Methods for early detection of cancer

A method for detecting a tumor marker or genetic variant among the sequence reads of a gene panel, wherein detection of the tumor marker or genetic variant indicates the presence of cancer, wherein the method comprises:

• a) providing a sample of nucleic acids from a subject, wherein the sample comprises cell-free deoxyribonucleic acid (cfDNA) molecules;
• b) amplifying the nucleic acids by polymerase chain reaction (PCR)-based amplification to provide amplified nucleic acids;
• c) enriching the amplified nucleic acids for a panel of genomic regions, wherein the panel comprises one or more loci from each of AKT1, ALK, APC, ATM, BRAF, CTNNB1, EGFR, ERBB2, ESR1, FGFR2, GATA3, GNAS, IDH1, IDH2, KIT, KRAS, MET, NRAS, PDGFRA, PIK3CA, PTEN, RB1, SMAD4, STK11, and TP53;
• d) sequencing the enriched set of amplified nucleic acids to generate sequence reads;
• e) determining consensus sequences from the sequence reads obtained from the sequencing to reduce errors from amplification or sequencing;
• and
• f) detecting a tumor marker or genetic variant among the consensus sequences of the gene panel.