Proposed minimum information guideline for kidney disease—research and clinical data reporting: a cross-sectional study

Objective This project aimed to develop and propose a standardised reporting guideline for kidney disease research and clinical data reporting, in order to improve kidney disease data quality and integrity, and combat challenges associated with the management and challenges of ‘Big Data’. Methods A list of recommendations was proposed for the reporting guideline based on the systematic review and consolidation of previously published data collection and reporting standards, including PhenX measures and Minimal Information about a Proteomics Experiment (MIAPE). Thereafter, these recommendations were reviewed by domain-specialists using an online survey, developed in Research Electronic Data Capture (REDCap). Following interpretation and consolidation of the survey results, the recommendations were mapped to existing ontologies using Zooma, Ontology Lookup Service and the Bioportal search engine. Additionally, an associated eXtensible Markup Language schema was created for the REDCap implementation to increase user friendliness and adoption. Results The online survey was completed by 53 respondents; the majority of respondents were dual clinician-researchers (57%), based in Australia (35%), Africa (33%) and North America (22%). Data elements within the reporting standard were identified as participant-level, study-level and experiment-level information, further subdivided into essential or optional information. Conclusion The reporting guideline is readily employable for kidney disease research projects, and also adaptable for clinical utility. The adoption of the reporting guideline in kidney disease research can increase data quality and the value for long-term preservation, ensuring researchers gain the maximum benefit from their collected and generated data. This is an open access article distributed in accordance with the Creative Commons Attribution Non Commercial (CC BY-NC 4.0) license, which permits others to distribute, remix, adapt, build upon this work non-commercially, and license their derivative works on different terms, provided the original work is properly cited, appropriate credit is given, any changes made indicated, and the use is non-commercial

Ten simple rules for providing effective bioinformatics research support.

Life scientists are increasingly turning to high-throughput sequencing technologies in their research programs, owing to the enormous potential of these methods. In a parallel manner, the number of core facilities that provide bioinformatics support are also increasing. Notably, the generation of complex large datasets has necessitated the development of bioinformatics support core facilities that aid laboratory scientists with cost-effective and efficient data management, analysis, and interpretation. In this article, we address the challenges-related to communication, good laboratory practice, and data handling-that may be encountered in core support facilities when providing bioinformatics support, drawing on our own experiences working as support bioinformaticians on multidisciplinary research projects. Most importantly, the article proposes a list of guidelines that outline how these challenges can be preemptively avoided and effectively managed to increase the value of outputs to the end user, covering the entire research project lifecycle, including experimental design, data analysis, and management (i.e., sharing and storage). In addition, we highlight the importance of clear and transparent communication, comprehensive preparation, appropriate handling of samples and data using monitoring systems, and the employment of appropriate tools and standard operating procedures to provide effective bioinformatics support

The H3ABioNet helpdesk: an online bioinformatics resource, enhancing Africa’s capacity for genomics research

Abstract Background Currently, formal mechanisms for bioinformatics support are limited. The H3Africa Bioinformatics Network has implemented a public and freely available Helpdesk (HD), which provides generic bioinformatics support to researchers through an online ticketing platform. The following article reports on the H3ABioNet HD (H3A-HD)‘s development, outlining its design, management, usage and evaluation framework, as well as the lessons learned through implementation. Results The H3A-HD evaluated using automatically generated usage logs, user feedback and qualitative ticket evaluation. Evaluation revealed that communication methods, ticketing strategies and the technical platforms used are some of the primary factors which may influence the effectivity of HD. Conclusion To continuously improve the H3A-HD services, the resource should be regularly monitored and evaluated. The H3A-HD design, implementation and evaluation framework could be easily adapted for use by interested stakeholders within the Bioinformatics community and beyond

African Genomic Medicine Portal: A Web Portal for Biomedical Applications

Genomics data are currently being produced at unprecedented rates, resulting in increased knowledge discovery and submission to public data repositories. Despite these advances, genomic information on African-ancestry populations remains significantly low compared with European- and Asian-ancestry populations. This information is typically segmented across several different biomedical data repositories, which often lack sufficient fine-grained structure and annotation to account for the diversity of African populations, leading to many challenges related to the retrieval, representation and findability of such information. To overcome these challenges, we developed the African Genomic Medicine Portal (AGMP), a database that contains metadata on genomic medicine studies conducted on African-ancestry populations. The metadata is curated from two public databases related to genomic medicine, PharmGKB and DisGeNET. The metadata retrieved from these source databases were limited to genomic variants that were associated with disease aetiology or treatment in the context of African-ancestry populations. Over 2000 variants relevant to populations of African ancestry were retrieved. Subsequently, domain experts curated and annotated additional information associated with the studies that reported the variants, including geographical origin, ethnolinguistic group, level of association significance and other relevant study information, such as study design and sample size, where available. The AGMP functions as a dedicated resource through which to access African-specific information on genomics as applied to health research, through querying variants, genes, diseases and drugs. The portal and its corresponding technical documentation, implementation code and content are publicly available

African Genomic Medicine Portal: A Web Portal for Biomedical Applications

Genomics data are currently being produced at unprecedented rates, resulting in increased knowledge discovery and submission to public data repositories. Despite these advances, genomic information on African-ancestry populations remains significantly low compared with European- and Asian-ancestry populations. This information is typically segmented across several different biomedical data repositories, which often lack sufficient fine-grained structure and annotation to account for the diversity of African populations, leading to many challenges related to the retrieval, representation and findability of such information. To overcome these challenges, we developed the African Genomic Medicine Portal (AGMP), a database that contains metadata on genomic medicine studies conducted on African-ancestry populations. The metadata is curated from two public databases related to genomic medicine, PharmGKB and DisGeNET. The metadata retrieved from these source databases were limited to genomic variants that were associated with disease aetiology or treatment in the context of African-ancestry populations. Over 2000 variants relevant to populations of African ancestry were retrieved. Subsequently, domain experts curated and annotated additional information associated with the studies that reported the variants, including geographical origin, ethnolinguistic group, level of association significance and other relevant study information, such as study design and sample size, where available. The AGMP functions as a dedicated resource through which to access African-specific information on genomics as applied to health research, through querying variants, genes, diseases and drugs. The portal and its corresponding technical documentation, implementation code and content are publicly available

GA4GH: International policies and standards for data sharing across genomic research and healthcare.

The Global Alliance for Genomics and Health (GA4GH) aims to accelerate biomedical advances by enabling the responsible sharing of clinical and genomic data through both harmonized data aggregation and federated approaches. The decreasing cost of genomic sequencing (along with other genome-wide molecular assays) and increasing evidence of its clinical utility will soon drive the generation of sequence data from tens of millions of humans, with increasing levels of diversity. In this perspective, we present the GA4GH strategies for addressing the major challenges of this data revolution. We describe the GA4GH organization, which is fueled by the development efforts of eight Work Streams and informed by the needs of 24 Driver Projects and other key stakeholders. We present the GA4GH suite of secure, interoperable technical standards and policy frameworks and review the current status of standards, their relevance to key domains of research and clinical care, and future plans of GA4GH. Broad international participation in building, adopting, and deploying GA4GH standards and frameworks will catalyze an unprecedented effort in data sharing that will be critical to advancing genomic medicine and ensuring that all populations can access its benefits

The role of DNA methylation in the aetiology of anxiety proneness in a cohort of South African adolescents: an exploratory study

Thesis (MSc)--Stellenbosch University, 2017.ENGLISH ABSTRACT: Anxiety disorders are a range of complex disorders characterised by abnormal anxiety in the absence of anxiety-provoking stimuli. The aetiology of anxiety disorders is attributed to interaction between genetic and environmental factors. It is crucial to identify and characterise risk factors that result in the development of anxiety disorders in adulthood. Anxiety proneness (AP) is one such risk factor and represents an endophenotype for anxiety disorders. Several studies have previously associated hypothalamic- pituitary- adrenal (HPA) axis related genes with anxiety disorder development, however these studies generally do not account for environmental contributors. Epigenetics provides a mechanism to study environment and gene interaction. DNA methylation is a well-studied epigenetic modification with the ability to influence gene expression. The present study aimed to investigate the role that genome-wide alterations in DNA methylation play in the development of AP by investigating South African adolescents who have experienced differing levels of childhood trauma (n = 63). The Illumina HumanMethylation450K BeadChip array was used to conduct genome-wide DNA methylation analysis on 46 individuals. EpiTYPER MassARRAY technology was used to verify selected differentially methylated genes from the initial analysis, as well as to analyse additional HPAaxis related genes. Several genes were found to be differentially methylated prior to correction for multiple testing, and the majority of these had designated brain functions. Additionally, a significant trend in methylation was observed in the promoter region of the serotonin transporter gene (SLC6A4). In conclusion, the current study indicates a role for the methylation of SLC6A4 in the development of AP in South African adolescents, however these results need to be replicated in a larger study sample.AFRIKAANSE OPSOMMING: Angsversteurings beskryf 'n verskeidenheid van komplekse siektes wat gekenmerk word deur abnormale angs in die afwesigheid van angs uitdagende stimuli. Die etiologie van angsversteurings word toegeskryf aan die interaksie tussen genetiese- en omgewings faktore. Daarom is dit noodsaaklik om risiko faktore wat lei tot die ontwikkeling van volwasse angsversteurings te identifiseer. Angs geneigheid verteenwoordig een van hierdie sogenoemde risiko faktore. Angs geneigheid verteenvoordig 'n angsversteurings endofenotipe wat in die huidige studie ondersoek word. Verskeie studies het voorheen hipotalamus-pituïtêre-adrenale siklus (HPA) verwante gene met die ontwikkeling van angsversteurings assosieer. Oor die algemeen, neem hierdie studies egter nie die bydrae van omgewings faktore in ag tydens analise nie. Epigenetika bied 'n metode om die interaksie tussen genetiese en omgewings faktore te bestudeer. DNS-metilering is 'n goed-bestudeerde epigenetiese modifikasie met die vermoë om geenuitdrukking te beïnvloed. Die huidige studie het ten doel om die rol wat genoom-wye veranderinge in DNS-metilering in die ontwikkeling van AP speel te ondersoek. Hierdie doel was bereik deur Suid-Afrikaanse tieners wat verskeie vlakke van trauma ervaar het tydens hul kinderjare, te ondersoek (N = 63). Die Illumina HumanMethylation450K BeadChip tegnologie is gebruik om genoom-wye DNS-metilering analise uit te voer op 46 individuele. Daarbenewens is die EpiTYPER MassARRAY tegnologie gebruik om selektiewe differensieël gemetileerde gene vanaf die aanvanklike ontleding te verifieer asook bykomende HPAverwante gene te analiseer. Verskeie differensieel gemetileerde gene was identifiseer voor statistiese korreksie vir veelvuldige toetsing. Die meerderheid hiervan besit toegeskrewe breinfunksies. Daarbenewens was 'n beduidende neiging in metilering ook waargeneem in die promotor streek van die serotonien karweier geen (SLC6A4). Ten slotte, dui die huidige studie op 'n moontlike rol vir die metilering van SLC6A4 in die ontwikkeling van AP in Suid-Afrikaanse tieners. Hierdie resultate moet egter herhaal word in 'n groter studie monster

Ten simple rules for providing effective bioinformatics research support.

Life scientists are increasingly turning to high-throughput sequencing technologies in their research programs, owing to the enormous potential of these methods. In a parallel manner, the number of core facilities that provide bioinformatics support are also increasing. Notably, the generation of complex large datasets has necessitated the development of bioinformatics support core facilities that aid laboratory scientists with cost-effective and efficient data management, analysis, and interpretation. In this article, we address the challenges-related to communication, good laboratory practice, and data handling-that may be encountered in core support facilities when providing bioinformatics support, drawing on our own experiences working as support bioinformaticians on multidisciplinary research projects. Most importantly, the article proposes a list of guidelines that outline how these challenges can be preemptively avoided and effectively managed to increase the value of outputs to the end user, covering the entire research project lifecycle, including experimental design, data analysis, and management (i.e., sharing and storage). In addition, we highlight the importance of clear and transparent communication, comprehensive preparation, appropriate handling of samples and data using monitoring systems, and the employment of appropriate tools and standard operating procedures to provide effective bioinformatics support

Consent codes: Maintaining consent in an ever-expanding open science ecosystem

We previously proposed a structure for recording consent-based data use 'categories' and 'requirements' - Consent Codes - with a view to supporting maximum use and integration of genomic research datasets, and reducing uncertainty about permissible re-use of shared data. Here we discuss clarifications and subsequent updates to the Consent Codes (v4) based on new areas of application (e.g., the neurosciences, biobanking, H3Africa), policy developments (e.g., return of research results), and further practical considerations, including developments in automated approaches to consent management.SOMD, SD, ACE and JK were supported by The Neuro Tanenbaum Open Science Institute, the Canadian Open Neuroscience Platform (funded in part by Brain Canada), and McGill Healthy Brains for Healthy Lives. NM and LZ are funded by the NIH under grant number U24HG006941. MM is funded by EUH2020 CINECA grant number 825775. NM, VN and NSM are funded by the NHLBI award number U24HL135600. JDS and GK are funded by the Wellcome Trust grant 360G-Wellcome-201535_Z_16_Z and previously the EU H2020 Corbel grant number 645248