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bierapp_ex3 [2016/09/27 16:14] fgarcia |
bierapp_ex3 [2017/05/24 14:23] (current) |
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+ | =====Data description===== | ||
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+ | {{:ex3.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 (mother is affected). | ||
+ | - For these region, only chromosome: 3,19 | ||
+ | - Evaluate the same regions, including start and end at the first region: 3:1000-200000,19 | ||
+ | - For this gene: SDC3 | ||
+ | - [[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) < 0.05 for AFR populations in 1000 Genomes phase 1 | ||
+ | - Variants with MAF (Minimum Allelic Frequency) < 0.05 for AFR populations in 1000 Genomes phase 3 | ||
+ | - Variants with MAF (Minimum Allelic Frequency) < 0.05 for African American population in ESP 6500 | ||
+ | - For sift<0.05 and polyphen >0.95, because it is likely pathogenic | ||
+ | |||
+ | \\ | ||
+ | ===B. Progressive selection=== | ||
+ | |||
+ | - Can you apply filters to search "Insuline Resistance" phenotype in recesive heritage? | ||
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+ | \\ | ||
+ | \\ | ||
+ | /* | ||
+ | ====Solutions==== | ||
+ | ===A. Individual filters=== | ||
+ | - Candidate variants: 964 | ||
+ | - Candidate variants: 10852 | ||
+ | - Candidate variants: 5015 | ||
+ | - Candidate variants: 975 | ||
+ | - Candidate variants: 2 | ||
+ | - 36307 SNVs, 3666 INDELs, 23 MNVs, 3 SVs, 0 CNVs | ||
+ | - Candidate variants in 1000 Genomes, phase 1: 16102 | ||
+ | - Candidate variants in 1000 Genomes, phase 3: 17468 | ||
+ | - Candidate variants in European American population: 24460 | ||
+ | - Candidate variants: 313 | ||
+ | |||
+ | ===B. Progressive selection=== | ||
+ | - sift<0.05, polyphen>0.95, AFR phase3 < 0.1 | ||
+ | |||
+ | */ |