stddata__2014_02_15 Samples Report
Overview
Introduction

The Broad GDAC mirrors data from the DCC on a daily basis. Although all data is mirrored, not every sample is ingested into Firehose. There are three main mechanisms that filter samples to ensure that only the most scientifically relevant samples make it into our standard data and analyses runs. These three mechanisms are redactions, replicate filtering, and blacklisting. This report summarizes the data that is ingested into Firehose, describes the three filtering mechanisms, lists those samples that are removed, and gives all available annotations from the DCC's Annotation Manager.

Summary

There were 160 redactions, 2850 replicate aliquots, 23 blacklisted aliquots, and 561 FFPE aliquots. The table below represents the sample counts for those samples that were ingested into firehose after filtering out redactions, replicates, and blacklisted data, and segregating FFPEs.

Table 1.  Get Full Table Summary of TCGA Tumor Data. Click on a tumor type to display a tumor type specific Samples Report.

Cohort BCR Clinical CN LowP Methylation mRNA mRNASeq miR miRSeq RPPA MAF
ACC 92 9 90 0 80 0 79 0 80 0 90
BLCA 268 197 241 112 242 0 223 0 212 127 28
BRCA 1061 977 1031 19 1024 526 1037 0 994 408 976
CESC 211 98 181 0 189 0 185 0 163 0 39
COAD 437 434 427 69 434 153 432 0 406 331 154
COADREAD 605 602 589 104 596 222 588 0 549 461 223
DLBC 38 21 28 0 28 0 28 0 17 0 0
ESCA 126 39 81 32 93 0 0 0 72 0 0
GBM 607 578 564 0 414 540 160 565 0 214 290
HNSC 517 399 509 108 457 0 424 0 456 212 306
KICH 113 92 66 0 66 0 66 0 66 0 66
KIRC 523 507 504 0 511 72 506 0 492 454 417
KIRP 246 160 172 0 172 16 172 0 172 0 168
LAML 200 200 197 0 194 0 179 0 188 0 197
LGG 516 298 463 52 403 27 365 0 306 258 289
LIHC 217 140 165 0 194 0 166 0 147 0 0
LUAD 563 465 493 120 555 32 488 0 491 237 229
LUSC 493 411 490 0 492 154 482 0 467 195 178
MESO 37 13 37 0 0 0 0 0 0 0 0
OV 592 580 576 0 584 574 296 570 453 412 316
PAAD 103 65 91 0 91 0 75 0 59 0 57
PANCAN12 5974 5398 5719 569 5601 2174 4860 1135 4815 2920 3408
PCPG 179 0 0 0 0 0 0 0 0 0 0
PRAD 381 190 295 115 300 0 297 0 259 164 251
READ 168 168 162 35 162 69 156 0 143 130 69
SARC 170 95 127 0 137 0 103 0 97 0 0
SKCM 386 333 374 119 374 0 372 0 343 205 344
STAD 373 311 332 107 308 0 274 0 323 264 221
THCA 496 484 494 98 496 0 494 0 495 222 402
UCEC 545 482 525 106 532 54 517 0 513 200 248
UCS 57 34 56 0 57 0 57 0 56 0 56
Totals 9715 7780 8771 1092 8589 2217 7633 1135 7470 4033 5391
Results
Sample Heatmaps
ACC

Figure 1.  Get High-res Image This figure depicts the distribution of available data on a per participant basis.

BLCA

Figure 2.  Get High-res Image This figure depicts the distribution of available data on a per participant basis.

BRCA

Figure 3.  Get High-res Image This figure depicts the distribution of available data on a per participant basis.

CESC

Figure 4.  Get High-res Image This figure depicts the distribution of available data on a per participant basis.

COAD

Figure 5.  Get High-res Image This figure depicts the distribution of available data on a per participant basis.

COADREAD

Figure 6.  Get High-res Image This figure depicts the distribution of available data on a per participant basis.

DLBC

Figure 7.  Get High-res Image This figure depicts the distribution of available data on a per participant basis.

ESCA

Figure 8.  Get High-res Image This figure depicts the distribution of available data on a per participant basis.

GBM

Figure 9.  Get High-res Image This figure depicts the distribution of available data on a per participant basis.

HNSC

Figure 10.  Get High-res Image This figure depicts the distribution of available data on a per participant basis.

KICH

Figure 11.  Get High-res Image This figure depicts the distribution of available data on a per participant basis.

KIRC

Figure 12.  Get High-res Image This figure depicts the distribution of available data on a per participant basis.

KIRP

Figure 13.  Get High-res Image This figure depicts the distribution of available data on a per participant basis.

LAML

Figure 14.  Get High-res Image This figure depicts the distribution of available data on a per participant basis.

LGG

Figure 15.  Get High-res Image This figure depicts the distribution of available data on a per participant basis.

LIHC

Figure 16.  Get High-res Image This figure depicts the distribution of available data on a per participant basis.

LUAD

Figure 17.  Get High-res Image This figure depicts the distribution of available data on a per participant basis.

LUSC

Figure 18.  Get High-res Image This figure depicts the distribution of available data on a per participant basis.

MESO

Figure 19.  Get High-res Image This figure depicts the distribution of available data on a per participant basis.

OV

Figure 20.  Get High-res Image This figure depicts the distribution of available data on a per participant basis.

PAAD

Figure 21.  Get High-res Image This figure depicts the distribution of available data on a per participant basis.

PANCAN12

Figure 22.  Get High-res Image This figure depicts the distribution of available data on a per participant basis.

PCPG

Figure 23.  Get High-res Image This figure depicts the distribution of available data on a per participant basis.

PRAD

Figure 24.  Get High-res Image This figure depicts the distribution of available data on a per participant basis.

READ

Figure 25.  Get High-res Image This figure depicts the distribution of available data on a per participant basis.

SARC

Figure 26.  Get High-res Image This figure depicts the distribution of available data on a per participant basis.

SKCM

Figure 27.  Get High-res Image This figure depicts the distribution of available data on a per participant basis.

STAD

Figure 28.  Get High-res Image This figure depicts the distribution of available data on a per participant basis.

THCA

Figure 29.  Get High-res Image This figure depicts the distribution of available data on a per participant basis.

UCEC

Figure 30.  Get High-res Image This figure depicts the distribution of available data on a per participant basis.

UCS

Figure 31.  Get High-res Image This figure depicts the distribution of available data on a per participant basis.

Filtered Samples

Redactions

Replicate Samples

Blacklisted Samples

FFPE Cases

FFPE Cases

Additional Annotations from the DCC's Annotations Manager

CenterNotifications

Notifications

Observations

Methods & Data
Redactions and Other Annotations

Annotation data was taken from theTCGA Data Portalusing the query string:

https://tcga-data.nci.nih.gov/annotations/resources/searchannotations/json?item=TCGA

Redaction information was generated by filtering for the annotationClassificationName "Redaction"

FFPE information was generated by filtering for "FFPE" in annotation note text

Additional FFPEs were garnered from clinical data

Remaining annotations were sorted into sections by annotationClassificationName

Preprocessors
mRNA Preprocessor

The mRNA preprocess median module chooses the matrix for the platform(Affymetrix HG U133, Affymetrix Exon Array and Agilent Gene Expression) with the largest number of samples.

mRNAseq Preprocessor

The mRNAseq preprocessor picks the "scaled_estimate" (RSEM) value from Illumina HiSeq/GA2 mRNAseq level_3 (v2) data set and makes the mRNAseq matrix with log2 transformed for the downstream analysis. If there are overlap samples between two different platforms, samples from illumina hiseq will be selected. The pipeline also creates the matrix with RPKM and log2 transform from HiSeq/GA2 mRNAseq level 3 (v1) data set.

miRseq Preprocessor

The miRseq preprocessor picks the "RPM" (reads per million miRNA precursor reads) from the Illumina HiSeq/GA miRseq Level_3 data set and makes the matrix with log2 transformed values.

Methylation Preprocessor

The methylation preprocessor filters methylation data for use in downstream pipelines. To learn more about this preprocessor, please visit the documentation.

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