Analyzing circulating nucleic acids to identify a biomarker representative of cancer presented by a patient population

A method of analyzing nucleic acid sequences, the method comprising:

• (a) sequencing amplified acellular DNA from a population of cancer patients having the same type of cancer subsequent to whole genome amplification of DNA extracted from serum or plasma from said population of cancer patients, wherein said sequencing is performed with one or more individual sequence tags for sample identification, and wherein said sequencing generates at least 50,000 sequences per sample;
• (b) electrically receiving sequence information obtained in (a) on a processor describing one or more of the sequenced amplified acellular DNA from the population of cancer patients;
• (c) electrically receiving sequence information on said processor describing one or more acellular DNA sequences from a control patient population;
• (d) electrically performing a cluster analysis comparing the information electrically received on the processor in steps (b) and (c) within a predetermined number of cluster regions of the human genome by aligning sequences within the predetermined number of cluster regions from said sequenced acellular DNA from the population of cancer patients with one or more sequences from acellular DNA obtained from the control patient population;
• and
• (e) electrically identifying a biomarker representative of the type of cancer presented by the population of cancer patients having the same type of cancer by the processor.