ContaminationDetection - Revision history

Gzajac: /* Overview */

2017-05-03T19:53:47Z

Overview

← Older revision		Revision as of 15:53, 3 May 2017
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	#** The method provides a well calibrated Type I error to test the null hypothesis of no contamination from a DNA sample.		#** The method provides a well calibrated Type I error to test the null hypothesis of no contamination from a DNA sample.
	#* [[VICES]] jointly estimates contamination and its sources from genotyping array intensities.		#* [[VICES]] jointly estimates contamination and its sources from genotyping array intensities.
			#** Can be useful to determine where in the process contamination occurred and whether DNA can be salvaged from leftover DNA earlier in the genotyping pipeline, or to revise laboratory protocols.

	== History ==		== History ==
	* Initial description of method 1 can be found at [[Verifying_Sample_Identities_-_Implementation]] (last modified in April 29, 2010)		* Initial description of method 1 can be found at [[Verifying_Sample_Identities_-_Implementation]] (last modified in April 29, 2010)

Gzajac: /* Overview */

2017-05-03T19:51:59Z

Overview

← Older revision		Revision as of 15:51, 3 May 2017
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	#** This method is sensitive to estimate low levels of contamination.		#** This method is sensitive to estimate low levels of contamination.
	#** The method provides a well calibrated Type I error to test the null hypothesis of no contamination from a DNA sample.		#** The method provides a well calibrated Type I error to test the null hypothesis of no contamination from a DNA sample.
			#* [[VICES]] jointly estimates contamination and its sources from genotyping array intensities.

	== History ==		== History ==
	* Initial description of method 1 can be found at [[Verifying_Sample_Identities_-_Implementation]] (last modified in April 29, 2010)		* Initial description of method 1 can be found at [[Verifying_Sample_Identities_-_Implementation]] (last modified in April 29, 2010)

Gjun at 21:19, 24 April 2012

2012-04-24T21:19:06Z

← Older revision		Revision as of 17:19, 24 April 2012
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	#* The key idea of the method is to capture the excessive heterozygosity in the contaminated sample by modeling the sequence reads as mixture of independent samples.		#* The key idea of the method is to capture the excessive heterozygosity in the contaminated sample by modeling the sequence reads as mixture of independent samples.
	# When a sample has array-based genotypes but not yet sequenced		# When a sample has array-based genotypes but not yet sequenced
	#* [[VerifyIDintensity]] software can estimate the levels of DNA sample contamination from ~~aligned sequence reads and population allele frequency~~		#* [[VerifyIDintensity]] software can estimate the levels of DNA sample contamination from pre-computed intensity data using likelihood-based model.
	#** The key idea is similar to that of [[VerifyBamID]] with sequence data alone		#** The key idea is similar to that of [[VerifyBamID]] with sequence data alone
	#** [[VerifyIDintensity]] models array intensity data instead of sequence reads		#** [[VerifyIDintensity]] models array intensity data instead of sequence reads

Gjun: /* Overview */

2012-04-24T20:48:21Z

Overview

← Older revision		Revision as of 16:48, 24 April 2012
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	#* The key idea of the method is to capture the excessive heterozygosity in the contaminated sample by modeling the sequence reads as mixture of independent samples.		#* The key idea of the method is to capture the excessive heterozygosity in the contaminated sample by modeling the sequence reads as mixture of independent samples.
	# When a sample has array-based genotypes but not yet sequenced		# When a sample has array-based genotypes but not yet sequenced
	#* [[~~VerifyIntensity~~]] software can estimate the levels of DNA sample contamination from aligned sequence reads and population allele frequency		#* [[VerifyIDintensity]] software can estimate the levels of DNA sample contamination from aligned sequence reads and population allele frequency
	#** The key idea is similar to that of [[VerifyBamID]] with sequence data alone		#** The key idea is similar to that of [[VerifyBamID]] with sequence data alone
	#** [[~~VerifyIntensity~~]] models array intensity data instead of sequence reads		#** [[VerifyIDintensity]] models array intensity data instead of sequence reads
	#** When a large number of samples are genotyped together, the 'multi-sample' option will estimate the intensity distribution for each marker across multiple samples. When only one a few samples are genotyped, 'per-sample' option will estimate the intensity distribution for each sample across all markers.		#** When a large number of samples are genotyped together, the 'multi-sample' option will estimate the intensity distribution for each marker across multiple samples. When only one a few samples are genotyped, 'per-sample' option will estimate the intensity distribution for each sample across all markers.
	#* [[BAFRegress]] software can estimate levels of sample contamination and test the presence of contamination by regressing the allele frequency with respect to the B allele frequency (BAF).		#* [[BAFRegress]] software can estimate levels of sample contamination and test the presence of contamination by regressing the allele frequency with respect to the B allele frequency (BAF).

Hmkang: /* Overview */

2012-04-24T11:11:27Z

Overview

← Older revision		Revision as of 07:11, 24 April 2012
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	DNA sample contamination (or sample swap) is quite common in sequencing studies. It is possible to detect DNA contamination from sequence reads of intensity data from SNP genotyping arrays by modeling the likelihood of sequence reads as a mixture of two samples and estimating the fraction of reads contributed by contaminating samples.		DNA sample contamination (or sample swap) is quite common in sequencing studies. It is possible to detect DNA contamination from sequence reads of intensity data from SNP genotyping arrays by modeling the likelihood of sequence reads as a mixture of two samples and estimating the fraction of reads contributed by contaminating samples.

	Depending on the types of available data, we can detect contamination in the following ways.		Depending on the types of available data, one can detect DNA sample contamination in the following ways.

	# When a sequenced sample has also external array-based genotypes available		# When a sequenced sample has also external array-based genotypes available

Hmkang: /* History */

2012-04-24T11:10:41Z

History

← Older revision		Revision as of 07:10, 24 April 2012
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	== History ==		== History ==
	* Initial description of ~~the first~~ method can be found at [[Verifying_Sample_Identities_-_Implementation]] (last modified in April 29, 2010)		* Initial description of method 1 can be found at [[Verifying_Sample_Identities_-_Implementation]] (last modified in April 29, 2010)

Hmkang: /* History */

2012-04-24T11:10:25Z

History

← Older revision		Revision as of 07:10, 24 April 2012
Line 21:		Line 21:

	== History ==		== History ==
	* Initial ~~version of mathematical~~ description of the first method can be found at [[Verifying_Sample_Identities_-_Implementation]] (last modified in April 29, 2010)		* Initial description of the first method can be found at [[Verifying_Sample_Identities_-_Implementation]] (last modified in April 29, 2010)

Hmkang: /* History */

2012-04-24T11:10:10Z

History

← Older revision		Revision as of 07:10, 24 April 2012
Line 21:		Line 21:

	== History ==		== History ==
	* Initial version of mathematical description of the first method can be found at [[Verifying_Sample_Identities_-_Implementation]]		* Initial version of mathematical description of the first method can be found at [[Verifying_Sample_Identities_-_Implementation]] (last modified in April 29, 2010)

Hmkang: Created page with '== Overview == DNA sample contamination (or sample swap) is quite common in sequencing studies. It is possible to detect DNA contamination from sequence reads of intensity data …'

2012-04-24T11:09:43Z

Created page with '== Overview == DNA sample contamination (or sample swap) is quite common in sequencing studies. It is possible to detect DNA contamination from sequence reads of intensity data …'

New page

== Overview ==

DNA sample contamination (or sample swap) is quite common in sequencing studies. It is possible to detect DNA contamination from sequence reads of intensity data from SNP genotyping arrays by modeling the likelihood of sequence reads as a mixture of two samples and estimating the fraction of reads contributed by contaminating samples.

Depending on the types of available data, we can detect contamination in the following ways.

# When a sequenced sample has also external array-based genotypes available
#* [[VerifyBamID]] software can estimate the levels of sample contamination and detect sample swap from alignment sequence reads and the external genotypes
#* The basic mathematical concept is described in [[Verifying_Sample_Identities_-_Implementation]]
# When a sequenced sample does not have external genotypes available
#* [[VerifyBamID]] software can still estimate sample contamination from aligned sequence reads and population minor allele frequency
#* The key idea of the method is to capture the excessive heterozygosity in the contaminated sample by modeling the sequence reads as mixture of independent samples.
# When a sample has array-based genotypes but not yet sequenced
#* [[VerifyIntensity]] software can estimate the levels of DNA sample contamination from aligned sequence reads and population allele frequency
#** The key idea is similar to that of [[VerifyBamID]] with sequence data alone
#** [[VerifyIntensity]] models array intensity data instead of sequence reads
#** When a large number of samples are genotyped together, the 'multi-sample' option will estimate the intensity distribution for each marker across multiple samples. When only one a few samples are genotyped, 'per-sample' option will estimate the intensity distribution for each sample across all markers.
#* [[BAFRegress]] software can estimate levels of sample contamination and test the presence of contamination by regressing the allele frequency with respect to the B allele frequency (BAF).
#** This method is sensitive to estimate low levels of contamination.
#** The method provides a well calibrated Type I error to test the null hypothesis of no contamination from a DNA sample.

== History ==
* Initial version of mathematical description of the first method can be found at [[Verifying_Sample_Identities_-_Implementation]]