Databases and Other Resources¶

hCNV Reference Resource Project¶

Started at Biohackathon 23, the cnv-reference-resources project aims to create a "modern" resource for germline CNV data without known disease association, e.g. collected in the context of reference genome screening projects. The dataset will be derived from projects such as 1000 Genomes and made available through different channels, chiefly by using the GA4GH Beacon protocol.

Databases

BANCCO - Banque Nationale de CNV Constitutionnelles

La banque nationale de CNV Constitutionnelles est développée afin de recenser les CNV (Copy Number Variation) issus du diagnostic clinique.

cancercelllines.org - Cell Line Genomics

A cancer cell line resource with focus on genomic variants and CNV profiles

The Cancercelllines genomic information resource contains genome profiling data, somatic mutation information and associated metadata for thousands of human cancer cell lines. Originally spun out of the Progenetix oncogenomic resource with its collection of more than 100’000 individual genomic copy number screening datasets, cancercelllines.org provides an entry point for genomic variants in cell lines as well as for the exploration of related publications.

Progenetix - Cancer Genome Data Resource

An Open Cancer Genomics Resource with Focus on CNV Profiles

The Progenetix database is the largest repository for annotated copy number profiling data in cancer. The website also tracks & analyses cancer genome profiling publications for provenance & content.

Domain Name: progenetix.net
Creation Date: 2000-11-29T18:17:38.000Z

Other Resources and Information

CNV Annotation Formats

Some Information about CNV Annotation Standards

Cytogenetics vs. Molecular Biology...¶

With the "dual origin" in cytogenetics ("chromosome based") and genomics ("sequencing based") analyses the annotation of copy number variants has evolved starting from different directions. From the cytogenetic side the use of cytogenetic bands as coordinate system, has been amended by increasing use of mapping positions (i.e. for molecular-cytogenetic or hybrid analyses with known probe positions) while for array and sequencing based CNV detection Continue reading

CNV File & Storage Formats

VCF¶

VCF 4.4 is the most appropriate VCF format to store Structural variants including copy number variants * VCF specification v4.4 PDF * VCF specification v4.3 PDF * VCF specification v4.2 PDF

BED files and other columnar segment files¶

BED file documentation at UCSC genome browser

CNV-related contributions to ontologies

h-CNV Community Members and their Involvement with Classifications and Ontologies

h-CNV community members have been contributors to several ontologies, for the representation of technologies relevant for CNV analysis as well as for the encoding of CNV data.

Ontology of bioscientific data analysis and data management (EDAM)¶

Copy number variation detection and child terms
contributed by David Salgado

Experimental Factor Ontology (EFO)¶

Genomic array types¶

Terms for genomic array types used in CNV detection were added to the existing DNA array concept (Michael Baudis):

Whole Exome Sequencing (WES) tools for detection of copy number variants and their status in Galaxy

A list of WES tools for detection of copy number variants and their status in Galaxy

A list of whole exome sequencing tools for detection of copy number variants including: description, web source/repository, conda status, Galaxy status including wrapper if exist hCNV-Galaxy