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Progenetix Publication Collection

Progenetix publication collection: Which scientific publications are included?

The Progenetix Publication DB contains articles describing whole genome screening (WGS, WES, aCGH, cCGH1) experiments in cancer. Genomic information about the analyzed cancer samples is extracted from these publications to generate cancer mutation data, with a focus on copy number abnormalities (CNV / CNA).

Data from a scientific publication is included in the Progenetix publication collection if the following three main criteria are fulfilled:

  1. Data was obtained from a human tumor sample
  2. Data represents the tumor at a whole-genome level
  3. Genomic resolution is at least comparable to molecular-cytogenetic assessment (i.e. cytoband / Megabase resolution).

The table below summarizes which genome sequencing technologies generally offer relevant tumor sample data for the Progenetix web resource, and which ones don't:

Relevant technologies Non-relevant technologies
whole-genome sequencing targeted genome-sequencing
whole-exome sequencing gene expression arrays / sequencing
chromosomal Comparative Genomic Hybridization (CGH) tissue microarrays
genomic arrays (SNP, aCGH) methylation arrays2

Note that, despite containing data about tumor samples at a whole-genome level, some publications might still not be relevant for the Progenetix publication collection. Examples of such publications are:

  • publications that report previously presented data (e.g. reviews, technical publications, ...)
  • publications with data that from certain in vitro experiments (e.g. drug exposure)
  • publications with tumor data obtained from animal models (i.e. not measuring a human genome)
  • articles which report germline analyses - e.g. GWAS studies of individuals with a risk for - or manifestation of - a malignancy are not included

  1. Whole-genome screening techniques: cCGH chromosomal Comparative Genomic Hybridization; aCGH genomic arrays (including single color oligonucleotide, SNP, and large-insert clone arrays); WES Whole Exome Sequencing; WGS Whole Genome Sequencing 

  2. In principle, methylation arrays could be considered as "genome screening experiments", since one may extract e.g. CNV profiles from some platforms/experiments. However, at this time we do not consider them as "compatible" platforms.