Cytogenomics data standards and tools

[ahwagner]

Submitter Name

Alex Wagner

Submitter Affiliation

Nationwide Children’s Hospital

Submitter Github Handle

Ahwagner

Additional Submitter Details

No response

Project Details

While several community resources exist to evaluate the clinical significance of cytogenomic abnormalities, a lack of data standards in this space limits computational exchange and search of this knowledge.

This session will explore potential use cases, standards, and tools that may inform development of GA4GH standards for the computable sharing and search of cytogenomics knowledge.

Relevant background material:

• Cytoband model in GA4GH VRS 1.3
• CCGA
• Mitelman Database
• Atlas of Genetics and Cytogenetics

Required Skills

Familiarity with cytogenomics databases, data standards, and/or analysis tools.

[malachig]

A preliminary survey of interest (where every participant was allowed to vote twice) resulted in 15 votes for this topic.

[henryhmo0]

Motive and opportunity: MYC rearrangements in high-grade B-cell lymphoma with MYC and BCL2 rearrangements (an LLMPP study) https://pubmed.ncbi.nlm.nih.gov/38701426/

[Laveniya]

One of the fusion databases that I use (in case useful):

https://www.kobic.re.kr/chimerdb/chimerkb

[ahwagner]

Contributor form

[henryhmo0]

CytoConverter : Cytogenetic Nomenclature to Genomic Coordinate Translator https://jxw773.shinyapps.io/Cytogenetic__software/

Used in Mitelman website

[ahwagner]

Summary slides