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| + | =====Data description===== | ||
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| + | {{:ex4.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 and the two daughters are affected). | ||
| + | - For this region, only chromosome: 7 | ||
| + | - Evaluate the same region, including start and end: 7:1000-200000 | ||
| + | - For these genes: PMS,ATRN | ||
| + | - Are there variants for these SNPs: rs104895545,rs79716074? | ||
| + | - [[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) < 0.001 for all populations in 1000 Genomes phase 1 | ||
| + | - Variants with MAF (Minimum Allelic Frequency) < 0.001 for all populations in 1000 Genomes phase 3 | ||
| + | - Variants with MAF (Minimum Allelic Frequency) < 0.001 for European American population in ESP 6500 | ||
| + | - Variants with the three preview MAFs at the same time | ||
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| + | ===B. Progressive selection=== | ||
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| + | - We have several clues about our candidate variants. In addition of knowing the pattern of recessive heritage, we search variants with MAF < 0.001 (for all populations in 1000 Genomes phase 1) because it is a rare disease. | ||
| + | *How many variants do you have including both characteristics? | ||
| + | *Include at the preview filter the consequence type "missense_variant". How many variants do you have now? | ||
| + | *Finally, include the Sift < 0.05 and Polyphen > 0.95, thus it is likely pathogenic variant. How many variants do you have now? | ||
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| + | /* | ||
| + | ====Solutions==== | ||
| + | Some of these solutions could be different when having updated databases | ||
| + | |||
| + | ===A. Individual filters=== | ||
| + | - Candidate variants: 950 | ||
| + | - Candidate variants: 1496 | ||
| + | - Candidate variants: 2181 | ||
| + | - Candidate variants: 2 | ||
| + | - Candidate variants: 18 | ||
| + | - Candidate variants: 2 | ||
| + | - 36499 SNVs, 3488 INDELs, 7 MNVs, 5 SVs, 0 CNVs | ||
| + | - Candidate variants in 1000 Genomes, phase 1: 11079 | ||
| + | - Candidate variants in 1000 Genomes, phase 3: 12027 | ||
| + | - Candidate variants in European American population: 21229 | ||
| + | - Candidate variants in the three MAFs: 7475 | ||
| + | |||
| + | ===B. Progressive selection=== | ||
| + | - 108-22-4 | ||
| + | |||
| + | */ | ||