Replicate Samples

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
BLCA 15
BLCA

Table S1. 

Participant Id DataType__Platform__Center__DataLevel__ProtocolName_Extension Filter Reason Removed Sample(s) Chosen Sample
TCGA-BL-A13J mirnaseq__illuminahiseq_mirnaseq__bcgsc_ca__Level_3__miR_isoform_expression__data Analyte Replicate Filter TCGA-BL-A13J-01A-11R-A10V-13 TCGA-BL-A13J-01B-04R-A27D-13
TCGA-BL-A0C8 mirnaseq__illuminahiseq_mirnaseq__bcgsc_ca__Level_3__miR_isoform_expression__data Analyte Replicate Filter TCGA-BL-A0C8-01A-11R-A10V-13 TCGA-BL-A0C8-01B-04R-A27D-13
TCGA-BL-A13J snp__genome_wide_snp_6__broad_mit_edu__Level_2__birdseed_genotype__birdseed Analyte Replicate Filter TCGA-BL-A13J-01A-11D-A10T-01 TCGA-BL-A13J-01B-04D-A273-01
TCGA-BL-A0C8 snp__genome_wide_snp_6__broad_mit_edu__Level_2__birdseed_genotype__birdseed Analyte Replicate Filter TCGA-BL-A0C8-01A-11D-A10T-01 TCGA-BL-A0C8-01B-04D-A273-01
TCGA-BL-A13J snp__genome_wide_snp_6__broad_mit_edu__Level_2__invariantset_medianpolish__data Analyte Replicate Filter TCGA-BL-A13J-01A-11D-A10T-01 TCGA-BL-A13J-01B-04D-A273-01
TCGA-BL-A0C8 snp__genome_wide_snp_6__broad_mit_edu__Level_2__invariantset_medianpolish__data Analyte Replicate Filter TCGA-BL-A0C8-01A-11D-A10T-01 TCGA-BL-A0C8-01B-04D-A273-01
TCGA-BL-A13J methylation__humanmethylation450__jhu_usc_edu__Level_3__within_bioassay_data_set_function__data Analyte Replicate Filter TCGA-BL-A13J-01A-11D-A10W-05 TCGA-BL-A13J-01B-04D-A276-05
TCGA-BL-A0C8 methylation__humanmethylation450__jhu_usc_edu__Level_3__within_bioassay_data_set_function__data Analyte Replicate Filter TCGA-BL-A0C8-01A-11D-A10W-05 TCGA-BL-A0C8-01B-04D-A276-05
TCGA-BL-A13I methylation__humanmethylation450__jhu_usc_edu__Level_3__within_bioassay_data_set_function__data Analyte Replicate Filter TCGA-BL-A13I-01A-11D-A13Z-05 TCGA-BL-A13I-01B-04D-A276-05
TCGA-BL-A13J snp__genome_wide_snp_6__broad_mit_edu__Level_2__byallele_copynumber__data Analyte Replicate Filter TCGA-BL-A13J-01A-11D-A10T-01 TCGA-BL-A13J-01B-04D-A273-01
TCGA-BL-A0C8 snp__genome_wide_snp_6__broad_mit_edu__Level_2__byallele_copynumber__data Analyte Replicate Filter TCGA-BL-A0C8-01A-11D-A10T-01 TCGA-BL-A0C8-01B-04D-A273-01
TCGA-BL-A13J snp__genome_wide_snp_6__broad_mit_edu__Level_2__raw_copynumber__data Analyte Replicate Filter TCGA-BL-A13J-01A-11D-A10T-01 TCGA-BL-A13J-01B-04D-A273-01
TCGA-BL-A0C8 snp__genome_wide_snp_6__broad_mit_edu__Level_2__raw_copynumber__data Analyte Replicate Filter TCGA-BL-A0C8-01A-11D-A10T-01 TCGA-BL-A0C8-01B-04D-A273-01
TCGA-BL-A13J mirnaseq__illuminahiseq_mirnaseq__bcgsc_ca__Level_3__miR_gene_expression__data Analyte Replicate Filter TCGA-BL-A13J-01A-11R-A10V-13 TCGA-BL-A13J-01B-04R-A27D-13
TCGA-BL-A0C8 mirnaseq__illuminahiseq_mirnaseq__bcgsc_ca__Level_3__miR_gene_expression__data Analyte Replicate Filter TCGA-BL-A0C8-01A-11R-A10V-13 TCGA-BL-A0C8-01B-04R-A27D-13