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Data from sample analysis and testing 

To gain access to comprehensive omics and high throughput screening datasets, together with minimal clinical information to support high-level integrative analysis, researchers are invited to complete and submit the following:

-  ZERO Data Access Application form (for ZERO datasets not listed on the EGA), or

-  EGA Data Access Application form (for ZERO datasets archived on the EGA; see below Section “ZERO Data on the European Genome-Phenome Archive (EGA)”)

These applications are based on the exacting standards of the European Genome-Phenome Archive. VCF, BAM, FASTQ, TXT and BED data are available. 

ZERO data is primarily comprised of: 

• whole genome sequencing (WGS) 
• RNA sequencing (RNASeq)  
• methylation array data  
• high-throughput drug screening
• aggregate base clinical information from children with high-risk cancer of various tissue origins.  

In addition, the successful generation of in vitro cell culture gives rise to drug screening data and, in turn, patient-derived xenografts (PDXs) enable in vivo drug efficacy data to be made available. (Note: Targeted sequencing was routinely performed on samples obtained earlier in the Program; however, it is now only completed on samples where the material is found to be insufficient for WGS.)   

Whole-genome sequencing  

DNA was extracted from tumour:normal matched pair tissue. Libraries were prepared and sequenced using Illumina next generation sequencers to generate 2x150bp reads at a target coverage of >30x for germline and >90x for tumour samples.

RNA sequencing  

Tumour RNA was extracted and RNA libraries were sequenced on Illumina. Gene expression analysis was performed using data from the patient-tumour to generate gene and isoform counts (Transcripts per million), and gene fusion detection.

Methylation analysis 

Tumour DNA was extracted followed by bisulfite conversion and hybridised on the Illumina EPIC Infinium Methylation BeadChip. Classification of tumours by methylation profiling was performed using the DKFZ Molecular Neuropathology portal (MNP).

High-throughput Drug Screening (HTS)

Primary or expanded tumour cells were validated by short tandem repeat profiling, single-nucleotide polymorphism profiling array and/or immunohistochemistry, and screened with up to 150 drugs approved or in (pre)clinical development for paediatric cancer.

ZERO Data on the European Genome-Phenome Archive (EGA)

ZERO Datasets archived on the European Genome-Phenome Archive (EGA) are listed in the table below. Click to explore these datasets on the EGA website:

To access ZERO Data archived on the EGA, researchers are invited to complete a EGA Data Access Application form .

This application is based on the exacting standards of the European Genome-Phenome Archive. VCF, BAM, FASTQ, TXT and BED data are available for the paper titled: Whole genome, transcriptome and methylome profiling enhances actionable target discovery in high-risk pediatric cancer; Nat Med. 2020 Nov;26(11):1742-1753. doi: 10.1038/s41591-020-1072-4. Epub 2020 Oct 5.

For all other ZERO Data requests, please use the general ZERO Data Access Application form here.

All submitted application form(s) and all supporting documentation must be provided in English. All submissions and enquiries should be addressed to the ZERO DAC via zeroDAC@ccia.org.au.

- Download the general ZERO Data Access Application Form