CTVT Variation Tracks
 
CTVT Variations from Germline and Somatic tracks

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CTVT Indels Somat  CTVT Indels Somatic  
CTVT Indels Germl  CTVT Indels Germline  
CTVT SNV Somatic  CTVT SNV Somatic  
CTVT SNV Germline  CTVT SNV Germline  
Assembly: Dog Sep. 2011 (Broad CanFam3.1/canFam3)

Canine Transmissible Venereal Tumor (CTVT) Germline and Somatic Variation

This track contains information for SNVs and insertion-deletion events for two categories of variants found in CTVT: alleles originating from the ancient founder canine genome, and subsequently derived somatic mutations (Decker and Davis et al.).

Display Conventions and Configuration

Tracks default to dense. When in full display, each marker is associated with detailed variant data:

  • Variant quality
  • Allele count in genotypes, for each ALT allele
  • Allele Frequency, for each ALT allele, in the same order as listed
  • Total number of alleles
  • Z-score from Wilcoxon rank sum test of Alt Vs. Ref base qualities
  • Approximate read depth
  • Phred-scaled p-value using Fisher's exact test to detect strand bias
  • Mean of all GQ values
  • Standard deviation of all GQ values
  • Inbreeding coefficient estimated from the genotype likelihoods per-sample compared to Hardy-Weinberg expectation
  • Maximum likelihood expectation for the allele counts for ALT allele
  • Maximum likelihood expectation for the allele frequency for ALT allele
  • RMS Mapping Quality
  • Total Mapping Quality Zero Reads
  • Z-score From Wilcoxon rank sum test of Alt vs. Ref read mapping qualities
  • Variant Confidence/Quality by Depth
  • Z-score from Wilcoxon rank sum test of Alt vs.Ref read position bias
  • Log odds ratio of being a true variant versus being false under the trained gaussian mixture model
  • Functional consequences as predicted by Ensembl Variant Effect Predictor.

Methods

Variants represent the union of two sequenced CTVT tumors (Murchison et al. 2014) after compareison to a panel of 186 canine whole genomes. For detailed methods see: (Decker and Davis et al.).

Credits

Data was generated, compiled and analyzed by Brian W. Davis and Brennan Decker in the lab of Elaine A. Ostrander (Cancer Genetics and Comparative Genomics Branch, National Human Genome Research Institute, National Institutes of Health). Sequencing was performed at the NIH Intramural Sequencing Center, as well as through collaboration with Tosso Leeb (University of Bern) and Matt Huntleman (Translational Genomics Research Institute).

References

Decker B, Davis BW et al. (2015) Comparison against 186 canid whole genome sequences reveals survival strategies of an ancient clonally transmissible canine tumor. Genome Research, doi: 10.1101/gr.190314.115

Contact

For questions or more information on the data in this Track Hub, please contact the Broad Institute Vertebrate Genome Biology group: vertebrategenomes@broadinstitute.org