Exercise 9

We have several candidate profiles of mutations to explore:

1. Description of variants. How many SNVs, INDELs, MNVs, SVs, CNVs?
2. Recessive heritage
3. Dominant heritage (mother is affected).
4. For this region: 3:10000-500000
5. Evaluate these regions at the same time: 3:10000-500000, 5:1000-500000, 13:500-100000
6. For theses genes related to Charcot-Marie-Tooth disease: BSCL2, DNM2, EGR2, FGD4, FIG4, GARS, GDAP1, GJB1, HSPB1, HSPB8, KIF1B, LITAF, LMNA, MFN2, MPZ, MTMR2, NDRG1, NEFL, PMP22, PRPS1, PRX, RAB7A, SBF2, SH3TC2, TRPV4, and YARS

1. We have several clues about our candidate variants:
   • Recessive heritage
   • For theses genes related to Charcot-Marie-Tooth disease: BSCL2, DNM2, EGR2, FGD4, FIG4, GARS, GDAP1, GJB1, HSPB1, HSPB8, KIF1B, LITAF, LMNA, MFN2, MPZ, MTMR2, NDRG1, NEFL, PMP22, PRPS1, PRX, RAB7A, SBF2, SH3TC2, TRPV4, and YARS
     • How many variants do you have including both characteristics? Only one!
     • Maybe this is our variant. We need several more things:
       • Select this variant and take a picture from the Genomic Browser.
       • Explore with detail information about “Genomic context”, “Pop. Frequencies”, “Phenotype”, “Effect”.
2. Another interesting profile for us:
   • Dominant heritage (mother is affected) where mother and daughters present a heterozygous variant.
   • Only chromosome 5.
     • How many variants do you have including both characteristics?
     • Download these final results in a csv file
3. Last scenario to explore:
   • Recessive heritage but…..
   • There are two affected daughters but one of them (F2) is more affected than (F3). Maybe there is a modifier for F2 not present in F3.
   • Only chromosome 5.

1. 36376 SNVs, 3602 INDELs, 14 MNVs, 6 SVs, 0 CNVs
2. Candidate variants: 319
3. Candidate variants: 1228
4. Candidate variants: 4
5. Candidate variants: 45
6. Candidate variants: 48

1. 319 → 1
2. 1186 → 63
3. 956 → 43