The TARGET neuroblastoma (NBL) project has produced comprehensive genomic profiles of more than 200 clinically annotated patient cases within the discovery dataset. This cohort includes nearly 200 high-risk patient cases, including some who have relapsed and subsets of low-risk and/or stage 4S NBL cases (tumors that spontaneously regress without treatment). Each fully-characterized TARGET NBL case includes data from nucleic acid samples extracted from tumor and normal tissues as follows:
- Primary tumor sample collected at diagnosis
- Normal tissue sample from peripheral blood or bone marrow (case-matched)
- Relapsed tumor sample (case-matched) when available; some cases have 3rd sample (those cases are considered a “trio”)
There are a large number of additional cases, varying in risk level, with partial molecular characterization and/or sequencing data that are available to the research community.
Case Selection Criteria
Tissues and clinical data used for the TARGET NBL project were obtained from patients enrolled on biology studies and clinical trials managed through the Children’s Oncology Group (COG). Patient samples with full characterization were chosen based on the following criteria:
- Tumor cellularity of >70% in tumor specimens and tumor necrosis of <30%
- High-quality nucleic acids in amounts adequate to complete comprehensive genomic profiling
- Preference for high-risk cases (Stage 4) who have relapsed or whose tumors spontaneously regress without treatment (Stage 4S)
The TARGET NBL project team relied on a variety of platforms to obtain a fully characterized dataset of more than 200 cases. The COG NBL Statistics and Data Center provided clinical annotations and outcome data for all cases. Visit the TARGET Project Experimental Methods page for detailed information and protocols.
||COG NBL Protocols
||Affymetrix Human Exon ST Array
|Chomosome Copy Number Analyses & Loss of Heterozygosity
||Affymetrix SNP 6.0 Array
|Epigenetics (DNA Methylation)
||Illumina Infinium 450K
|Whole Genome Sequencing
||Complete Genomics Incorporated,
Illumina Genome Analyzer IIx or Hi-Seq 2000
|Whole Exome Sequencing
||Illumina Genome Analyzer II or Hi-Seq 2000
||Illumina Genome Analyzer IIx or Hi-Seq 2000
Verification of Discovery Variants
The TARGET NBL project team utilized a variety of sequencing approaches to confirm candidate variants identified in the discovery sample cohort as somatic. For example, mRNA-seq results are being used to determine variants which were expressed and originally identified through whole genome or exome sequencing. These verified variants will be made available as open-access data.
Some sequence mutations identified in the discovery cohort, along with some previously published variants, were further analyzed in an additional 500 cases. The TARGET NBL project team employed targeted capture sequencing to look at the presence and frequency of alterations in 400 gene variants. This validation effort was performed in an unbiased cohort that was randomly selected from patients enrolled on a single COG protocol, which allowed for determination of the frequency of these changes across a broader spectrum of NBL subtypes.
All data from the discovery cohort and this validation effort are available through the TARGET Data Matrix. These data must be used as specified in the TARGET Publication Guidelines.