Rare variant tests - Revision history

Ppwhite: /* Summary of rare variant tests for sequence data */

2017-02-02T15:35:35Z

Summary of rare variant tests for sequence data

← Older revision		Revision as of 11:35, 2 February 2017
Line 112:		Line 112:
	\|-		\|-
	\| WHaIT \|\| [http://www.ncbi.nlm.nih.gov/pubmed/21055717 Li et al. 2010]		\| WHaIT \|\| [http://www.ncbi.nlm.nih.gov/pubmed/21055717 Li et al. 2010]
	\| http://~~www~~.sph.umich.edu/~~csg~~/yli/whait/ \|\|		\| http://csg.sph.umich.edu//yli/whait/ \|\|
	\|-		\|-
	\| EMMPAT*		\| EMMPAT*

Zhanxw: /* Summary of rare variant tests for sequence data */

2012-03-07T15:07:09Z

Summary of rare variant tests for sequence data

← Older revision		Revision as of 11:07, 7 March 2012
Line 168:		Line 168:
	\| Sequence dissimilarity* \|\| Schork et al. 2008, Wessel et al. 2006 \|\| \|\|		\| Sequence dissimilarity* \|\| Schork et al. 2008, Wessel et al. 2006 \|\| \|\|
	\|-		\|-
	\| Ridge regression * \|\| Malo et al. 2008 \|\| \|\|		\| Ridge regression * \|\| [http://www.cell.com/AJHG/abstract/S0002-9297(08)00091-8 Malo et al. 2008] \|\| \|\|
	\|}		\|}

Goncalo: /* Summary of rare variant tests for sequence data */

2011-02-07T21:58:35Z

Summary of rare variant tests for sequence data

← Older revision		Revision as of 17:58, 7 February 2011
Line 61:		Line 61:
	! scope="col" align="left" \| Notes		! scope="col" align="left" \| Notes
	\|-		\|-
	\| 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] \|		\| 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] \|\| \|\| [http://atgu.mgh.harvard.edu/plinkseq/ Will be implemented in PlinkSeq] \|		\| 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, [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, [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, [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, [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] \|\| \|\|
	\|-		\|-
	\| ANRV/GRANVIL* \|\| [http://www.ncbi.nlm.nih.gov/pubmed/19810025 Morris & Zeggini] \|\| \|\| \|		\| 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] \|\| \|\| \|		\| 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/ \|\| \|		\| 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, [http://atgu.mgh.harvard.edu/plinkseq/ Will be implemented in PlinkSeq] \|		\| RVE (rare variant exclusive) \|\| Cohen & Hobbs \|\|
			\| underpowered, [http://atgu.mgh.harvard.edu/plinkseq/ Will be implemented in PlinkSeq]
	\|}		\|}

Line 91:		Line 99:
	! scope="col" align="left" \| Notes		! scope="col" align="left" \| Notes
	\|-		\|-
	\| C-alpha \|\| [Neale et al., submitted] \|\| \|\| [http://atgu.mgh.harvard.edu/plinkseq/ Will be implemented in PlinkSeq] \|		\| 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] \|\| \|\| \|
	\|-		\|-
	\| DASH* \|\| [http://www.ncbi.nlm.nih.gov/pubmed/20413981 Han & Pan] \|\| \|\| Computational burden \|		\| 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 \|		\| 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/ \|\| \|		\| 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 \|\| \|		\| 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 \|\|
	\|}		\|}

Line 115:		Line 130:
	! 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, [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% 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] \|\| \|\| [http://atgu.mgh.harvard.edu/plinkseq/ Will be implemented in PlinkSeq] \|		\| 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] \|		\| 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 \|\| \|		\| MENDEL* \|\| [http://www.ncbi.nlm.nih.gov/pubmed/21121038 Zhou et al. 2011]
			\| http://www.genetics.ucla.edu/software/download?package=1 \|\|
	\|}		\|}

Line 141:		Line 162:
	! scope="col" align="left" \| Notes		! scope="col" align="left" \| Notes
	\|-		\|-
	\| Logic regression* \|\| [http://kooperberg.fhcrc.org/papers/2001gaw.pdf Kooperberg et al. 2001] \|\| \|\| \|		\| Logic regression* \|\| [http://kooperberg.fhcrc.org/papers/2001gaw.pdf Kooperberg et al. 2001] \|\| \|\|
	\|-		\|-
	\| Sequence diversity \|\| Anderson et al. 2006 \|\| \|\| \|		\| Sequence diversity \|\| Anderson et al. 2006 \|\| \|\|
	\|-		\|-
	\| Sequence dissimilarity* \|\| Schork et al. 2008, Wessel et al. 2006 \|\| \|\| \|		\| Sequence dissimilarity* \|\| Schork et al. 2008, Wessel et al. 2006 \|\| \|\|
	\|-		\|-
	\| Ridge regression * \|\| Malo et al. 2008 \|\| \|\| \|		\| Ridge regression * \|\| Malo et al. 2008 \|\| \|\|
	\|}		\|}

Cristen: /* Summary of rare variant tests for sequence data */

2011-02-05T01:48:30Z

Summary of rare variant tests for sequence data

← Older revision		Revision as of 21:48, 4 February 2011
Line 48:		Line 48:

	* indicates applicability to quantitative data		* 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/)~~

	~~[http://atgu.mgh.harvard.edu/plinkseq/ Will be implemented in PlinkSeq]~~

Cristen: /* Summary of rare variant tests for sequence data */

2011-02-05T01:47:46Z

Summary of rare variant tests for sequence data

@@ Line 1: / Line 1: @@
 === Summary of rare variant tests for sequence data  ===
@@ Line 9: / Line 52: @@
 [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'''
@@ Line 37: / Line 82: @@
 | RVE (rare variant exclusive) || Cohen & Hobb || || underpowered, [http://atgu.mgh.harvard.edu/plinkseq/ Will be implemented in PlinkSeq] |
 |}
 '''2)   Aggregate tests for protective and detrimental variants (recommend 1% cutoff)'''
@@ Line 59: / Line 106: @@
 | 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 || |
 |}
 '''3) Analyzing common and rare variants together (could down-weight or threshold common variants)'''
@@ Line 79: / Line 128: @@
 | 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'''

Cristen: /* Summary of rare variant tests for sequence data */

2011-02-05T01:44:11Z

Summary of rare variant tests for sequence data

← Older revision		Revision as of 21:44, 4 February 2011
Line 8:		Line 8:
	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'''
Line 18:		Line 19:
	! 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] \|\| \|\| \|
Line 34:		Line 35:
	\| 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] \|
	\|}		\|}

Line 46:		Line 47:
	! 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] \|\| \|\| \|
Line 66:		Line 67:
	! 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 \|\| \|\| \|
			\|}

Cristen: /* Summary of rare variant tests for sequence data */

2011-02-05T01:27:24Z

Summary of rare variant tests for sequence data

Cristen: /* Summary of rare variant tests for sequence data */

2011-02-05T01:25:24Z

Summary of rare variant tests for sequence data

@@ Line 16: / Line 16: @@
 ! scope="col" align="left" | Reference
 ! 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] || || |
 |-
 |}

Cristen: 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…'

2011-02-05T01:05:13Z

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…'

New page

=== 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'''

{| 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
|-
| CMC/T1 test* || Li & Leal, 2008 || || ||
|-
| KBAC || Liu & Leal, 2010 || || ||
|-
| VT* || Price et al., 2010 || http://genetics.bwh.harvard.edu/rare_variants/ || Incorporating functional weights but not VT
|-
| WSS || Madsen & Browning, 2009 || || with 1% cutoff
|-
| CMAT || Zawistowski et al. 2010 ||
|-
|}

← Older revision		Revision as of 21:27, 4 February 2011
Line 16:		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* \|\| [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] \|\| \|\| \|
Line 44:		Line 44:
	! 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
	\|-		\|-
	\| C-alpha \|\| [Neale et al., submitted] \|\| \|\| \|		\| C-alpha \|\| [Neale et al., submitted] \|\| \|\| \|
Line 59:		Line 59:
	\|}		\|}

	'''Analyzing common and rare variants together (could down-weight or threshold common variants)'''		'''3) Analyzing common and rare variants together (could down-weight or threshold common variants)'''

	{\| width="75%" cellspacing="0" cellpadding="5" border="1"		{\| width="75%" cellspacing="0" cellpadding="5" border="1"
Line 72:		Line 72:
	\| 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		\| Step-Up Collapsing* \|\| [http://www.plosone.org/article/info:doi/10.1371/journal.pone.0013584 Hoffman et al. 2010] \|\| \|\| \|
			\|-