MTPpilot Web Application

Allowed values for the columns of the tab separated file for data upload. Example files: tab separated and excel format.

Variant types (VARIANT_TYPE):

• Short variants
  VARIANT_TYPE: short-variant
• Copy number alterations
  VARIANT_TYPE: copy-number-alteration
• Rearrangements
  VARIANT_TYPE: rearrangement

Gene names (GENE):

• Alphabetical and numerical values, no special characters:
  GENE: CARD11
  GENE: FGFR2

Functional impact (SOMATIC_STATUS_FUNCTIONAL_IMPACT):

• Variant of known significance:
  SOMATIC_STATUS_FUNCTIONAL_IMPACT: known
  
• Variant of unknown significance:
  SOMATIC_STATUS_FUNCTIONAL_IMPACT: unknown
  

Short variants amino acid changes (SV_PROTEIN_CHANGE):

• Missense mutations
  SV_PROTEIN_CHANGE: V2070L
• Stop codons
  SV_PROTEIN_CHANGE: R196*
• Frame shifts
  SV_PROTEIN_CHANGE: R112fs*25
• Amino acid deletions
  SV_PROTEIN_CHANGE: A147_P151del
• Amino acid insertions
  SV_PROTEIN_CHANGE: R506_K507insVLR
• Promotor mutations (note: same value as in SV_CDS_CHANGE required)
  SV_PROTEIN_CHANGE: -124C>A
• Splice site mutations (note: same value as in SV_CDS_CHANGE required)
  SV_PROTEIN_CHANGE: 1984-19_1998del34

Short variants nucleotide changes (SV_CDS_CHANGE):

• Single nucleotide mutations
  SV_CDS_CHANGE: 6208G>A
• Base pair deletions
  SV_CDS_CHANGE: 439_453delGCCGCGGAAGGTCCC
• Base pair insertions
  SV_CDS_CHANGE: 1276_1277insGTGC
• Promotor mutations (note: same value as in SV_PROTEIN_CHANGE required)
  SV_CDS_CHANGE: -124C>A
• Splice site mutations (note: same value as in SV_PROTEIN_CHANGE required)
  SV_CDS_CHANGE: 1984-19_1998del34

Short variants chromosomal positions (SV_GENOME_POSITION)

• For single nucleotide variants:
  SV_GENOME_POSITION: chr17:7578263
  SV_GENOME_POSITION: chrX:122434

Short variants chromosomal positions (SV_GENOME_POSITION)

• Mandatory value including chromosome number, or X/Y value for sex chromosomes:
  SV_GENOME_POSITION: chr17:7578263
  SV_GENOME_POSITION: chrX:122434

Short variants variant allele frequency (SV_PERCENT_READS)

• Mandatory value as float number:
  SV_PERCENT_READS: 49.15

Copy number alterations fold change (CNA_COPY_NUMBER)

• Amplifications:
  CNA_COPY_NUMBER: 5
• Losses:
  CNA_COPY_NUMBER: 0

First gene in rearrangement (REARR_GENE1)

• Alphabetical and numerical values, no special characters:
  REARR_GENE1: NTRK1
  REARR_GENE1: ALK

Second gene in rearrangement (REARR_GENE2)

• Alphabetical and numerical values, no special characters:
  REARR_GENE2: ETV4
  REARR_GENE2: ERG

Rearrangement chromosomal position first gene (REARR_POS1)

• Exact chromosomal location or location range
  REARR_POS1: chr17:7578263
  REARR_POS1: chr16:2122099-2122412

Rearrangement chromosomal position second gene (REARR_POS2)

• Exact chromosomal location or location range
  REARR_POS2: chr12:134522
  REARR_POS2: chr16:2129381-2129779

Rearrangement number of reads (REARR_NUMBER_OF_READS)

• Required integer value
  REARR_NUMBER_OF_READS: 124