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16 Cards in this Set
- Front
- Back
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cost-effectiveness issues in GWAS (4)
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------ 1. balance between false positives and false negatives
2.choice of larger sample sizes or ore genetic markers 3.choice of larger sample sizes and more informative subjects 4.splitting resources between initial GW scan and follow-up |
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most popular solution to cost-effectiveness problem
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GWAS studies
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why GWAS (4)
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---- 1. powerful design to gain global dissection of etiology
2.many successful replications 3.takes advantage of exisiting database (HAPMAP) to gain new information (genotype imputation/CNVs) 4.design of choice for studying complex diseases |
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unique issues for GW study design (4)
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----- 1. hypothesis generating vs testing
2.population specific polymorphisms 3.genome coverage 4.choice of sampling units |
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in reporting resutls of hypotheis tets, what must occur? -----
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- p-value adjustment for multiple testing MUST occur
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what is key for GWAS: hypothesis
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------ REPLICATION!
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procedures for adjustment of multiple tesgting that are suitable for GWAS -----
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- 1. step down bonferroni
2.sequential mutliple decision proces 3.false discover rate 4.multi-stage design 5.genomic control |
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gwas marker issues ------
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1. limited platforms
2.genome coverage 3.problems with population specific polymorphisms 4.marker density 5.marker frequency |
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what are copies of a gene in the genotype of an individual -
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----- DNA copy number
polymorphic loci with varying DNA copy numbers in a population |
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varying gene CN is related to...
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its exprssion level
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choice of samples in GWA
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1. population-based
2.family-based |
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con with GWAS population based data
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spurious association
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pro of popoulation based choice of sampling units
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more efficient
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types of sampling units with populaiton based GWAS
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1. case -control
2.case only |
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pros of family based choice of sample units in GWAS
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1. control for population stratification
2.may be performed on existing samples 3.better haplotype estimate 4. natural to combine with linkage analysis |
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cons of family based choice of sample units in GWAS
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1.cost more
2.missing data may compromise power |
