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Rare variant tests (view source)

Revision as of 17:58, 7 February 2011

23 bytes removed ,  17:58, 7 February 2011
→‎Summary of rare variant tests for sequence data
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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] ||  || [http://atgu.mgh.harvard.edu/plinkseq/ Will be implemented in PlinkSeq] |
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| CMC/T1 test* || [http://www.ncbi.nlm.nih.gov/pubmed/18691683 Li & Leal, 2008]  
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| [http://atgu.mgh.harvard.edu/plinkseq/ Will be implemented in PlinkSeq]  
 
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| KBAC || [http://www.ncbi.nlm.nih.gov/pubmed/20976247 Liu & Leal, 2010] || || [http://atgu.mgh.harvard.edu/plinkseq/ Will be implemented in PlinkSeq] |
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| KBAC || [http://www.ncbi.nlm.nih.gov/pubmed/20976247 Liu & Leal, 2010] ||  
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| [http://atgu.mgh.harvard.edu/plinkseq/ Will be implemented in PlinkSeq]  
 
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| 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] |
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| VT* || [http://www.ncbi.nlm.nih.gov/pubmed/20471002 Price et al., 2010]  
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| http://genetics.bwh.harvard.edu/rare_variants/  
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| Incorporating functional weights but not VT, [http://atgu.mgh.harvard.edu/plinkseq/ Will be implemented in PlinkSeq] |
 
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| 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] |
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| WSS || [http://www.ncbi.nlm.nih.gov/pubmed/19214210 Madsen & Browning, 2009] ||  
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| with 1% cutoff, [http://atgu.mgh.harvard.edu/plinkseq/ Will be implemented in PlinkSeq]  
 
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| CMAT || [http://www.ncbi.nlm.nih.gov/pubmed/21070896 Zawistowski et al. 2010] || || |
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| CMAT || [http://www.ncbi.nlm.nih.gov/pubmed/21070896 Zawistowski et al. 2010] || ||  
 
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| ANRV/GRANVIL* || [http://www.ncbi.nlm.nih.gov/pubmed/19810025 Morris & Zeggini] || || |
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| ANRV/GRANVIL* || [http://www.ncbi.nlm.nih.gov/pubmed/19810025 Morris & Zeggini] || ||  
 
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| RARECOVER || [http://www.ploscompbiol.org/article/info:doi/10.1371/journal.pcbi.1000954 Bhati et al. 2010] || || |
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| RARECOVER || [http://www.ploscompbiol.org/article/info:doi/10.1371/journal.pcbi.1000954 Bhati 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/ || |
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| CCRaVAT and QuTie* || [http://www.ncbi.nlm.nih.gov/pubmed/20964851 Lawrence et al. 2010]  
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| http://www.sanger.ac.uk/resources/software/rarevariant/ ||  
 
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| RVE (rare variant exclusive) || Cohen & Hobb || || underpowered, [http://atgu.mgh.harvard.edu/plinkseq/ Will be implemented in PlinkSeq] |
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| RVE (rare variant exclusive) || Cohen & Hobbs ||  
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| underpowered, [http://atgu.mgh.harvard.edu/plinkseq/ Will be implemented in PlinkSeq]  
 
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| C-alpha || [Neale et al., submitted] ||  || [http://atgu.mgh.harvard.edu/plinkseq/ Will be implemented in PlinkSeq] |
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| C-alpha || [Neale et al., submitted] ||   
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| [http://atgu.mgh.harvard.edu/plinkseq/ Will be implemented in PlinkSeq]  
 
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| Ionita-Laza & Lange || [http://www.plosgenetics.org/article/info%3Adoi%2F10.1371%2Fjournal.pgen.1001289 Ionita-Laza & Lange, 2011] || || |
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| Ionita-Laza & Lange  
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| [http://www.plosgenetics.org/article/info%3Adoi%2F10.1371%2Fjournal.pgen.1001289 Ionita-Laza & Lange, 2011] || || |
 
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| DASH* || [http://www.ncbi.nlm.nih.gov/pubmed/20413981 Han & Pan] || || Computational burden |
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| DASH* || [http://www.ncbi.nlm.nih.gov/pubmed/20413981 Han & Pan] || || Computational burden  
 
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| SKAT* || [http://www.ncbi.nlm.nih.gov/pubmed/20560208 Wu et al., 2010] || http://www.hsph.harvard.edu/~xlin/software.html || For some kernel choices, need to code 0=major homozygote, 1=het, 2-minor homozygote |
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| SKAT* || [http://www.ncbi.nlm.nih.gov/pubmed/20560208 Wu et al., 2010]  
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| http://www.hsph.harvard.edu/~xlin/software.html  
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| For some kernel choices, need to code 0=major homozygote, 1=het, 2-minor homozygote  
 
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| WHaIT || [http://www.ncbi.nlm.nih.gov/pubmed/21055717 Li et al. 2010] || http://www.sph.umich.edu/csg/yli/whait/ || |
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| WHaIT || [http://www.ncbi.nlm.nih.gov/pubmed/21055717 Li et al. 2010]  
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| http://www.sph.umich.edu/csg/yli/whait/ ||  
 
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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 || |
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| EMMPAT*  
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| [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2978703/pdf/pgen.1001202.pdf King et al. 2010]  
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| http://home.uchicago.edu/~crk8e/papersup.html ||  
 
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! scope="col" align="left" | Notes
 
! scope="col" align="left" | Notes
 
|-
 
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| 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] |
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| WSS || [http://www.ncbi.nlm.nih.gov/pubmed/19214210 Madsen & Browning, 2009] ||  
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| with 1% or 5% cutoff, [http://atgu.mgh.harvard.edu/plinkseq/ Will be implemented in PlinkSeq]  
 
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| RARECOVER || [http://www.ploscompbiol.org/article/info:doi/10.1371/journal.pcbi.1000954 Bhati et al. 2010] || || |
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| RARECOVER  
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| [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 Hoffman et al. 2010] || || [http://atgu.mgh.harvard.edu/plinkseq/ Will be implemented in PlinkSeq] |
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| Step-Up Collapsing*  
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| [http://www.plosone.org/article/info:doi/10.1371/journal.pone.0013584 Hoffman et al. 2010] ||  
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| [http://atgu.mgh.harvard.edu/plinkseq/ Will be implemented in PlinkSeq]  
 
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| 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] |
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| CMC/T5 test* || [http://www.ncbi.nlm.nih.gov/pubmed/18691683 Li & Leal, 2008] ||   
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| [http://atgu.mgh.harvard.edu/plinkseq/ Will be implemented in PlinkSeq]  
 
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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 || |
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| MENDEL* || [http://www.ncbi.nlm.nih.gov/pubmed/21121038 Zhou et al. 2011]  
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| http://www.genetics.ucla.edu/software/download?package=1 ||  
 
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| Logic regression* || [http://kooperberg.fhcrc.org/papers/2001gaw.pdf Kooperberg et al. 2001] ||  || |
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| Logic regression* || [http://kooperberg.fhcrc.org/papers/2001gaw.pdf Kooperberg et al. 2001] ||  ||  
 
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| Sequence diversity || Anderson et al. 2006 || || |
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| Sequence diversity || Anderson et al. 2006 || ||  
 
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| Sequence dissimilarity* || Schork et al. 2008, Wessel et al. 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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| Ridge regression * || Malo et al. 2008 || ||  
 
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Retrieved from "http://genome.sph.umich.edu/wiki/Special:MobileDiff/2866"

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