Patent ID: 11929144
Assignee: GENOME RESEARCH LIMITED
Field: Computer technology (Electrical engineering)
Classification: CPC G | IPC G

Claim 12:
13. A computer program product containing non-transitory memory storing a computer program which, when run on a computer, performs a method comprising:
obtaining whole genome DNA sequence data that was previously obtained by sequencing a DNA sample, the DNA sample comprising fresh-frozen derived DNA, circulating tumor DNA, or formalin-fixed paraffin-embedded (FFPE) DNA representative of a suspected or known tumor from a patient;
obtaining a file of somatic mutations in the DNA sample, the somatic mutations obtained from the whole genome DNA sequence data;
filtering, using data obtained from one or more databases, the somatic mutations in the file to remove one or more germline rearrangements and copy number polymorphisms;
filtering, using data in alignment mapping files, the somatic mutations in the file to remove known sequencing artifacts;
cataloguing the somatic mutations in the file to produce a rearrangement catalogue for the DNA sample which classifies rearrangement mutations identified in the sequence data into a plurality of categories, the cataloguing comprising:
identifying mutations as one of: tandem duplications, deletions, inversions or translocations and grouping mutations identified as tandem duplications, deletions or inversions by size, and
identifying mutations as being clustered or non-clustered;

determining the contributions of known rearrangement signatures to said rearrangement catalogue using a measure of similarity between the rearrangement mutations in said rearrangement catalogue and the known rearrangement signatures, wherein each of the known rearrangement signatures comprises proportions of rearrangements in the plurality of categories and wherein said known rearrangement signatures are indicative of the presence of mutational processes contributing to cancer; and
determining if the number or proportion of rearrangements in the rearrangement catalogue which are determined to be associated with a particular one of the known rearrangement signatures exceeds a predetermined threshold and, if so, determining that the particular one rearrangement signature is present in the DNA sample.