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bierapp_ex7 [2017/03/05 16:26] fgarcia |
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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 | ||
+ | |||
+ | */ |