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| + | === Summary of discussion from ESP rare variant working group === |
| + | |
| + | The rare variant working group within ESP has discussed the issue of |
| + | rare variant tests on several conference calls. The end result is |
| + | that we recommend selecting one test from each of these three |
| + | categories; |
| + | |
| + | 1. Aggregate tests (typically with 1% threshold, nonsynonymous SNPs |
| + | only, with meta-analysis across different ethnic groups) |
| + | |
| + | 2. Tests that allow for risk and/or protective variants (again, |
| + | probably 1% threshold, nonsynonymous SNPs only, with meta-analysis |
| + | across different ethnic groups) |
| + | |
| + | 3. Weighted tests that allow incorporation of more common variants |
| + | (possibly apply 5% threshold?, nonsynonymous only, etc.) |
| + | |
| + | A brief summary of the RV discussion; |
| + | |
| + | - Permutations (where we permute phenotype while maintaining ethnic |
| + | group) will likely be required to get empirical p-values. These RV |
| + | tests typically provide conservative p-values (deflated QQ plot), but |
| + | not always. Thus, a computationally intensive test will not be |
| + | practical for performing large numbers of permutations (at least |
| + | 1000). |
| + | |
| + | - Using too many tests will decrease the power overall because of |
| + | correction for family-wise error. |
| + | |
| + | - Although we'd like to evaluate power and type I error rates of these |
| + | tests under a variety of genetic models, the reality is that we have |
| + | so few known positive examples it would be difficult to assess them |
| + | all in a fair way at this time. Instead, we expect to re-convene this |
| + | discussion group at a later date once some true positive associations |
| + | are identified. |
| + | |
| + | - Shamil Sunyaev is performing a bake-off with some of these tests, |
| + | and we look forward to seeing his results in the future. |
| + | |
| + | - PLINKSeq is on its way, but is likely a month away from release (end Feb 2011) |
| + | |
| + | |
| + | |
| === Summary of rare variant tests for sequence data === | | === Summary of rare variant tests for sequence data === |
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| [http://atgu.mgh.harvard.edu/plinkseq/ Will be implemented in PlinkSeq] | | [http://atgu.mgh.harvard.edu/plinkseq/ Will be implemented in PlinkSeq] |
| + | |
| + | |
| | | |
| '''1) Aggregate tests using a cut off e.g. 1 % analyzing nonsynonymous variants to detect detrimental variants''' | | '''1) Aggregate tests using a cut off e.g. 1 % analyzing nonsynonymous variants to detect detrimental variants''' |
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| | RVE (rare variant exclusive) || Cohen & Hobb || || underpowered, [http://atgu.mgh.harvard.edu/plinkseq/ Will be implemented in PlinkSeq] | | | | RVE (rare variant exclusive) || Cohen & Hobb || || underpowered, [http://atgu.mgh.harvard.edu/plinkseq/ Will be implemented in PlinkSeq] | |
| |} | | |} |
| + | |
| + | |
| | | |
| '''2) Aggregate tests for protective and detrimental variants (recommend 1% cutoff)''' | | '''2) Aggregate tests for protective and detrimental variants (recommend 1% cutoff)''' |
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| | EMMPAT* || [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2978703/pdf/pgen.1001202.pdf King et al. 2010] || http://home.uchicago.edu/~crk8e/papersup.html || | | | | EMMPAT* || [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2978703/pdf/pgen.1001202.pdf King et al. 2010] || http://home.uchicago.edu/~crk8e/papersup.html || | |
| |} | | |} |
| + | |
| + | |
| | | |
| '''3) Analyzing common and rare variants together (could down-weight or threshold common variants)''' | | '''3) Analyzing common and rare variants together (could down-weight or threshold common variants)''' |
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| | MENDEL* || [http://www.ncbi.nlm.nih.gov/pubmed/21121038 Zhou et al. 2011] || http://www.genetics.ucla.edu/software/download?package=1 || | | | | MENDEL* || [http://www.ncbi.nlm.nih.gov/pubmed/21121038 Zhou et al. 2011] || http://www.genetics.ucla.edu/software/download?package=1 || | |
| |} | | |} |
| + | |
| + | |
| | | |
| '''4.) Analyze higher frequency rare variants >1% individually''' | | '''4.) Analyze higher frequency rare variants >1% individually''' |
| Use same regression frame work which has been used for common variants* | | Use same regression frame work which has been used for common variants* |
| Use meta analysis to combine results from sequence data and imputed genotypes to increase power* | | Use meta analysis to combine results from sequence data and imputed genotypes to increase power* |
− |
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− |
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− | Additional tests
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− | Test Name Notes Reference Website/Code
| |
− | Logic Regression* Kooperberg et al. (2001)
| |
− | http://kooperberg.fhcrc.org/papers/2001gaw.pdf
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− | Sequence diversity Anderson (2006)
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− | Sequence dissimilarity* Schork et al. (2008), Wessel et al. (2006)
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− | Ridge Regression* Malo et al. (2008)
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− |
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| | | |
| '''Additional tests''' | | '''Additional tests''' |