Exome Chip Design - Revision history

Cfuchsb: /* Second Generation Arrays */

2013-08-06T11:42:17Z

Second Generation Arrays

← Older revision		Revision as of 07:42, 6 August 2013
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	A second generation of exome arrays will be available in 2013, from both Illumina and Affymetrix. In addition to the original exome array content, each of these includes a grid of SNPs across the genome that facilitates analysis of common variants when a suitably large reference panel is available. These grids were selected both to ensure good coverage of the genome and to ensure that assays could be manufactured inexpensively, taking into account proprietary platform specific constraints.		A second generation of exome arrays will be available in 2013, from both Illumina and Affymetrix. In addition to the original exome array content, each of these includes a grid of SNPs across the genome that facilitates analysis of common variants when a suitably large reference panel is available. These grids were selected both to ensure good coverage of the genome and to ensure that assays could be manufactured inexpensively, taking into account proprietary platform specific constraints.

	To evaluate the accuracy of these grids, we have used data from the Go T2D project (led by David Altshuler, Mike Boehnke and Mark McCarthy). The dataset includes ~2,650 individuals that have been whole genome sequenced (depth ~4x) and whole exome sequenced (depth ~80-100x). We focused on 600 samples from the UK and, for each of these in turn, tried to impute missing genotypes using the remaining sequenced individuals as a reference panel. The results show both the Affymetrix and Illumina arrays are expected to provide excellent coverage of the genome provided that a suitably large reference panel is available.		To evaluate the accuracy of these grids, we have used data from the Go T2D project (led by David Altshuler, Mike Boehnke and Mark McCarthy). The dataset includes ~2,650 individuals that have been whole genome sequenced (depth ~4x) and whole exome sequenced (depth ~80-100x). We focused on chr20 and 600 samples from the UK and, for each of these in turn, tried to impute missing genotypes using the remaining sequenced individuals as a reference panel. The results show both the Affymetrix and Illumina arrays are expected to provide excellent coverage of the genome provided that a suitably large reference panel is available.

	The specific numbers are that:		The specific numbers are that:

Cfuchsb: /* Second Generation Arrays */

2013-08-06T11:40:47Z

Second Generation Arrays

← Older revision		Revision as of 07:40, 6 August 2013
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	* For variants with MAF >5%, 94.6% (Affymetrix) and 89.2% (Illumina)		* For variants with MAF >5%, 94.6% (Affymetrix) and 89.2% (Illumina)

	The evaluation is based on imputation of ~600 UK samples that have been whole genome and whole exome sequenced (comparing imputed genotypes and the sequenced based calls) and using a panel of 2,~~500~~ sequenced individuals from the T2D-Go Project (Altshuler, Boehnke, McCarthy) as a reference.		The evaluation is based on imputation of ~600 UK samples that have been whole genome and whole exome sequenced (comparing imputed genotypes and the sequenced based calls) and using a panel of 2,650 sequenced individuals from the T2D-Go Project (Altshuler, Boehnke, McCarthy) as a reference.

	All evaluations used [[Minimac]] and were carried out by [mailto:cfuchsb@umich.edu Christian Fuchsberger].		All evaluations used [[Minimac]] and were carried out by [mailto:cfuchsb@umich.edu Christian Fuchsberger].

Goncalo: /* Cautious Sites */

2013-06-12T07:30:00Z

Cautious Sites

← Older revision		Revision as of 03:30, 12 June 2013
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	== ~~Cautious~~ Sites ==		== Sites to be Careful About ==

	333 exome chip variants sites should be treated ~~cautiously~~.		Peter Chines, working with Francis Collins, provided a list of 333 exome chip variants sites that should be treated with caution. The sites include variants for which the SNP probe differs from the expected reference genome sequence, could not be mapped back to the reference, mapped to multiple places, or where neither allele matches the reference genome.
	~~Refer to this~~ plain text ~~files~~ of ~~those~~ sites [ftp://share.sph.umich.edu/exomeChip/IlluminaDesigns/cautiousSites/cautiousSite.sorted.sites list] and [ftp://share.sph.umich.edu/exomeChip/IlluminaDesigns/cautiousSites/cautiousSite.sorted.README descriptions].
			A plain text list of these sites [ftp://share.sph.umich.edu/exomeChip/IlluminaDesigns/cautiousSites/cautiousSite.sorted.sites list] and corresponding [ftp://share.sph.umich.edu/exomeChip/IlluminaDesigns/cautiousSites/cautiousSite.sorted.README descriptions] are available.

	= Affymetrix Exome Arrays =		= Affymetrix Exome Arrays =

Goncalo: /* Second Generation Arrays */

2013-01-09T16:50:11Z

Second Generation Arrays

← Older revision		Revision as of 12:50, 9 January 2013
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	The specific numbers are that:		The specific numbers are that:

	For variants with MAF >1%, the average r<sup>2</sup> correlation between imputed and true genotypes will be 0.8879 (Affymetrix) and 0.8590 (Illumina).		* For variants with MAF >1%, the average r<sup>2</sup> correlation between imputed and true genotypes will be 0.8879 (Affymetrix) and 0.8590 (Illumina).
	For variants with MAF >5%, the average r<sup>2</sup> correlation between imputed and true genotypes will be 0.9458 (Affymetrix) and 0.9256 (Illumina).		* For variants with MAF >5%, the average r<sup>2</sup> correlation between imputed and true genotypes will be 0.9458 (Affymetrix) and 0.9256 (Illumina).

	The fraction of variants imputed with r<sup>2<sup> > 0.80 will be:		The fraction of variants imputed with r<sup>2</sup> > 0.80 will be:

	For variants with MAF >1%, 82.1% (Affymetrix) and 76.5% (Illumina)		* For variants with MAF >1%, 82.1% (Affymetrix) and 76.5% (Illumina)
	For variants with MAF >5%, 94.6% (Affymetrix) and 89.2% (Illumina)		* For variants with MAF >5%, 94.6% (Affymetrix) and 89.2% (Illumina)

	The evaluation is based on imputation of ~600 UK samples that have been whole genome and whole exome sequenced (comparing imputed genotypes and the sequenced based calls) and using a panel of 2,500 sequenced individuals from the T2D-Go Project (Altshuler, Boehnke, McCarthy) as a reference.		The evaluation is based on imputation of ~600 UK samples that have been whole genome and whole exome sequenced (comparing imputed genotypes and the sequenced based calls) and using a panel of 2,500 sequenced individuals from the T2D-Go Project (Altshuler, Boehnke, McCarthy) as a reference.

Goncalo: /* Second Generation Arrays */

2013-01-09T16:49:39Z

Second Generation Arrays

← Older revision		Revision as of 12:49, 9 January 2013
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	The evaluation is based on imputation of ~600 UK samples that have been whole genome and whole exome sequenced (comparing imputed genotypes and the sequenced based calls) and using a panel of 2,500 sequenced individuals from the T2D-Go Project (Altshuler, Boehnke, McCarthy) as a reference.		The evaluation is based on imputation of ~600 UK samples that have been whole genome and whole exome sequenced (comparing imputed genotypes and the sequenced based calls) and using a panel of 2,500 sequenced individuals from the T2D-Go Project (Altshuler, Boehnke, McCarthy) as a reference.

	All evaluations used [[Minimac]] and were carried out by ~~Christian Fuchsberger~~ [mailto:cfuchsb@umich.edu].		All evaluations used [[Minimac]] and were carried out by [mailto:cfuchsb@umich.edu Christian Fuchsberger].

	= Illumina Exome Arrays =		= Illumina Exome Arrays =

Goncalo: /* Illumina Exome Arrays */

2013-01-09T16:49:13Z

Illumina Exome Arrays

@@ Line 233: / Line 233: @@
 Paul De Bakker's HLA tag SNPs are listed here:
 http://www.broadinstitute.org/~debakker/hla_tags_exome.txt
 = Illumina Exome Arrays =

Zhanxw: /* Cautious Sites */

2012-06-07T19:08:12Z

Cautious Sites

← Older revision		Revision as of 15:08, 7 June 2012
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	== Cautious Sites ==		== Cautious Sites ==

	~~487~~ exome chip variants sites should be treated cautiously.		333 exome chip variants sites should be treated cautiously.
	~~Detailed~~ sites list and ~~explanations can be found in a FTPlink, which will be provided soon~~.		Refer to this plain text files of those sites [ftp://share.sph.umich.edu/exomeChip/IlluminaDesigns/cautiousSites/cautiousSite.sorted.sites list] and [ftp://share.sph.umich.edu/exomeChip/IlluminaDesigns/cautiousSites/cautiousSite.sorted.README descriptions].

	= Affymetrix Exome Arrays =		= Affymetrix Exome Arrays =

Zhanxw: /* Assay Design Rates */

2012-06-07T02:14:47Z

Assay Design Rates

← Older revision		Revision as of 22:14, 6 June 2012
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			== Cautious Sites ==

			487 exome chip variants sites should be treated cautiously.
			Detailed sites list and explanations can be found in a FTPlink, which will be provided soon.

	= Affymetrix Exome Arrays =		= Affymetrix Exome Arrays =

Benjamin Neale: /* Non-synonymous Variants */

2012-05-01T18:34:04Z

Non-synonymous Variants

← Older revision		Revision as of 14:34, 1 May 2012
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	== Non-synonymous Variants ==		== Non-synonymous Variants ==

	We tallied 1,107,05 nonsynonymous variants seen at least once across ~12,000 sequenced samples. Among the non-synonymous variants, the majority were seen only once (646,888) or twice (163,044), as expected. Of the remaining variants (297,119), a total of 260,054 were seen in at least 2 datasets and are considered as candidates for inclusion in exome SNP arrays. The transition transversion ratio of this class of variants was 2.0 in the full set of variants and 2.49 in the set of variants that were seen at least three times and in two or more studies.		We tallied 1,107,051 nonsynonymous variants seen at least once across ~12,000 sequenced samples. Among the non-synonymous variants, the majority were seen only once (646,888) or twice (163,044), as expected. Of the remaining variants (297,119), a total of 260,054 were seen in at least 2 datasets and are considered as candidates for inclusion in exome SNP arrays. The transition transversion ratio of this class of variants was 2.0 in the full set of variants and 2.49 in the set of variants that were seen at least three times and in two or more studies.

	The set of variants selected for array design is estimated to include 97-98% of the nonsynonymous variants detected in average genome through exome sequencing.		The set of variants selected for array design is estimated to include 97-98% of the nonsynonymous variants detected in average genome through exome sequencing.

Jeanette Schmidt: /* Coding Variants: Design Criteria */

2012-04-27T06:32:40Z

Coding Variants: Design Criteria

← Older revision		Revision as of 02:32, 27 April 2012
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	\| bgcolor="lightgray" scope="row" align="right" \| 56,095		\| bgcolor="lightgray" scope="row" align="right" \| 56,095
	\| bgcolor="lightgray" scope="row" align="right" \| 35,137		\| bgcolor="lightgray" scope="row" align="right" \| 35,137
	\| bgcolor="lightgray" scope="row" \|   Includes biallelic indels from the draft Phase 1 1000 Genomes Project ~~<br>  ~~and previously validated indels in the Axiom Genomic Database; <br>   indel size ranges from 1-138bp.		\| bgcolor="lightgray" scope="row" \|   Includes biallelic indels from the draft Phase 1 1000 Genomes Project and previously validated indels in the Axiom Genomic Database; <br>   indel size ranges from 1-138bp.
	\|-		\|-
	! scope="row" \|		! scope="row" \|

← Older revision		Revision as of 02:32, 27 April 2012
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	\| bgcolor="lightgray" scope="row" align="right" \| 56,095		\| bgcolor="lightgray" scope="row" align="right" \| 56,095
	\| bgcolor="lightgray" scope="row" align="right" \| 35,137		\| bgcolor="lightgray" scope="row" align="right" \| 35,137
	\| bgcolor="lightgray" scope="row" \|   Includes biallelic indels from the draft Phase 1 1000 Genomes Project ~~<br>  ~~and previously validated indels in the Axiom Genomic Database; <br>   indel size ranges from 1-138bp.		\| bgcolor="lightgray" scope="row" \|   Includes biallelic indels from the draft Phase 1 1000 Genomes Project and previously validated indels in the Axiom Genomic Database; <br>   indel size ranges from 1-138bp.
	\|-		\|-
	! scope="row" \|		! scope="row" \|