Getting started

Searching any variant

To start using CNVS can access the CNVS web on this link.

The CNVS tool provides various search filters.

1. Position: This filters have two possibilities:

   • Chromosomal Location: Region where narrow your search. Chromosome:Start-End. Ex.: 1:10004570-1004646.
   • Gene: Visualize a particular gene. If you want see more than one gene,separate them with commas. Ex.: BRCA2,FAT3

2. Identifiers: This filters have two possibilities:

   • Code: Reference of the center.
   • Decipher Id: Decipher Identifier. Exists if the CNV exists int the BD.

3. Type of variant: You can check three possibilities: Gain, Loss and LOH neutral.

4. Doses: x0, x1, x2(XY) and x3.

5. Clinical Significance: Benign, Pahtogenic, VOUS, Likely Benign or Likely Pathogenic.

6. Cell line: Germline and Somatic.

7. Chromosomal Gender: XX or XY.

8. Status: Proband, Father, Mother or Control.

9. Type of Sample: Blood, Amniotic Fluid, Chorionic villi, Tumour or Etc.

10. Phenotyphe (HPO): Many of our samples contain the associated phenotypes. You can search for it to find the desired variation.

11. Year of Birth: This filter corresponds to the year of birth of the patient.

12. Ethnic Group: Example: Ethnic group to which the patient belongs sequenced. Ex.White Mediterranean

13. Geographic Origin: Although all our variants correspond to Spanish population, given our cultural diversity, samples include the country where the patient comes.

After inserting the ID and set the desired filter, you must press the "search" button to search. To reset the search parameters, you can press the "Clear" button.

The search result is displayed in a result table (blue) and graphical display spaces (green).

The table offers the possibility to close or minimize it by pressing the upper right of the same button. It also offers the possibility to increase or decrease the size of the columns. If you are interested in a CNV of those shown in the table, you can click on it to center the graphical display in the region where the CNV is located.

The display table offers different display areas:

• Karyotype:
• Chromosome: All human chromosomes are shown. the current display area is indicated by an orange line.
• Gene overview: Region genes shown. This area is less than the area zoom genes. It is to have a global vision to the user that there are genes around.
• Sequence: Bases of chromosomal sequence. If the viewing area is very large sequence it will not be shown.
• Gene: Gene found in that region.
• SNP: SNP found in that region. If the size of the region is no longer the snp grnade be displayed , if not a histogram of these .
• CNVS: This area has two parts: first a histogram showing the amount of features there of each type of CNV ; gain , lossh and neutral LOH , the second zone is the Copy Number Variants found in the database for that region.

When you mouse over the display area, an orange line follows you for the user to know which chromosome area is. If you hover your mouse over a feature, a tooltip with the information we have about it is displayed. If you want to view adjacent areas to which you checked, you can click and drag the mouse to see the left or right.