Experimental Data Submission File Specifications
Types of experimental data being supported:
- Simple mutations/variations: - single and multiple base substitutions, and small (<=200bp) insertions and deletions that appear in the tumour tissue, but not in the normal control tissues.
- Copy number mutations: - DNA copy number alterations (ie. gain, losses, LOH) of genes and other loci in tumour tissues relative to normal control samples.
- Structural mutations: - chromosomal rearrangements including deletions, insertions, inversions, and translocations detected by high-throughput sequencing technologies.
- Gene expression: - gene expression measured at the transcriptional level (mRNA) using array-based or sequencing platforms.
- miRNA: - genome wide analyses of microRNA (miRNA) expression generated by array-based and sequencing platforms.
- Exon junctions: - genomic events that affect the splicing of genes, including aberrant/novel splice forms and gene fusions
- Protein expression: - translational level expression data using for example, Reverse Phase Protein Array (RPPA) platform.
- Methylation: - A type of epigenetic modification that does not affect the primary DNA sequence, but affects secondary interactions and play a role in the regulation of gene expression in the normal setting and in the context of many diseases such as cancer. In the context of ICGC methylation refers to the comprehensive analysis of DNA cytosine methylation states of promoter CpG islands, and readout of differential methylated regions (DMRs) on microarrays.
Types of Files:
Certain data elements (ie. analysis_id, analyzed_sample_id) regarded as identifiers must be consistent across prepared submission files.
- Data that provides useful background information on the experimental data. This can include for example, a detailed description of procedures, protocols and calculations that were applied to produce experimental data, or information on a public repository where raw data is deposited.
- This file is mandatory when submitting a primary experimental file.
- Molecular information describing experimental feature (ie. variation/mutation). Information can include type of mutation, chromosome location of mutation, normalized/raw expression level values, control/tumour genotype.
- Additional experimental information, such as genes/transcript affected, annotation etc.
- This file is optional.