Table of Contents

Exercise 7

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. 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


B. Progressive selection

  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?
  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.