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

Claim 14:
15. A method of selecting a subject for a particular treatment for cancer and treating the subject using the particular treatment for cancer, the method comprising:
detecting rearrangement signatures in a previously obtained DNA sample from said subject wherein each of the rearrangement signatures comprises proportions of rearrangements in each of a plurality of categories, wherein the rearrangement signatures include a rearrangement signature characterized by the presence of non-clustered tandem duplications less than 10kb in length, and wherein detecting the rearrangement signatures comprises:
cataloguing, by a processor, somatic mutations in sample using whole genome DNA sequence data obtained from the DNA sample to produce a rearrangement catalogue for the DNA sample which classifies rearrangement mutations identified in the whole genome DNA sequence data into the plurality of categories; and
determining, by said processor, the contributions of the rearrangement signatures, including the rearrangement signature characterized by the presence of non-clustered tandem duplications less than 10kb in length, to said rearrangement catalogue by computing a measure of similarity between the rearrangement mutations in said rearrangement catalogue and the rearrangement signatures, the computing comprising computing the measure of similarity between the rearrangement mutations in said rearrangement catalogue and the rearrangement signature characterized by the presence of non-clustered tandem duplications less than 10kb in length;

determining that the rearrangement signature characterized by the presence of non-clustered tandem duplications less than 10kb in length is present in the DNA sample by determining if the number or proportion of rearrangements in the rearrangement catalogue which are determined to be associated with the rearrangement signature characterized by the presence of non-clustered tandem duplications less than 10kb in length exceeds a predetermined threshold;
selecting the subject for treatment with a particular cancer therapy for subjects whose cancer exhibit homologous recombination deficiency (HRD) when it is determined that the rearrangement signature characterized by the presence of non-clustered tandem duplications less than 10kb in length is present in the DNA sample; and
administering the particular cancer therapy to the subject, and
wherein the processor cataloguing the somatic mutations in said DNA sample to produce said rearrangement catalogue includes:
said processor identifying mutations as one of: tandem duplications, deletions, inversions or translocations and grouping mutations identified as tandem duplications, deletions or inversions by size, and
said processor identifying mutations as being clustered or non-clustered, and wherein the presence or absence of one or more of the rearrangement signatures is associated with said type of cancer or a response to said particular cancer therapy.