Patent ID: 11875899
Assignee: VERINATA HEALTH, INC.
Field: Biotechnology (Chemistry)
Classification: CPC G  A  C | IPC C  G

Claim 15:
16. A computer program product for use in determining the presence of a cancer and/or an increased risk of a cancer in a mammal, said computer program product comprising:
(a) code for providing sequence reads of nucleic acids in a test sample from said mammal, wherein said test sample comprises both genomic nucleic acids from cancerous or precancerous cells and genomic nucleic acids from constitutive cells, and wherein the sequence reads are provided in an electronic format;
(b) code for aligning the sequence reads to one or more chromosome reference sequences and thereby providing sequence tags corresponding to the sequence reads;
(c) code for identifying a number of sequence tags from nucleic acids for one or more sequences of interest amplification of which or deletions of which are associated with cancers, wherein said one or more sequences of interest are on chromosomes 1-22, X, or Y, and identifying a number of sequence tags for at least one normalizing sequence for each of the one or more sequences of interest;
(d) code for calculating, using said number of sequence tags identified for each of said one or more sequences of interest and said number of sequence tags identified for each said at least one normalizing sequence, a single sequence dose for each of said one or more sequences of interest,
wherein the at least one normalizing sequence is a sequence that yields sequence doses for a sequence of interest having: (a) the smallest variability among unaffected samples, (b) the greatest differentiability between affected and unaffected samples, (c) the smallest variability and the greatest differentiability, or (d) an optimal combination of small variability and large differentiability; and
(e) code for evaluating each of said single sequence doses for each of one or more sequences of interest, and thereby determining the presence or absence of copy number variations (CNVs) of the one or more sequences of interest in said test sample, where the presence of said CNVs is an indicator of the presence and/or increased risk of a cancer.