Table of Contents

Exercise 5

Data description




Working plan

We have several candidate profiles of mutations to explore:

How many variants do you detect for each scenario?

A. Individual filters

  1. Recessive heritage
  2. Dominant heritage (mother is affected).
  3. For chromosomes 1 and 3
  4. Evaluate these regions at the same time: 1:10000-500000, 11:1000-500000, 13:500-100000
  5. For theses genes: BRCA1,BRCA2
  6. Are there variants for these SNPs: rs6682385,rs75478250,rs147502335,rs368140013,rs7951297?
  7. Description of variants. How many SNVs, INDELs, MNVs, SVs, CNVs?
  8. Variants with MAF (Minimum Allelic Frequency) < 0.005 for Asian population in 1000 Genomes phase 1
  9. Variants with MAF (Minimum Allelic Frequency) < 0.005 for East Asian population in 1000 Genomes phase 3
  10. Variants with MAF (Minimum Allelic Frequency) < 0.005 for South Asian population in 1000 Genomes phase 3


B. Progressive selection

  1. There are clear information about our candidate variants:
    • Recessive heritage
    • Chromosomes 5 and 7
    • INDEL
      • How many variants do you have including both characteristics?
      • Download these final results in a csv file
  2. We have other interesting scenario where we are sure there are several candidate variants:
    • Heterozygous variant for mother and daughter and father is reference (0/0)
    • Consequence type: “stop lost”
    • We search new variants without rs ID
    • BiERapp includes details about “Genomic context”, “Pop. Frequencies”, “Phenotype” and “Effect”. Please, could you explain a bit this information?