Fast and exact quantification of motif occurrences in biological sequences

Abstract Background Identification of motifs and quantification of their occurrences are important for the study of genetic diseases, gene evolution, transcription sites, and other biological mechanisms. Exact formulae for estimating count distributions of motifs under Markovian assumptions have high computational complexity and are impractical to be used on large motif sets. Approximated formulae, e.g. based on compound Poisson, are faster, but reliable p value calculation remains challenging. Here, we introduce ‘motif_prob’, a fast implementation of an exact formula for motif count distribution through progressive approximation with arbitrary precision. Our implementation speeds up the exact calculation, usually impractical, making it feasible and posit to substitute currently employed heuristics. Results We implement motif_prob in both Perl and C+ + languages, using an efficient error-bound iterative process for the exact formula, providing comparison with state-of-the-art tools (e.g. MoSDi) in terms of precision, run time benchmarks, along with a real-world use case on bacterial motif characterization. Our software is able to process a million of motifs (13–31 bases) over genome lengths of 5 million bases within the minute on a regular laptop, and the run times for both the Perl and C+ + code are several orders of magnitude smaller (50–1000× faster) than MoSDi, even when using their fast compound Poisson approximation (60–120× faster). In the real-world use cases, we first show the consistency of motif_prob with MoSDi, and then how the p-value quantification is crucial for enrichment quantification when bacteria have different GC content, using motifs found in antimicrobial resistance genes. The software and the code sources are available under the MIT license at https://github.com/DataIntellSystLab/motif_prob. Conclusions The motif_prob software is a multi-platform and efficient open source solution for calculating exact frequency distributions of motifs. It can be integrated with motif discovery/characterization tools for quantifying enrichment and deviation from expected frequency ranges with exact p values, without loss in data processing efficiency.

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The Evolution of Isochores: Evidence From SNP Frequency Distributions

Genetics ◽

10.1093/genetics/162.4.1805 ◽

2002 ◽

Vol 162 (4) ◽

pp. 1805-1810 ◽

Cited By ~ 1

Author(s):

Martin J Lercher ◽

Nick G C Smith ◽

Adam Eyre-Walker ◽

Laurence D Hurst

Keyword(s):

Population Genetics ◽

Large Scale ◽

Gc Content ◽

Nucleotide Composition ◽

Compositional Variation ◽

Mutation Bias ◽

Single Nucleotide ◽

Frequency Distributions ◽

Noncoding Regions ◽

Standard Population

AbstractThe large-scale systematic variation in nucleotide composition along mammalian and avian genomes has been a focus of the debate between neutralist and selectionist views of molecular evolution. Here we test whether the compositional variation is due to mutation bias using two new tests, which do not assume compositional equilibrium. In the first test we assume a standard population genetics model, but in the second we make no assumptions about the underlying population genetics. We apply the tests to single-nucleotide polymorphism data from noncoding regions of the human genome. Both models of neutral mutation bias fit the frequency distributions of SNPs segregating in low- and medium-GC-content regions of the genome adequately, although both suggest compositional nonequilibrium. However, neither model fits the frequency distribution of SNPs from the high-GC-content regions. In contrast, a simple population genetics model that incorporates selection or biased gene conversion cannot be rejected. The results suggest that mutation biases are not solely responsible for the compositional biases found in noncoding regions.

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AB0799 REAL-WORLD EXPERIENCE OF SECUKINUMAB FOR PSORIATIC ARTHRITIS WITH AXIAL INVOLVEMENT.

Annals of the Rheumatic Diseases ◽

10.1136/annrheumdis-2020-eular.6564 ◽

2020 ◽

Vol 79 (Suppl 1) ◽

pp. 1699.3-1699

Author(s):

M. Martin Lopez ◽

B. Joven-Ibáñez ◽

J. L. Pablos

Keyword(s):

Psoriatic Arthritis ◽

Adverse Events ◽

Real World ◽

Spinal Pain ◽

Tender Joint Count ◽

P Value ◽

X Ray ◽

Activity Assessment ◽

Real World Setting ◽

Axial Involvement

Background:Evidence on the efficacy of biologics in the treatment of psoriatic arthritis (PsA) patients with axial manifestations affecting 30-70% of PsA patients is limited. Secukinumab (SEC) has provided significant and sustained improvement in the signs and symptoms of active PsA and ankylosing spondylitis.Objectives:This study aims to analyze the experience of using SEC for PsA patients with axial involvement in real-world setting.Methods:Multicentric observational, longitudinal, retrospective study conducted in a tertiary hospital between January 2016 and December 2019. Patients with PsA (CASPAR criteria) and clinical and/or image diagnosis of axial involvement receiving at least one dose of SEC were included. Patients with non-pathological sacroiliacs x-ray and MRI had to have spinal pain VAS ≥4/10 after failure to NSAIDs, prior to the onset of SEC, to be included. Medical records were reviewed to collect demographic and clinical data, features of PsA (manifestations, treatments and activity assessment). Descriptive statistics and then a comparative analysis with the Studentt-test to analyze the effectiveness of SEC were performed.Results:Of 98 PsA patients treated with SEC, 58 (59.2%) had axial involvement, of which 41 (71%) female. Mean age was 54 y.o (SD 10) and average duration of the disease was 10 years (SD 8). All 58 patients had peripheral disease (33% joint erosions), 55 (95%) had psoriasis, 20 (34%) showed dactilitis and 39 (67%) had enthesitis. Sacroiliacs x-ray was damaged in 38 (66%) patients (grade I-IV) and 23 (40%) pathological MRI, with HLAB27+ at 8 (14%) patients. Average BMI was 29 (SD 8), with an obesity rate of 33% (19 pt). Observed comorbidities were hypertension (27 pt, 47%), diabetes mellitus (6 pt, 10%), dyslipidemia (23 pt, 40%), active smoking (18 pt, 31%) and malignancy (6 pt, 10%). Regarding previous treatments, 90% had received cDMARDs, particularly methotrexate (86%) and 40 (69%) had been exposed to at least one bDMARD (15 pt to one, 9 to two, 6 to three and 10 to four or more). 7 patients were on 300 mg dose and 51 patients on 150 mg dose (dose escalation to 300 mg was performed in 16 patients and 44% respond and maintain SEC). Average drug survival time was 1.4 (SD 1) years. At 6 months of SEC therapy, tender and swollen joint count, spinal pain VAS, CRP, ASDAS-CRP and DAPSA had significantly decreased (Table 1). 29 (50%) patients suspended SEC during follow-up due to primary ineffectiveness (8), secondary ineffectiveness (16), adverse events (3), latex allergy (1) and remission (1). Adverse events do not differ from those reported in clinical trials.Table 1.Disease activity assessment at 6 months of secukinumab therapy.Baseline6 months after SECMean differenceP valueSJC4,8±5,41,9±3,1-2,8 (IC95% -3,9 a -1,7)p<0,0001TJC7,7±5,83,9±4,1-3,8 (IC95% -5,1 a -2,4)p<0,0001Spinal pVAS6,1±3,24,2±2,9-1,9 (IC95% -2,4 a -1,4)p<0,0001CRP (mg/L)7,7±9,94,9±5,9-2,9 (IC95% -4,5 a -1,2)p=0,0009ASDAS-CRP2,5±1,91,8±1,3-0,7 (IC95% -0,9 a -0,4)p<0,0001DAPSA27,7±12,116,7±10,4-11 (IC95% -15,3 a -6,8)p<0,0001SJC: swollen joint count, TJC: tender joint count, Spinal pVAS: spinal pain visual analog scale, CRP: C-reactive protein, SEC: secukinumab.Conclusion:Secukinumab in real-world setting provided improvements in the axial and peripheral manifestations of PsA, using both the 150 mg and 300 mg doses.Disclosure of Interests:MARIA MARTIN LOPEZ: None declared, Beatriz Joven-Ibáñez Speakers bureau: Abbvie, Celgene, Janssen, Merck Sharp & Dohme, Novartis, Pfizer, José Luis Pablos: None declared

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Utility of routinely collected electronic health records data to support effectiveness evaluations in inflammatory bowel disease: a pilot study of tofacitinib

BMJ Health & Care Informatics ◽

10.1136/bmjhci-2021-100337 ◽

2021 ◽

Vol 28 (1) ◽

pp. e100337

Author(s):

Vivek Ashok Rudrapatna ◽

Benjamin Scott Glicksberg ◽

Atul Janardhan Butte

Keyword(s):

Inflammatory Bowel Disease ◽

Pilot Study ◽

Disease Activity ◽

Real World ◽

Bowel Disease ◽

P Value ◽

Health Records ◽

Real World Evidence ◽

Inflammatory Bowel

ObjectivesElectronic health records (EHR) are receiving growing attention from regulators, biopharmaceuticals and payors as a potential source of real-world evidence. However, their suitability for the study of diseases with complex activity measures is unclear. We sought to evaluate the use of EHR data for estimating treatment effectiveness in inflammatory bowel disease (IBD), using tofacitinib as a use case.MethodsRecords from the University of California, San Francisco (6/2012 to 4/2019) were queried to identify tofacitinib-treated IBD patients. Disease activity variables at baseline and follow-up were manually abstracted according to a preregistered protocol. The proportion of patients meeting the endpoints of recent randomised trials in ulcerative colitis (UC) and Crohn’s disease (CD) was assessed.Results86 patients initiated tofacitinib. Baseline characteristics of the real-world and trial cohorts were similar, except for universal failure of tumour necrosis factor inhibitors in the former. 54% (UC) and 62% (CD) of patients had complete capture of disease activity at baseline (month −6 to 0), while only 32% (UC) and 69% (CD) of patients had complete follow-up data (month 2 to 8). Using data imputation, we estimated the proportion achieving the trial primary endpoints as being similar to the published estimates for both UC (16%, p value=0.5) and CD (38%, p-value=0.8).Discussion/ConclusionThis pilot study reproduced trial-based estimates of tofacitinib efficacy despite its use in a different cohort but revealed substantial missingness in routinely collected data. Future work is needed to strengthen EHR data and enable real-world evidence in complex diseases like IBD.

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POS0619 MODELLING OF DISEASE ACTIVITY IN PATIENTS WITH INFLAMMATORY ARTHROPATHIES TREATED WITH ETANERCEPT ORIGINATOR OR BIOSIMILAR AS FIRST-LINE BIOLOGIC IN AN AUSTRALIAN REAL-WORLD DATASET

Annals of the Rheumatic Diseases ◽

10.1136/annrheumdis-2021-eular.2265 ◽

2021 ◽

Vol 80 (Suppl 1) ◽

pp. 547.1-547

Author(s):

C. Deakin ◽

G. Littlejohn ◽

H. Griffiths ◽

T. Smith ◽

C. Osullivan ◽

...

Keyword(s):

Disease Activity ◽

Clinical Data ◽

Real World ◽

Rank Test ◽

P Value ◽

Continuous Variables ◽

Linear Quadratic ◽

First Line ◽

Modest Improvement ◽

Over Time

Background:The availability of biosimilars as non-proprietary versions of established biologic disease-modifying anti-rheumatic drugs (bDMARDs) is enabling greater access for patients with rheumatic diseases to effective medications at a lower cost. Since April 2017 both the originator and a biosimilar for etanercept (trade names Enbrel and Brenzys, respectively) have been available for use in Australia.Objectives:[1]To model effectiveness of etanercept originator or biosimilar in reducing Disease Activity Score 28-joint count C reactive protein (DAS28CRP) in patients with rheumatoid arthritis (RA), psoriatic arthritis (PsA) or ankylosing spondylitis (AS) treated with either drug as first-line bDMARD[2]To describe persistence on etanercept originator or biosimilar as first-line bDMARD in patients with RA, PsA or ASMethods:Clinical data were obtained from the Optimising Patient outcomes in Australian rheumatoLogy (OPAL) dataset, derived from electronic medical records. Eligible patients with RA, PsA or AS who initiated etanercept originator (n=856) or biosimilar (n=477) as first-line bDMARD between 1 April 2017 and 31 December 2020 were identified. Propensity score matching was performed to select patients on originator (n=230) or biosimilar (n=136) with similar characteristics in terms of diagnosis, disease duration, joint count, age, sex and concomitant medications. Data on clinical outcomes were recorded at 3 months after baseline, and then at 6-monthly intervals. Outcomes data that were missing at a recorded visit were imputed.Effectiveness of the originator, relative to the biosimilar, for reducing DAS28CRP over time was modelled in the matched population using linear mixed models with both random intercepts and slopes to allow for individual heterogeneity, and weighting of individuals by inverse probability of treatment weights to ensure comparability between treatment groups. Time was modelled as a combination of linear, quadratic and cubic continuous variables.Persistence on the originator or biosimilar was analysed using survival analysis (log-rank test).Results:Reduction in DAS28CRP was associated with both time and etanercept originator treatment (Table 1). The conditional R-squared for the model was 0.31. The average predicted DAS28CRP at baseline, 3 months, 6 months, 9 months and 12 months were 4.0 and 4.4, 3.1 and 3.4, 2.6 and 2.8, 2.3 and 2.6, and 2.2 and 2.4 for the originator and biosimilar, respectively, indicating a clinically meaningful effect of time for patients on either drug and an additional modest improvement for patients on the originator.Median time to 50% of patients stopping treatment was 25.5 months for the originator and 24.1 months for the biosimilar (p=0.53). An adverse event was the reason for discontinuing treatment in 33 patients (14.5%) on the originator and 18 patients (12.9%) on the biosimilar.Conclusion:Analysis using a large national real-world dataset showed treatment with either the etanercept originator or the biosimilar was associated with a reduction in DAS28CRP over time, with the originator being associated with a further modest reduction in DAS28CRP that was not clinically significant. Persistence on treatment was not different between the two drugs.Table 1.Respondent characteristics.Fixed EffectEstimate95% Confidence Intervalp-valueTime (linear)0.900.89, 0.911.5e-63Time (quadratic)1.011.00, 1.011.3e-33Time (cubic)1.001.00, 1.007.1e-23Originator0.910.86, 0.960.0013Acknowledgements:The authors acknowledge the members of OPAL Rheumatology Ltd and their patients for providing clinical data for this study, and Software4Specialists Pty Ltd for providing the Audit4 platform.Supported in part by a research grant from Investigator-Initiated Studies Program of Merck & Co Inc, Kenilworth, NJ, USA. The opinions expressed in this paper are those of the authors and do not necessarily represent those of Merck & Co Inc, Kenilworth, NJ, USA.Disclosure of Interests:Claire Deakin: None declared, Geoff Littlejohn Consultant of: Over the last 5 years Geoffrey Littlejohn has received educational grants and consulting fees from AbbVie, Bristol Myers Squibb, Eli Lilly, Gilead, Novartis, Pfizer, Janssen, Sandoz, Sanofi and Seqirus., Hedley Griffiths Consultant of: AbbVie, Gilead, Novartis and Lilly., Tegan Smith: None declared, Catherine OSullivan: None declared, Paul Bird Speakers bureau: Eli Lilly, abbvie, pfizer, BMS, UCB, Gilead, Novartis

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NCDB Analysis of Melanoma 2004–2015: Epidemiology and Outcomes by Subtype, Sociodemographic Factors Impacting Clinical Presentation, and Real-World Survival Benefit of Immunotherapy Approval

Cancers ◽

10.3390/cancers13061455 ◽

2021 ◽

Vol 13 (6) ◽

pp. 1455

Author(s):

Sunny R. K. Singh ◽

Sindhu J. Malapati ◽

Rohit Kumar ◽

Christopher Willner ◽

Ding Wang

Keyword(s):

Metastatic Melanoma ◽

Metastatic Disease ◽

Real World ◽

Care Delivery ◽

Sociodemographic Factors ◽

P Value ◽

Real World Data ◽

Factors Associated ◽

Improvement In Survival ◽

The Impact

Background: The incidence of invasive melanoma is rising, and approval for the first immune checkpoint inhibitor (ICI) to treat metastatic melanoma occurred in 2011. We aim to describe the epidemiology and outcomes in recent years, sociodemographic factors associated with the presence of metastasis at diagnosis, and the real‐world impact of ICI approval on survival based on melanoma subtype and race. Methods: This is a retrospective analysis of the National Cancer Database (NCDB) from the years 2004–2015. The primary outcome was the overall survival of metastatic melanoma by subtype. Secondary outcomes included sociodemographic factors associated with the presence of metastasis at diagnosis and the impact of treatment facility type and ICI approval on the survival of metastatic melanoma. Results: Of the 419,773 invasive melanoma cases, 93.80% were cutaneous, and 4.92% were metastatic at presentation. The odds of presenting with metastatic disease were higher in African Americans (AA) compared to Caucasians (OR 2.37; 95% CI 2.11–2.66, p < 0.001). Treatment of metastatic melanoma at an academic/research facility was associated with lower mortality versus community cancer programs (OR 0.75, 95 % CI 0.69–0.81, p-value<0.001). Improvement in survival of metastatic melanoma was noted for Caucasians after the introduction of ICI (adjusted HR 0.80, 95% CI 0.78–0.83, p < 0.001); however, this was not statistically significant for AA (adjusted HR 0.80, 95% CI 0.62–1.02, p‐value = 0.073) or ocular cases (HR 1.03, 95% CI 0.81–1.31, p‐value 0.797). Conclusion: Real‐world data suggest a 20% improvement in survival of metastatic melanoma since the introduction of ICI. The disproportionately high odds of metastatic disease at presentation in AA patients with melanoma suggest the need for a better understanding of the disease and improvement in care delivery.

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AB0337 TOFACITINIB MONOTHERAPY OR COMBINED WITH METHOTREXATE IN PATIENTS WITH RHEUMATOID ARTHRITIS SHOW SIMILAR RETENTION OVER FOUR YEARS. REPORT FROM RHUMADATA ®

Annals of the Rheumatic Diseases ◽

10.1136/annrheumdis-2020-eular.2479 ◽

2020 ◽

Vol 79 (Suppl 1) ◽

pp. 1467.1-1467

Author(s):

D. Choquette ◽

L. Bessette ◽

L. Choquette Sauvageau ◽

I. Ferdinand ◽

B. Haraoui ◽

...

Keyword(s):

Rheumatoid Arthritis ◽

Disease Activity ◽

Real World ◽

Treatment Initiation ◽

Retention Rate ◽

Janus Kinase ◽

P Value ◽

Research Support ◽

Medication Discontinuation ◽

Kaplan Meier

Background:Since the introduction of biologic agents around the turn of the century, the scientific evidence shows that the majority of agents, independent of the therapeutic target, have a better outcome when used in combination with methotrexate (MTX). In 2014, tofacitinib (TOFA), an agent targeting Janus kinase 1 and 3, has reached the Canadian market with data showing that the combination with MTX may not be necessary [1,2].Objectives:To evaluate the efficacy and retention rate of TOFA in real-world patients with rheumatoid arthritis (RA).Methods:Two cohorts of patients prescribed TOFA was created. The first cohort was formed of patients who were receiving MTX concomitantly with TOFA (COMBO) and the other of patients using TOFA in monotherapy (MONO). MONO patients either never use MTX or were prescribed MTX post-TOFA initiation for at most 20% of the time they were on TOFA. COMBO patients received MTX at the time of TOFA initiation or were prescribed MTX post-TOFA initiation for at least 80% of the time. For all those patients, baseline demographic data definitions. Disease activity score and HAQ-DI were compared from the initiation of TOFA to the last visit. Time to medication discontinuation was extracted, and survival was estimated using Kaplan-Meier calculation for MONO and COMBO cohorts.Results:Overall, 194 patients were selected. Most were women (83%) on average younger than the men (men: 62.6 ± 11.0 years vs. women: 56.9 ± 12.1 years, p-value=0.0130). The patient’s assessments of global disease activity, pain and fatigue were respectively 5.0 ± 2.7, 5.2 ± 2.9, 5.1 ± 3.1 in the COMBO group and 6.2 ± 2.5, 6.5 ± 2.6, 6.3 ± 2.8 in the MONO group all differences being significant across groups. HAQ-DI at treatment initiation was 1.3 ± 0.7 and 1.5 ± 0.7 in the COMBO and MONO groups, respectively, p-value=0.0858. Similarly, the SDAI score at treatment initiation was 23.9 ± 9.4 and 25.2 ± 11.5, p-value=0.5546. Average changes in SDAI were -13.4 ± 15.5 (COMBO) and -8.9 ± 13.5 (MONO), p-value=0.1515, and changes in HAQ -0.21 ± 0.63 and -0.26 ± 0.74, p-value 0.6112. At treatment initiation, DAS28(4)ESR were 4.4 ± 1.4 (COMBO) and 4.6 ± 1.3 (MONO), p-value 0.5815, with respective average changes of -1.06 ± 2.07 and -0.70 ± 1.96, p-value=0.2852. The Kaplan-Meier analysis demonstrated that the COMBO and MONO retention curves were not statistically different (log-rank p-value=0.9318).Conclusion:Sustainability of TOFA in MONO or COMBO are not statistically different as are the changes in DAS28(4)ESR and SDAI. Despite this result, some patients may still benefit from combination with MTX.References:[1]Product Monograph - XELJANZ ® (tofacitinib) tablets for oral administration Initial U.S. Approval: 2012.[2] Reed GW, Gerber RA, Shan Y, et al. Real-World Comparative Effectiveness of Tofacitinib and Tumor Necrosis Factor Inhibitors as Monotherapy and Combination Therapy for Treatment of Rheumatoid Arthritis [published online ahead of print, 2019 Nov 9].Rheumatol Ther. 2019;6(4):573–586. doi:10.1007/s40744-019-00177-4.Disclosure of Interests:Denis Choquette Grant/research support from: Rhumadata is supported by grants from Pfizer, Amgen, Abbvie, Gylead, BMS, Novartis, Sandoz, eli Lilly,, Consultant of: Pfizer, Amgen, Abbvie, Gylead, BMS, Novartis, Sandoz, eli Lilly,, Speakers bureau: Pfizer, Amgen, Abbvie, Gylead, BMS, Novartis, Sandoz, eli Lilly,, Louis Bessette Grant/research support from: AbbVie, Amgen, Bristol-Myers Squibb, Celgene, Eli Lilly, Janssen, Merck, Novartis, Pfizer, Roche, Sanofi, UCB Pharma, Consultant of: AbbVie, Amgen, Bristol-Myers Squibb, Celgene, Eli Lilly, Janssen, Merck, Novartis, Pfizer, Roche, Sanofi, UCB Pharma, Speakers bureau: AbbVie, Amgen, Bristol-Myers Squibb, Celgene, Eli Lilly, Janssen, Merck, Novartis, Pfizer, Sanofi, Loïc Choquette Sauvageau: None declared, Isabelle Ferdinand Consultant of: Pfizer, Abbvie, Amgen, Novartis, Speakers bureau: Pfizer, Amgen, Boulos Haraoui Grant/research support from: Abbvie, Amgen, Pfizer, UCB, Grant/research support from: AbbVie, Amgen, BMS, Janssen, Pfizer, Roche, and UCB, Consultant of: Abbvie, Amgen, Lilly, Pfizer, Sandoz, UCB, Consultant of: AbbVie, Amgen, BMS, Celgene, Eli Lilly, Janssen, Merck, Pfizer, Roche, and UCB, Speakers bureau: Pfizer, Speakers bureau: Amgen, BMS, Janssen, Pfizer, and UCB, Frédéric Massicotte Consultant of: Abbvie, Janssen, Lilly, Pfizer, Speakers bureau: Janssen, Jean-Pierre Pelletier Shareholder of: ArthroLab Inc., Grant/research support from: TRB Chemedica, Speakers bureau: TRB Chemedica and Mylan, Jean-Pierre Raynauld Consultant of: ArthroLab Inc., Marie-Anaïs Rémillard Consultant of: Abbvie, Amgen, Eli Lilly, Novartis, Pfizer, Sandoz, Paid instructor for: Abbvie, Amgen, Eli Lilly, Novartis, Pfizer, Sandoz, Speakers bureau: Abbvie, Amgen, Eli Lilly, Novartis, Pfizer, Sandoz, Diane Sauvageau: None declared, Édith Villeneuve Consultant of: Abbvie, Amgen, BMS, Celgene, Pfizer, Roche, Sanofi-Genzyme,UCB, Paid instructor for: Abbvie, Speakers bureau: AbbVie, BMS, Pfizer, Roche, Louis Coupal: None declared

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Efficacy of BRAF and MEK Inhibition in Patients with BRAF-Mutant Advanced Melanoma and Germline CDKN2A Pathogenic Variants

Cancers ◽

10.3390/cancers13102440 ◽

2021 ◽

Vol 13 (10) ◽

pp. 2440

Author(s):

Francesco Spagnolo ◽

Bruna Dalmasso ◽

Enrica Tanda ◽

Miriam Potrony ◽

Susana Puig ◽

...

Keyword(s):

Real World ◽

Response Rate ◽

Suppressor Gene ◽

Phase Iii ◽

Clinical Activity ◽

P Value ◽

Pathogenic Variants ◽

Phase Iii Trials ◽

The Difference ◽

First Time

Inherited pathogenic variants (PVs) in the CDKN2A tumor suppressor gene are among the strongest risk factors for cutaneous melanoma. Dysregulation of the p16/RB1 pathway may intrinsically limit the activity of MAPK-directed therapy due to the interplay between the two pathways. In our study, we assessed, for the first time, whether patients with germline CDKN2A PVs achieve suboptimal results with BRAF inhibitors (BRAFi)+/−MEK inhibitors (MEKi). We compared the response rate of nineteen CDKN2A PVs carriers who received first-line treatment with BRAFi+/−MEKi with an expected rate derived from phase III trials and “real-world” studies. We observed partial response in 16/19 patients (84%), and no complete responses. The overall response rate was higher than that expected from phase III trials (66%), although not statistically significant (p-value = 0.143; 95% CI = 0.60–0.97); the difference was statistically significant (p-value = 0.019; 95% CI = 0.62–0.97) in the comparison with real-world studies (57%). The clinical activity of BRAFi+/−MEKi in patients with germline CDKN2A PV was not inferior to that of clinical trials and real-world studies, which is of primary importance for clinical management and genetic counseling of this subgroup of patients.

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Smoking Cessation Services by Community Pharmacists: Real-World Practice in Thailand

International Journal of Environmental Research and Public Health ◽

10.3390/ijerph182211890 ◽

2021 ◽

Vol 18 (22) ◽

pp. 11890

Author(s):

Sunee Lertsinudom ◽

Pentipa Kaewketthong ◽

Tamonwan Chankaew ◽

Dujrudee Chinwong ◽

Surarong Chinwong

Keyword(s):

Smoking Cessation ◽

Community Pharmacy ◽

Real World ◽

Community Pharmacists ◽

Self Report ◽

P Value ◽

Quit Smoking ◽

Smoking Cessation Services ◽

Before And After ◽

Exhaled Carbon Monoxide

This study aimed to report the effectiveness of community pharmacy smoking cessation services in 13 health regions in Thailand using a retrospective data-collecting method from the Foundation of Community Pharmacy database. The participants were smokers aged at least 18 years. The outcomes were the abstinence of smoking at least 30 consecutive days by self-report only and self-report with exhaled CO level <7 ppm (if available), the number of cigarettes smoked daily, exhaled carbon monoxide (exhaled CO), and % peak expiratory flow rate (%PEFR); smokers measured these outcomes before and after receiving the smoking cessation services. Of 58 community pharmacies, 532 smokers (93% male, mean age of 42.4 ± 14.9 years) received smoking cessation services from community pharmacists. Of 235 smokers with complete data, 153 (28.8%, 153/532) smokers reported smoking abstinence by self-report. The mean number of cigarettes smoked daily reduced from 15.3 ± 8.7 to 1.9 ± 3.8 cigarettes, p-value < 0.001. The exhaled CO levels of smokers significantly reduced from 11.7 ± 5.9 ppm to 7.2 ± 4.4 ppm, p-value < 0.001. The %PEFR also significantly increased from 84.2 ± 19.4 to 89.5 ± 19.5, p-value < 0.001. In conclusion, Thai community pharmacy smoking cessation services could aid smokers to quit smoking. This study is the outcome of the real-world community pharmacy smoking cessation service; policymakers should consider this service to be included in the national healthcare policy.

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Retrospective, observational study on usage of evogliptin in T2DM patients: A real-World experience in Indian patients

Indian Journal of Pharmacy and Pharmacology ◽

10.18231/j.ijpp.2021.035 ◽

2021 ◽

Vol 8 (3) ◽

pp. 205-207

Author(s):

Abhijit Trailokya ◽

Amol Aiwale ◽

Roshan Pawar ◽

Suhas Erande

Keyword(s):

Real World ◽

Small Sample Size ◽

Small Sample ◽

Hypoglycemic Agents ◽

P Value ◽

Base Line ◽

Oral Hypoglycemic Agents ◽

Naive Patient ◽

Indian Patients ◽

Treatment Naïve

This study aimed to assess effectiveness and safety of Evogliptin 5 mg in patients with T2DM who were prescribed Evogliptin alone or with other oral hypoglycemic agents in real world scenario. Overall 20 patients who received Evogliptin as routine clinical practice in management of T2DM were analyzed retrospectively from single center. Data collected from past medical records. Primary endpoint was mean changes in HbA1c from baseline to weeks 24 and secondary endpoints were Change in HbA1c from baseline to weeks 12 Change from baseline in FPG & PPG at weeks 12 & 24.Significant reduction in HbA1c at the end of 12 and 24 weeks of Evogliptin therapy was - 0.9% and -1.45% respectively from the baseline of HbA1c 8.6% (p value <0.001). At the end of 12 and 24 weeks of addition of Evogliptin, significant reduction in FBG were seen i.e -49.5 mg/dl and -90.7mg/dl respectively from base line of 182 mg/dl and reduction in PPG was -79.4mg/dl and -116.6mg/dl respectively from base line 277 mg/dl (p value <0.001). Evogliptin was found to be effective when added to the patients who were uncontrolled on dual / triple oral anti-diabetic medications and even in treatment naïve patient. It effectively showed reduction in HbA1c, FBG and PPG and the end of 12 and 24 weeks when added to existing anti-diabetic medications & well tolerated in type 2 diabetes Indian patients.Small sample size and retrospective study

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Cabozantinib versus other TKIs after CPI treatment in the real-world management of patients with metastatic renal cell carcinoma (mRCC).

Journal of Clinical Oncology ◽

10.1200/jco.2021.39.6_suppl.293 ◽

2021 ◽

Vol 39 (6_suppl) ◽

pp. 293-293

Author(s):

Florence Marteau ◽

Brooke Harrow ◽

Christine McCarthy ◽

Joel Wallace ◽

Alisha Monnette ◽

...

Keyword(s):

Renal Cell Carcinoma ◽

Cell Carcinoma ◽

Metastatic Renal Cell Carcinoma ◽

Real World ◽

Renal Cell ◽

Response Rate ◽

Checkpoint Inhibitors ◽

P Value ◽

The Real ◽

The Us

293 Background: Checkpoint inhibitors (CPIs) are a treatment option for patients with metastatic renal cell carcinoma (mRCC), but there is limited clinical data on the efficacy of targeted therapies following CPI treatment. Cabozantinib is a tyrosine kinase inhibitor (TKI) that targets multiple receptor kinases implicated in tumorigenesis. In the US, cabozantinib is approved for use in patients with advanced RCC including after CPI treatment. Methods: This retrospective observational cohort study (NCT04353765) evaluated outcomes associated with cabozantinib or other TKIs (axitinib, lenvatinib, pazopanib, sorafenib, sunitinib) in patients with mRCC following CPI treatment. Eligible patients initiated TKI therapy between May 1, 2016 and Sep 31, 2019 and had received a CPI as their last systemic treatment prior to TKI therapy. Patients were identified from the US Oncology Network iKnowMed electronic health record database through structured queries and a targeted chart review. The following real-world outcomes were assessed: 6-month response rate (RR6months; primary); overall response rate (ORR); overall survival (OS); time to treatment discontinuation (TTD); rates of dose reductions, and discontinuation due to adverse events (AEs). The p value for RR6months was used to test for non-inferiority. Results: Eligible patients ( n = 247) had a mean (SD) age of 65.9 (10.5) years and 74.1% were male; 75.7% ( n = 187) received cabozantinib and 24.3% ( n = 60) received other TKIs. All patients had intermediate or poor MSKCC score; more poor-risk patients received cabozantinib than other TKIs (28.9% vs 20%). Outcomes data are shown in the Table. Compared with other TKIs, cabozantinib was associated with a significantly higher RR6months and ORR, and TTD was twice as long with cabozantinib. Discontinuation due to AEs was more frequent with other TKIs than with cabozantinib, although this was not statistically significant; 21.7% of discontinuations occurred during the first 3 months of treatment. AEs leading to discontinuation were consistent with the known safety profile of the products. Conclusions: In this mRCC population receiving routine care in the US, cabozantinib was used more frequently than other TKIs after CPI treatment. Cabozantinib was an effective and well tolerated option post-CPI, with a high response rate in the real-world setting.abozantinib was associated with a significantly higher response rate and a lower discontinuation rate due to AEs; TTD was double that of other TKIs. [Table: see text]

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