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Use Cases

Explore Gene CNVs

One of the main use cases for the Progenetix resource is the exploration of frequency and disease specificity of genes of interest. Traditionally, the relevance of somatic CNVs hitting a gene in the context of cancer are judged by

  • the CNV frequency (i.e. in what fraction of samples the a CNV in this gene is being observed)
  • the relative specificity, i.e. how CNVs in this gene compare to
    • the overall amount of CNVs in the samples
    • the local specificity, i.e. the "focality" of the CNVs

The Progenetix Search Page supports the exploration of regional CNVs through

  • support for inserting positions of genes or cytobands into standard Beacon query parameter fields
  • selection support for hierarchical disease annotations
  • providing example queries as templates

The response of the queries for genomic variants provide some basic statistics, e.g. the relative frequencies of these variants for each classification code (e.g. NCIT, ICD-O) encountered in teh matched samples.

Example Procedure

  • go to the Progenetix Search Page (or the equivalent page at other resources)
  • retrive the gene coordinates by clicking the Gene Spans button and typing the start f a HUGO gene symbol (e.g. CDK); select the gene of interest
  • the panel should now show the coordinates (start + end + reference/chromosome); select Apply to insert the values into the form
  • the values represent the genome coordinates for the maximum coding region of the gene; if you want to include the flanking regions, you can change the values accordingly or convert into a bracket query by changing those to ranges around start end end
    • e.g. change the start value from 60778331 to 60000000-60778330 and the end value from 60794852 to 60794853-61500000; here the start bracket and the end brackets cover regions just outside the CDR, e.g. to match small CNVs that cober the whole region
  • select the Variant Type
  • Query Database

Visualize CNV patterns

The Progenetix resource contains pre-computed CNV frequency profiles for all diagnostic and technical (e.g. derived from a publication or technical platform) categories. These profiles provide a rapid overview of CNV events along the genome but also can serve for the exploration of possible genomic subsets hidden behind the overview profiles.

CNV profile clustering

Example Procedure

TBD

Download or Plot CNV Frequencies

Collation plots

The Progenetix resource provides pre-computed CNV frequencies for all its "collations" such as

  • cancer types by e.g. NCIt, ICD-O morphology and topography codes
  • experimental series, e.g. all samples from a given publication
  • custom cohorts, e.g. all samples used in a Progenetix meta-analysis or external project such as TCGA

This data can be accessed through the Progenetix API in data and image format.

Example CNV histogram with custom parameters

Interval frequencies are per default stored in a 1Mb binned format. More information about the API use can be found in the IntervalFrequencies API documentation.

Query-based histograms

The Progenetix Beacon responses - depending on their type - usually contain a handover URL to retrieve CNV histogram and/or sample plots of the samples matched by the query. The bycon API now offers a direct access to the histograms without the need to deparse JSON response first. The switch to the histogram is ionitiated by adding &output=histoplot to the Beacon query URL. Then, the API will first query the samples and then perfor a handover to the plotting API. Please be aware that this procedure is best suited for limited queries and may lead to a time-out.

Examples:

Example query-based CNV histogram

Example Procedure - Download CNV Frequencies

Typical cases for the use of collation-specific frequency data could be e.g. the visualization of CNV tracks with 3rd party tools such as Circos or integration in data analysis workflows, e.g. for comparing target genes to local, disease-specific CNV frequencies.

Getting cancer type CNV frequencies

All cancer codes for a given classification system can be retrieved though:

Download the data file

For any of those codes one can create a .pgxseg file downloader link for the "IntervalFrequencies" service:

Examples

Example Procedure - Download or embed CNV frequency plot

For the generation of CNV frequency plots, the same procedure as above for identifying existing frequency maps can be applied. CNV hsitograms in SVG format can be generated for download or embedding through a canonical service URL with added (single) collation code.

Examples

Download Sample Data

The sample annotations for any type of query - particularly but not limited to single identifier values - can be downloaded in either Beacon v2 JSON or in a tab-delimited text format. You can also use &limit= to limit the number of samples to download, &limit=0 indicates no limitations.

Examples

User-Provided CNV Data

The Progenetix resource has a limited option to visualize CNV data provided by the users. Data has to be formatted in a standard tab-delimited columnar format, preferably using the .pgxseg file format. Additional information can be found on the upload service page:

The data is only temporary stored on the server with a randomiized access path. At this time we do not provide any long term or login protected data storage and do not store access data.

Example Procedure

TBD