Project description:The Human Cytochrome P450 (CYP) Allele Nomenclature Database, a critical resource for the pharmacogenetics and genomics communities, has transitioned to the Pharmacogene Variation (PharmVar) Consortium. In this report we provide a summary of the current database, provide an overview of the PharmVar consortium, and highlight the PharmVar database which will serve as the new home for pharmacogene nomenclature.

| S-EPMC5836850 | biostudies-literature

Exploratory pharmacogene variation in Ghanaian population

Project description:Genetic variations in drug metabolising enzymes play a role in how individuals respond to drugs. Pharmacogene variation data in the Ghanaian population is limited and this study looks at exploring common variations that exist in our population for commonly used drugs. Samples were validated with PCR-RFLP for accuracy

2023-11-22 | GSE232865 | GEO

NIDDK International IBD Genetics Consortium Repository Global Screening Array

Project description:NIDDK International IBD Genetics Consortium Repository Global Screening Array

| PRJNA695808 | ENA

NIDDK International IBD Genetics Consortium Repository Global Screening Array

Project description:NIDDK International IBD Genetics Consortium Repository Global Screening Array

| PRJNA695809 | ENA

Exploratory pharmacogene variation in Ghanaian population

Project description:Exploratory pharmacogene variation in Ghanaian population

| PRJNA974254 | ENA

PlasmoView: a web-based resource to visualise global Plasmodium falciparum genomic variation.

Project description:Malaria is a global public health challenge, with drug resistance a major barrier to disease control and elimination. To meet the urgent need for better treatments and vaccines, a deeper knowledge of Plasmodium biology and malaria epidemiology is required. An improved understanding of the genomic variation of malaria parasites, especially the most virulent Plasmodium falciparum (Pf) species, has the potential to yield new insights in these areas. High-throughput sequencing and genotyping is generating large amounts of genomic data across multiple parasite populations. The resulting ability to identify informative variants, particularly single-nucleotide polymorphisms (SNPs), will lead to the discovery of intra- and inter-population differences and thus enable the development of genetic barcodes for diagnostic assays and clinical studies. Knowledge of genetic variability underlying drug resistance and other differential phenotypes will also facilitate the identification of novel mutations and contribute to surveillance and stratified medicine applications. The PlasmoView interactive web-browsing tool enables the research community to visualise genomic variation and annotation (eg, biological function) in a geographic setting. The first release contains over 600,000 high-quality SNPs in 631 Pf isolates from laboratory strains and four malaria-endemic regions (West Africa, East Africa, Southeast Asia and Oceania).

| S-EPMC4017360 | biostudies-literature

Resource profile and user guide of the Polygenic Index Repository.

Project description:Polygenic indexes (PGIs) are DNA-based predictors. Their value for research in many scientific disciplines is growing rapidly. As a resource for researchers, we used a consistent methodology to construct PGIs for 47 phenotypes in 11 datasets. To maximize the PGIs' prediction accuracies, we constructed them using genome-wide association studies-some not previously published-from multiple data sources, including 23andMe and UK Biobank. We present a theoretical framework to help interpret analyses involving PGIs. A key insight is that a PGI can be understood as an unbiased but noisy measure of a latent variable we call the 'additive SNP factor'. Regressions in which the true regressor is this factor but the PGI is used as its proxy therefore suffer from errors-in-variables bias. We derive an estimator that corrects for the bias, illustrate the correction, and make a Python tool for implementing it publicly available.

| S-EPMC8678380 | biostudies-literature

<i>rbcL</i> gene in global molecular data repository.

Project description:The ribulose-bisphosphate carboxylase (rbcL) gene sequence data in the molecular data repository has been increasing significantly, over the years with contributions from different parts of the world. The abundance of the gene has enhanced its applications in several ways. Bulk records were obtained from National Center for Biotechnology Information (NCBI) GenBank database using the entrez efetch utility as implemented in the Biopython package version 1.77. Records corresponding to the following keywords "rbcL AND plants [filter] AND biomol_genomic [PROP] AND is _nuccore [filter]" were created. Generated records were cleaned and then further analysed using the code file in the supplementary materials. Country information was obtained by searching reference information for matches to countries present in the pycountry package. Where no match was found, null was returned. This data article contains information about the plant family and species whose rbcL gene sequence has been deposited on the NCBI and regions of the world that has contributed to the rbcL repository growth. This data can be used to analyse the intra and inter family relatedness of plant and compare with existing relationships the molecular characterization of plants, evolutionary relationship studies, inferring biogeography origin of plant.

| S-EPMC8987485 | biostudies-literature

ProteomeScout: a repository and analysis resource for post-translational modifications and proteins.

Project description:ProteomeScout (https://proteomescout.wustl.edu) is a resource for the study of proteins and their post-translational modifications (PTMs) consisting of a database of PTMs, a repository for experimental data, an analysis suite for PTM experiments, and a tool for visualizing the relationships between complex protein annotations. The PTM database is a compendium of public PTM data, coupled with user-uploaded experimental data. ProteomeScout provides analysis tools for experimental datasets, including summary views and subset selection, which can identify relationships within subsets of data by testing for statistically significant enrichment of protein annotations. Protein annotations are incorporated in the ProteomeScout database from external resources and include terms such as Gene Ontology annotations, domains, secondary structure and non-synonymous polymorphisms. These annotations are available in the database download, in the analysis tools and in the protein viewer. The protein viewer allows for the simultaneous visualization of annotations in an interactive web graphic, which can be exported in Scalable Vector Graphics (SVG) format. Finally, quantitative data measurements associated with public experiments are also easily viewable within protein records, allowing researchers to see how PTMs change across different contexts. ProteomeScout should prove useful for protein researchers and should benefit the proteomics community by providing a stable repository for PTM experiments.

| S-EPMC4383955 | biostudies-literature

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