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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| 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] ||  || |
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! scope="col" align="left" | Reference
 
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| C-alpha || [Neale et al., submitted] ||  || |
 
| C-alpha || [Neale et al., submitted] ||  || |
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'''Analyzing common and rare variants together (could down-weight or threshold common variants)'''
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'''3) Analyzing common and rare variants together (could down-weight or threshold common variants)'''
  
 
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{| width="75%" cellspacing="0" cellpadding="5" border="1"
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| 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] || || |
 
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| Step-Up Collapsing* || [http://www.plosone.org/article/info:doi/10.1371/journal.pone.0013584
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| Step-Up Collapsing* || [http://www.plosone.org/article/info:doi/10.1371/journal.pone.0013584 Hoffman et al. 2010] || || |
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Revision as of 21:27, 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/)


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