stddata__2015_04_02 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 159 redactions, 3166 replicate aliquots, 23 blacklisted aliquots, and 685 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 rawMAF
ACC 92 92 90 0 80 0 79 0 80 46 90 0
BLCA 412 393 410 112 412 0 408 0 409 127 130 395
BRCA 1098 1080 1089 19 1081 526 1093 0 1078 410 977 0
CESC 307 304 295 0 307 0 304 0 307 173 194 0
CHOL 36 36 36 0 36 0 36 0 36 30 35 0
COAD 460 453 450 69 457 153 457 0 406 331 154 367
COADREAD 631 624 615 104 622 222 623 0 549 461 223 489
DLBC 58 47 48 0 48 0 28 0 47 33 0 0
ESCA 185 174 184 32 185 0 184 0 184 126 0 0
FPPP 38 38 0 0 0 0 0 0 22 0 0 0
GBM 613 592 577 0 420 540 160 565 0 214 290 290
GBMLGG 1129 1067 1090 52 936 567 676 565 512 472 576 803
HNSC 528 522 522 108 528 0 520 0 523 212 279 508
KICH 113 110 66 0 66 0 66 0 66 0 66 66
KIPAN 973 914 883 0 892 88 889 0 873 661 644 678
KIRC 537 533 528 0 535 72 533 0 516 454 417 451
KIRP 323 271 289 0 291 16 290 0 291 207 161 161
LAML 200 200 197 0 194 0 179 0 188 0 197 0
LGG 516 475 513 52 516 27 516 0 512 258 286 513
LIHC 377 363 370 0 377 0 371 0 372 0 198 0
LUAD 585 521 516 120 578 32 515 0 513 181 230 542
LUSC 504 495 501 0 503 154 501 0 478 195 178 0
MESO 87 77 87 0 87 0 86 0 87 0 0 0
OV 602 591 586 0 594 574 296 570 453 412 316 469
PAAD 185 174 184 0 184 0 178 0 178 106 146 0
PCPG 179 179 175 0 179 0 179 0 179 80 178 0
PRAD 499 489 492 115 498 0 497 0 494 352 425 0
READ 171 171 165 35 165 69 166 0 143 130 69 122
SARC 260 250 256 0 260 0 258 0 258 221 0 0
SKCM 470 447 469 118 470 0 468 0 448 204 343 366
STAD 443 438 442 107 443 0 274 0 442 264 289 0
STES 628 612 626 139 628 0 458 0 626 390 289 0
TGCT 150 133 150 0 150 0 150 0 150 118 149 0
THCA 503 501 501 98 503 0 501 0 502 222 402 0
THYM 124 122 123 0 124 0 120 0 124 90 0 0
UCEC 560 537 540 106 547 54 545 0 538 200 248 0
UCS 57 57 56 0 57 0 57 0 56 48 57 0
UVM 80 80 80 0 80 0 80 0 80 12 80 0
Totals 11352 10945 10987 1091 10955 2217 10095 1135 10160 5456 6584 4250
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.

CHOL

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

COAD

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

COADREAD

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

DLBC

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

ESCA

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

FPPP

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

GBM

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

GBMLGG

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

HNSC

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

KICH

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

KIPAN

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

KIRC

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

KIRP

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

LAML

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

LGG

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

LIHC

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

LUAD

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

LUSC

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

MESO

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

OV

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

PAAD

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

PCPG

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

PRAD

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

READ

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

SARC

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

SKCM

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

STAD

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

STES

Figure 32.  Get High-res Image This figure depicts the distribution of available data on a per participant basis.

TGCT

Figure 33.  Get High-res Image This figure depicts the distribution of available data on a per participant basis.

THCA

Figure 34.  Get High-res Image This figure depicts the distribution of available data on a per participant basis.

THYM

Figure 35.  Get High-res Image This figure depicts the distribution of available data on a per participant basis.

UCEC

Figure 36.  Get High-res Image This figure depicts the distribution of available data on a per participant basis.

UCS

Figure 37.  Get High-res Image This figure depicts the distribution of available data on a per participant basis.

UVM

Figure 38.  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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