Difference between revisions of "Rare variant tests"

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(Summary of rare variant tests for sequence data)
(Summary of rare variant tests for sequence data)
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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