Regions of high linkage disequilibrium (LD) - Revision history

Mflick at 02:38, 11 October 2021

2021-10-11T02:38:39Z

← Older revision		Revision as of 22:38, 10 October 2021
Line 1:		Line 1:
	There are regions of long-range, high linkage diequilibrium in the human genome <ref>Price et al. (2008) Long-Range LD Can Confound Genome Scans in Admixed Populations. Am. J. Hum. Genet. 86, 127-147</ref><ref>Weale M. (2010) Quality Control for Genome-Wide Association Studies from Michael R. Barnes and Gerome Breen (eds.), Genetic Variation: Methods and Protocols, Methods in Molecular Biology, vol. 628, DOI 10.1007/978-1-60327-367-1_19, © Springer Science+Business Media, LLC 2010</ref>. These regions should be excluded when performing certain analyses such as principal component analysis on genotype data.		There are regions of long-range, high linkage diequilibrium in the human genome <ref>Price et al. (2008) Long-Range LD Can Confound Genome Scans in Admixed Populations. Am. J. Hum. Genet. 86, 127-147</ref><ref>Weale M. (2010) Quality Control for Genome-Wide Association Studies from Michael R. Barnes and Gerome Breen (eds.), Genetic Variation: Methods and Protocols, Methods in Molecular Biology, vol. 628, DOI 10.1007/978-1-60327-367-1_19, © Springer Science+Business Media, LLC 2010</ref>. These regions should be excluded when performing certain analyses such as principal component analysis on genotype data.

	[[Image:High-ld.png]]		[[Image:High-ld-b38.png]]


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	Here is a list of positions for GRCH Build 37		Here is a list of positions for GRCH Build 37

			[[Image:High-ld.png]]

	<tab border="1" head="top">		<tab border="1" head="top">
	Chr Start Stop		Chr Start Stop

Mflick at 03:12, 10 October 2021

2021-10-10T03:12:00Z

@@ Line 3: / Line 3: @@
 [[Image:High-ld.png]]
-Here is a lost of positions for GRCH Build 37
 <tab border="1" head="top">
 Chr	Start	Stop

Mflick at 17:02, 27 July 2017

2017-07-27T17:02:23Z

← Older revision		Revision as of 13:02, 27 July 2017
Line 5:		Line 5:
	Here is a lost of positions for GRCH Build 37		Here is a lost of positions for GRCH Build 37
	<tab border="1" head="top">		<tab border="1" head="top">
	Chr Start Stop ID		Chr Start Stop
	1 48000000 52000000		1 48000000 52000000
	2 86000000 100500000		2 86000000 100500000

Mflick at 17:02, 27 July 2017

2017-07-27T17:02:03Z

← Older revision		Revision as of 13:02, 27 July 2017
Line 2:		Line 2:

	[[Image:High-ld.png]]		[[Image:High-ld.png]]

			Here is a lost of positions for GRCH Build 37
			<tab border="1" head="top">
			Chr Start Stop ID
			1 48000000 52000000
			2 86000000 100500000
			2 134500000 138000000
			2 183000000 190000000
			3 47500000 50000000
			3 83500000 87000000
			3 89000000 97500000
			5 44500000 50500000
			5 98000000 100500000
			5 129000000 132000000
			5 135500000 138500000
			6 25000000 35000000
			6 57000000 64000000
			6 140000000 142500000
			7 55000000 66000000
			8 7000000 13000000
			8 43000000 50000000
			8 112000000 115000000
			10 37000000 43000000
			11 46000000 57000000
			11 87500000 90500000
			12 33000000 40000000
			12 109500000 112000000
			20 32000000 34500000
			</tab>


	These positions are for GRCH build 36.		These positions are for GRCH build 36.
Line 30:		Line 60:
	12 109521663 112021663 hild23		12 109521663 112021663 hild23
	20 32000000 34500000 hild24		20 32000000 34500000 hild24
	23 14150264 16650264 hild25		X 14150264 16650264 hild25
	23 25650264 28650264 hild26		X 25650264 28650264 hild26
	23 33150264 35650264 hild27		X 33150264 35650264 hild27
	23 55133704 60500000 hild28		X 55133704 60500000 hild28
	23 65133704 67633704 hild29		X 65133704 67633704 hild29
	23 71633704 77580511 hild30		X 71633704 77580511 hild30
	23 80080511 86080511 hild31		X 80080511 86080511 hild31
	23 100580511 103080511 hild32		X 100580511 103080511 hild32
	23 125602146 128102146 hild33		X 125602146 128102146 hild33
	23 129102146 131602146 hild34		X 129102146 131602146 hild34
	</tab>		</tab>

Mflick at 16:55, 27 July 2017

2017-07-27T16:55:31Z

← Older revision		Revision as of 12:55, 27 July 2017
Line 3:		Line 3:
	[[Image:High-ld.png]]		[[Image:High-ld.png]]

			These positions are for GRCH build 36.
	<tab border="1" head="top">		<tab border="1" head="top">
	Chr Start Stop ID		Chr Start Stop ID

Mflick: used new SimpleTable extension

2012-01-25T14:39:13Z

used new SimpleTable extension

← Older revision		Revision as of 10:39, 25 January 2012
Line 1:		Line 1:
	There are regions of long-range, high linkage diequilibrium in the human genome <ref>Price et al. (2008) Long-Range LD Can Confound Genome Scans in Admixed Populations. Am. J. Hum. Genet. 86, 127-147</ref><ref>Weale M. (2010) Quality Control for Genome-Wide Association Studies from Michael R. Barnes and Gerome Breen (eds.), Genetic Variation: Methods and Protocols, Methods in Molecular Biology, vol. 628, DOI 10.1007/978-1-60327-367-1_19, © Springer Science+Business Media, LLC 2010</ref>. These regions should be excluded when performing certain analyses such as principal component analysis on genotype data.		There are regions of long-range, high linkage diequilibrium in the human genome <ref>Price et al. (2008) Long-Range LD Can Confound Genome Scans in Admixed Populations. Am. J. Hum. Genet. 86, 127-147</ref><ref>Weale M. (2010) Quality Control for Genome-Wide Association Studies from Michael R. Barnes and Gerome Breen (eds.), Genetic Variation: Methods and Protocols, Methods in Molecular Biology, vol. 628, DOI 10.1007/978-1-60327-367-1_19, © Springer Science+Business Media, LLC 2010</ref>. These regions should be excluded when performing certain analyses such as principal component analysis on genotype data.

	[[~~File~~:High-ld.png]]		[[Image:High-ld.png]]

	~~{\| class~~="~~wikitable~~" ~~border~~=1		<tab border="1" head="top">
	! Chr		Chr Start Stop ID
	! Start		1 48060567 52060567 hild1
	! Stop		2 85941853 100407914 hild2
	! ID		2 134382738 137882738 hild3
	\|-		2 182882739 189882739 hild4
	\| 1 \|\| 48060567 \|\| 52060567 \|\| hild1		3 47500000 50000000 hild5
	\|-		3 83500000 87000000 hild6
	\| 2 \|\| 85941853 \|\| 100407914 \|\| hild2		3 89000000 97500000 hild7
	\|-		5 44500000 50500000 hild8
	\| 2 \|\| 134382738 \|\| 137882738 \|\| hild3		5 98000000 100500000 hild9
	\|-		5 129000000 132000000 hild10
	\| 2 \|\| 182882739 \|\| 189882739 \|\| hild4		5 135500000 138500000 hild11
	\|-		6 25500000 33500000 hild12
	\| 3 \|\| 47500000 \|\| 50000000 \|\| hild5		6 57000000 64000000 hild13
	\|-		6 140000000 142500000 hild14
	\| 3 \|\| 83500000 \|\| 87000000 \|\| hild6		7 55193285 66193285 hild15
	\|-		8 8000000 12000000 hild16
	\| 3 \|\| 89000000 \|\| 97500000 \|\| hild7		8 43000000 50000000 hild17
	\|-		8 112000000 115000000 hild18
	\| 5 \|\| 44500000 \|\| 50500000 \|\| hild8		10 37000000 43000000 hild19
	\|-		11 46000000 57000000 hild20
	\| 5 \|\| 98000000 \|\| 100500000 \|\| hild9		11 87500000 90500000 hild21
	\|-		12 33000000 40000000 hild22
	\| 5 \|\| 129000000 \|\| 132000000 \|\| hild10		12 109521663 112021663 hild23
	\|-		20 32000000 34500000 hild24
	\| 5 \|\| 135500000 \|\| 138500000 \|\| hild11		23 14150264 16650264 hild25
	\|-		23 25650264 28650264 hild26
	\| 6 \|\| 25500000 \|\| 33500000 \|\| hild12		23 33150264 35650264 hild27
	\|-		23 55133704 60500000 hild28
	\| 6 \|\| 57000000 \|\| 64000000 \|\| hild13		23 65133704 67633704 hild29
	\|-		23 71633704 77580511 hild30
	\| 6 \|\| 140000000 \|\| 142500000 \|\| hild14		23 80080511 86080511 hild31
	\|-		23 100580511 103080511 hild32
	\| 7 \|\| 55193285 \|\| 66193285 \|\| hild15		23 125602146 128102146 hild33
	\|-		23 129102146 131602146 hild34
	\| 8 \|\| 8000000 \|\| 12000000 \|\| hild16		</tab>
	\|-
	\| 8 \|\| 43000000 \|\| 50000000 \|\| hild17
	\|-
	\| 8 \|\| 112000000 \|\| 115000000 \|\| hild18
	\|-
	\| 10 \|\| 37000000 \|\| 43000000 \|\| hild19
	\|-
	\| 11 \|\| 46000000 \|\| 57000000 \|\| hild20
	\|-
	\| 11 \|\| 87500000 \|\| 90500000 \|\| hild21
	\|-
	\| 12 \|\| 33000000 \|\| 40000000 \|\| hild22
	\|-
	\| 12 \|\| 109521663 \|\| 112021663 \|\| hild23
	\|-
	\| 20 \|\| 32000000 \|\| 34500000 \|\| hild24
	\|-
	\| 23 \|\| 14150264 \|\| 16650264 \|\| hild25
	\|-
	\| 23 \|\| 25650264 \|\| 28650264 \|\| hild26
	\|-
	\| 23 \|\| 33150264 \|\| 35650264 \|\| hild27
	\|-
	\| 23 \|\| 55133704 \|\| 60500000 \|\| hild28
	\|-
	\| 23 \|\| 65133704 \|\| 67633704 \|\| hild29
	\|-
	\| 23 \|\| 71633704 \|\| 77580511 \|\| hild30
	\|-
	\| 23 \|\| 80080511 \|\| 86080511 \|\| hild31
	\|-
	\| 23 \|\| 100580511 \|\| 103080511 \|\| hild32
	\|-
	\| 23 \|\| 125602146 \|\| 128102146 \|\| hild33
	\|-
	\| 23 \|\| 129102146 \|\| 131602146 \|\| hild34
	\|}

	== Excluding Regions With Plink ==		== Excluding Regions With Plink ==

	You can remove these regions from a PED file using the following PLINK commands. Assuming you have the data stored in a file named "high-ld.txt"		You can remove these regions from a PED file using the following PLINK commands. Assuming you have the data stored in a file named "high-ld.txt"

	plink --file mydata --make-set high-ld.txt --write-set --out hild		plink --file mydata --make-set high-ld.txt --write-set --out hild
	plink --file mydata --exclude hild.set --recode --out mydatatrimmed		plink --file mydata --exclude hild.set --recode --out mydatatrimmed

	=References=		= References =
	<references/>
			<references />

Mflick at 04:57, 23 January 2012

2012-01-23T04:57:13Z

← Older revision		Revision as of 00:57, 23 January 2012
Line 1:		Line 1:
	There are regions of high linkage diequilibrium in the human genome. These regions should be excluded when performing certain analyses such as principal component analysis on genotype data.		There are regions of long-range, high linkage diequilibrium in the human genome <ref>Price et al. (2008) Long-Range LD Can Confound Genome Scans in Admixed Populations. Am. J. Hum. Genet. 86, 127-147</ref><ref>Weale M. (2010) Quality Control for Genome-Wide Association Studies from Michael R. Barnes and Gerome Breen (eds.), Genetic Variation: Methods and Protocols, Methods in Molecular Biology, vol. 628, DOI 10.1007/978-1-60327-367-1_19, © Springer Science+Business Media, LLC 2010</ref>. These regions should be excluded when performing certain analyses such as principal component analysis on genotype data.

	[[File:High-ld.png]]		[[File:High-ld.png]]
Line 84:		Line 84:
	plink --file mydata --make-set high-ld.txt --write-set --out hild		plink --file mydata --make-set high-ld.txt --write-set --out hild
	plink --file mydata --exclude hild.set --recode --out mydatatrimmed		plink --file mydata --exclude hild.set --recode --out mydatatrimmed

			=References=
			<references/>

Mflick at 03:14, 19 January 2012

2012-01-19T03:14:09Z

← Older revision		Revision as of 23:14, 18 January 2012
Line 77:		Line 77:
	\| 23 \|\| 129102146 \|\| 131602146 \|\| hild34		\| 23 \|\| 129102146 \|\| 131602146 \|\| hild34
	\|}		\|}

			== Excluding Regions With Plink ==

			You can remove these regions from a PED file using the following PLINK commands. Assuming you have the data stored in a file named "high-ld.txt"

			plink --file mydata --make-set high-ld.txt --write-set --out hild
			plink --file mydata --exclude hild.set --recode --out mydatatrimmed

Mflick: Created page with 'There are regions of high linkage diequilibrium in the human genome. These regions should be excluded when performing certain analyses such as principal component analysis on gen…'

2012-01-19T03:07:11Z

Created page with 'There are regions of high linkage diequilibrium in the human genome. These regions should be excluded when performing certain analyses such as principal component analysis on gen…'

New page

There are regions of high linkage diequilibrium in the human genome. These regions should be excluded when performing certain analyses such as principal component analysis on genotype data.

[[File:High-ld.png]]

{| class="wikitable" border=1
! Chr
! Start
! Stop
! ID
|-
| 1 || 48060567 || 52060567 || hild1
|-
| 2 || 85941853 || 100407914 || hild2
|-
| 2 || 134382738 || 137882738 || hild3
|-
| 2 || 182882739 || 189882739 || hild4
|-
| 3 || 47500000 || 50000000 || hild5
|-
| 3 || 83500000 || 87000000 || hild6
|-
| 3 || 89000000 || 97500000 || hild7
|-
| 5 || 44500000 || 50500000 || hild8
|-
| 5 || 98000000 || 100500000 || hild9
|-
| 5 || 129000000 || 132000000 || hild10
|-
| 5 || 135500000 || 138500000 || hild11
|-
| 6 || 25500000 || 33500000 || hild12
|-
| 6 || 57000000 || 64000000 || hild13
|-
| 6 || 140000000 || 142500000 || hild14
|-
| 7 || 55193285 || 66193285 || hild15
|-
| 8 || 8000000 || 12000000 || hild16
|-
| 8 || 43000000 || 50000000 || hild17
|-
| 8 || 112000000 || 115000000 || hild18
|-
| 10 || 37000000 || 43000000 || hild19
|-
| 11 || 46000000 || 57000000 || hild20
|-
| 11 || 87500000 || 90500000 || hild21
|-
| 12 || 33000000 || 40000000 || hild22
|-
| 12 || 109521663 || 112021663 || hild23
|-
| 20 || 32000000 || 34500000 || hild24
|-
| 23 || 14150264 || 16650264 || hild25
|-
| 23 || 25650264 || 28650264 || hild26
|-
| 23 || 33150264 || 35650264 || hild27
|-
| 23 || 55133704 || 60500000 || hild28
|-
| 23 || 65133704 || 67633704 || hild29
|-
| 23 || 71633704 || 77580511 || hild30
|-
| 23 || 80080511 || 86080511 || hild31
|-
| 23 || 100580511 || 103080511 || hild32
|-
| 23 || 125602146 || 128102146 || hild33
|-
| 23 || 129102146 || 131602146 || hild34
|}