Table of Contents
Data description
Working plan
We have several candidate profiles of mutations because it is clear the kind of mutation we are searching but sometimes we do not have a specific clues.
How many variants do you detect for each scenario?
A. Individual filters
- Recessive heritage
- Dominant heritage (mother is affected)
- For this region: 4
- For these genes: RET,BRCA2
- Are there variants for this SNPId: rs5064
- Description of variants. How many MNVs?
- Variants with MAF (Minimum Allelic Frequency) < 0.001 for European American population in ESP 6500
- Variants with MAF (Minimum Allelic Frequency) < 0.001 for African American population in ESP 6500
- Variants with the two preview MAFs at the same time
B. Progressive selection
- Can you apply filters to search “Cardiomyopathy” phenotype in dominant heritage(mother is affected)? (You can see a solution at the end, it could be more than one)
- Download these final results in a csv file.
Solutions
A. Individual filters
- Candidate variants: 944
- Candidate variants: 10925
- Candidate variants: 1675
- Candidate variants: 18
- Candidate variants: 1
- 14 MNVs
- Candidate variants in European American population: 21399
- Candidate variants in African American population: 21433
- Candidate variants in the two MAFs: 21207
B. Progressive selection
- MAF ALL phase 1 < 0.1, MAF ALL phase3 < 0.1, Phylop > 0.5, PhastCons >0.5, GENE: VCL