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

Claim 0:
1. A method, implemented using a computer system comprising one or more processors and system memory, for identifying the presence of a cancer and/or an increased risk of a cancer in a mammal, said method comprising:
(a) providing, to the computer system, 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) aligning, by the one or more processors, the sequence reads to one or more chromosome reference sequences, thereby providing sequence tags corresponding to the sequence reads;
(c) identifying, by the one or more processors, a number of sequence tags from the 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, by the one or more processors, a number of sequence tags for at least one normalizing sequence for each of the one or more sequences of interest;
(d) calculating, by the one or more processors and 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 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) evaluating, using the one or more processors, 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.