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bierapp_ex7 [2017/03/05 16:26]
fgarcia
bierapp_ex7 [2017/05/24 14:23] (current)
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 +====== Exercise 7======
  
 +=====Data description=====
 +
 +\\ 
 +{{:ex7.png?500|}}
 +\\
 +\\
 +=====Working plan=====
 +We have several candidate profiles of mutations to explore:
 + 
 +
 +====How many variants do you detect for each scenario?====
 +===A. Individual filters===
 +   - [[http://www.clcsupport.com/clcgenomicsworkbench/650/Variant_types.html|Description of variants]]. How many SNVs, INDELs, MNVs, SVs, CNVs?
 +  - Recessive heritage
 +  - Dominant heritage (mother is affected).
 +  - For this region:   3:10000-500000
 +  - Evaluate these regions at the same time:  3:10000-500000, 5:1000-500000, 13:500-100000
 +  - 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===
 +
 +  - 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".
 +  - 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?**
 +  - 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.
 +\\
 +\\
 +/*
 +====Solutions====
 +Some of these solutions could be different when having updated  databases
 +
 +===A. Individual filters===
 +  - 36376 SNVs, 3602 INDELs, 14 MNVs, 6 SVs, 0 CNVs
 +  - Candidate variants: 319 
 +  - Candidate variants: 1228
 +  - Candidate variants: 4
 +  - Candidate variants: 45
 +  - Candidate variants: 48
 +
 +
 +===B. Progressive selection===
 +  - 319  ->  1
 +  - 1186 -> 63 
 +  - 956  -> 43
 +
 +*/