scholarly journals Should deep-sequenced amplicons become the new gold-standard for analysing malaria drug clinical trials?

Author(s):  
Sam Jones ◽  
Katherine Kay ◽  
Eva Maria Hodel ◽  
Maria Gruenberg ◽  
Anita Lerch ◽  
...  

Background. Regulatory clinical trials are required to ensure the continued supply and deployment of effective antimalarial drugs. Patient follow-up in such trials typically lasts several weeks as the drugs have long half-lives and new infections often occur during this period. “Molecular correction” is therefore used to distinguish drug failures from new infections. The current WHO-recommend method for molecular correction uses length-polymorphic alleles at highly diverse loci but is inherently poor at detecting low density clones in polyclonal infections. This likely leads to substantial underestimates of failure rates, delaying the replacement of failing drugs with potentially lethal consequences. Deep sequenced amplicons (AmpSeq) substantially increase the detectability of low-density clones and may offer a new “gold standard” for molecular correction. Methods. Pharmacological simulation of clinical trials was used to evaluate the suitability of AmpSeq for molecular correction. We investigated the impact of factors such as the number of amplicon loci analysed, the informatics criteria used to distinguish genotyping ‘noise’ from real low density signals, the local epidemiology of malaria transmission, and the potential impact of genetic signals from gametocytes. Results. AmpSeq greatly improved molecular correction and provided accurate drug failure rate estimates. The use of 3 to 5 amplicons was sufficient, and simple, non-statistical, criteria could be used to classify recurrent infections as drug failures or new infections. Conclusions. These results suggest AmpSeq is strongly placed to become the new standard for molecular correction in regulatory trials, with its potential extension into routine surveillance once the requisite technical support becomes established.

2021 ◽  
Author(s):  
Sam Jones ◽  
Katherine Kay ◽  
Eva Maria Hodel ◽  
Maria Gruenberg ◽  
Anita Lerch ◽  
...  

Background. Regulatory clinical trials are required to ensure the continued supply and deployment of effective antimalarial drugs. Patient follow-up in such trials typically lasts several weeks as the drugs have long half-lives and new infections often occur during this period. Molecular correction is therefore used to distinguish drug failures from new infections. The current WHO-recommend method for molecular correction uses length-polymorphic alleles at highly diverse loci but is inherently poor at detecting low density clones in polyclonal infections. This likely leads to substantial underestimates of failure rates, delaying the replacement of failing drugs with potentially lethal consequences. Deep sequenced amplicons (AmpSeq) substantially increase the detectability of low-density clones and may offer a new gold standard for molecular correction. Methods. Pharmacological simulation of clinical trials was used to evaluate the suitability of AmpSeq for molecular correction. We investigated the impact of factors such as the number of amplicon loci analysed, the informatics criteria used to distinguish genotyping noise from real low density signals, the local epidemiology of malaria transmission, and the potential impact of genetic signals from gametocytes. Results. AmpSeq greatly improved molecular correction and provided accurate drug failure rate estimates. The use of 3 to 5 amplicons was sufficient, and simple, non-statistical, criteria could be used to classify recurrent infections as drug failures or new infections. Conclusions. These results strongly endorse the deployment of AmpSeq as the standard for molecular correction in regulatory trials, with its potential extension into routine surveillance once the requisite technical support becomes established.


2015 ◽  
Vol 8 (8) ◽  
pp. 74 ◽  
Author(s):  
Maryam Kardan-Souraki ◽  
Zeinab Hamzehgardeshi ◽  
Ismail Asadpour ◽  
Reza Ali Mohammadpour ◽  
Soghra Khani

<p><strong>BACKGROUND:</strong> Lack of intimacy is currently the main concern rather than main concern of the experts in psychology and counseling. It is considered as one of the most important causes for divorce and as such to improve marital intimacy a great number of interventions have been proposed in the literature. Intimacy training and counseling make the couples take effective and successful steps to increase marital intimacy. No study has reviewed the interventions promoting marital intimacy after marriage. Thus, this review study aimed to classify the articles investigating the impact of interventional programs on marital intimacy after marriage.</p><p><strong>SEARCH METHODS:</strong> In April 2015, we performed a general search in Google Scholar search engines, and then we did an advanced search the databases of Science Direct, ProQuest, SID, Magiran, Irandoc, Pubmed, Scopus, <a href="http://www.cochranelibrary.com/">Cochrane Library</a>, and Psych info; Cumulative Index to Nursing and Allied Health Literature (CINAHL). Also, lists of the references of the relevant articles were reviewed for additional citations. Using Medical Subject Headings (MESH) keywords: Intervention (Clinical Trials, Non-Randomized Controlled Trials, Randomized Controlled Trials, Education), intimacy, marital (Marriage) and selected related articles to the study objective were from 1995 to April 2015. Clinical trials that evaluated one or more behavioral interventions to improve marital intimacy were reviewed in the study.</p><p><strong>MAIN RESULTS:</strong> 39 trials met the inclusion criteria. Eleven interventions had follow-up, and 28 interventions lacked follow-up. The quality evidence for 22 interventions was low, for 15 interventions moderate, and for one intervention was considered high. Findings from studies were categorized in 11 categories as the intimacy promoting interventions in dimensions of emotional, psychological, physical, sexual, temporal, communicational, social and recreational, aesthetic, spiritual, intellectual intimacy, and total intimacy.</p><p><strong>AUTHORS’ CONCLUSIONS:</strong> Improving and promoting communication, problem solving, self-disclosure and empathic response skills and sexual education and counseling in the form of cognitive-behavioral techniques and based on religious and cultural context of each society, an effective step can be taken to enhance marital intimacy and strengthen family bonds and stability. Health care providers should consider which interventions are appropriate to the couple characteristics and their relationships.</p>


2020 ◽  
Vol 5 (2) ◽  
pp. 86
Author(s):  
I.D. Rusen

The COVID-19 pandemic has caused unforeseen and extreme changes in societal and health system functioning not previously experienced in most countries in a lifetime. The impact of the pandemic on clinical trials can be especially profound given their complexities and operational requirements. The STREAM Clinical Trial is the largest trial for MDR-TB ever conducted. Currently operating in seven countries, the trial had 126 participants on treatment and 312 additional participants in active follow up as of March 31, 2020. Areas of particular concern during this global emergency include treatment continuity, supply chain management and participant safety monitoring. This commentary highlights some of the challenges faced due to the pandemic and the steps taken to protect the safety of trial participants and the integrity of the trial.


2017 ◽  
Vol 35 (15_suppl) ◽  
pp. e18228-e18228
Author(s):  
Dazhi Liu ◽  
Thu Oanh Dang ◽  
Stephen Harnicar ◽  
Katherine Kargus ◽  
Lauren A Evans ◽  
...  

e18228 Background: Early phase clinical trials have broadened treatment options for patients with cancer. Expert management of these new therapies is essential to positive patient outcomes. At Memorial Sloan Kettering Cancer Center, the Developmental Therapeutic Center (DTC) satisfies this need. Oncology clinical pharmacists collaborate with other healthcare professionals to maximize the benefits of drug therapy and minimize toxicities. The purpose of this project is to describe the interventions from a clinical pharmacist assigned to the DTC. Methods: A clinical pharmacist joined DTC to serve adult patients with cancer undergoing clinical trials. The clinical pharmacist acted as a liaison between pharmacy team and medical team, and sees patients during their trial eligibility screening and follow-up visits. The interventions were documented by the clinical pharmacist in patients’ medical charts and email communications. All interventions during 1 month were retrospectively collected and categorized into supportive care optimization, protocol violation prevention, and operational. Results: The oncology clinical pharmacist was involved in 115 patient visits for trial eligibility screening or protocol follow-up. A total of 769 interventions were addressed including supportive care optimization (40.2%), protocol violation prevention (24.7%), and operational (35.1%). Conclusions: The oncology clinical pharmacist is actively engaged in many aspects of cancer care at the early phase trial clinic. Our results demonstrate the vital role of an oncology clinical pharmacist. The impact of these categorized intervention areas would require a formal outcome and cost-saving analysis. [Table: see text]


2009 ◽  
Vol 37 (1) ◽  
pp. 54-63 ◽  
Author(s):  
Sarra L. Hedden ◽  
Robert F. Woolson ◽  
Rickey E. Carter ◽  
Yuko Palesch ◽  
Himanshu P. Upadhyaya ◽  
...  

Blood ◽  
2014 ◽  
Vol 124 (21) ◽  
pp. 2599-2599 ◽  
Author(s):  
Marlise R. Luskin ◽  
Ju-Whei Lee ◽  
Hugo F. Fernandez ◽  
Hillard M. Lazarus ◽  
Jacob M. Rowe ◽  
...  

Abstract Background: Novel therapies are required to improve the outcome of patients with AML. New agents are asked to demonstrate an overall survival (OS) benefit before qualifying for FDA approval. The long duration of clinical trials required in order to achieve this endpoint hampers quick evaluation of candidate therapies, including novel agents. Identification of reliable surrogate endpoints for OS in AML is needed. Here we compare the results of therapy for patients with untreated AML ages 16-60 years on the Eastern Cooperative Oncology Group 1900 trial (E1900) of induction chemotherapy followed by consolidation and autologous transplant in order to evaluate the validity of an event free survival (EFS) endpoint as a surrogate for OS. Methods:OS was measured from randomization for induction therapy to death from any cause (censored at last contact). EFS was measured from randomization to induction treatment failure, relapse after compete response (CR), or death in remission (censored at last contact). Hazard ratios (HR) were computed using Cox proportional hazards models. The association between EFS and OS was evaluated using the Kendall tau-a rank correlation for censored data. Results:There were657 patients enrolled of which 426 patients relapsed or had induction treatment failure before death or date of last contact. Median EFS and OS were 8.0 months (95% CI, 6.3 to 9.7 months) and 23.6 months (95% CI, 16.9 to 23.6 months), respectively. With a median follow-up of 80.1 months, there is a statistically significant correlation between EFS and OS (Kendall tau-a = 0.467, 95% confidence interval (CI) = (0.425, 0.510), p<0.001). This correlation was similarly significant at a median follow-up of 25.2 months (Kendall tau-a = 0.361, 95% CI (0.323, 0.400), p <0.001) when the E1900 trial was originally reported (Fernandez et al. NEJM 2009). Key findings reported based on the original OS endpoint are similar when analyzed with an EFS endpoint (Table 1). High-dose daunorubicin (90 mg/m2) (DNR 90) confers both an EFS and OS benefit in patients aged < 50 years and patients with intermediate cytogenetic risk, and does not confer an EFS or OS benefit in older patients and patients with unfavorable cytogenetic risk, on univariate analysis. Divergent results are only seen in the small subset of favorable cytogenetic risk patients, where DNR 90 conferred an OS benefit (p=0.027) without an EFS benefit (p=0.32). Both EFS and OS endpoints consistently reflect the impact of mutation status on survival. The presence of a FLT3-ITD or DNMT3A mutation has a negative impact on both EFS and OS while an IDH2 mutation has a favorable impact on EFS and OS. The presence of a NPM1 mutation confers a favorable impact on EFS and OS in patients who received DNR 90 and did not impact EFS or OS in patients receiving standard-dose daunorubicin (45 mg/m2) (DNR 45). The presence of an IDH1 mutation does not impact EFS or OS. Conclusions:The results of E1900 demonstrating superiority of DNR 90 in AML induction in patients up to age 60 are concordant when using an EFS or OS endpoint. This is true for the group as a whole as well as for subgroups for which targeted agents are in development (FLT3/IDH2 inhibitors). Further investigation of whether EFS is a reliable surrogate for OS is warranted in AML. If confirmed, its use as a primary endpoint could be adopted by regulatory agencies in order to allow more rapid completion of clinical trials in AML and bring new therapies to AML patients in a timely fashion. Table 1. Results of E1900 based on an EFS endpoint versus an OS endpoint. Subgroup N OS HR (DNR 90/DNR 45) & 95% CI Wald P EFS HR (DNR 90/DNR 45) & 95% CI Wald P DNR 45 DNR 90 Age < 50 yrs ³ 50 yrs 188 142 172 155 0.66 (0.50, 0.85) 0.81 (0.62, 1.06) 0.002 0.118 0.64 (0.50, 0.82) 0.86 (0.67, 1.10) 0.0004 0.23 Cytogenetic Favorable Intermediate Unfavorable 38 141 59 51 127 63 0.51 (0.28, 0.93) 0.68 (0.50, 0.92) 0.79 (0.54, 1.16) 0.027 0.012 0.225 0.76 (0.44, 1.31) 0.63 (0.47, 0.83) 0.72 (0.49, 1.05) 0.32 0.001 0.09 Subgroup N OS HR (MUT/WT) & 95% CI Wald P EFS HR (MUT/WT) & 95% CI Wald P FLT3-ITD WT MUT 456 147 1.62 (1.31, 2.01) <.0001 1.48 (1.21, 1.82) 0.0002 DNMT3A WT MUT 371 119 1.30 (1.03, 1.65) 0.03 1.23 (0.98, 1.54) 0.07 IDH1 WT MUT 465 36 0.88 (0.59, 1.33) 0.55 0.91 (0.62, 1.34) 0.64 IDH2 WT MUT 451 50 0.63 (0.43, 0.93) 0.02 0.68 (0.48, 0.97) 0.03 NPM1 DNR 45 DNR 90 245 257 0.84 (0.61, 1.16) 0.60 (0.41, 0.89) 0.30 0.01 0.90 (0.66, 1.22) 0.59 (0.41, 0.84) 0.49 0.004 Disclosures No relevant conflicts of interest to declare.


2016 ◽  
Vol 37 (5) ◽  
pp. 600-602 ◽  
Author(s):  
Dominik Mertz ◽  
Richard Whitlock ◽  
Alicia Y. Kokoszka ◽  
Stephanie W. Smith ◽  
Alex Carignan ◽  
...  

Based on a cohort of 966 patients, routine surveillance data were not sufficiently accurate for use in clinical trials investigating surgical site infections. Surveillance data can only be used if adequate 90-day follow-up is provided and if cases identified by surveillance are independently reviewed by a blinded outcome adjudication committee.Infect Control Hosp Epidemiol 2016;37:600–602


2021 ◽  
Vol 27 (Supplement_1) ◽  
pp. S8-S8
Author(s):  
Bixuan Lin ◽  
Poonam Beniwal-Patel

Abstract Background Total psoas muscle cross sectional area, as identified with computed tomography (CT), has been associated with clinical outcomes in various disease states. Unfortunately, total psoas CSA does not differentiate muscle density nor fat, both of which may be abnormal in obesity. Using a novel CT method to partition psoas muscle into low and high density muscle, recent studies have demonstrated low and high attenuating psoas muscle may be superior to total psoas CSA in identifying sarcopenic obesity. The impact of varying muscle composition in patients with inflammatory bowel disease is unknown. Methods We conducted a retrospective cohort study of IBD patients from a tertiary care center. Psoas muscle composition was determined using a novel and validated CT method. High and low attenuating bilateral psoas muscle was measured at the level of the 3rd lumbar vertebra. Clinical remission, surgery, hospitalization, and corticosteroid use were stratified by low and high density muscle and evaluated 6 weeks from the index CT. Results We identified 115 consecutive patients with a routine CT scan. Majority of patients had a greater quantity of low-density muscle (LDM), 95% had CD and 71% were not in clinical remission at the time of baseline CT. Of those with a greater quantity of LDM, 68% had history of IBD surgery and 60% were current/former smokers. The mean pre-CT body mass index (BMI) for the greater quantity LDM was significantly higher (p=0.002) than the mean pre-CTE BMI for those with low LDMC. Seventy percent with greater quantity of low-density muscle were either overweight or obese and 20% had a normal range BMI. Six months after the baseline CT, 53% in the lower quantity LDM had clinical remission, whereas 33.3% had remission in the high LDMC (p=0.05). Patients with greater quantity LDM were more likely to require corticosteroids in the 6 months after index CT, as compared to those with lower quantity LDM (p=0.02). Conclusion This observational study showed an association between greater quantity of LDM and obesity and worse IBD-related outcomes. This is the first study to evaluate the impact of muscle composition on IBD outcomes and our results offer a novel tool to risk stratify patients with IBD. Our study is limited by the retrospective nature, limited sample size, and narrow longitudinal follow-up. Larger prospective studies with greater longitudinal follow-up are needed to confirm our retrospective findings.


Stroke ◽  
2015 ◽  
Vol 46 (suppl_1) ◽  
Author(s):  
Casey Olm-Shipman ◽  
Victoria Marquevich ◽  
Jonathan Rosand ◽  
Aman Patel ◽  
Emad Eskandar ◽  
...  

Background: Recent AHA Acute Stroke Guidelines endorse DHC (Class 1, Level B) based on clinical trials showing benefit of early DHC on outcome and mortality. In 2011, our multidisciplinary quality improvement team developed a process to translate DHC guideline recommendations into clinical practice. Methods: Our consensus guideline includes a tool (STATE Criteria, based on inclusion/exclusion criteria of DHC clinical trials) to rapidly identify and triage potential DHC candidates, and provide specific guidelines for pre- and post-surgical management, adjunctive therapy, and DHC after IV/IA thrombolysis. Patients meeting all STATE Criteria including age ≤ 60 years are sent for urgent DHC. Patients meeting all criteria except age ≤ 60 years receive DHC only if age < 75 years and Neurology and Neurosurgery teams reach consensus about benefit. Patients not meeting criteria are observed and referred for DHC if criteria are met within 48 hours of onset. The guideline was disseminated to all stakeholders via email, conferences, and intranet. In this study, we retrospectively analyzed process and outcome measures for DHC before and after guideline implementation in February 2011. Results: Of 1518 stroke patients age ≤ 60 years admitted between January 2007 and April 2014, 47 (3%) received DHC (22 pre- and 25 post-guideline implementation; 28% female, 13% Hispanic). Mean admission NIHSS was similar (17±7 vs 18±5; p=.82). Mean time from admission to DHC improved significantly from 45±30 hours to 29±18 hours (p=0.04). The percentage of patients undergoing DHC beyond 48 hours decreased from 27% to 16% (p=0 .35). The degree of midline shift evident on CT or MRI prior to DHC significantly decreased from 9±4 mm to 5±4 mm (p=.01). There was no significant difference in length of stay, frequency of tracheostomy, gastrostomy, pneumonia, or urinary tract infection, or percentage of patients who died within 30 days of DHC. Conclusion: Our institutional guideline has facilitated the rapid identification and triage of patients with large MCA stroke to DHC. Follow-up is ongoing to determine the impact of our guideline on functional outcome after stroke.


2021 ◽  
Vol 1 (58) ◽  
pp. 4-7
Author(s):  
Adam Wojtaszczyk ◽  
Paweł Ptaszyński ◽  
Krzysztof Kaczmarek

Atrial fibrillation (AF) is one of the most important problems in cardiology. Thermal ablation therapies are “gold standard” to treat symptomatic patients. Despite the improvements, both success rate and safety are limited by their thermal nature. Pulsed filed ablation is a new non-thermal ablation method. It is based on the phenomenon of unrecoverable permeabilization of cell membranes caused by pulses of high voltage (irreversible electroporation). Several preclinical studies suggest its safety. Clinical trials published so far have showed high efficacy. Further studies especially with longer follow-up period are needed.


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