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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''' |
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| ! scope="col" align="left" | Notes | | ! scope="col" align="left" | Notes |
| |- | | |- |
− | | 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] | |
| |- | | |- |
− | | 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] | |
| |- | | |- |
− | | 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] | |
| |- | | |- |
− | | 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] | |
| |- | | |- |
| | 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] || || | |
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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/ || | | | | 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 | | + | | 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 |
| |- | | |- |
− | | C-alpha || [Neale et al., submitted] || || | | + | | C-alpha || [Neale et al., submitted] || || [http://atgu.mgh.harvard.edu/plinkseq/ Will be implemented in PlinkSeq] | |
| |- | | |- |
| | 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] || || | |
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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 |
| |- | | |- |
− | | 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] | |
| |- | | |- |
| | 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] || || | |
| |- | | |- |
− | | 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] | |
| |- | | |- |
| + | | 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] | |
| + | |- |
| + | | MENDEL* || [http://www.ncbi.nlm.nih.gov/pubmed/21121038 Zhou et al. 2011] || http://www.genetics.ucla.edu/software/download?package=1 || | |
| + | |} |
| + | |
| + | '''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" |
| + | |- |
| + | ! scope="col" align="left" | Test Name |
| + | ! scope="col" align="left" | Reference |
| + | ! scope="col" align="left" | Software |
| + | ! scope="col" align="left" | Notes |
| + | |- |
| + | | Logic regression* || [http://kooperberg.fhcrc.org/papers/2001gaw.pdf Kooperberg et al. 2001] || || | |
| + | |- |
| + | | Sequence diversity || Anderson et al. 2006 || || | |
| + | |- |
| + | | Sequence dissimilarity* || Schork et al. 2008, Wessel et al. 2006 || || | |
| + | |- |
| + | | Ridge regression * || Malo et al. 2008 || || | |
| + | |} |