ABSTRACT
The European Nucleotide Archive (ENA, https://www.ebi.ac.uk/ena), maintained at the European Molecular Biology Laboratory's European Bioinformatics Institute (EMBL-EBI) provides freely accessible services, both for deposition of, and access to, open nucleotide sequencing data. Open scientific data are of paramount importance to the scientific community and contribute daily to the acceleration of scientific advance. Here, we outline the major updates to ENA's services and infrastructure that have been delivered over the past year.
Subject(s)
Computational Biology , Databases, Nucleic Acid , Nucleotides/genetics , Software , High-Throughput Nucleotide Sequencing , Humans , Internet , Molecular Sequence Annotation , Nucleotides/classificationABSTRACT
The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) pandemic will be remembered as one of the defining events of the 21st century. The rapid global outbreak has had significant impacts on human society and is already responsible for millions of deaths. Understanding and tackling the impact of the virus has required a worldwide mobilisation and coordination of scientific research. The COVID-19 Data Portal (https://www.covid19dataportal.org/) was first released as part of the European COVID-19 Data Platform, on April 20th 2020 to facilitate rapid and open data sharing and analysis, to accelerate global SARS-CoV-2 and COVID-19 research. The COVID-19 Data Portal has fortnightly feature releases to continue to add new data types, search options, visualisations and improvements based on user feedback and research. The open datasets and intuitive suite of search, identification and download services, represent a truly FAIR (Findable, Accessible, Interoperable and Reusable) resource that enables researchers to easily identify and quickly obtain the key datasets needed for their COVID-19 research.
Subject(s)
Biomedical Research , COVID-19 , Databases, Factual , Datasets as Topic , Information Dissemination , Open Access Publishing , SARS-CoV-2 , COVID-19/epidemiology , COVID-19/genetics , COVID-19/virology , Databases, Bibliographic , Disease Outbreaks , Humans , Pandemics , SARS-CoV-2/chemistry , SARS-CoV-2/genetics , SARS-CoV-2/metabolism , SARS-CoV-2/ultrastructure , Time Factors , Viral Proteins/chemistry , Viral Proteins/geneticsABSTRACT
INTRODUCTION: Various genome wide association studies have manifested that Major Histocompatibility Complex (MHC) region on chromosome 6p21 houses many potential candidate genes for asthma. OBJECTIVE: This Case-Control association study was planned to determine the association of 10 Single Nucleotide Polymorphisms (SNPs), residing within and around MHC genes' region on chromosome 6p21, with Asthma in Punjabi population of Lahore, Pakistan. METHODS: A total of 161 subjects, 61 physician-diagnosed asthma patients and 100 age-matched healthy controls, were recruited from Lahore, a city in Punjab. Ten single nucleotide polymorphisms (SNPs) (rs9378249, rs2070600, rs404860, rs6689, rs1049124, rs1063355, rs1049225, rs1049219, rs7773955 and rs928976) located within or near AGER, NOTCH and HLA genes in MHC region, were genotyped in both patients and controls using single base extension reaction and capillary electrophoresis-based genetic analyser. Statistical models were applied using SHEsis Plus. Results were adjusted for various cofactors (age, gender and environment) and by applying multiple corrections. Haplotype and linkage disequilibrium analyses were performed on Haploview software v4.1. RESULTS: Three of the studied SNPs rs1049124, rs1049219 and rs7773955 show independent significant association with asthma under allelic and genotypic models. Two of the haplotypes, H7 and H13, "CTAATTT" and "CCACTAT", respectively, for rs2070600, rs404860, rs6689, rs1049124, rs1063355, rs1049219 and rs7773955, are found to be significantly associated with the disease. CONCLUSION: This study reports association of SNP variants residing on HLA-DQB1 and HLA-DQA2 genes and haplotypes H7 and H13 on genomic region 6p21 with Asthma in the Punjabi population of Lahore, Pakistan.
Subject(s)
Asthma , Genes, MHC Class II , Genome-Wide Association Study , Asthma/epidemiology , Asthma/genetics , Genetic Predisposition to Disease , Humans , Pakistan , Polymorphism, Single NucleotideABSTRACT
The European Nucleotide Archive (ENA; https://www.ebi.ac.uk/ena), provided by the European Molecular Biology Laboratory's European Bioinformatics Institute (EMBL-EBI), has for almost forty years continued in its mission to freely archive and present the world's public sequencing data for the benefit of the entire scientific community and for the acceleration of the global research effort. Here we highlight the major developments to ENA services and content in 2020, focussing in particular on the recently released updated ENA browser, modernisation of our release process and our data coordination collaborations with specific research communities.
