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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'''
! 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] |
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| 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] |
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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 |
| 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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| 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] |
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| 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] || || |
| 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] |
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| 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] || || |
! 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
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| 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] |
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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 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] |
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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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| 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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'''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"
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! scope="col" align="left" | Test Name
! scope="col" align="left" | Reference
! scope="col" align="left" | Software
! scope="col" align="left" | Notes
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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 dissimilarity* || Schork et al. 2008, Wessel et al. 2006 || || |
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| Ridge regression * || Malo et al. 2008 || || |
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