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Line 16: |
| ! 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 |