How to understand ESP database

How to understand the ESP database, I believe that many inexperienced people do not know what to do. Therefore, this paper summarizes the causes and solutions of the problem. Through this article, I hope you can solve this problem.

ESP, whose full name is NHLBI Exome Sequencing Project, is a large exon sequencing project carried out by many universities and research structures. the main purpose is to carry out SNP typing in different populations through NGS technology to assist the study of heart, lung and blood related diseases.

The database can be retrieved through the Data Browser button on the front page. You can retrieve it in the following four ways:

Gene symbol named by HUGO

Entrez Gene ID

Chromosome region

DbSNP rs ID

The results of two populations are provided in the search results.

EuropeanAmerican

AfricanAmerican

On the page of the results display, detailed information about each mutation site is given.

1. Gene related information

This section will give the basic information such as symbol, ID and chromosome region of the gene, as well as links to databases such as pathway, COSMIC, STRING, OMIM, etc.

two。 Variation point header information

The header of the variation site is screened by using the single check box.

3. Details page of the mutation site

Display the information corresponding to each mutation site according to the previously screened header

The filling colors of different types of variation sites are different, and the corresponding relationship between color and variation types is as follows.

The search results can be downloaded by clicking the download button in the upper right corner. Both text and vcf formats are supported.

In addition to retrieval, you can also download the contents of the entire database at once, and click the Download button on the home page to jump to the download page.

The data provided on this page is the analysis results of 6503 samples. The location of the mutation site is based on the hg19 version. In order to adapt to the hg38 version, a new field is added to store the location information on the hg38 version. Five files are available for download, which can be divided into three categories

1.SNP typing result

ESP6500SI-V2-SSA137.GRCh48-liftover.snps_indels.txt.tar.gzESP6500SI-V2-SSA137.GRCh48-liftover.snps_indels.vcf.tar.gz

two。 Sequencing coverage result

ESP6500SI-V2.GRCh48-liftover.coverage.all_sites.txt.tar.gzESP6500SI-V2.coverage.seq_blocks.txt.tar.gz

3. Exon destination area file

Agilent_nimblegen_exome_targets_esp_project.tar.gz

Usually, you can download the VCF file.

After reading the above, have you mastered how to understand the ESP database? If you want to learn more skills or want to know more about it, you are welcome to follow the industry information channel, thank you for reading!