Disease and Phenotype Data at Ensembl

Spudich, Giulietta; Fernández‐Suárez, Xosé M.

doi:10.1002/0471142905.hg0611s69

Cited by 4 publications

(1 citation statement)

References 54 publications

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“…GTEx offers various tools for searching gene, variant, and tissue-related databases with molecular genomic and phenotypic datasets (Stanfill & Cao, 2021). Additionally, the Ensembl Genome Browser is a single-scale genomic data entry with a graphical user interface that incorporates OMIM, dbSNP, and the NHGRI GWAS catalog (Spudich & Fernandez-Suarez, 2012). The Ensembl Genome Browser provides comprehensive human genome annotation data from various sources, facilitating biomedical analysis and understanding of their relationships with human genetic diseases.…”

Section: Figure 3 Expression Of the Tnfrsf1b Gene In Human Body Tissuesmentioning

confidence: 99%

UTILIZING A GENOMIC DATABASE FOR IDENTIFYING GENOMIC VARIATION FOR SARS-CoV-2 RECEPTORS

Rezadhini

Irham

Puspitaningrum

et al. 2023

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Coronavirus disease 2019 (COVID-19) is a severe acute respiratory syndrome caused by the coronavirus SARS-CoV-2. This disease progresses through different stages, and its common symptoms include fever, malaise, dry cough, dyspnea, and pneumonia. Since its discovery in Wuhan, Hubei, China, in December 2019, SARS-CoV-2 transmission has rapidly spread. Unfortunately, the number of cases is increasing beyond expectations, making the spread of confirmed COVID-19 cases easier. To detect specific symptoms in a large population, the relationship between gene variants and patients with COVID-19 can be determined. The data of COVID-19 variations can be obtained from the Ensembl Genome Browser. Herein, the gene associated with 19 variants was selected according to the Haploreg 4.1 version. Additionally, protein expression of missense genes variants using the GTEx portal to determine 2 selected variants: rs200553089 encode the TLR7 gene and rs1061622 encode the TNFRSF1B gene, respectively. The highest protein expression of the TLR7 gene is found in lymphocyte cells, while TNFRSF1B shows the highest expression in the whole blood system. According to the data obtained from the Ensembl Genome Browser, the two most prevalent populations for SNP rs19085059, which is associated with the GPHN gene, are in Africa and East Asia, while SNP rs74956615, linked to the RAVER1 gene, is most prevalent in East Asia. The allele frequency for the TLR7 gene cannot be found in five countries, except in America. Keywords: COVID-19, SARS-CoV-2, Single nucleotide polymorphism, Variants.

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Section: Figure 3 Expression Of the Tnfrsf1b Gene In Human Body Tissuesmentioning

confidence: 99%

UTILIZING A GENOMIC DATABASE FOR IDENTIFYING GENOMIC VARIATION FOR SARS-CoV-2 RECEPTORS

Rezadhini

Irham

Puspitaningrum

et al. 2023

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Reporting of Clinical Genome Sequencing Results

2018

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High-throughput sequencing and high-performance computing technologies have become powerful tools in clinical genetic diagnosis of hereditary disorders and genetic screening of healthy individuals to provide information for the diagnosis, treatment, and prevention of diseases or impairment and assessment of health. For patients with undiagnosed disorders, including many rare disorders, the whole-genome sequencing (WGS) test may end the diagnostic odyssey, ultimately guiding clinical care for them and their families. A clinical WGS test relies on high-quality genome-sequencing data as well as sophisticated data-interpretation approaches. Results are returned to the ordering physician in a concise report featuring an overall test result and in-depth phenotype-driven interpretation of the known or plausible genetic explanation of test indications. Patients have the option to decide whether the report should include secondary and incidental findings. Protocols and templates for reporting clinical WGS results and supplementary information are described in this article. © 2018 by John Wiley & Sons, Inc.

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Deciphering the complexities of human diseases and disorders by coupling induced‐pluripotent stem cells and systems genetics

Chang

Garcha²,

Manias

et al. 2012

WIREs Mechanisms of Disease

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The recent discovery that adult mouse and human somatic cells can be ‘reprogrammed’ to a state of pluripotency by ectopic expression of only a few transcription factors has already made a major impact on the biomedical community. For the first time, it is possible to study diseases on an individual patient basis, which may eventually lead to the realization of personalized medicine. The utility of induced‐pluripotent stem cells (iPSCs) for modeling human diseases has greatly benefitted from established human embryonic stem cell (ESC) differentiation and tissue engineering protocols developed to generate many different cell and tissue types. The limited access to preimplantation genetic tested embryos and the difficulty in gene targeting human ESCs have restricted the use of human ESCs in modeling human disease. Afforded by iPSC technology is the ability to study disease pathogenesis as it unfolds during tissue morphogenesis. The complexities of molecular signaling and interplay with protein transduction during disease progression necessitate a systems approach to studying human diseases, whereby data can be statistically integrated by sorting out the signal to noise issues that arise from global biological changes associated with disease versus experimental noise. Using a systems approach, biomarkers can be identified that define the initiation or progression of disease and likewise can serve as putative therapeutic targets. WIREs Syst Biol Med 2012 doi: 10.1002/wsbm.1170This article is categorized under: Models of Systems Properties and Processes > Cellular Models Laboratory Methods and Technologies > Genetic/Genomic Methods Translational, Genomic, and Systems Medicine > Translational Medicine

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Disease and Phenotype Data at Ensembl

Cited by 4 publications

References 54 publications

UTILIZING A GENOMIC DATABASE FOR IDENTIFYING GENOMIC VARIATION FOR SARS-CoV-2 RECEPTORS

UTILIZING A GENOMIC DATABASE FOR IDENTIFYING GENOMIC VARIATION FOR SARS-CoV-2 RECEPTORS

Reporting of Clinical Genome Sequencing Results

Deciphering the complexities of human diseases and disorders by coupling induced‐pluripotent stem cells and systems genetics

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