Difference between revisions of "Rare variant tests"
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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 | ||
|- | |- | ||
− | | 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/ || | | ||
|- | |- | ||
− | | 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 | ||
|- | |- | ||
− | | 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 |