CVCDAP

You can create your own Project by uploading somatic mutations and clinical data here, to be seamless integrated with exisitng public projects in CVCDAP, for cohort query and analysis.

If you wish to make use of additional public datasets/studies with a large amount of multi-omics data, no hesitate to let us know, and we will prioritize them for integration in the future release.

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(required)
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Somatic Mutation data (required)
The following columns are mandatory (click to open)
  • Sample_ID: tumor sample ID
  • Hugo_Symbol: HUGO gene symbol
  • Chromosome: The affected chromosome (1..22,"X","Y")
  • Start_Position: Mutation start coordinate
  • End_Position: Mutation end coordinate
  • Variant_Classification: Translational effect of variant allele. Frame_Shift_Del, Frame_Shift_Ins, In_Frame_Del, In_Frame_Ins, Missense_Mutation, Nonsense_Mutation, Silent, Splice_Site, Translation_Start_Site, Nonstop_Mutation, 3'UTR, 3'Flank, 5'UTR, 5'Flank, IGR ( More details)
  • Variant_Type: Type of mutation. SNP, DNP, TNP, ONP, INS, DEL, or Consolidated.( More details)
  • Reference_Allele: The plus strand reference allele. Includes the deleted sequence for a deletion or "-" for an insertion
  • t_ref_count: Read depth supporting the Reference Allele in tumor BAM
  • Mutant_Allele: Primary data genotype, usually from column Tumor sequencing (discovery) allele 2 of a MAF-format file. " -" for a deletion represents a variant. "-" for an insertion represents wild-type allele.
  • t_alt_count: Read depth supporting the variant allele (Mutant Allele) in the tumor BAM file
  • HGVSp_Short: The protein sequence of the variant in HGVS recommended format, using 1-letter amino-acid codes, e.g. p.R296Q
  • Homozygosity: Inferred homozygous, Inferred heterozygous, NA

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Clinical data (optional)
Column description (click to open)
  • Sample_ID: This column is mandatory, and other clinical columns are optional.
  • Gender: FEMALE , MALE , Unknown
  • Grade: G1 , G2 , G3 , G4 , GB , GX , High Grade , Low Grade , Unknown
  • Stage: I , I/II NOS , II , III , IS , IV , Unknown , X
  • Race: AMERICAN INDIAN OR ALASKA NATIVE , ASIAN , BLACK OR AFRICAN AMERICAN , NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER , Unknown , WHITE
  • Age: integer values.
  • OS_status: 0 for censoring, 1 for event
  • OS_time: Overall survival (days)

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Please note: Uploaded projects will be permanently preserved for registered users, while 7 days for guest users.
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