Rare variant tests: Difference between revisions
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Blue font indicates implementation in upcoming PLINKSeq release (http://atgu.mgh.harvard.edu/plinkseq/) | Blue font indicates implementation in upcoming PLINKSeq release (http://atgu.mgh.harvard.edu/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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! scope="col" align="left" | Notes | ! scope="col" align="left" | Notes | ||
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| CMC/T1 test* || [http://www.ncbi.nlm.nih.gov/pubmed/18691683 Li & Leal, 2008] || || | | | CMC/T1 test* || [http://www.ncbi.nlm.nih.gov/pubmed/18691683 Li & Leal, 2008] || || [http://atgu.mgh.harvard.edu/plinkseq/ Will be implemented in PlinkSeq] | | ||
|- | |- | ||
| KBAC || [http://www.ncbi.nlm.nih.gov/pubmed/20976247 Liu & Leal, 2010] || || | | | KBAC || [http://www.ncbi.nlm.nih.gov/pubmed/20976247 Liu & Leal, 2010] || || [http://atgu.mgh.harvard.edu/plinkseq/ Will be implemented in PlinkSeq] | | ||
|- | |- | ||
| VT* || [http://www.ncbi.nlm.nih.gov/pubmed/20471002 Price et al., 2010] || http://genetics.bwh.harvard.edu/rare_variants/ || Incorporating functional weights but not VT | | | VT* || [http://www.ncbi.nlm.nih.gov/pubmed/20471002 Price et al., 2010] || http://genetics.bwh.harvard.edu/rare_variants/ || Incorporating functional weights but not VT, [http://atgu.mgh.harvard.edu/plinkseq/ Will be implemented in PlinkSeq] | | ||
|- | |- | ||
| WSS || [http://www.ncbi.nlm.nih.gov/pubmed/19214210 Madsen & Browning, 2009] || || with 1% cutoff | | | WSS || [http://www.ncbi.nlm.nih.gov/pubmed/19214210 Madsen & Browning, 2009] || || with 1% cutoff, [http://atgu.mgh.harvard.edu/plinkseq/ Will be implemented in PlinkSeq] | | ||
|- | |- | ||
| CMAT || [http://www.ncbi.nlm.nih.gov/pubmed/21070896 Zawistowski et al. 2010] || || | | | CMAT || [http://www.ncbi.nlm.nih.gov/pubmed/21070896 Zawistowski et al. 2010] || || | | ||
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| CCRaVAT and QuTie* || [http://www.ncbi.nlm.nih.gov/pubmed/20964851 Lawrence et al. 2010] || http://www.sanger.ac.uk/resources/software/rarevariant/ || | | | CCRaVAT and QuTie* || [http://www.ncbi.nlm.nih.gov/pubmed/20964851 Lawrence et al. 2010] || http://www.sanger.ac.uk/resources/software/rarevariant/ || | | ||
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| RVE (rare variant exclusive) || Cohen & Hobb || || underpowered | | | RVE (rare variant exclusive) || Cohen & Hobb || || underpowered, [http://atgu.mgh.harvard.edu/plinkseq/ Will be implemented in PlinkSeq] | | ||
|} | |} | ||
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! scope="col" align="left" | Notes | ! scope="col" align="left" | Notes | ||
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| C-alpha || [Neale et al., submitted] || || | | | C-alpha || [Neale et al., submitted] || || [http://atgu.mgh.harvard.edu/plinkseq/ Will be implemented in PlinkSeq] | | ||
|- | |- | ||
| Ionita-Laza & Lange || [http://www.plosgenetics.org/article/info%3Adoi%2F10.1371%2Fjournal.pgen.1001289 Ionita-Laza & Lange, 2011] || || | | | Ionita-Laza & Lange || [http://www.plosgenetics.org/article/info%3Adoi%2F10.1371%2Fjournal.pgen.1001289 Ionita-Laza & Lange, 2011] || || | | ||
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! scope="col" align="left" | Reference | ! scope="col" align="left" | Reference | ||
! scope="col" align="left" | Software | ! scope="col" align="left" | Software | ||
! scope="col" align="left" | Notes | ! scope="col" align="left" | Notes | ||
|- | |- | ||
| WSS || [http://www.ncbi.nlm.nih.gov/pubmed/19214210 Madsen & Browning, 2009] || || with 1% or 5% cutoff | | | WSS || [http://www.ncbi.nlm.nih.gov/pubmed/19214210 Madsen & Browning, 2009] || || with 1% or 5% cutoff, [http://atgu.mgh.harvard.edu/plinkseq/ Will be implemented in PlinkSeq] | | ||
|- | |- | ||
| RARECOVER || [http://www.ploscompbiol.org/article/info:doi/10.1371/journal.pcbi.1000954 Bhati et al. 2010] || || | | | RARECOVER || [http://www.ploscompbiol.org/article/info:doi/10.1371/journal.pcbi.1000954 Bhati et al. 2010] || || | | ||
|- | |- | ||
| Step-Up Collapsing* || [http://www.plosone.org/article/info:doi/10.1371/journal.pone.0013584 Hoffman et al. 2010] || || | | | Step-Up Collapsing* || [http://www.plosone.org/article/info:doi/10.1371/journal.pone.0013584 Hoffman et al. 2010] || || [http://atgu.mgh.harvard.edu/plinkseq/ Will be implemented in PlinkSeq] | | ||
|- | |- | ||
| CMC/T5 test* || [http://www.ncbi.nlm.nih.gov/pubmed/18691683 Li & Leal, 2008] || || [http://atgu.mgh.harvard.edu/plinkseq/ Will be implemented in PlinkSeq] | | |||
|- | |||
| 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''' | |||
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* | |||
Additional tests | |||
Test Name Notes Reference Website/Code | |||
Logic Regression* Kooperberg et al. (2001) | |||
http://kooperberg.fhcrc.org/papers/2001gaw.pdf | |||
Sequence diversity Anderson (2006) | |||
Sequence dissimilarity* Schork et al. (2008), Wessel et al. (2006) | |||
Ridge Regression* Malo et al. (2008) | |||
'''Additional tests''' | |||
{| width="75%" cellspacing="0" cellpadding="5" border="1" | |||
|- | |||
! scope="col" align="left" | Test Name | |||
! scope="col" align="left" | Reference | |||
! scope="col" align="left" | Software | |||
! scope="col" align="left" | Notes | |||
|- | |||
| Logic regression* || [http://kooperberg.fhcrc.org/papers/2001gaw.pdf Kooperberg et al. 2001] || || | | |||
|- | |||
| Sequence diversity || Anderson et al. 2006 || || | | |||
|- | |||
| Sequence dissimilarity* || Schork et al. 2008, Wessel et al. 2006 || || | | |||
|- | |||
| Ridge regression * || Malo et al. 2008 || || | | |||
|} | |||
Revision as of 21:44, 4 February 2011
Summary of rare variant tests for sequence data
Compiled by Cristen Willer and Suzanne Leal for the ESP Feb 1, 2011
* indicates applicability to quantitative data
? indicates possible applicability to quantitative data with adaptation Blue font indicates implementation in upcoming PLINKSeq release (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
| Test Name | Reference | Software | Notes |
|---|---|---|---|
| CMC/T1 test* | Li & Leal, 2008 | ||
| KBAC | Liu & Leal, 2010 | ||
| VT* | Price et al., 2010 | http://genetics.bwh.harvard.edu/rare_variants/ | |
| WSS | Madsen & Browning, 2009 | ||
| CMAT | Zawistowski et al. 2010 | ||
| ANRV/GRANVIL* | Morris & Zeggini | ||
| RARECOVER | Bhati et al. 2010 | ||
| CCRaVAT and QuTie* | Lawrence et al. 2010 | http://www.sanger.ac.uk/resources/software/rarevariant/ | |
| RVE (rare variant exclusive) | Cohen & Hobb |
2) Aggregate tests for protective and detrimental variants (recommend 1% cutoff)
| Test Name | Reference | Software | Notes |
|---|---|---|---|
| C-alpha | [Neale et al., submitted] | ||
| Ionita-Laza & Lange | Ionita-Laza & Lange, 2011 | ||
| DASH* | Han & Pan | ||
| SKAT* | Wu et al., 2010 | http://www.hsph.harvard.edu/~xlin/software.html | |
| WHaIT | Li et al. 2010 | http://www.sph.umich.edu/csg/yli/whait/ | |
| EMMPAT* | 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)
| Test Name | Reference | Software | Notes |
|---|---|---|---|
| WSS | Madsen & Browning, 2009 | ||
| RARECOVER | Bhati et al. 2010 | ||
| Step-Up Collapsing* | Hoffman et al. 2010 | ||
| CMC/T5 test* | Li & Leal, 2008 | ||
| MENDEL* | Zhou et al. 2011 | http://www.genetics.ucla.edu/software/download?package=1 |
4.) Analyze higher frequency rare variants >1% individually
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*
Additional tests
Test Name Notes Reference Website/Code
Logic Regression* Kooperberg et al. (2001)
http://kooperberg.fhcrc.org/papers/2001gaw.pdf
Sequence diversity Anderson (2006)
Sequence dissimilarity* Schork et al. (2008), Wessel et al. (2006)
Ridge Regression* Malo et al. (2008)
Additional tests
| Test Name | Reference | Software | Notes |
|---|---|---|---|
| Logic regression* | Kooperberg et al. 2001 | ||
| Sequence diversity | Anderson et al. 2006 | ||
| Sequence dissimilarity* | Schork et al. 2008, Wessel et al. 2006 | ||
| Ridge regression * | Malo et al. 2008 |
