Table of Contents

Activity 2

Create new user and upload the data

  1. Please create your own user and login with this new user.
  2. Upload the required VCF file in “Default Study” and wait 4-5 min to indexing tool. http://bioinfo.cipf.es/apps-beta/gda16/team/patients.vcf
  3. While the file is indexing we will design all the panels.

Design panels

Cataracts

  1. Use the “+ Panel” menu and create a new panel for “Cataracts”.
  2. Select the next phenotypes: “Cataract” and “Cataracts”.
  3. Use Panel App and Search if we can get more genes for this panel (select only genes with “HighEvidence”).
  4. With this panel search 1 or more samples with the disease.

Hyperammonaemia

  1. Use the “+ Panel” menu and create a new panel for “Hyperammonaemia”.
  2. Select the next phenotype: “Hyperammonaemia”.
  3. Use Panel App and Search if we can get more genes for this panel (select only genes with “HighEvidence”).
  4. With this panel search 1 or more samples with the disease.

Sotos syndrome

  1. Use the “+ Panel” menu and create a new panel for “Sotos syndrome”.
  2. Select the next phenotypes: “Sotos syndrome 1, Sotos syndrome 2 and Sotos' syndrome”.
  3. Use Panel App and Search if we can get more genes for this panel (select only genes with “HighEvidence”).
  4. With this panel search 1 or more samples with the disease.

Osteogenesis imperfecta

  1. Use the “+ Panel” menu and create a new panel for “Osteogenesis imperfecta”.
  2. Select the next phenotype: “Osteogenesis imperfecta”.
  3. Use Panel App and Search if we can get more genes for this panel (select only genes with “HighEvidence”).
  4. With this panel search 1 or more samples with the disease.

Ketotic hyperglycinemia

  1. Use the “+ Panel” menu and create a new panel for “Ketotic hyperglycinemia”.
  2. Select the next phenotype: “Ketotic hyperglycinemia”.
  3. Use Panel App and Search if we can get more genes for this panel (select only genes with “HighEvidence”).
  4. With this panel search 1 or more samples with the disease.

Fanconi anemia

  1. Use the “+ Panel” menu and create a new panel for “Fanconi anemia”.
  2. Select the next phenotype: “Fanconi anemia”.
  3. With this panel search 1 or more samples with the disease.

My disease

  1. We will create a panel for a new disease: “my disease”.
  2. Copy genes from this file: genes.txt
  3. Import mutations from this CSV file: mutations.txt (NOTE: this is a TXT file but you should import it using “import CSV”)
  4. These genes and these mutations are from a real disease. Do you know the name of this disease?