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bierapp_ex1 [2016/09/27 16:05] fgarcia |
bierapp_ex1 [2017/05/24 11:26] (current) |
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+ | =====Data description===== | ||
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+ | {{:ex1.png?nolink|}} | ||
+ | \\ | ||
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+ | =====Working plan===== | ||
+ | We have several candidate profiles of mutations because it is clear the kind of mutation we are searching but sometimes we do not have a specific clues. | ||
+ | |||
+ | ====How many variants do you detect for each scenario?==== | ||
+ | ===A. Individual filters=== | ||
+ | |||
+ | - Recessive heritage | ||
+ | - Dominant heritage (father is affected). | ||
+ | - For this region: 1:1000-50000 | ||
+ | - For this gene: BRD9 | ||
+ | - For these genes at the same time: BRD9,CDK11A,RET | ||
+ | - [[http://www.clcsupport.com/clcgenomicsworkbench/650/Variant_types.html|Description of variants]]. How many SNVs and INDELs can you search? | ||
+ | - Variants with MAF (Minimum Allelic Frequency) < 0.1 for all populations in 1000 Genomes phase 3 | ||
+ | - Variants with MAF (Minimum Allelic Frequency) < 0.01 for all populations in 1000 Genomes phase 3 | ||
+ | - Variants with MAF (Minimum Allelic Frequency) < 0.001 for all populations in 1000 Genomes phase 3 | ||
+ | \\ | ||
+ | ===B. Progressive selection=== | ||
+ | - We have several clues about our candidate variants. In addition of knowing the pattern of recessive heritage, we search variants with MAF < 0.1 (for all populations in 1000 Genomes phase 3) because it is a rare disease. Consequence type must be "synonymous variant" | ||
+ | ***How many variants do you have including both characteristics?** | ||
+ | - We have several clues about our candidate variants. In addition of knowing the pattern of dominant heritage (father is affected), we search variants with MAF < 0.1 (for all populations in 1000 Genomes phase 3) because it is a rare disease. Consequence type must be "synonymous variant" | ||
+ | ***How many variants do you have including both characteristics?** | ||
+ | |||
+ | \\ | ||
+ | \\ | ||
+ | /* | ||
+ | ====Solutions==== | ||
+ | ===A. Individual filters=== | ||
+ | - Candidate variants: 1312 | ||
+ | - Candidate variants: 10722 | ||
+ | - Candidate variants: 1 | ||
+ | - Candidate variants: 9 | ||
+ | - Candidate variants: 34 | ||
+ | - 39980 SNVs and INDELs | ||
+ | - Candidate variants in 1000 Genomes, phase 3:17333 | ||
+ | - Candidate variants in 1000 Genomes, phase 3:13190 | ||
+ | - Candidate variants in 1000 Genomes, phase 3:12270 | ||
+ | |||
+ | ===B. Progressive selection=== | ||
+ | - 1312-449-46 | ||
+ | - 10722-5171-655 | ||
+ | |||
+ | */ |