stddata__2014_06_14 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 161 redactions, 2872 replicate aliquots, 23 blacklisted aliquots, and 595 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	80	90	0	80	0	79	0	80	0	91
BLCA	367	218	252	112	352	0	252	0	267	127	130
BRCA	1096	999	1052	19	1044	526	1048	0	1041	408	976
CESC	257	180	203	0	257	0	196	0	257	0	39
CHOL	36	0	0	0	0	0	0	0	0	0	0
COAD	460	439	427	69	445	153	432	0	406	331	154
COADREAD	631	610	589	104	607	222	595	0	549	461	223
DLBC	58	33	28	0	48	0	28	0	27	0	0
ESCA	185	81	126	32	176	0	70	0	125	0	0
GBM	613	582	571	0	414	540	160	565	0	214	290
HNSC	528	422	511	108	527	0	497	0	512	212	306
KICH	113	94	66	0	66	0	66	0	66	0	66
KIRC	537	509	514	0	535	72	518	0	506	454	417
KIRP	274	197	212	0	242	16	198	0	242	0	168
LAML	200	200	197	0	194	0	179	0	188	0	197
LGG	516	388	486	52	512	27	486	0	504	258	289
LIHC	377	164	208	0	238	0	200	0	268	0	202
LUAD	585	473	493	120	555	32	488	0	491	237	229
LUSC	504	414	490	0	492	154	489	0	467	195	178
MESO	87	17	37	0	37	0	36	0	26	0	0
OV	602	587	576	0	584	574	296	570	453	412	316
PAAD	185	89	102	0	130	0	96	0	96	0	91
PCPG	179	57	172	0	179	0	178	0	179	0	0
PRAD	500	257	373	115	336	0	374	0	417	164	261
READ	171	171	162	35	162	69	163	0	143	130	69
SARC	261	108	169	0	170	0	103	0	194	0	0
SKCM	470	366	384	118	403	0	371	0	409	204	343
STAD	443	337	370	107	373	0	274	0	353	264	221
THCA	503	490	494	98	496	0	494	0	495	222	402
UCEC	560	490	525	106	543	54	527	0	534	200	248
UCS	57	57	56	0	57	0	57	0	56	0	57
UVM	80	0	0	0	0	0	0	0	0	0	0
Totals	10896	8499	9346	1091	9647	2217	8355	1135	8802	4032	5740

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.

GBM

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

HNSC

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

KICH

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

KIRC

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

KIRP

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

LAML

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

LGG

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

LIHC

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

LUAD

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

LUSC

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

MESO

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

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

PAAD

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.

UVM

Figure 32. 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.

Made with Nozzle