Wilms tumor (WT) is the most common type of childhood kidney cancer and usually occurs before the age of six years. Most cases present with a favorable histology and respond well to standard treatment, however there are patients who relapse unexpectedly. A subset of WT patients are diagnosed with anaplasia, an unfavorable histology WT which does not respond to current therapies. TARGET investigators analyzed tumors from patients with anaplasia at diagnosis, or those who relapsed and for whom standard therapies were ineffective in order to identify biomarkers that correlate with poor clinical outcome and/or new therapeutic approaches.
The TARGET Kidney Tumors project team members (like other TARGET researchers) are generating data in two phases: Discovery and Validation. Visit the TARGET Research page to learn more.
Discovery Dataset
The TARGET Wilms tumor (WT) project has produced comprehensive genomic profiles of nearly 130 poor outcome, clinically annotated patient cases that make up the discovery dataset. This cohort includes around 80 favorable histology Wilms tumors (FHWT) that relapsed and approximately 50 anaplastic WT cases. Each fully-characterized TARGET WT 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 and/or tumor adjacent normal kidney (case-matched)
- Relapsed tumor sample (case-matched) when available; some cases have 3rd sample (those cases are considered a “trio”)
Additional cases with partial molecular characterization and/or sequencing data are available to the research community.
Case Selection Criteria
Tissues and clinical data used for the TARGET WT project were obtained from patients enrolled in the National Wilms Tumor Study (mostly NWTS-5) clinical trial that is now run through the Children's Oncology Group (COG). Patient samples with full characterization were chosen based on the following criteria:
- Tumor cellularity of >80% in tumor specimens and tumor necrosis of <20%
- High-quality nucleic acids in amounts adequate to complete comprehensive genomic profiling
- Unfavorable histology (anaplasia) or relapse event in favorable histology (FHWT) cases
Molecular Characterization
The TARGET KT project team relied on a variety of platforms to obtain a fully characterized dataset of nearly 130 hard to cure WT cases. The COG renal tumors 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.
| General Methodology |
Platform |
|---|
| Clinical Annotation |
NWTS – 5 Protocol |
| Gene Expression |
Affymetrix U133 Plus 2.0 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 Hi-Seq 2000 |
| Whole Exome Sequencing |
Illumina Hi-Seq 2000 |
| mRNA-seq |
Illumina Hi-Seq 2000 |
| miRNA-seq |
Illumina Hi-Seq 2000 |
Verification of Discovery Variants
The TARGET KT 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 that were expressed and originally identified through whole genome or exome sequencing. These verified variants will be made available as open-access data. The TARGET KT project team has additionally employed the same targeted capture sequencing approach described in the validation strategy below to verify variants seen in diagnostic tumor samples from a majority of fully-characterized patient cases in the TARGET WT discovery cohort.
Validation Strategy
Some sequence mutations identified in the poor outcome discovery cohort, along with some previously published variants, were further analyzed in an additional 550-plus cases. The TARGET KT 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 WT subtypes.
All data from the discovery and validation efforts are made available as specified in the Using TARGET Data and TARGET Publication Guidelines pages. The TARGET Data Matrix provides an overview of the data generated and described above.
