Replicate Samples

2016_01_28 Data Snapshot

In many instances there is more than one aliquot for a given combination of individual, platform, and data type. However, only one aliquot may be ingested into Firehose. Therefore, a set of precedence rules are applied to select the most scientifically advantageous one among them. Two filters are applied to achieve this aim: an Analyte Replicate Filter and a Sort Replicate Filter.

Analyte Replicate Filter

The following precedence rules are applied when the aliquots have differing analytes. For RNA aliquots, T analytes are dropped in preference to H and R analytes, since T is the inferior extraction protocol. If H and R are encountered, H is the chosen analyte. This is somewhat arbitrary and subject to change, since it is not clear at present whether H or R is the better protocol. If there are multiple aliquots associated with the chosen RNA analyte, the aliquot with the later plate number is chosen. For DNA aliquots, D analytes (native DNA) are preferred over G, W, or X (whole-genome amplified) analytes, unless the G, W, or X analyte sample has a higher plate number.

Sort Replicate Filter

The following precedence rules are applied when the analyte filter still produces more than one sample. The sort filter chooses the aliquot with the highest lexicographical sort value, to ensure that the barcode with the highest portion and/or plate number is selected when all other barcode fields are identical.

Table 1. Get Full Table Click on any filtered samples count to display a table detailing the filtered samples for the associated tumor type.

Tumor Type	Filtered Samples Count
HNSC	18

HNSC

Table S1.

Participant Id	DataType__Platform__Center__DataLevel__ProtocolName_Extension	Filter Reason	Removed Sample(s)	Chosen Sample
TCGA-CV-6955	snp__genome_wide_snp_6__broad_mit_edu__Level_2__tangent_copynumber__data	Analyte Replicate Filter	TCGA-CV-6955-01A-11D-2010-01	TCGA-CV-6955-01A-11D-2062-01
TCGA-CV-6956	snp__genome_wide_snp_6__broad_mit_edu__Level_2__tangent_copynumber__data	Analyte Replicate Filter	TCGA-CV-6956-01A-21D-2010-01	TCGA-CV-6956-01A-21D-2062-01
TCGA-CV-6955	snp__genome_wide_snp_6__broad_mit_edu__Level_2__byallele_copynumber__data	Analyte Replicate Filter	TCGA-CV-6955-01A-11D-2010-01	TCGA-CV-6955-01A-11D-2062-01
TCGA-CV-6956	snp__genome_wide_snp_6__broad_mit_edu__Level_2__byallele_copynumber__data	Analyte Replicate Filter	TCGA-CV-6956-01A-21D-2010-01	TCGA-CV-6956-01A-21D-2062-01
TCGA-CV-6955	snp__genome_wide_snp_6__broad_mit_edu__Level_2__invariantset_medianpolish__data	Analyte Replicate Filter	TCGA-CV-6955-01A-11D-2010-01	TCGA-CV-6955-01A-11D-2062-01
TCGA-CV-6956	snp__genome_wide_snp_6__broad_mit_edu__Level_2__invariantset_medianpolish__data	Analyte Replicate Filter	TCGA-CV-6956-01A-21D-2010-01	TCGA-CV-6956-01A-21D-2062-01
TCGA-CV-6955	snp__genome_wide_snp_6__broad_mit_edu__Level_2__birdseed_genotype__birdseed	Analyte Replicate Filter	TCGA-CV-6955-01A-11D-2010-01	TCGA-CV-6955-01A-11D-2062-01
TCGA-CV-6956	snp__genome_wide_snp_6__broad_mit_edu__Level_2__birdseed_genotype__birdseed	Analyte Replicate Filter	TCGA-CV-6956-01A-21D-2010-01	TCGA-CV-6956-01A-21D-2062-01
TCGA-CV-6955	snp__genome_wide_snp_6__broad_mit_edu__Level_3__segmented_scna_minus_germline_cnv_hg18__seg	Analyte Replicate Filter	TCGA-CV-6955-01A-11D-2010-01	TCGA-CV-6955-01A-11D-2062-01
TCGA-CV-6956	snp__genome_wide_snp_6__broad_mit_edu__Level_3__segmented_scna_minus_germline_cnv_hg18__seg	Analyte Replicate Filter	TCGA-CV-6956-01A-21D-2010-01	TCGA-CV-6956-01A-21D-2062-01
TCGA-CV-6955	snp__genome_wide_snp_6__broad_mit_edu__Level_3__segmented_scna_hg19__seg	Analyte Replicate Filter	TCGA-CV-6955-01A-11D-2010-01	TCGA-CV-6955-01A-11D-2062-01
TCGA-CV-6956	snp__genome_wide_snp_6__broad_mit_edu__Level_3__segmented_scna_hg19__seg	Analyte Replicate Filter	TCGA-CV-6956-01A-21D-2010-01	TCGA-CV-6956-01A-21D-2062-01
TCGA-CV-6955	snp__genome_wide_snp_6__broad_mit_edu__Level_3__segmented_scna_minus_germline_cnv_hg19__seg	Analyte Replicate Filter	TCGA-CV-6955-01A-11D-2010-01	TCGA-CV-6955-01A-11D-2062-01
TCGA-CV-6956	snp__genome_wide_snp_6__broad_mit_edu__Level_3__segmented_scna_minus_germline_cnv_hg19__seg	Analyte Replicate Filter	TCGA-CV-6956-01A-21D-2010-01	TCGA-CV-6956-01A-21D-2062-01
TCGA-CV-6955	snp__genome_wide_snp_6__broad_mit_edu__Level_3__segmented_scna_hg18__seg	Analyte Replicate Filter	TCGA-CV-6955-01A-11D-2010-01	TCGA-CV-6955-01A-11D-2062-01
TCGA-CV-6956	snp__genome_wide_snp_6__broad_mit_edu__Level_3__segmented_scna_hg18__seg	Analyte Replicate Filter	TCGA-CV-6956-01A-21D-2010-01	TCGA-CV-6956-01A-21D-2062-01
TCGA-CV-6955	snp__genome_wide_snp_6__broad_mit_edu__Level_2__raw_copynumber__data	Analyte Replicate Filter	TCGA-CV-6955-01A-11D-2010-01	TCGA-CV-6955-01A-11D-2062-01
TCGA-CV-6956	snp__genome_wide_snp_6__broad_mit_edu__Level_2__raw_copynumber__data	Analyte Replicate Filter	TCGA-CV-6956-01A-21D-2010-01	TCGA-CV-6956-01A-21D-2062-01

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