Differences
This shows you the differences between two versions of the page.
bierapp_ex5 [2017/03/05 16:25] fgarcia |
bierapp_ex5 [2017/05/24 14:23] (current) |
||
---|---|---|---|
Line 1: | Line 1: | ||
+ | ====== Exercise 5====== | ||
+ | =====Data description===== | ||
+ | |||
+ | \\ | ||
+ | {{:ex5.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=== | ||
+ | |||
+ | - Recessive heritage | ||
+ | - Dominant heritage (mother is affected). | ||
+ | - For chromosomes 1 and 3 | ||
+ | - Evaluate these regions at the same time: 1:10000-500000, 11:1000-500000, 13:500-100000 | ||
+ | - For theses genes: BRCA1,BRCA2 | ||
+ | - Are there variants for these SNPs: rs6682385,rs75478250,rs147502335,rs368140013,rs7951297? | ||
+ | - [[http://www.clcsupport.com/clcgenomicsworkbench/650/Variant_types.html|Description of variants]]. How many SNVs, INDELs, MNVs, SVs, CNVs? | ||
+ | - Variants with MAF (Minimum Allelic Frequency) < 0.005 for Asian population in 1000 Genomes phase 1 | ||
+ | - Variants with MAF (Minimum Allelic Frequency) < 0.005 for East Asian population in 1000 Genomes phase 3 | ||
+ | - Variants with MAF (Minimum Allelic Frequency) < 0.005 for South Asian population in 1000 Genomes phase 3 | ||
+ | |||
+ | \\ | ||
+ | ===B. Progressive selection=== | ||
+ | |||
+ | - 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** | ||
+ | - 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? | ||
+ | |||
+ | /* | ||
+ | |||
+ | \\ | ||
+ | \\ | ||
+ | ====Solutions==== | ||
+ | Some of these solutions could be different when having updated databases | ||
+ | |||
+ | ===A. Individual filters=== | ||
+ | - Candidate variants: 1688 | ||
+ | - Candidate variants: 6084 | ||
+ | - Candidate variants: 6459 | ||
+ | - Candidate variants: 60 | ||
+ | - Candidate variants: 13 | ||
+ | - Candidate variants: 1 | ||
+ | - 36385 SNVs, 3596 INDELs, 13 MNVs, 4 SVs, 0 CNVs | ||
+ | - Candidate variants in 1000 Genomes, phase 1: 14948 | ||
+ | - Candidate variants in 1000 Genomes, phase 3: 15730 | ||
+ | - Candidate variants in European American population: 13029 | ||
+ | |||
+ | ===B. Progressive selection=== | ||
+ | - 1688 -> 164 -> 20 | ||
+ | - 4432 -> 2 -> 1 | ||
+ | |||
+ | */ |