Blacklisted Samples
2016_07_15 Data Snapshot

In certain circumstances, replicate filtering may choose the less favorable among two or more aliquots. For instance, an analyst may manually review two aliquots for a given individual and determine that one is superior. If the replicate filtering would choose the inferior sample, then the inferior sample can be added to this blacklist. This would result in the desired sample being chosen. This table lists those blacklisted samples and a reason for their being blacklisted.

Table 1.  Get Full Table These samples were blacklisted and removed from the run.

TCGA.ID Tumor.Type Blacklist.Reason
TCGA-38-4626-01A-01D-1549-01 LUAD Andrew Cherniack determined the earlier sample is better than this later one.
TCGA-44-2655-01A-01D-1549-01 LUAD Andrew Cherniack determined the earlier sample is better than this later one.
TCGA-44-2656-01A-02D-1549-01 LUAD Andrew Cherniack determined the earlier sample is better than this later one.
TCGA-44-2662-01A-01D-1549-01 LUAD Andrew Cherniack determined the earlier sample is better than this later one.
TCGA-44-2665-01A-01D-1549-01 LUAD Andrew Cherniack determined the earlier sample is better than this later one.
TCGA-44-3396-01A-01D-1549-01 LUAD Andrew Cherniack determined the earlier sample is better than this later one.
TCGA-AR-A0U1-01A-11R-A115-07 BRCA Katherine Hoadley identified this sample as having a low read count or no confirmed SNP comparison.
TCGA-A7-A0DC-01A-11R-A00Z-07 BRCA Katherine Hoadley identified this sample as having a low read count or no confirmed SNP comparison.
TCGA-BH-A0B2-11A-11R-A10J-07 BRCA Katherine Hoadley identified this sample as having a low read count or no confirmed SNP comparison.
TCGA-BH-A0B2-01A-11R-A10J-07 BRCA Katherine Hoadley identified this sample as having a low read count or no confirmed SNP comparison.
TCGA-A7-A0DC-11A-41R-A089-07 BRCA Katherine Hoadley identified this sample as having a low read count or no confirmed SNP comparison.
TCGA-E2-A1IP-01A-11R-A14D-07 BRCA Katherine Hoadley identified this sample as having a low read count or no confirmed SNP comparison.
TCGA-AA-3695-01A-01R-0905-07 BRCA Katherine Hoadley identified this sample as having a low read count or no confirmed SNP comparison.
TCGA-A6-2670-01A-02R-0821-07 BRCA Katherine Hoadley identified this sample as having a low read count or no confirmed SNP comparison.
TCGA-14-0871-01A-01R-1849-01 BRCA Katherine Hoadley identified this sample as having a low read count or no confirmed SNP comparison.
TCGA-33-4579-01A-01R-1443-07 BRCA Katherine Hoadley identified this sample as having a low read count or no confirmed SNP comparison.
TCGA-31-1950-01A-01R-1568-13 BRCA Katherine Hoadley identified this sample as having a low read count or no confirmed SNP comparison.
TCGA-BJ-A0ZF THCA Per Lisa Iype, pathology reports indicated that this sample was a follicular carcinoma and not a papillary thyroid carcinoma.
TCGA-EM-A2CM THCA Per Lisa Iype, pathology reports indicated that this sample was a poorly differentiated oncocytic carcinoma and not a papillary thyroid carcinoma
TCGA-DJ-A3V6 THCA Per Lisa Iype, pathology reports indicated that this patient has a pretreatment
TCGA-DJ-A3UV THCA Per Lisa Iype, pathology reports indicated that this patient has a pretreatment
TCGA-BR-4376 STAD Henry Song, Chris Bristow, and Sahil Seth at Harvard GCC uncovered a sample swap for this sample.
TCGA-FG-5965-02B-11D-A323-01 LGG Andrew Cherniack determined the earlier sample is better than this later one.