While the pgx prefix had been registered in 2017 with identifiers.org
we recently changed the resolver and target mappings on the Progenetix server.
This went hand-in-hand with the generation of unique & persistant identifiers
for the main data items.
2020-10-09: more ...
After some months of dormancy, the arrayMap resource has been relaunched through integration with the new Progenetix site. All of the oiginal arrayMap data has now been integrated into Progenetix, and of today the arraymap.org domain maps to a standard Progenetix search page, where only data samples with existing source data (e.g. probe specific array files) will be presented.
@mbaudis 2021-02-06: more ...
2012-04-02: more ...
The new year brings some refinements to biosamples search and display:
@mbaudis 2021-01-04: more ...
This article provides an overview of recent changes and additions to the Progenetix database and the services provided through the resource.
2021-06-30: more ...
]So far (and still as standard), any
selected filter will also include matches on its child terms; i.e. “NCIT:C3052 -
Digestive System Neoplasm” will include results from gastric, esophagus, colon
… cancer. Here we introduce a selector for the search panel to make use of the Beacon v2
filters includeDescendantTerms pragma, which can be set to false if one only
wants to query for the term itself and exclude any child terms from the matching.
@mbaudis 2022-01-17: more ...
While the Progenetix resource has provided access to the CNV data from The Cancer Genome Annotation Project (TCGA*; www.cancer.gov/tcga) for quite some time, we have now launched a dedicated search page to facilitate data access and visualization using the standard Progenetix tools.
@mbaudis 2021-02-06: more ...
Copy number aberrations (CNA) are one of the most important classes of genomic mutations relatedto oncogenetic effects. In the past three decades, a vast amount of CNA data has been generated bymolecular-cytogenetic and genome sequencing based methods. While this data has been instrumentalin the identification of cancer-related genes and promoted research into the relation between CNA andhisto-pathologically defined cancer types, the heterogeneity of source data and derived CNV profilespose great challenges for data integration and comparative analysis. Furthermore, a majority of exist-ing studies have been focused on the association of CNA to pre-selected ”driver” genes with limitedapplication to rare drivers and other genomic elements.
2021-04-15: more ...
progenetixuse PageWe have introduced a new publications listing page which contains links to articles that cite or use Progenetix and resources from this “ecosystem.” Please let us know if you are aware of other such cases - frequently the publications do not use a proper citation format but just refer to “according tho the Progenetix resource” or similar in the text.
For proper citation please follow these instructions.
The pop-up in th Publication maps has been updated with a proper short text listing and direct links to the article pages on EuropePMC.
@mbaudis 2021-10-12: more ...
After many years of using a CreativeCommons CC-BY-SA (“attribution + share alike”), the Progenetix resource has dropped the “SA - share alike” attribute and is now “attribution” only. This may facilitate the use of the data in more complex and/or commercial scenarios - enjoy!
@mbaudis 2020-08-05: more ...
The Progenetix oncogenomics resource provides sample-specific cancer genome profiling data and biomedical annotations as well as provenance data from cancer studies. Especially through currently 113322 curated genomic copy number number (CNV) profiles from 1600 individual studies representing over 500 cancer types (NCIt), Progenetix empowers aggregate and comparative analyses which vastly exceed individual studies or single diagnostic concepts.
2020-09-30: more ...
2021-08-03: more ...
2020-03-16: more ...
The group is an active contributor to several public ontologies, both through mapping efforts (ICDOntologies, icdot2uberon) and by requesting terms relevant for genomic and metadata e.g. for EFO.
@mbaudis 2021-01-14: more ...
Loss of heterozygosity (LOH) is a phenomenon frequently observed in cancer genomes where the selective pressure to keep only the susceptible gene product from one allele removes the other healthy allele from the pool; In this context, copy neutral - loss of heterozygosity (CN-LOH) is commonly observed in haematological malignancies (O’keefe et al., 2010 and Mulligan et al., 2007). To Progenetix oncogenomic resource, comprising of nearly 800 cancer types (by NCIt classification) as of 2021, we expanded the new feature of LOH in our data collection, in addition to the total copy number, to open the door for the analysis of frequency and impact of this phenomenon.
Update 2021-01-28:
LOH variants can now be queried through the Search and Beacon+ interfaces, either as specific variants or together with deletions.
Please be aware that in contrast to the “complete for chromosomes 1-22” DUP and DEL calls, LOH is only determined for a subset of samples and therefore will be underreported in the statistics section.
@qingyao 2021-01-14: more ...
The Progenetix website has been completely rebuilt using a JavaScript / React based framework and API based content delivery. At its core, the site is built around the Beacon standard, with some extensions for data colections and advanced query options.
@mbaudis 2020-09-21: more ...
@mbaudis 2019-07-31: more ...
@mbaudis 2021-04-29: more ...
@mbaudis 2020-04-02: more ...
2020-12-18: more ...
The Beacon driver project was one of the earliest initiatives of the Global Alliance for Genomics and Health with the Beacon v1.0 API as first approved GA4GH standard. Version 2 of the protocol is slated to provide fundamental changes, towards a Internet of Genomics foundational standard:
2020-09-30: more ...
2020-05-06: more ...
Diffuse Intrinsic Pontine Glioma (DIPG) is a highly aggressive tumor type that originate from glial cells in the pon area of brainstem, which controls vital functions including breathing, blood pressure and heart rate. DIPG occurs frequently in the early childhood and has a 5-year survival rate below 1 percent. Progenetix has now incorporated the DIPG cohort, consisting of 1067 individuals from 18 publications. The measured data include copy number variation as well as (in part) point mutations on relevant genes, e.g. TP53, NF1, ATRX, TERT promoter.
@qingyao 2021-02-15: more ...
Wherever possible, data annotation in Progenetix uses {S}[B] OntologyClass
objects for categorical values, with CURIEs as id values. So far, the
Progenetix databases had used pubmed: for PubMed identifiers and ncit:
for NCI Metathesaurus (Neoplasm) ids.
@mbaudis 2020-03-30: more ...
The Beacon+ implementation of the GA4GH Beacon protocol has become a part of the ELIXIR Beacon Network, an expanding Beacon service to query multiple Beacon resources and aggregate their query results.
@mbaudis 2020-01-20: more ...
We have introduced a simple option to search directly by Gene Symbol, which will match to any genomic variant with partial overlap to the specified gene. This works by expanding the Gene Symbol (e.g. TP53, CDKN2A …) into a range query for its genomic coordinates (maximum CDR).
Such queries - which would e.g. return all whole-chromosome CNV events covering the gene of interest, too - should be narrowed by providing e.g. Variant Type and Maximum Size (e.g. 2000000) values.
@mbaudis 2021-02-22: more ...
The response element of the Beacon+ interface now contains a link for displaying the matched variants e.g. of e.g. a CNV query in the UCSC genome browser.
@mbaudis 2019-10-14: more ...
In “forward-looking” conformity with the Beacon v2
API, the JSON attributes of the API responses has been changed from snake_cased
to camelCased. Please adjust your code, where necessary.
@mbaudis 2021-07-01: more ...
The Biosample schema used for exporting Progenetix data has been adjusted with respect to representation of “bio-“classifications. The previous biocharacteristics list parameter has been deprecated and its previous content is now expressed in1:
histologicalDiagnosis (PXF)sampledTissue (PXF)icdoMorphology (pgx)icdoTopography (pgx)Here, “PXF” means that the attribute is part of the Phenopackets standard, while “pgx” labels it as specific to Progenetix. ↩
@mbaudis 2021-08-31: more ...
The Progenetix resource’s API utilizes the bycon framework for data query and
delivery and basically represents a custom implementation of the Beacon API.
@mbaudis 2021-05-05: more ...
For testing the rapidly evolving Beacon v2 API, we have now implemented more paths/endpoints which mostly conform to the brand new & still “flexible” v2.0.0-draft.4 version. Please check the documentation and examples.
@mbaudis 2021-07-02: more ...
Following the launch of the updated Progenetix website (new interface, now much
more data with >130’000 samples…) and the recent introduction of the new
Python based bycon API for BeaconPlus and Progenetix Services
we now also have some structured information for the different API options.
2020-10-21: more ...