
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Beech R, Burgess K, Stratford J. Process evaluation of treatment times in a large radiotherapy department. Radiography (Lond) 2016. [DOI: 10.1016/j.radi.2016.03.001] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
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Stratford J, Hariani G, Jasper J, Brown C, Jones W, Weigman VJ. Abstract 5276: Impact of duplicate removal on low frequency NGS somatic variant calling. Cancer Res 2016. [DOI: 10.1158/1538-7445.am2016-5276] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Abstract
Cancer genomic profiles created by analysis of targeted Next Generation Sequencing (NGS) panels is emerging as a powerful tool for making informed clinical decisions. Of the critical informatics challenges to address, accurate mutation calls and allele frequency estimations after accounting for PCR-mediated artifacts are debated. The process of sample preparation for NGS sequencing involves amplification by PCR. While PCR is relatively error-free, mistakes early in DNA synthesis can be compounded, driving detection of spurious mutations and having an adverse impact on clinical reporting. Previous reports have addressed the utility of detecting and removing PCR duplicate reads in Mendelian applications but have rarely examined its use with targeted NGS panels.
We performed deduplication with 3 widely used tools (Samtools, Samblaster, and Picard) to understand sensitivity to call low frequency alleles and any impact on false positive/negative rates. Furthermore, we evaluated effects of duplicate removal on targeted panels of varying sizes and effects of sample matrices using replicates of 7 verified reference samples with several digitally confirmed alleles with frequencies ranging from 1-5%.
It is not practical to perform deduplication on PCR-enriched panels, therefore, we assessed 3 different hybrid enrichment panels of varying size (387kb, 1.3Mb, and 54Mb). Deduplication by Picard resulted in a greater decrease in the mean depth for the smaller panels (32-59%) compared to Exome (15%), showing that higher molecular diversity lowers duplication rates. Uniformity (percent of ROI with depth within 20% of the mean depth) improved 6-18% after deduplication for the smaller panels, but only 1% for the Exome.
Independent of panel size, about 32% of the total reads were marked as duplicates, reducing the power to call low frequency variants by 18%. Importantly, after added sequencing 95-96% of onco-specific variants were detected post-deduplication with a lower limit of detection of 3% compared to 2.5% pre-removal. For low-quality DNA samples we find no benefit in added sequencing for any panel. We also generally observed higher sensitivity (0% to 10% for SNV and -3% to 3% for indels) post deduplication.
Molecular diversity also varies by sample type. Intact DNA show higher molecular diversity and lower duplication rates than degraded FFPE samples. We profiled mixed-quality FFPE samples (n = 85), good-quality fresh frozen samples (n = 3), and NA12878 (n = 1) on our smallest panel and noted duplication rates of 64±14%, 40±5% and 30% respectively. On average, deduplication cut the number of SNV calls by 17.4%, with the FFPE samples affected the most (2-88%).
From our analysis we recommend performing deduplication during analysis of targeted panels. While we observed the most benefit for smaller panels with low uniformity, improved variant sensitivity was seen regardless of panel size. During experimental design, we advise a worksheet to guide deduplication decisions.
Citation Format: Jeran Stratford, Gunjan Hariani, Jeff Jasper, Chad Brown, Wendell Jones, Victor J. Weigman. Impact of duplicate removal on low frequency NGS somatic variant calling. [abstract]. In: Proceedings of the 107th Annual Meeting of the American Association for Cancer Research; 2016 Apr 16-20; New Orleans, LA. Philadelphia (PA): AACR; Cancer Res 2016;76(14 Suppl):Abstract nr 5276.
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Tignanelli CJ, Stratford J, Moffitt R, Reuther R, Johnson GL, Yeh JJ. Abstract B71: Multiplexed kinase inhibitor beads identify multiple pathways of resistance to PI3K inhibition facilitating the rational selection of novel combination therapies in pancreatic cancer. Cancer Res 2015. [DOI: 10.1158/1538-7445.panca2014-b71] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Abstract
KRAS mutational activation plays a critical role in tumorigenesis, but exactly which downstream KRAS effector pathway is critical for this role remains less clear. One of the most studied downstream pathways is the phosphatidylinositol-3-kinase (PI3K) pathway which mediates cellular metabolism, growth, and survival. We have previously shown using validated pancreatic ductal adenocarcinoma (PDAC) patient derived xenograft (PDX) mouse models that treatment with BKM120 (a pan-class 1 PI3K inhibitor, currently in Phase I/II clinical trials) resulted in tumor growth inhibition (p = 0.017) but not regression. In this study, we evaluated possible mechanisms of resistance to BKM120 therapy. We developed a novel multiplex inhibitor bead/mass spectrometry (MIB/MS) assay to measure the activation state of the kinome. We have recently shown that kinome response to kinase inhibitor therapy (i.e. kinome reprogramming) is a potential mechanism of resistance in triple negative breast cancer in response to MEK inhibition and in drug-resistant leukemia in response to imatinib. We hypothesized that kinome reprogramming may play a role in resistance to PI3K inhibition in PDAC and used MIB/MS to identify second targets that may be used in combination with PI3K inhibitors.
We found kinome reprogramming in response to PI3K inhibition through both previously known as well as less studied pathways. For instance, we found MEK1 and MEK2 activation in response to BKM120 treatment. MEK activation has previously been implicated in resistance to PI3K inhibition and combined MEK and PI3K inhibition has been shown to be synergistic in PDAC. However, our results suggest that resistance to PI3K may be mediated through many more pathways than MEK alone. We found ErbB1, ErbB2 and ErbB3 activation in response to BKM120 treatment in both cell lines and PDX tumors. ErbB2 and ErbB3 activation has previously been noted in response to PI3K inhibition in breast cancer. However, no studies have evaluated this combination in PDAC. Thus we evaluated the effect of combined PI3K and pan-ErbB inhibition in a panel of 10 PDAC cell lines using BKM120 and dacomitinib (a pan-ErbB inhibitor currently in Phase III clinical trials). Combined treatment with BKM120 and dacomitinib inhibited proliferation in 10 of 10 PDAC cell lines evaluated. This combination showed impressive synergy across all cell lines with a mean combination index of 0.24 (0.00245 – 0.49).
MIB/MS is a powerful unbiased approach to identify second targets for combination therapy. We identified both known and novel kinase pathways that may mediate resistance to PI3K inhibition in PDAC. Our results suggest that pan-ErbB inhibition may be a promising second target in combination with PI3K inhibition in PDAC. Combination studies in PDX models are ongoing. Pan-ErbB and PI3K inhibition in PDAC may be more effective than either single agent alone and should be considered in clinical trials.
Citation Format: Christopher J. Tignanelli, Jeran Stratford, Richard Moffitt, Rachel Reuther, Gary L. Johnson, Jen Jen Yeh. Multiplexed kinase inhibitor beads identify multiple pathways of resistance to PI3K inhibition facilitating the rational selection of novel combination therapies in pancreatic cancer. [abstract]. In: Proceedings of the AACR Special Conference on Pancreatic Cancer: Innovations in Research and Treatment; May 18-21, 2014; New Orleans, LA. Philadelphia (PA): AACR; Cancer Res 2015;75(13 Suppl):Abstract nr B71.
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Price G, Faivre-Finn C, Stratford J, Bayman N, Chauhan S, Bewley M, Clarke L, Moore C. EP-1527: Early results from a clinical trial of visual feedback from dynamic optical surface sensing in lung cancer patients. Radiother Oncol 2015. [DOI: 10.1016/s0167-8140(15)41519-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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Bewley M, Marchant T, Stratford J, Chauhan S, Faivre-Finn C. PO-1119 Suitability of lung margins following analysis of set up data within a multi-national lung trial. Radiother Oncol 2015. [DOI: 10.1016/s0167-8140(15)41111-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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Brand D, Thompson C, McWilliam A, Barton S, Taylor C, Logue J, Wylie J, Coyle C, Stratford J, Choudhury A. EP-1223: Endorectal balloons in prostate cancer radiotherapy: effects on seminal vesicle positioning. Radiother Oncol 2015. [DOI: 10.1016/s0167-8140(15)41215-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
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Chauhan S, Stratford J, Patel I, Lander H, Anandadas C, Loncaster J. EP-1665: Do radiotherapy tattoos reliably guide patient set up for breast tumour bed treatment? - A review of current practice. Radiother Oncol 2015. [DOI: 10.1016/s0167-8140(15)41657-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
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Stratford J, Aitkenhead A, Chauhan S, Thompson C, Taylor C, Choudhury A. EP-1670: Does the use of an endorectal balloon stabilise the rectum for patients receiving prostate radiotherapy? Radiother Oncol 2015. [DOI: 10.1016/s0167-8140(15)41662-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
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Chauhan S, Clarke L, Stratford J, Bewley M, Choudhury A, Faivre-Finn C, Marchant T. 135: Intra-fractional tumour motion and an isotropic margin: lung stereotactic ablative body radiotherapy treatment – practice evaluation. Lung Cancer 2015. [DOI: 10.1016/s0169-5002(15)50129-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
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Thompson C, Mayes S, Aitkenhead A, Logue J, Wylie J, Elliot P, Livsey J, Coyle C, Alam N, Tran A, Stratford J, Boylan C, Choudhury A. Simultaneous Cone Beam Computed Tomography (CBCT) Acquisition During Arc Radiation Therapy (SCART): A Comparison of Volume Delineation on Simultaneous and Standard CBCT in Prostate Radiation Therapy. Int J Radiat Oncol Biol Phys 2014. [DOI: 10.1016/j.ijrobp.2014.05.1324] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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Thompson C, Anandadas C, Liptrot T, Sanderson B, Lyons J, Stratford J, Tran A, Alam N, Livsey J, Wylie J, Elliott P, Logue J, Choudhury A. Tolerability of Neoadjuvant Chemotherapy and Concurrent Chemoradiation Therapy With Gemcitabine in Muscle Invasive Bladder Cancer: Physician and Patient-Reported Outcomes. Int J Radiat Oncol Biol Phys 2014. [DOI: 10.1016/j.ijrobp.2014.05.1447] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
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Mayes S, Hamlett L, Stratford J, Boylan C, Aitkenhead A, Choudhury A. Simultaneous Cone Beam Computed Tomography (CBCT) Acquisition during Volumetric Modulated Arc Therapy (VMAT): A Comparison of Volume Delineation and Organ Position on Simultaneous and Peri-radiotherapy CBCT. Clin Oncol (R Coll Radiol) 2014. [DOI: 10.1016/j.clon.2013.11.014] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
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Thompson C, Anandadas C, Stratford J, Lyons J, Elliott P, Livsey J, Logue J, Wylie J, Cowan R, Choudhury A. EP-1290: Neoadjuvant chemotherapy and chemoradiotherapy with gemcitabine in muscle invasive bladder cancer. Radiother Oncol 2014. [DOI: 10.1016/s0167-8140(15)31408-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
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Minchell L, Whitehurst P, Faivre-Finn C, Bayman N, Choudhury A, Stratford J. PO-0988: Evaluation of set up margins and a correction protocol in radical radiotherapy for lung cancer. Radiother Oncol 2014. [DOI: 10.1016/s0167-8140(15)31106-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
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Chauhan S, Bewley M, Stratford J, Davidson L, Choudhury A, Faivre –Finn C, Golby C. PO-0993: Free breathing stereotactic ablative body radiotherapy with isotropic margins: evaluation of current practice. Radiother Oncol 2014. [DOI: 10.1016/s0167-8140(15)31111-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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Davidson L, Chauhan S, Bewley M, Davidson S, Choudhury C, Stratford J. EP-1844: An investigation into the use of a drinking protocol to stabilise bladder volume in cervical radiotherapy. Radiother Oncol 2014. [DOI: 10.1016/s0167-8140(15)31962-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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Anandadas C, Thompson C, Sanderson B, Lyons J, Stratford J, Logue J. Bladder Preservation by Neoadjuvant Chemotherapy followed by Concurrent Chemoradiotherapy with Gemcitabine in Muscle Invasive Bladder Cancer (MIBC). Clin Oncol (R Coll Radiol) 2013. [DOI: 10.1016/j.clon.2012.12.009] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
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Mayes S, Hamlett L, Stratford J, Dickinson P, Livsey J, Faivre-Finn C, Boylan C, Choudhury A, Aitkenhead A. PO-0724: Comparison of volume delineation on simultaneous and standard cone beam CT images during arc radiotherapy (SCART). Radiother Oncol 2013. [DOI: 10.1016/s0167-8140(15)33030-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
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Webster GJ, Stratford J, Rodgers J, Livsey JE, Macintosh D, Choudhury A. Comparison of adaptive radiotherapy techniques for the treatment of bladder cancer. Br J Radiol 2013; 86:20120433. [PMID: 23255547 PMCID: PMC4651060 DOI: 10.1259/bjr.20120433] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2012] [Revised: 10/02/2012] [Accepted: 10/10/2012] [Indexed: 11/05/2022] Open
Abstract
OBJECTIVE Day-to-day anatomical variations complicate bladder cancer radiotherapy treatment. This work quantifies the impact on target coverage and irradiated normal tissue volume for different adaptive strategies. METHODS 20 patients were retrospectively planned using different three-dimensional conformal radiotherapy treatment strategies for whole-bladder carcinoma: (i) "conventional" treatment used isotropic expansion of the clinical target volume (CTV) by 15 mm to the planning target volume (PTV) for daily treatment; (ii) "plan of the day" used daily volumetric on-treatment imaging [cone beam CT (CBCT)] to select from four available plans with varying superior PTV margins; (iii) "composite" strategies used on-treatment CBCTs from Fractions 1-3 to inform a composite CTV and adapted PTV (5- and 10-mm margins for composite 1 and composite 2, respectively) for subsequent treatment. Target coverage was evaluated from available CBCTs (the first three fractions then the minimum weekly thereafter), and the reduction in the irradiated volume (i.e. within the 95% isodose) was quantified. RESULTS Plan of the day improved target coverage (i.e. all of the bladder within the 95% isodose throughout the treatment) relative to conventional treatment (p=0.10), while no such benefit was observed with composite 2. Target coverage was reduced with composite 1 relative to conventional treatment. The mean irradiated volume was reduced by 17.2%, 35.0% and 14.6% relative to conventional treatment, for plan of the day, composite 1 and composite 2, respectively (p<0.01 in all cases). No parameters predictive of large changes in bladder volume later in the treatment were identified. CONCLUSIONS Adaptive techniques can maintain or improve target coverage while allowing for reduced irradiated volume and possibly reduced toxicity. The plan-of-the-day technique appeared to provide the optimal balance between target coverage and normal tissue sparing. ADVANCES IN KNOWLEDGE This study suggests that plan-of-the-day techniques will provide optimal outcomes for adaptive bladder radiotherapy.
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Boylan CJ, Marchant TE, Stratford J, Malik J, Choudhury A, Shrimali R, Rodgers J, Rowbottom CG. A megavoltage scatter correction technique for cone-beam CT images acquired during VMAT delivery. Phys Med Biol 2012; 57:3727-39. [PMID: 22617805 DOI: 10.1088/0031-9155/57/12/3727] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
Kilovoltage cone-beam CT (kV CBCT) can be acquired during the delivery of volumetric modulated arc therapy (VMAT), in order to obtain an image of the patient during treatment. However, the quality of such CBCTs is degraded by megavoltage (MV) scatter from the treatment beam onto the imaging panel. The objective of this paper is to introduce a novel MV scatter correction method for simultaneous CBCT during VMAT, and to investigate its effectiveness when compared to other techniques. The correction requires the acquisition of a separate set of images taken during VMAT delivery, while the kV beam is off. These images--which contain only the MV scatter contribution on the imaging panel--are then used to correct the corresponding kV/MV projections. To test this method, CBCTs were taken of an image quality phantom during VMAT delivery and measurements of contrast to noise ratio were made. Additionally, the correction was applied to the datasets of three VMAT prostate patients, who also received simultaneous CBCTs. The clinical image quality was assessed using a validated scoring system, comparing standard CBCTs to the uncorrected simultaneous CBCTs and a variety of correction methods. Results show that the correction is able to recover some of the low and high-contrast signal to noise ratio lost due to MV scatter. From the patient study, the corrected CBCT scored significantly higher than the uncorrected images in terms of the ability to identify the boundary between the prostate and surrounding soft tissue. In summary, a simple MV scatter correction method has been developed and, using both phantom and patient data, is shown to improve the image quality of simultaneous CBCTs taken during VMAT delivery.
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