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.

Kidney Tumors

The TARGET Kidney Tumor projects elucidate comprehensive molecular characterization to determine the genetic changes that drive the initiation and progression of high-risk or hard-to-treat childhood cancers. Pediatric kidney tumors fall into four primary categories: Wilms tumors (~85% of all cases), clear cell sarcomas of the kidney (~5%), congenital mesoblastic nephromas (~4%), and rhabdoid tumors of the kidney (~3%). The TARGET initiative is investigating three of these tumor types. TARGET initiated the Kidney Tumor Project to elucidate the mutation spectrums of highly aggressive forms of the disease in relapsed favorable histology Wilms tumor, anaplastic Wilms tumor, clear cell sarcoma of the kidney (CSSK) and rhabdoid tumor (RT). The tissues used in this study were collected from patients enrolled in the National Wilms Tumor Study (mostly NWTS-5) clinical trial that was completed by the Children's Oncology Group (COG).
Kidney tumors are rare and generally curable in children. However, there are subsets of patients afflicted with these diseases that do not respond to treatment or eventually relapse. These patients usually have poor clinical outcomes as compared with the majority of children diagnosed with kidney tumors. All patients undergo therapy regimens that can be detrimental later in life. Through genome-wide characterization, TARGET investigators are identifying critical molecular alterations in these tumors, mostly from relapsed patients. Future research may identify treatments tailored to these alterations to improve outcomes for children afflicted with these kidney tumors. To learn more about pediatric kidney cancers and current treatment strategies, visit the NCI childhood kidney tumor website.

The Kidney Tumor Projects have been completed; the Wilms tumor (WT), CCSK, and RT datasets are now available without restrictions on their use in publications or presentations.

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TARGET Wilms Tumor Project Summary

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 3^rd 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.

TARGET Clear Cell Sarcoma of the Kidney Subproject

Clear cell sarcoma of the kidney (CCSK) is a rare kidney tumor that usually occurs in children age 3 or younger. Although treatment outcomes are generally favorable, patients undergo highly toxic therapies, which can lead to complications later in life (e.g., additional cancers or infertility). As CCSK is uncommon, the lack of tumor tissues for research makes studying the underlying biology of the disease difficult. The TARGET Kidney Tumors (KT) project team analyzed tumors from pediatric CCSK patients using a comprehensive, integrated genomic approach to identify new therapeutic approaches and/or biomarkers that correlate with poor clinical outcome.

Discovery Dataset

The TARGET CCSK subproject has produced comprehensive genomic profiles of 13 clinically annotated patient cases. Each fully-characterized TARGET CCSK case consists of data generated from nucleic acid samples extracted from case-matched tumor and normal tissues as follows:

Primary tumor sample collected at diagnosis
Normal tissue sample from peripheral blood or tumor adjacent normal kidney (case-matched)

Case Selection Criteria

Tissues and clinical data used for the TARGET CCSK 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
Relapse event (~50 patient cases studied)

Molecular Characterization

The TARGET KT project team relied on a variety of platforms to obtain a fully characterized dataset of 13 CCSK cases, including some who have relapsed. 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
mRNA-seq	Illumina Hi-Seq 2000

Verification & Validation of Discovery Variants

The TARGET KT project team analyzed 9 additional CCSK cases, using the molecular profiling and sequencing approaches described above (see table), to confirm the presence and frequency of candidate variants found in the discovery dataset. This validation effort was performed in an unbiased cohort that was selected based on availability of tissue from patients enrolled on a single protocol (NWTS-5, like the discovery cohort; cases were chosen without regard for relapse). In addition, mRNA-seq results from both discovery and validation cases are being used to determine variants which were expressed and originally identified through whole genome sequencing. These verified variants will be made available as open-access data.

TARGET Rhabdoid Tumor Subproject

Rhabdoid tumors (RT) are rare and very aggressive kidney tumors found mostly in young children. These patients typically have poor prognoses. Malignant rhabdoid tumors (MRT) are also rare, highly lethal tumors that most commonly present in the kidney of infants. MRT may present within the brain, and these are classified as atypical teratoid/rhabdoid tumors. Very rarely, MRT may develop in the soft tissue. TARGET researchers characterized RT genomes, transcriptomes, and epigenomes through extensive second generation sequencing efforts. These data will increase understanding of the disease and facilitate the development of better therapeutic options for this tumor subtype.

Discovery Dataset

The TARGET RT subproject has produced comprehensive genomic profiles of 40 clinically annotated patient cases. Each fully-characterized TARGET RT case consists of data generated from nucleic acid samples extracted from case-matched tumor and normal tissues as follows:

Primary tumor sample collected at diagnosis
Normal tissue sample from peripheral blood or tumor adjacent normal kidney (case-matched)

Case Selection Criteria

Tissues and clinical data used for the TARGET RT project were obtained from patients enrolled in renal tumor protocols 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, transcriptomic and epigenomic profiling

Molecular Characterization

The TARGET KT project team relied on a variety of sequencing platforms to obtain a fully characterized dataset of 40 RT 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	AREN03B2 or NWTS-5 Protocols
Whole Genome Sequencing	Illumina Hi-Seq 2000
mRNA-seq	Illumina Hi-Seq 2000
miRNA-seq	Illumina Hi-Seq 2000
Bisulfite-seq	Illumina Hi-Seq 2500
ChIP-seq	Illumina Hi-Seq 2000

Verification & Validation of Discovery Variants

The TARGET KT project team analyzed 29 additional RT cases, using the same sequencing approaches described above (see table), to confirm the presence and frequency of candidate variants found in the discovery dataset. This validation effort was performed in an unbiased cohort that was selected based on availability of tissue from patients enrolled on COG renal tumor protocols (AREN03B2 or NWTS-5, like the discovery cohort). In addition, mRNA-seq results from both discovery and validation cases are being used to determine variants that were expressed and originally identified through whole genome sequencing. These verified variants will be made available as open-access data.

RT Cell Line and Xenograft Samples

In order to facilitate data analysis by non-TARGET users, all cell line and xenograft data generated as part of the RT project have been moved to the TARGET-MDLS study. MDLS includes cell line and xenograft data from many TARGET studies. These are the samples used in RT manuscripts whose data is at MDLS:

TARGET-00-NAAEMA	TARGET-00-NAAEMC	TARGET-52-NAAELY
TARGET-00-NAAEMB	TARGET-52-NAAELV	TARGET-52-NAAELZ

Investigators

The TARGET Kidney Tumor Project team consists of COG investigators at various institutions who work together with the scientists, analysts, project managers, and technicians from the COG (Biorepository, Data and Statistics Core) and NCI offices (Office of Cancer Genomics, Clinical Therapy Evaluation Program, Center for Cancer Research, and Center for Bioinformatics and Information Technology). This collaborative network is led by:

Principal Investigator

Elizabeth J. Perlman, M.D.
- Pathologist-in-Chief, Ann & Robert H. Lurie Children's Hospital of Chicago
- Professor, Northwestern University Feinberg School of Medicine

Publications

Gadd S, Huff V, Walz AL, et al. (2017) A Children's Oncology Group and TARGET initiative exploring the genetic landscape of Wilms tumor. Nature Genetics 49(10):1487-1494 (PMID: 28825729) View PubMed abstract View GDC Publication Page
Ooms AH, Gadd S, Gerhard DS, et al. (2016) Significance of TP53 Mutation in Wilms Tumors with Diffuse Anaplasia: A Report from the Children's Oncology Group. Clinical Cancer Research 22(22):5582-5591. View PubMed abstract
Chun HJ, Lim EL, Heravi-Moussavi A, et al. (2016) Genome-Wide Profiles of Extra-cranial Malignant Rhabdoid Tumors Reveal Heterogeneity and Dysregulated Developmental Pathways. Cancer Cell 29(3):394-406. (PMID: 26977886) View PubMed abstract
Perlman EJ, Gadd S, Arold ST, et al. (2015) MLLT1 YEATS domain mutations in clinically distinctive Favourable Histology Wilms tumours. Nature Communications 6:10013. (PMID: 26635203) View PubMed abstract
Gooskens SL, Gadd S, Guidry Auvil JM, et al. (2015) TCF21 hypermethylation in genetically quiescent clear cell sarcoma of the kidney. Oncotarget 6(18):15828-41. (PMID: 26158413) View PubMed abstract
Walz AL, Ooms A, Gadd S, et al. (2015) Recurrent DGCR8, DROSHA, and SIX homeodomain mutations in favorable histology Wilms tumors. Cancer Cell 27(2):286-97. (PMID: 25670082) View PubMed abstract

Last updated: January 09, 2020