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Why do CNVs of different genes in the GDC Data Portal differ from other genomic portals?

Submitted by gaheens on

This discrepancy is due to differences in the data processing pipelines used by the GDC and other genomic portals. At the GDC, gene-level CNVs are derived from a mix of standardized pipelines. For TCGA projects, the CNV values are prioritized in the following order: SNP6 ABSOLUTE (LiftOver) > SNP6 ASCAT3 > WGS AscatNGS > SNP6 ASCAT2. All of these workflows produce absolute integer copy number values. 

Date: Saturday, July 26, 2025
Time: 5:45 PM - 5:45 PM EDT
Location: Web Conference (See WebEx information below)
Speakers:
Dr. Bill Wysocki, Director of User Services, University of Chicago (UChicago)
Dr. Zhenyu Zhang, GDC Co-Principal Investigator, University of Chicago (UChicago)
Dr. Xin Zhou, Assistant Member, St. Jude Children's Research Hospital
Intended Audience

This webinar is designed for researchers interested in learning how the GDC generates copy number variation (CNV) data and provides an overview of the new GDC Copy Number Segment Tool for visualizing copy number variation over a gene or region. It is ideal for anyone interested in analyzing copy number data for cancer research, regardless of their prior experience in genomics.

Abstract

Join us for an in-depth exploration of the GDC workflows and tools supporting Copy Number Variation (CNV) analysis. This webinar will cover copy number workflows for whole-genome sequencing and SNP array data, including allele-specific segmentation with ASCAT, gene-level CNV profiling with ABSOLUTE, and circular binary segmentation with DNACopy. Data processing steps, output formats, and how the GDC generates CNV data for cancer genomics research will be discussed. This webinar will also demonstrate existing GDC analysis tools for analyzing copy number variation data, as well as the new Copy Number Segment Tool available in the GDC Data Portal for visualizing copy number variation over a gene or regions. A review of GDC CNV Application Programming Interface (API) endpoints for programmatic access will also be provided.

Included Topics
  • Overview of GDC workflows for generating copy number segmentation and gene-level copy number data 
  • Demonstration of GDC tools for visualizing copy number data including the new Copy Number Segment Tool 
  • Review of the CNV API endpoint for programmatic access 
  • Live Q&A session to address user questions and gather feedback
Webex Information

Exploring GDC Copy Number Variation (CNV) Analysis Workflows and Tools

  • Monday, August 25, 2025
  • 2:00 pm    |    Eastern Standard Time (New York, GMT-04:00)    |    1 hr
  • Meeting number (access code): 2304 255 2981
  • Meeting password: 9Pfy452JCc@ (97394525 when dialing from a phone or video system)

REGISTER/JOIN WEBEX MEETING.

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How does the GDC choose the default transcript for each variant?

Submitted by gaheens on

When a mutation overlaps multiple transcripts or genes, the GDC annotates all consequences in the all_effects column of the MAF file and in the CONSEQUENCE table on the Mutation Summary Page. One transcript is then selected as the default for detailed annotation and visualization where a single consequence is shown. 

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