Table of Contents
Activity 2
Create new user and upload the data
Design panels
Cataracts
Hyperammonaemia
Sotos syndrome
Osteogenesis imperfecta
Ketotic hyperglycinemia
Fanconi anemia
My disease
Activity 2
Create new user and upload the data
Please create your own user and login with this new user.
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
While the file is indexing we will design all the panels.
Design panels
Cataracts
Use the ”+ Panel” menu and create a new panel for “Cataracts”.
Select the next phenotypes: “Cataract” and “Cataracts”.
Use Panel App and Search if we can get more genes for this panel (select only genes with “HighEvidence”).
With this panel search 1 or more samples with the disease.
Hyperammonaemia
Use the ”+ Panel” menu and create a new panel for “Hyperammonaemia”.
Select the next phenotype: “Hyperammonaemia”.
Use Panel App and Search if we can get more genes for this panel (select only genes with “HighEvidence”).
With this panel search 1 or more samples with the disease.
Sotos syndrome
Use the ”+ Panel” menu and create a new panel for “Sotos syndrome”.
Select the next phenotypes: “Sotos syndrome 1, Sotos syndrome 2 and Sotos' syndrome”.
Use Panel App and Search if we can get more genes for this panel (select only genes with “HighEvidence”).
With this panel search 1 or more samples with the disease.
Osteogenesis imperfecta
Use the ”+ Panel” menu and create a new panel for “Osteogenesis imperfecta”.
Select the next phenotype: “Osteogenesis imperfecta”.
Use Panel App and Search if we can get more genes for this panel (select only genes with “HighEvidence”).
With this panel search 1 or more samples with the disease.
Ketotic hyperglycinemia
Use the ”+ Panel” menu and create a new panel for “Ketotic hyperglycinemia”.
Select the next phenotype: “Ketotic hyperglycinemia”.
Use Panel App and Search if we can get more genes for this panel (select only genes with “HighEvidence”).
With this panel search 1 or more samples with the disease.
Fanconi anemia
Use the ”+ Panel” menu and create a new panel for “Fanconi anemia”.
Select the next phenotype: “Fanconi anemia”.
With this panel search 1 or more samples with the disease.
My disease
We will create a panel for a new disease: “my disease”.
Copy genes from this file:
genes.txt
Import mutations from this CSV file:
mutations.txt
(NOTE: this is a TXT file but you should import it using “import CSV”)
These genes and these mutations are from a real disease. Do you know the name of this disease?