stddata__2014_01_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, 2802 replicate aliquots, 23 blacklisted aliquots, and 541 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	10	90	0	80	0	79	0	80	0	90
BLCA	253	186	223	112	242	0	223	0	212	127	28
BRCA	1051	975	1016	19	1024	526	1019	0	994	408	976
CESC	200	84	171	0	179	0	159	0	163	0	39
COAD	437	434	427	69	434	153	418	0	406	331	154
COADREAD	605	602	589	104	596	222	574	0	549	461	223
DLBC	38	21	28	0	28	0	28	0	17	0	0
ESCA	103	22	73	32	73	0	0	0	72	0	0
GBM	606	576	560	0	414	540	160	565	0	214	290
HNSC	517	379	452	108	457	0	424	0	456	212	306
KICH	113	70	66	0	66	0	66	0	66	0	66
KIRC	523	505	504	0	511	72	506	0	492	454	417
KIRP	230	139	172	0	172	16	161	0	172	0	112
LAML	200	200	197	0	194	0	179	0	188	0	197
LGG	466	282	365	52	403	27	365	0	306	258	289
LIHC	205	128	165	0	169	0	147	0	147	0	0
LUAD	563	461	493	120	555	32	488	0	491	237	229
LUSC	493	408	490	0	492	154	482	0	467	195	178
MESO	37	13	0	0	0	0	0	0	0	0	0
OV	592	580	576	0	584	574	296	570	453	412	316
PAAD	92	58	81	0	91	0	56	0	59	0	57
PANCAN12	5948	5353	5615	569	5591	2174	4824	1135	4815	2920	3408
PCPG	179	0	0	0	0	0	0	0	0	0	0
PRAD	338	186	278	115	300	0	278	0	259	164	251
READ	168	168	162	35	162	69	156	0	143	130	69
SARC	150	82	127	0	127	0	103	0	97	0	0
SKCM	386	320	374	119	374	0	354	0	343	205	344
STAD	353	308	332	106	308	0	274	0	323	264	221
THCA	496	484	494	98	496	0	488	0	495	222	402
UCEC	545	481	515	106	522	54	513	0	513	200	248
UCS	57	33	56	0	57	0	56	0	56	0	56
Totals	9483	7593	8487	1091	8514	2217	7478	1135	7470	4033	5335

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.

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

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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