Exercise 7

We have several candidate profiles of mutations to explore:

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

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?

1. Candidate variants: 1688
2. Candidate variants: 6084
3. Candidate variants: 6459
4. Candidate variants: 60
5. Candidate variants: 13
6. Candidate variants: 1
7. 36385 SNVs, 3596 INDELs, 13 MNVs, 4 SVs, 0 CNVs
8. Candidate variants in 1000 Genomes, phase 1: 14948
9. Candidate variants in 1000 Genomes, phase 3: 15730
10. Candidate variants in European American population: 13029

1. 1688 → 164 → 20
2. 4432 → 2 → 1