TruSeq 48 Gene Cancer Panel Indication: Next generation sequencing (NGS) assay for detection of hot spot mutations in 48 cancer-related genes: ABL1, AKT1, ALK, APC, ATM, BRAF, CDH1, CDKN2A, CSF1R, CTNNB1, EGFR, ERBB2, ERBB4, FBXW7, FGFR1, FGFR2, FGFR3, FLT3, GNA11, GNAQ, GNAS, HNF1A, HRAS, IDH1, JAK2, JAK3, KDR, KIT, KRAS, MET, MLH1, MPL, NOTCH1, NPM1, NRAS, PDGFRA, PIK3CA, PTEN, PTPN11, RB1, RET, SMAD4, SMARCB1, SMO, SRC, STK11, TP53 and VHL. The specific mutations are detected by amplification of the corresponding exons by polymerase chain reaction (PCR). The PCR product is sequenced on a Illumina's MiSeqDx NGS Sequencer. Annotation is provided by Cartagenia Bench Lab NGS. Clinical Panel Gene Exon / Amino Acid (AA) Coverage ABL1 Exons 4-7 (AA 243-362, 395-424) ALK Exons 23, 25 (AA 1172-1176, 1248-1275) BRAF Exon 15 (AA 581-606) EGFR Exons 3, 7, 18-21 (AA 108-142, 287-297, 598-627, 708-728, 729-761, 762-817, 857-875) GNA11 Exons 4-7 (AA 159-172, 172-202, 202-216, 255-297, 304-349, 349-360) GNAQ Exons 4- 7 (AA 159-202, 202-210, 210-263, 261-297, 297-325, 326-360, 355-360) IDH1 Exon 4 (AA 95-133) JAK2 Exon 14 (AA 615-622) KIT Exons 11, 13, 17 (AA 550-587, 641-664, 814-828) KRAS Exons 2-3 (AA 1-22, 38-63) MPL Exon 10 (AA 514-522) NRAS Exons 2-3 (AA 1-19, 38-62) NPM1 Exon 11 (AA 283-295) PIK3CA Exons 2, 5, 8, 10, 21 (AA 84-118, 345-353, 418-441, 538-555, 987-1068) Investigational Panel Gene Exon / Amino Acid (AA) Coverage AKT1 Exon 4 (AA 16-49) APC Exon 16 (AA 875-918, 1113-1153, 1257-1575) ATM Exons 8, 9, 12, 17, 26, 34-36, 50, 54-56, 59, 61, 63 (AA 352-355, 409-412, 601- 633, 846-880, 1308-1331, 1678-1715,1740-1773, 1794-1830,1940-1973, 2441- 2477, 2665-2670, 2695-2717, 2724-2756, 2889-2891, 2947-2950, 3007-3044) BRAF Exon 11 (AA 439-472) CDH1 Exons 3, 8, 9 (AA 77-114, 369-379, 398-436) CDKN2A Exon 2 (AA 51-71) CSF1R Exons 7, 22 (AA 297-302, 933-970) CTNNB1 Exon 3 (AA 11-49) ERBB2 Exons 19-21 (AA 754-769, 772-818, 839-883) ERBB4 Exons 3, 4, 6-9, 15, 23 (AA 104-141, 154-186, 208-245, 250-287, 295-306, 333- 350, 582-620, 907-935) FBXW7 Exons 5, 8-11 (AA 243-278, 375-394, 434-472, 473-509, 549-582) FGFR1 Exons 5, 8 (AA 153-159, 280-283) FGFR2 Exons 7, 9, 12 (AA 250-313, 363-383, 522-551) FGFR3 Exons 7, 9, 14, 15, 16, 18 (AA 247-288, 379-422, 639-658, 692-723, 792-806) FLT3 Exons 11, 14, 16, 20 (AA 437-454, 569-605, 648-683, 807-843) - only insertions less than 25bp in length are detected GNAS Exon 8 (AA 842-863) HNF1A Exons 3-4 (AA 205-238, 271-309) HRAS Exons 2-3 (AA 1-16, 38-63) JAK3 Exons 13, 16 (AA 683-724, 568-572) KDR Exons 6, 7, 11, 19, 21, 26, 27, 30 (AA 220-249, 267-276, 471-476, 872-874, 948- 985, 1135-1146, 1174-1210, 1308-1345, 1353-1356) KIT Exons 2, 9, 10, 14, 15, 18 (AA 51-88, 502-514, 515-549, 670-707, 715-745, 838- 866) KRAS Exon 4 (AA 110-147) MET Exons 2, 14, 16, 19 (AA 168-205, 375-400, 990-1010, 1093-1114, 1229-1266) MLH1 Exon 12 (AA 383-421) MPL Exon 10 (AA 514-522) NOTCH1 Exons 26, 27 (AA 1563-1601, 1673-1678) PDGFRA Exons 12, 14, 15, 18 (AA 552-589, 659-668, 673-711, 823-854) PIK3CA Exons 14 (AA 700-729) PTEN Exons 1, 3, 6-8 (AA 5-27, 66-70, 170-207, 212-218, 229-266, 288-325, 335-342) PTPN11 Exons 3, 13 (AA 60-97, 501-533) RB1 Exons 4, 6, 11, 17, 18, 20-22 (AA 127-153, 198-203, 357-376, 550-565, 569- 605,659-696,703-731,746-775) RET Exons 10, 11, 13, 15, 16 (AA 610-627, 630-667, 768-798, 880-910, 917-934) SMAD4 Exons 3, 5 (AA 118-142, 167-204) SMAD4 Exons 6, 8, 9, 10-12 (AA 243-263, 310-319, 329-366, 385-422, 442-479, 495-533) SMARCB1 Exons 2, 4, 5, 9 (AA 40-76, 156-167, 199-210, 381-386) SMO Exons 3, 5, 6, 9, 11 (AA 198-235, 322-360, 405-422, 535-551, 638-646) SRC Exon 14 (AA 531-537) STK11 Exons 1, 4-6, 8 (AA 36-73, 193-199, 200-205, 264-288, 333-370) TP53 Exons 2, 4-8, 10 (AA 1-12, 75-113, 147-185, 187-224, 225-253, 268-306, 332-342) VHL Exons 1-3 (AA 88-114, 129-155, 157-194) Testing Method: Amplicon based targeted next generation sequencing. Test Parameters: Diagnostic sensitivity: This assay is designed to detect known single nucleotide variants only within defined regions. Nucleotide insertions and deletions more than 25bp or outside of the defined regions may not be detected. Gene rearrangements are not detected. Technical sensitivity: This assay may not detect certain mutations if the proportion of tumor cells in the sample studied is less than 5%. Test Parameters: Diagnostic sensitivity: This assay is designed to detect known single nucleotide variants only within defined regions. Nucleotide insertions and deletions more than 25bp or outside of the defined regions may not be detected. Gene rearrangements are not detected. Technical sensitivity: This assay may not detect certain mutations if the proportion of tumor cells in the sample studied is less than 5%. Turnaround Time: 5-10 business days Sample Requirements: The presence of adequate tumor in the material submitted for analysis should be confirmed by a surgical pathologist. A section from archival paraffin material or frozen surgical biopsies should be confirmed to contain > 50% tumor by a surgical pathologist. If the submitted material for analysis contains < 50% of tumor, areas of predominant tumor will be microdissected to enrich for neoplastic cells. • Formalin-fixed, paraffin-embedded tissue • 5-6 tissue sections (please include H&E slide and a copy of pathology report) • Cytology slides • Fresh frozen tissue (ship frozen) CPT Codes: 81445, G0452. 88381 may apply. .