Blacklisted Samples
2016_01_28 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. |