What is dbGaP used for?

Database of Genotype and Phenotype (dbGaP) refers to NIH maintained database of datasets and was developed to archive and distribute the results of studies that have investigated the interaction of genotype and phenotype. dbGaP provides two types of data – open access and controlled access.

How do I access dbGaP?

A dbGaP Data Access Application after logging into the NCBI dbGaP website (www.ncbi.nlm.nih.gov) using their eRA Commons account. After selecting the desired data sets and completing all requested information, the Investigator must then submit the application for Signing Official (SO) approval.

How do I download data from dbGaP?

To download non-SRA data, go to the “Phenotype and Genotype files” sub-tab and click on the “dbGaP File Selector” link. To download SRA data, go to the “SRA data (reads and reference alignments)” sub-tab and click on the “SRA RUN Selector” link. Wait until the page loading is complete.

What is genotype data?

Overview. Genotyping is the process of determining the DNA sequence, called a genotype, at specific positions within the genome of an individual. Sequence variations can be used as markers in linkage and association studies to determine genes relevant to specific traits or disease.

What is controlled access data?

While stripped of direct patient identifiers as defined by HIPAA, controlled-access data contain specific demographic, clinical, and genotypic information that are excluded in open-access data. Controlled-access data are unique and valuable to research projects for which open-access data are insufficient.

What is phenotypic data?

Phenotypic data are all kinds of clinical information regarding patients’ disease symptoms, as well as relevant demographic data, such as age, ethnicity and sex. This type of information is collected and stored by patient registries and biobanks.

How do I access my TCGA data?

Commonly requested files such as descriptions of somatic mutations or clinical data are open access. Please go to this page: https://tcga-data.nci.nih.gov/docs/publications/ to access all data associated with TCGA tumor specific publications.

How do I access Tcga?

Popular Answers (1)

1. Connect to https://tcga-data.nci.nih.gov/tcga/
2. Select the cancer subtype you are interested in (i.e breast invasive carcinoma)
3. Select mRNA.
4. Now you can see a table where rows are representing different patients.

How do I download SRA run selector?

Download sequence data from the Run Browser

1. Open the selected run in the Run Browser .
2. Click the Reads tab.
3. Find certain reads by applying a Filter or leave the Filter field empty.
4. Click on the Filtered Download button.
5. Select available download format and click Download link.

What data is in dbGaP?

The information contained in dbGaP includes individual-level molecular and phenotype data, analysis results, medical images, general information about the study and documents that contextualize phenotypic variables, such as research protocols and questionnaires.

What are the 3 types of phenotypes?

Polygenic inheritance can be explained by additive effects of many loci: if each “capital” allele contributes one increment to the phenotype. With one locus and additive effects we have three phenotypic classes: AA, Aa and aa.

What is A phenotype test?

Drug resistance testing allows clinicians to evaluate a patient’s viral resistance profile with confidence by showing which drugs are suitable to use for treatment and which drugs should be avoided.

How do I get RNA Seq data?

You can download the FASTQ files using the sra-toolkit, and some of the records also have links to the GEO databases cited by Albolfazi Bahrami. RNAseq from normal breast is also available from the gtex portal. you can download from TCGA database by TCGAbiolinks package in R.

What is TCGA in DNA?

The Cancer Genome Atlas (TCGA), a landmark cancer genomics program, molecularly characterized over 20,000 primary cancer and matched normal samples spanning 33 cancer types.

What is UCSC Xena?

UCSC Xena is a visual exploration resource for both public and private omics data, supported through the web-based Xena Browser and multiple turn-key Xena Hubs.

What is SRA run selector?

Run Selector is a tool available through the Sequence Read Archive (SRA) that allows you to fine-tune your web-based search results. There are over two dozen fields that can be used to filter SRA data in Run Selector.

What is SRA run?

The Sequence Read Archive (SRA, previously known as the Short Read Archive) is a bioinformatics database that provides a public repository for DNA sequencing data, especially the “short reads” generated by high-throughput sequencing, which are typically less than 1,000 base pairs in length.

What is AA genotype sickness?

According to the social media posts, some of the symptoms exhibited by persons who came down with the purported “AA sickness” include fever, sore throat, catarrh, headache and body pains. These are some of the symptoms associated with COVID-19.

What is dbGaP?

Database of Genotype and Phenotype (dbGaP) refers to NIH maintained database of datasets and was developed to archive and distribute the results of studies that have investigated the interaction of genotype and phenotype. dbGaP provides two types of data – open access and controlled access.

When will the dbGaP data browser be retired?

The dbGaP Data Browser will be retired in April 2022. View dbGaP study data and additional gene and SNP annotation in the Genome Data Viewer browser. Read more .

What is a cada file in dbGaP?

CADA stands for the Compilation of Aggregate Genomic Data and is a collection of analyses across many dbGaP studies that can be accessed with a single Data Access Request. Submitting Files 24. Who can submit files to dbGaP? A dbGaP study must be registered in the dbGaP Submission System before data can be submitted.

Who needs an era account to access dbGaP?

Investigators not affiliated with NIH must have an eRA account to access dbGaP. NIH intramural investigators may use their NIH credentials to access dbGaP, but must first obtain permission from their Institute or Center.