The Hospital for Sick Children

Adam Shlien

Uri Tabori

Matthew Zatzman

The present invention relates a system and method for cancer-cell specific transcription identification. The method including: receiving nucleic acid data from one or more samples; determining variant allele fraction (VAF) of markers in ribonucleic acid (RNA) in the nucleic acid data and markers for deoxyribonucleic acid (DNA) in the nucleic acid data; comparing the VAF of the RNA relative to the DNA for each of the markers; and outputting the comparison as a quantification of cancer-cell specific changes in transcriptional output as a marker of prognosis or therapeutic response in cancer.

System and method for cancer-cell specific transcription identification

There is provided a method of profiling a tumour, the method comprising determining a relative proportion for each of 96 mutation types, wherein the 96 mutation types are defined as the six possible sequence changes C&#x3e;A, C&#x3e;G, C&#x3e;T, T&#x3e;A, T&#x3e;C, or T&#x3e;G in the context of each of four possible nucleotides (A, C, G, or T) at the position immediately 5' to the mutation and each of four possible nucleotides at the position immediately 3&#x2032; to the mutation; assigning the tumour, using the determined relative proportion for each of the 96 mutation types, to at least one of eight clusters defined herein; and determining at least one tumour characteristic based on the assignment to a cluster.

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Toronto, Canada

Adam Shlien