For some TARGET cases, additional clinical data are missing, and OCG is currently working with the GDC to populate those fields. Some “Recurrent Blood Derived Cancer-Bone Marrow” samples are currently incorrectly identified and users should identify these samples as sample_type_id of “04” in both the aliquot barcode and in the GDC’s sample.sample_type_id field.

TARGET Data Matrix

Last Updated: August 24, 2020

TARGET Program

Link to instructions on how to use the data

Using TARGET Data

TARGET Methods

TARGET Analysis Working Group

Pediatric Resource

The Genomic Data Commons (GDC) is currently working on developing their whole genome sequencing (WGS) analysis pipeline. While some TARGET analyzed WGS data is already available via the GDC Data Portal, not all aliquots have completed the analysis phase. The TARGET aliquots that are currently still undergoing WGS analysis at the GDC are listed here: https://ocg.cancer.gov/TARGET-WGS-Aliquots-Undergoing-Analysis-At-GDC.

Disease

Patient Data

Gene Expression

Copy Number

Methylation

miRNA

Sequence

Other

Acute Lymphoblastic Leukemia (ALL)

ALL Phase 1 (B-ALL)

Clinical File
Sample Matrix

Affymetrix U133 Plus 2
DCC Open*

Affymetrix SNP 500k
DCC Open* DCC Controlled†

Whole Genome
View Cases* DCC Controlled† FASTQ/BAM†

Whole Genome Lite
View Cases* FASTQ/BAM†

mRNA-seq
DCC Open* DCC Controlled† FASTQ/BAM†

Kinome
113 Genes* Kinome Linking Table†

ALL Phase 2 (B-ALL, T-ALL, Dicentric, Xenograft)

Clinical File
Sample Matrix

Affymetrix U133 Plus 2
DCC Open*

Affymetrix SNP 6.0
DCC Open* DCC Controlled†

NimbleGen HELP
DCC Open*

miRNA-seq
DCC Open* FASTQ/BAM†

Whole Genome
DCC Open* DCC Controlled† FASTQ/BAM†

Whole Exome
DCC Open* DCC Controlled† FASTQ/BAM†

mRNA-seq
DCC Open* DCC Controlled† FASTQ/BAM†

ALL Phase 3 (ALAL)

Clinical File
Sample Matrix

Affymetrix SNP 6.0
DCC Open* DCC Controlled†

miRNA-seq
DCC Open* FASTQ/BAM†

Whole Genome
DCC Open* DCC Controlled† FASTQ/BAM†

mRNA-seq
DCC Open* DCC Controlled† FASTQ/BAM†

Acute Myeloid Leukemia (AML)

AML

Clinical File
Sample Matrix

Affymetrix Gene ST
DCC Open*

Affymetrix SNP 6.0
DCC Open* DCC Controlled†

Illumina Infinium 27k
DCC Open*

miRNA-seq
DCC Open* FASTQ/BAM†

Whole Genome
DCC Open* DCC Controlled† FASTQ/BAM†

Whole Exome
DCC Open* DCC Controlled† FASTQ/BAM†

mRNA-seq
DCC Open* DCC Controlled† FASTQ/BAM†

Targeted Resequencing
DCC Open* DCC Controlled† FASTQ/BAM†

Kidney Tumors

Wilms Tumor (WT)

Clinical File
Clinical File†
Sample Matrix

Affymetrix U133 Plus 2
DCC Open*

Affymetrix SNP 6.0
DCC Open* DCC Controlled†

Illumina Infinium 450k
DCC Open*

miRNA-seq
DCC Open* FASTQ/BAM†

Whole Genome
DCC Open* DCC Controlled† FASTQ/BAM†

Whole Exome
DCC Open* DCC Controlled† FASTQ/BAM†

mRNA-seq
DCC Open* DCC Controlled† FASTQ/BAM†

Targeted Resequencing
DCC Open* DCC Controlled† FASTQ/BAM†

Clear Cell Sarcoma of the Kidney (CCSK)

Clinical File
Clinical File†
Sample Matrix

Affymetrix U133 Plus 2
DCC Open*

Affymetrix SNP 6.0
DCC Open* DCC Controlled†

Illumina Infinium 450k
DCC Open*

Whole Genome
DCC Open* DCC Controlled† FASTQ/BAM†

mRNA-seq
DCC Open* DCC Controlled† FASTQ/BAM†

Rhabdoid Tumor (RT)

Clinical File
Clinical File†
Sample Matrix

Illumina Human Methylation450
DCC Open*

miRNA-seq
DCC Open* FASTQ/BAM†

Whole Genome
DCC Open* DCC Controlled† FASTQ/BAM†

mRNA-seq
DCC Open* DCC Controlled† FASTQ/BAM†

Bisulfite-seq
DCC Open* DCC Controlled† FASTQ/BAM†

ChIP-seq
DCC Open* DCC Controlled† FASTQ/BAM†

Neuroblastoma (NBL)

NBL

Clinical File
Sample Matrix

Affymetrix Exon ST
DCC Open* DCC Controlled†

Illumina 550k SNP
DCC Open* DCC Controlled†

Illumina Infinium 450k
DCC Open*

miRNA-seq

Whole Genome
DCC Open* DCC Controlled† FASTQ/BAM†

Whole Exome
DCC Open* DCC Controlled† FASTQ/BAM†

mRNA-seq
DCC Open* DCC Controlled† FASTQ/BAM†

Targeted Resequencing
DCC Open* DCC Controlled† FASTQ/BAM†

Osteosarcoma (OS)

Clinical File
Sample Matrix

Affymetrix Exon ST
DCC Open* DCC Controlled†

Affymetrix SNP 6.0
DCC Open* DCC Controlled†

Illumina Infinium 450k
DCC Open*

MegaPlex TaqMan
DCC Open*

Whole Genome
DCC Open* DCC Controlled† FASTQ/BAM†

Whole Exome
DCC Open* DCC Controlled† FASTQ/BAM†

mRNA-seq
DCC Open* FASTQ/BAM†

Pan-cancer Model Systems (MDLS)

NBL Model Systems

Clinical File

Whole Genome
DCC Open* DCC Controlled† FASTQ/BAM†

Whole Exome
DCC Open* DCC Controlled† FASTQ/BAM†

Pediatric Preclinical Testing Program (PPTP)

Clinical File
Sample Matrix

Agilent SurePrint G3; Affymetrix U133 Plus 2
DCC Open*

Affymetrix SNP6 Illumina Omni5
DCC Open* DCC Controlled†

Whole Exome
DCC Open* FASTQ/BAM†

Projects and assays with available information or data are hyperlinked

ALL Phase 1 (B-ALL)

Patient Data:

Clinical File

Sample Matrix

Gene Expression:

Affymetrix U133 Plus 2

DCC Open*

Copy Number:

Affymetrix SNP 500k

DCC Open*
DCC Controlled†

Methylation:

MiRNA:

Sequence:

Whole Genome

View Cases*
DCC Controlled†
FASTQ/BAM†

Whole Genome Lite

View Cases*
FASTQ/BAM†

mRNA-seq

DCC Open*
DCC Controlled†
FASTQ/BAM†

Other:

Kinome

113 Genes*
Kinome Linking Table†

ALL Phase 2 (B-ALL, T-ALL, Dicentric, Xenograft)

Patient Data:

Clinical File

Sample Matrix

Gene Expression:

Affymetrix U133 Plus 2

DCC Open*

Copy Number:

Affymetrix SNP 6.0

DCC Open*
DCC Controlled†

Methylation:

NimbleGen HELP

DCC Open*

MiRNA:

miRNA-seq

DCC Open*
FASTQ/BAM†

Sequence:

Whole Genome

DCC Open*
DCC Controlled†
FASTQ/BAM†

Whole Exome

DCC Open*
DCC Controlled†
FASTQ/BAM†

mRNA-seq

DCC Open*
DCC Controlled†
FASTQ/BAM†

Other:

ALL Phase 3 (ALAL)

Patient Data:

Clinical File

Sample Matrix

Gene Expression:

Copy Number:

Affymetrix SNP 6.0

DCC Open*
DCC Controlled†

Methylation:

MiRNA:

miRNA-seq

DCC Open*
FASTQ/BAM†

Sequence:

Whole Genome

DCC Open*
DCC Controlled†
FASTQ/BAM†

mRNA-seq

DCC Open*
DCC Controlled†
FASTQ/BAM†

Other:

AML

Patient Data:

Clinical File

Sample Matrix

Gene Expression:

Affymetrix Gene ST

DCC Open*

Copy Number:

Affymetrix SNP 6.0

DCC Open*
DCC Controlled†

Methylation:

Illumina Infinium 27k

DCC Open*

MiRNA:

miRNA-seq

DCC Open*
FASTQ/BAM†

Sequence:

Whole Genome

DCC Open*
DCC Controlled†
FASTQ/BAM†

Whole Exome

DCC Open*
DCC Controlled†
FASTQ/BAM†

mRNA-seq

DCC Open*
DCC Controlled†
FASTQ/BAM†

Targeted Resequencing

DCC Open*
DCC Controlled†
FASTQ/BAM†

Other:

Wilms Tumor (WT)

Patient Data:

Clinical File

Sample Matrix

Gene Expression:

Affymetrix U133 Plus 2

DCC Open*

Copy Number:

Affymetrix SNP 6.0

DCC Open*
DCC Controlled†

Methylation:

Illumina Infinium 450k

DCC Open*

MiRNA:

miRNA-seq

DCC Open*
FASTQ/BAM†

Sequence:

Whole Genome

DCC Open*
DCC Controlled†
FASTQ/BAM†

Whole Exome

DCC Open*
DCC Controlled†
FASTQ/BAM†

mRNA-seq

DCC Open*
DCC Controlled†
FASTQ/BAM†

Targeted Resequencing

DCC Open*
DCC Controlled†
FASTQ/BAM†

Other:

Clear Cell Sarcoma of the Kidney (CCSK)

Patient Data:

Clinical File

Sample Matrix

Gene Expression:

Affymetrix U133 Plus 2

DCC Open*

Copy Number:

Affymetrix SNP 6.0

DCC Open*
DCC Controlled†

Methylation:

Illumina Infinium 450k

DCC Open*

MiRNA:

Sequence:

Whole Genome

DCC Open*
DCC Controlled†
FASTQ/BAM†

mRNA-seq

DCC Open*
DCC Controlled†
FASTQ/BAM†

Other:

Rhabdoid Tumor (RT)

Patient Data:

Clinical File

Sample Matrix

Gene Expression:

Copy Number:

Methylation:

Illumina Human Methylation450

DCC Open*

MiRNA:

miRNA-seq

DCC Open*
FASTQ/BAM†

Sequence:

Whole Genome

DCC Open*
DCC Controlled†
FASTQ/BAM†

mRNA-seq

DCC Open*
DCC Controlled†
FASTQ/BAM†

Bisulfite-seq

DCC Open*
DCC Controlled†
FASTQ/BAM†

Other:

ChIP-seq

DCC Open*
DCC Controlled†
FASTQ/BAM†

NBL

Patient Data:

Clinical File

Sample Matrix

Gene Expression:

Affymetrix Exon ST

DCC Open*
DCC Controlled†

Copy Number:

Illumina 550k SNP

DCC Open*
DCC Controlled†

Methylation:

Illumina Infinium 450k

DCC Open*

MiRNA:

miRNA-seq

Sequence:

Whole Genome

DCC Open*
DCC Controlled†
FASTQ/BAM†

Whole Exome

DCC Open*
DCC Controlled†
FASTQ/BAM†

mRNA-seq

DCC Open*
DCC Controlled†
FASTQ/BAM†

Targeted Resequencing

DCC Open*
DCC Controlled†
FASTQ/BAM†

Other:

Patient Data:

Clinical File

Sample Matrix

Gene Expression:

Affymetrix Exon ST

DCC Open*
DCC Controlled†

Copy Number:

Affymetrix SNP 6.0

DCC Open*
DCC Controlled†

Methylation:

Illumina Infinium 450k

DCC Open*

MiRNA:

MegaPlex TaqMan

DCC Open*

Sequence:

Whole Genome

DCC Open*
DCC Controlled†
FASTQ/BAM†

Whole Exome

DCC Open*
DCC Controlled†
FASTQ/BAM†

mRNA-seq

DCC Open*
FASTQ/BAM†

Other:

NBL Model Systems

Patient Data:

Clinical File

Gene Expression:

Copy Number:

Methylation:

MiRNA:

Sequence:

Whole Genome

DCC Open*
DCC Controlled†
FASTQ/BAM†

Whole Exome

DCC Open*
DCC Controlled†
FASTQ/BAM†

Other:

Pediatric Preclinical Testing Program (PPTP)

Patient Data:

Clinical File

Sample Matrix

Gene Expression:

Agilent SurePrint G3; Affymetrix U133 Plus 2

DCC Open*

Copy Number:

Affymetrix SNP6 Illumina Omni5

DCC Open*
DCC Controlled†

Methylation:

MiRNA:

Sequence:

Whole Exome

DCC Open*
FASTQ/BAM†
*

Other:

TARGET Data Legend
Blue: Public* Red: Protected† Black: Unavailable	All DCC Controlled† access links require an eRA Commons account via Globus.org All FASTQ/BAM† are controlled access links and require an eRA Commons account