Rare variant tests: Difference between revisions

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Created page with '=== 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 ? i…'
 
Cristen (talk | contribs)
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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 |
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| CMC/T1 test* || Li & Leal, 2008 ||  || ||
| CMC/T1 test* || [http://www.ncbi.nlm.nih.gov/pubmed/18691683 Li & Leal, 2008] ||  || |
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| KBAC || Liu & Leal, 2010 || || ||
| KBAC || [http://www.ncbi.nlm.nih.gov/pubmed/20976247 Liu & Leal, 2010] || || |
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| 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 |
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| WSS || Madsen & Browning, 2009 || || with 1% cutoff
| WSS || [http://www.ncbi.nlm.nih.gov/pubmed/19214210 Madsen & Browning, 2009] || || with 1% cutoff |
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| CMAT || Zawistowski et al. 2010 ||
| 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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| 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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| 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] ||  || |
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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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| 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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| 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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| 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
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