Determining a nucleic acid sequence imbalance associated with cancer using multiple markers

A non-transitory computer readable storage medium storing one or more programs configured to be executed by a system to perform a method for determining whether a nucleic acid sequence imbalance associated with cancer exists within a biological sample from a subject, the biological sample including cell-free nucleic acid molecules originating from non-malignant cells and potentially from tumor cells associated with cancer, the method comprising:

• separating the cell-free nucleic acid molecules of the biological sample into a plurality of reactions;
• measuring signals from the plurality of reactions;
• receiving, by one or more processors, first quantitative data indicating a first total amount of a plurality of clinically relevant nucleic acid sequences in a plurality of reactions involving cell-free nucleic acid molecules from the biological sample;
• receiving, by the one or more processors, second quantitative data indicating a second total amount of a plurality of background nucleic acid sequences in the plurality of reactions, wherein the plurality of background nucleic acid sequences is different from any one of the plurality of clinically relevant nucleic acid sequences, wherein the measured signals include the first quantitative data and the second quantitative data;
• determining, by the one or more processors, the first total amount of the plurality of clinically relevant nucleic acid sequences from the first quantitative data;
• determining, by the one or more processors, the second total amount of the plurality of background nucleic acid sequences from the second quantitative data;
• determining a parameter from the first total amount and the second total amount, wherein the parameter is based on a numerical value characterizing the first total amount and the second total amount;
• and
• based on the parameter, determining a classification of whether the nucleic acid sequence imbalance associated with cancer exists in the biological sample for the plurality of clinically relevant nucleic acid sequences in the subject.

An system for determining whether a nucleic acid sequence imbalance associated with cancer exists within a biological sample from a subject, the biological sample including cell-free nucleic acid molecules originating from non-malignant cells and potentially from tumor cells associated with cancer, the system comprising:

• an assay device configured to measure signals from a plurality of reactions within which the cell-free nucleic acid molecules of the biological sample are separated;
• and
• a computer system comprising:
• one or more processors;
• a memory storing one or more programs that are configured to be executed by the one or more processors to perform:
• receiving first quantitative data indicating a first total amount of a plurality of clinically relevant nucleic acid sequences in a plurality of reactions involving cell-free nucleic acid molecules from the biological sample;
• receiving second quantitative data indicating a second total amount of a plurality of background nucleic acid sequences in the plurality of reactions, wherein the plurality of background nucleic acid sequences is different from any one of the plurality of clinically relevant nucleic acid sequences, wherein the measured signals include the first quantitative data and the second quantitative data;
• determining the first total amount of the plurality of clinically relevant nucleic acid sequences from the first quantitative data;
• determining the second total amount of the plurality of background nucleic acid sequences from the second quantitative data;
• determining a parameter from the first total amount and the second total amount, wherein the parameter is based on a numerical value characterizing the first total amount and the second total amount;
• and
• based on the parameter, determining a classification of whether the nucleic acid sequence imbalance associated with cancer exists in the biological sample for the plurality of clinically relevant nucleic acid sequences in the subject.