ELIMU-MDx: A Web-Based, Open-Source Platform for Storage, Management and Analysis of Diagnostic qPCR Data

Krähenbühl, Silvan; Studer, Florian; Guirou, Etienne A; Deal, Anna; Mächler, Philipp; Hosch, Salome; Mpina, Maximilian; Mswata, Sarah; Daubenberger, Claudia; Schindler, Tobias

doi:10.2144/btn-2019-0064

Cited by 10 publications

(13 citation statements)

References 11 publications

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“…Kato-Katz results were calculated as mean egg counts of the two slides of each time point assessment (baseline day 1, baseline day 2, follow-up day 1 and follow-up day 2) and samples considered positive if at least 0.5 eggs per sample were identified. Data of the amplification curves were cleaned and standardised according to the standard curves with CFX Maestro ™ Software and then uploaded to ELIMU-MDx, an open-source platform for storage, management and analysis of diagnostic qPCR data [39]. Subsequent statistical analyses were conducted using Stata IC15 (StataCorp., College Station, TX).…”

Section: Data Preparationmentioning

confidence: 99%

Performance of the Kato-Katz method and real time polymerase chain reaction for the diagnosis of soil-transmitted helminthiasis in the framework of a randomised controlled trial: treatment efficacy and day-to-day variation

et al. 2020

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Background Accurate, scalable and sensitive diagnostic tools are crucial in determining prevalence of soil-transmitted helminths (STH), assessing infection intensities and monitoring treatment efficacy. However, assessments on treatment efficacy comparing traditional microscopic to newly emerging molecular approaches such as quantitative Polymerase Chain Reaction (qPCR) are scarce and hampered partly by lack of an established diagnostic gold standard. Methods We compared the performance of the copromicroscopic Kato-Katz method to qPCR in the framework of a randomized controlled trial on Pemba Island, Tanzania, evaluating treatment efficacy based on cure rates of albendazole monotherapy versus ivermectin-albendazole against Trichuris trichiura and concomitant STH infections. Day-to-day variability of both diagnostic methods was assessed to elucidate reproducibility of test results by analysing two stool samples before and two stool samples after treatment of 160 T. trichiura Kato-Katz positive participants, partially co-infected with Ascaris lumbricoides and hookworm, per treatment arm (n = 320). As negative controls, two faecal samples of 180 Kato-Katz helminth negative participants were analysed. Results Fair to moderate correlation between microscopic egg count and DNA copy number for the different STH species was observed at baseline and follow-up. Results indicated higher sensitivity of qPCR for all three STH species across all time points; however, we found lower test result reproducibility compared to Kato-Katz. When assessed with two samples from consecutive days by qPCR, cure rates were significantly lower for T. trichiura (23.2 vs 46.8%), A. lumbricoides (75.3 vs 100%) and hookworm (52.4 vs 78.3%) in the ivermectin-albendazole treatment arm, when compared to Kato-Katz. Conclusions qPCR diagnosis showed lower reproducibility of test results compared to Kato-Katz, hence multiple samples per participant should be analysed to achieve a reliable diagnosis of STH infection. Our study confirms that cure rates are overestimated using Kato-Katz alone. Our findings emphasize that standardized and accurate molecular diagnostic tools are urgently needed for future monitoring within STH control and/or elimination programmes.

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Section: Data Preparationmentioning

confidence: 99%

Performance of the Kato-Katz method and real time polymerase chain reaction for the diagnosis of soil-transmitted helminthiasis in the framework of a randomised controlled trial: treatment efficacy and day-to-day variation

et al. 2020

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“…Finally, ELIMU-MDx, is a web-based interface conceived to collect specific information regarding qPCR assays for diagnostic purposes. EILMU-MDx functions as a data management system, processes qPCR data generated using the absolute quantification method and requires an account and login information (Krahenbuhl et al, 2020).…”

Section: A Comparison Of Auto-qpcr Relative To Available To Qpcr Analmentioning

confidence: 99%

Auto-qPCR: A Python-based web app for automated and reproducible analysis of qPCR data

Maussion

Thomas

Demirova

et al. 2021

Preprint

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Quantifying changes in DNA and RNA levels is an essential component of any molecular biology toolkit. Quantitative real time PCR (qPCR) techniques, in both clinical and basic research labs, have evolved to become both routine and standardized. However, the analysis of qPCR data includes many steps that are time consuming and cumbersome, which can lead to mistakes and misinterpretation of data. To address this bottleneck, we have developed an open source software, written in Python, to automate the processing of csv output files from any qPCR machine, using standard calculations that are usually performed manually. Auto-qPCR is a tool that saves time when computing this type of data, helping to ensure standardization of qPCR experiment analyses. Unlike other software packages that process qPCR data, our web-based app (http://auto-q-pcr.com/) is easy to use and does not require programming knowledge or software installation. Additionally, we provide examples of four different data processing modes within one program: (1) cDNA quantification to identify genomic deletion or duplication events, (2) assessment of gene expression levels using an absolute model, (3) relative quantification, and (4) relative quantification with a reference sample. Auto-qPCR also includes options for statistical analysis of the data. Using this software, we performed analysis of differential gene expression following an initial data processing and provide graphs of the findings prepared through the Auto-qPCR program. Thus, our open access Auto-qPCR software saves the time of manual data analysis and provides a more systematic workflow, minimizing the risk of errors when done manually. Our program constitutes a new tool that can be incorporated into bioinformatic and molecular biology pipelines in clinical and research labs.

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“…The RT-qPCR cycling conditions were: 55 o C for 10 min, 95 o C for 1 min, 45 cycles at 95 o C for 15 sec and 55 o C for 1 min. The generated data were uploaded to an in-house available analysis platform where quanti cation cycle values (Cq) were calculated automatically [40]. HPgV viral quanti cation was done as described by Stapleton et al using in vitro transcribed (IVT) viral RNA [25].…”

Section: Rt-qpcr For Detection and Quanti Cation Of Hpgv-1 And Hpgv-2mentioning

confidence: 99%

Role of human Pegivirus infections in whole Plasmodium falciparum sporozoite vaccination and controlled human malaria infection in African volunteers

Tumbo

Schindler

Dangy

et al. 2021

Preprint

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Background: Diverse vaccination outcomes and protection levels among different populations pose a serious challenge to the development of an effective malaria vaccine. Co-infections are among many factors associated with immune dysfunction and sub-optimal vaccination outcomes. Chronic, asymptomatic viral infections can contribute to the modulation of vaccine efficacy through various mechanisms. Human Pegivirus-1 (HPgV-1) persists in immune cells thereby potentially modulating immune responses. We investigated whether Pegivirus infection influences vaccine-induced responses and protection in African volunteers undergoing whole P. falciparum sporozoites-based malaria vaccination and controlled human malaria infections (CHMI). Methods: HPgV-1 prevalence was quantified by RT-qPCR in plasma samples of 96 individuals before, post vaccination with PfSPZ Vaccine and after CHMI in cohorts from Tanzania and Equatorial Guinea. The impact of HPgV-1 infection was evaluated on (1) systemic cytokine and chemokine levels measured by Luminex, (2) PfCSP-specific antibody titers quantified by ELISA, (3) asexual blood-stage parasitemia pre-patent periods and parasite multiplication rates, (4) HPgV-1 RNA levels upon asexual blood-stage parasitemia induced by CHMI.Results: The prevalence of HPgV-1 was 29.2% (28/96) and sequence analysis of the 5' UTRand E2 regions revealed the predominance of genotypes 1, 2 and 5. HPgV-1 infection was associated with elevated systemic levels of IL-2 and IL-17A. Comparable vaccine-induced anti-PfCSP antibody titers, asexual blood-stage multiplication rates and pre-patent periods were observed in HPgV-1 positive and negative individuals. However, a tendency for higher protection levels was detected in the HPgV-1 positive group (62.5%) compared to the negative one (51.6%) following CHMI. HPgV-1 viremia levels were not significantly altered after CHMI. Conclusions: HPgV-1 infection did not alter PfSPZ Vaccine elicited levels of PfCSP-specific antibody responses and parasite multiplication rates. Ongoing HPgV-1 infection appears to improve to some degree protection against CHMI in PfSPZ-vaccinated individuals. This is likely through modulation of immune system activation and systemic cytokines as higher levels of IL-2 and IL17A were observed in HPgV-1 infected individuals. CHMI is safe and well tolerated in HPgV-1 infected individuals. Identification of cell types and mechanisms of both silent and productive infection in individuals will help to unravel the biology of this widely present but largely under-researched virus.

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ELIMU-MDx: A Web-Based, Open-Source Platform for Storage, Management and Analysis of Diagnostic qPCR Data

Cited by 10 publications

References 11 publications

Performance of the Kato-Katz method and real time polymerase chain reaction for the diagnosis of soil-transmitted helminthiasis in the framework of a randomised controlled trial: treatment efficacy and day-to-day variation

Performance of the Kato-Katz method and real time polymerase chain reaction for the diagnosis of soil-transmitted helminthiasis in the framework of a randomised controlled trial: treatment efficacy and day-to-day variation

Auto-qPCR: A Python-based web app for automated and reproducible analysis of qPCR data

Role of human Pegivirus infections in whole Plasmodium falciparum sporozoite vaccination and controlled human malaria infection in African volunteers

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