Browse
Submit Data
Databases
API
Help

Dataset Information

16 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Best Practices for Preclinical In Vivo Testing of Cancer Nanomedicines.

ABSTRACT: Significant advances have been made in the development of nanoparticles for cancer treatment in recent years. Despite promising results in preclinical animal models, cancer nanomedicines often fail in clinical trials. This failure rate could be reduced by defining stringent criteria for testing and quality control during the design and development stages, and by performing carefully planned preclinical studies in relevant animal models. This article discusses best practices for the evaluation of nanomedicines in murine tumor models. First, a recommended set of experiments to perform is introduced, including discussion of the types of data to collect during these studies. This is followed by an outline of various tumor models and their clinical relevance. Next, different routes of nanoparticle administration are overviewed, followed by a summary of important controls to include in in vivo studies of nanomedicine. Finally, animal welfare considerations are discussed, and an overview of the steps involved in achieving US Food and Drug Administration approval after animal studies are completed is provided. Researchers should use this report as a guideline for effective preclinical evaluation of cancer nanomedicine. As the community adopts best practices for in vivo testing, the rate of clinical translation of cancer nanomedicines is likely to improve.

SUBMITTER: Valcourt DM

PROVIDER: S-EPMC7473451 | biostudies-literature |

REPOSITORIES: biostudies-literature

ACCESS DATA

Json Xml

Similar Datasets

Best practices for eCLIP experiments and analysis

Project description:This SuperSeries is composed of the SubSeries listed below.

2018-06-08 | GSE107768 | GEO

Best practices for eCLIP experiments and analysis [poor quality]

Project description:Enhanced cross-linking immunoprecipitation (eCLIP) featuring a size-matched input control has been recently applied to profile the binding sites of more than one hundred RNA binding proteins (RBPs). However computational pipelines and quality control metrics needed to process CLIP data at scale have yet to be well defined. Here, we describe our ENCODE eCLIP processing pipeline (https://github.com/YeoLab/eclip), enabling users to go from raw reads to processed peaks that are enriched above paired input, reproducible across biological replicates, and can be directly compared against the public ENCODE eCLIP resource. In particular, we discuss processing steps designed to address common artifacts, including properly quantifying unique RNA fragments bound by both unique genomic- and repetitive element-mapped reads. Using manual quality annotation of 350 ENCODE eCLIP experiments, we develop metrics for quality assessment of eCLIP experiments prior to and after sequencing, including library yield, number of unique fragments in the library, total binding relative information, and biological reproducibility. In particular, we quantify the commonly believed linkage between depth of sequencing and peak discovery, and derive methods for estimating required sequencing depth based on pre-sequencing metrics. Finally we provide recommendations for the common question of integrating RBP binding information with RNA-seq to generate splicing maps representing the positional effect of binding on alternative splicing. These pipelines and QC metrics enable large-scale processing and analysis of eCLIP data, and will help to standardize rigorous analysis of RBP binding data.

2018-06-08 | GSE107767 | GEO

Best practices for eCLIP experiments and analysis [uncertain quality]

2018-06-08 | GSE107766 | GEO

Best practices for differential accessibility analysis in single-cell epigenomics

Project description:This submission is a dataset of single-nucleus multi-omics of uninjured and injured spinal cords of mice harvested and profiled using 10x Multiome ATAC + Gene Expression kit.

2024-04-30 | GSE230765 | GEO

Best practices for the visualization, mapping, and manipulation of R-loops

Project description:R-loops represent an abundant class of large non-B DNA structures in genomes. Even though they form transiently and at modest frequencies, interfering with R-loop formation or dissolution significantly impacts genome stability. Addressing the mechanism(s) of R-loop-mediated genome destabilization requires a precise characterization of their distribution in genomes. A number of independent methods have been developed to visualize and map R-loops, but their results are at times discordant, leading to confusion. Here we review the main existing methodologies underlying R-loop mapping and assess their limitations and the robustness of existing datasets. We offer a set of best practices to improve the reproducibility of maps, hoping that such guidelines could be useful for authors and referees alike. Finally, we offer a possible resolution to the apparent contradictions in R-loop mapping outcomes between antibody-based and RNase H1-based mapping approaches.

2021-02-24 | GSE158480 | GEO

Survey of renin and aldosterone testing practices by Ontario laboratories - Providing insight into best practices.

Project description:ObjectivesTesting for renin and aldosterone in clinical laboratories is complicated by pre-analytical considerations such as the posture for blood collection and susceptibility to cryoactivation of renin. From an analytical perspective, there are both renin activity and renin mass or concentration assays available. There can also be variability in result reporting practices and the aldosterone-renin ratio (ARR) cut-off applied to screen for primary aldosteronism (PA). The Institute for Quality Management in Healthcare (IQMH) Centre for Proficiency Testing surveyed laboratories on their handling of renin and aldosterone testing to better understand current practices.Design and methodsAn online survey was prepared and sent to 134 Canadian laboratories enrolled in endocrinology proficiency testing with IQMH.ResultsOne hundred twenty Ontario laboratories submitted responses. While only six (5%) laboratories perform testing for both renin and aldosterone, 108 (90%) collect and process specimens to be tested by reference laboratories. The survey revealed considerable variation in practices including the recommended state of patients prior to sample collection (for example, regarding medications or salt intake), the patient posture specifications for sample collection, the precautions taken against cryoactivation of renin, the choice of renin activity or mass assay, and the ARR cut-off used. The available literature on these factors was then reviewed.ConclusionsAlthough there is no standardized procedure for specimen collection, analysis, or result reporting for renin or aldosterone testing, we have attempted to summarize the available literature to develop evidence-based recommendations. Where laboratory practice differs from peers and/or recommended protocols, laboratories should review their practices.

| S-EPMC8145751 | biostudies-literature

Recommendations for Benchmarking Preclinical Studies of Nanomedicines.

Project description:Nanoparticle-based delivery systems provide new opportunities to overcome the limitations associated with traditional small-molecule drug therapy for cancer and to achieve both therapeutic and diagnostic functions in the same platform. Preclinical trials are generally designed to assess therapeutic potential and not to optimize the design of the delivery platform. Consequently, progress in developing design rules for cancer nanomedicines has been slow, hindering progress in the field. Despite the large number of preclinical trials, several factors restrict comparison and benchmarking of different platforms, including variability in experimental design, reporting of results, and the lack of quantitative data. To solve this problem, we review the variables involved in the design of preclinical trials and propose a protocol for benchmarking that we recommend be included in in vivo preclinical studies of drug-delivery platforms for cancer therapy. This strategy will contribute to building the scientific knowledge base that enables development of design rules and accelerates the translation of new technologies.

| S-EPMC4592474 | biostudies-literature

Consensus and controversies in best practices for molecular genetic testing of spinocerebellar ataxias.

Project description:Many laboratories worldwide are offering molecular genetic testing for spinocerebellar ataxias (SCAs). This is essential for differential diagnosis and adequate genetic counselling. The European Molecular Genetics Quality Network (EMQN) started an SCA external quality assessment scheme in 2004. There was a clear need for updated laboratory guidelines. EMQN and EuroGentest organized a Best Practice (BP) meeting to discuss current practices and achieve consensus. A pre-meeting survey showed that 36 laboratories (20 countries) conducted nearly 18?000 SCA tests the year before, and identified issues to discuss. Draft guidelines were produced immediately after the meeting and discussed online for several months. The final version was endorsed by EMQN, and harmonized with guidelines from other oligonucleotide repeat disorders. We present the procedures taken to organize the survey, BP meeting, as well as drafting and approval of BP guidelines. We emphasize the most important recommendations on (1) pre-test requirements, (2) appropriate methodologies and (3) interpretation and reporting, and focus on the discussion of controversial issues not included in the final document. In addition, after an extensive review of scientific literature, and responding to recommendations made, we now produce information that we hope will facilitate the activities of diagnostic laboratories and foster quality SCA testing. For the main loci, this includes (1) a list of repeat sequences, as originally published; (2) primers in use; and (3) an evidence-based description of the normal and pathogenic repeat-size ranges, including those of reduced penetrance and those in which there is still some uncertainty. This information will be maintained and updated in http://www.scabase.eu.

| S-EPMC2987480 | biostudies-literature

Endophenotype best practices.

Project description:This review examines the current state of electrophysiological endophenotype research and recommends best practices that are based on knowledge gleaned from the last decade of molecular genetic research with complex traits. Endophenotype research is being oversold for its potential to help discover psychopathology relevant genes using the types of small samples feasible for electrophysiological research. This is largely because the genetic architecture of endophenotypes appears to be very much like that of behavioral traits and disorders: they are complex, influenced by many variants (e.g., tens of thousands) within many genes, each contributing a very small effect. Out of over 40 electrophysiological endophenotypes covered by our review, only resting heart, a measure that has received scant advocacy as an endophenotype, emerges as an electrophysiological variable with verified associations with molecular genetic variants. To move the field forward, investigations designed to discover novel variants associated with endophenotypes will need extremely large samples best obtained by forming consortia and sharing data obtained from genome wide arrays. In addition, endophenotype research can benefit from successful molecular genetic studies of psychopathology by examining the degree to which these verified psychopathology-relevant variants are also associated with an endophenotype, and by using knowledge about the functional significance of these variants to generate new endophenotypes. Even without molecular genetic associations, endophenotypes still have value in studying the development of disorders in unaffected individuals at high genetic risk, constructing animal models, and gaining insight into neural mechanisms that are relevant to clinical disorder.

| S-EPMC5219856 | biostudies-literature