Methods and materials for assessing and treating cancer

A method for identifying the presence of cancer in a human comprising:

• a) sequencing at least a portion of each of at least 12 genes from cell-free DNA derived from a plasma sample from said human, wherein said at least 12 genes are selected from NRAS, CTNNB1, PIK3CA, FBXW7, APC, EGFR, BRAF, CDKN2A, PTEN, FGFR2, HRAS, KRAS, AKT1, TP53, PPP2R1A, and GNAS,
• wherein said human has not been determined to have cancer, and
• wherein the sequencing of at least a portion of each of the at least 12 genes detects the presence or absence of at least the following mutations:
• when the at least 12 genes comprise NRAS, a 175G>A, 35G>A, and 182A>G mutation in NRAS,
• when the at least 12 genes comprise CTNNB1, a 134C>T, 121A>G, 127G>A, 133T>G, 113G>A, 110C>T, 104T>G, 98C>A, 101G>T, and 100G>A mutation in CTNNB1,
• when the at least 12 genes comprise PIK3CA, a 3140A>G, 3137C>T, 1635G>T, 1624G>A, 1634A>C, 1633G>A, 3141T>G, 3132T>A, 3145G>C, 241G>A, 1637A>G, 1030G>A, 3140A>T, 1035T>A, 3131A>G, 263G>A, 1638G>T, and 1633G>C mutation in PIK3CA,
• when the at least 12 genes comprise FBXW7, a 1393C>T, 1514G>A, 1394G>A, 1436G>A, 1435C>T, 1412insA, 1105G>T, and 1099C>T mutation in FBXW7,
• when the at least 12 genes comprise APC, a 3916G>T, 4348C>T, 3927delAAAGA, and 393 linsA mutation in APC,
• when the at least 12 genes comprise EGFR, a 2570G>A, 2590G>A, 2588G>A, 2603A>G, and 2573T>G mutation in EGFR,
• when the at least 12 genes comprise BRAF, a 1798G>A, 1781A>G, 1801A>G, 1799T>A, 1796C>T, 1785T>G, 1790T>G, 1792G>A, and 1786G>C mutation in BRAF,
• when the at least 12 genes comprise CDKN2A, a 226G>A, 251A>T, 172C>T, 236C>T, 250G>T, 227C>T, 151G>C, 247C>T, 260G>A, and 262G>T mutation in CDKN2A,
• when the at least 12 genes comprise PTEN, a 388C>G, 406T>C, 377C>T, 376G>T, 275A>C, 389G>A, 451G>A, and 388C>T in PTEN,
• when the at least 12 genes comprise FGFR2, a 758C>G mutation in FGFR2,
• when the at least 12 genes comprise HRAS, a 35G>A, 38G>T, and 34G>A mutation in HRAS,
• when the at least 12 genes comprise KRAS, a 38G>A, 34G>T, 35G>A, 181C>A, 35G>T, 437C>T, 436G>A, 40G>A, 32C>T, 35G>C, 34G>A, 169G>A, 38G>T, 34G>C, 31G>A, 176C>A, 35G>T, 183A>C, 175G>A, and 183A>T mutation in KRAS,
• when the at least 12 genes comprise AKT1, a 49G>A mutation in AKT1,
• when the at least 12 genes comprise TP53, a 747G>T, 742C>T, 818G>T, 473G>A, 743G>A, 818G>A, 844C>T, 455C>T, 817C>T, 527G>T, 524G>A, 733G>A, and 659A>G mutation in TP53,
• when the at least 12 genes comprise PPP2R1A, a 547C>T, 544C>T, and 551C>T mutation in PPP2R1A, and
• when the at least 12 genes comprise GNAS, a 602G>A, 601C>T, 608T>C, and 601C>A mutation in GNAS;
• b) sequencing at least a portion of each of said at least 12 genes from genomic DNA derived from a white blood cell sample from the human to detect in the genomic DNA the presence or absence of each of the mutations detected as present or absent in said cell-free DNA;
• c) detecting a level of each of at least four of the following protein biomarkers derived from a plasma sample obtained from the human:
• CA19-9, CEA, HGF, OPN, CA125, AFP, prolactin, TIMP-1, follistatin, G-CSF, and CA15-3;
• d) comparing the detected levels of each of the at least four protein biomarkers to reference levels of each of the protein biomarkers;
• and
• e) identifying the presence of cancer in the human when:
• i) at least one of the mutations is detected as present in said cell-free DNA and is detected as absent in said genomic DNA;
• or
• ii) the detected level of at least one of said at least four protein biomarkers is higher than its reference level.