Difference between revisions of "Rare variant tests"
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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 | |
|- | |- | ||
− | | CMC/T1 test* || Li & Leal, 2008 || | + | | CMC/T1 test* || [http://www.ncbi.nlm.nih.gov/pubmed/18691683 Li & Leal, 2008] || || | |
|- | |- | ||
− | | KBAC || Liu & Leal, 2010 | + | | KBAC || [http://www.ncbi.nlm.nih.gov/pubmed/20976247 Liu & Leal, 2010] || || | |
|- | |- | ||
− | | VT* || 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 | |
|- | |- | ||
− | | WSS || Madsen & Browning, 2009 || || with 1% cutoff | + | | WSS || [http://www.ncbi.nlm.nih.gov/pubmed/19214210 Madsen & Browning, 2009] || || with 1% cutoff | |
|- | |- | ||
− | | CMAT || Zawistowski et al. 2010 || | + | | CMAT || [http://www.ncbi.nlm.nih.gov/pubmed/21070896 Zawistowski et al. 2010] || || | |
|- | |- | ||
+ | | ANRV/GRANVIL* || [http://www.ncbi.nlm.nih.gov/pubmed/19810025 Morris & Zeggini] || || | | ||
+ | |- | ||
+ | | RARECOVER || [http://www.ploscompbiol.org/article/info:doi/10.1371/journal.pcbi.1000954 Bhati 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/ || | | ||
+ | |- | ||
+ | | RVE (rare variant exclusive) || Cohen & Hobb || || underpowered | | ||
|} | |} | ||
+ | |||
+ | '''2) Aggregate tests for protective and detrimental variants (recommend 1% cutoff)''' | ||
+ | |||
+ | {| 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 | | ||
+ | |- | ||
+ | | C-alpha || [Neale et al., submitted] || || | | ||
+ | |- | ||
+ | | Ionita-Laza & Lange || [http://www.plosgenetics.org/article/info%3Adoi%2F10.1371%2Fjournal.pgen.1001289 Ionita-Laza & Lange, 2011] || || | | ||
+ | |- | ||
+ | | DASH* || [http://www.ncbi.nlm.nih.gov/pubmed/20413981 Han & Pan] || || Computational burden | | ||
+ | |- | ||
+ | | 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 | | ||
+ | |- | ||
+ | | WHaIT || [http://www.ncbi.nlm.nih.gov/pubmed/21055717 Li et al. 2010] || http://www.sph.umich.edu/csg/yli/whait/ || | | ||
+ | |- | ||
+ | | 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 || | | ||
+ | |} | ||
+ | |||
+ | '''Analyzing common and rare variants together (could down-weight or threshold common variants)''' | ||
+ | |||
+ | {| 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 | | ||
+ | |- | ||
+ | | WSS || [http://www.ncbi.nlm.nih.gov/pubmed/19214210 Madsen & Browning, 2009] || || with 1% or 5% cutoff | | ||
+ | |- | ||
+ | | 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 |
Revision as of 21:25, 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 |
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* | [http://www.plosone.org/article/info:doi/10.1371/journal.pone.0013584 |