Format specifications

Clinical information table

An Excel table with data from clinical routine diagnostics can be provided during the filtering step of this pipeline (Part II). This data will be used to check whether a reported fusion event shows evidence by cytogenetics (Karyotype in ISCN format) and/or molecular diagnostics (FISH/PCR). The Excel file must contain the following columns:

• cohort: Name of the cohort that the sample should be associated with.
• sample: Name of sample
  (has to match the name that was used in part I of this pipeline).
• Karyotype: Karyotype from cytogenetic analysis in ISCN format
  (e.g.: "46,XX,t(11;19)(q23;p13.1)[20]").
• otherCyto: Comma-separated results from FISH/PCR analyses for the identification of gene rearrangements.
  • Positive result for a fusion gene should be indicated by concatenating the official HGNC symbols with '-'
    (e.g.: "KMT2A-MLLT3").
  • Negative result for a fusion gene should be indicated by concatenating the official HGNC symbols with '!'
    (e.g.: "KMT2A!MLLT3").
  • Results from break-apart FISH analyses indicating the rearrangement of only one loci should be indicated by '#'
    (e.g.: "KMT2A#").