Our NGS Panel Details

Note: For all of the following assays, sequence data (from the specified regions) will be assessed for the presence of all unique coding variants contained within version 79 of the COSMIC database. A full list of these variants (excel format) can be downloaded by clicking the appropriate link in each section. Any variants outside of this designation are not routinely assessed or reported.

MGP-1 (22 Gene panel, on ISO scope)

SNVs & Small Indels

SNV – A single nucleotide variant; Small Indel – An Insertion, deletion or substitution of between 1 and 50 nucleotides
Gene RefSeq Transcript Exons Codons
AKT1 NM_001014432.1 4 17-52
ALK NM_004304.3 22, 23, 25 1151-1171, 1173-1215, 1251-1278
BRAF NM_004333.4 11, 15 439-472, 582-609
CTNNB1 NM_001904.3 3 9-48
DDR2 NM_001014796.1 5, 8, 12, 13, 14, 15, 17 92-135, 226-265, 440-483, 503-537, 577-607, 621-668, 762-790
EGFR NM_005228.3 12, 18, 19, 20, 21 472-499, 693-726, 729-761, 762-800, 854-875
ERBB2 NM_004448.2 19, 20, 21 753-769, 770-797, 839-882
ERBB4 NM_005235.2 3, 4, 6, 7, 8, 9, 15, 23 135-140, 167-185, 226-247, 254-290, 296-323, 334-368, 578-622, 917-947
FBXW7 NM_0033632.3 5, 8, 9, 10, 11 261-287, 377-402, 434-472, 478-508, 567-597
FGFR1 NM_0023110.2 4, 7 121-149, 250-275
FGFR2 NM_000141.4 7, 9, 12 251-278, 363-399, 542-557
FGFR3 NM_000142.4 7, 9, 14, 16, 18 248-277, 367-402, 631-653, 689-719, 772-807
KRAS NM_004985.4 2, 3, 4 5-37, 38-66, 114-150
MAP2K1 NM_002755.3 2 43-83
MET NM_001127500.1 2, 14, 16, 19 339-378, 982-1014, 1106-1131, 1244-1274
NOTCH1 NM_017617.3 26, 27 1566-1602, 1674-1680
NRAS NM_002524.3 2, 3, 4 3-31, 41-69, 112-150
PIK3CA NM_006218.2 10, 14, 21 522-550, 676-720, 1017-1051, 1063-1069
PTEN NM_000314.4 1, 3, 6, 7, 8 1-25, 56-69, 165-184, 213-218, 230-267, 280-302, 312-342
SMAD4 NM_005359.5 3, 5, 6, 8, 9, 10, 11, 12 98-136, 165-202, 241-262, 307-318, 326-365, 384-426, 444-473, 494-533
STK11 NM_00455.4 1, 6, 8, 4-5 22-64, 254-286, 317-361, 192-207
TP53 NM_00546.5 2, 4, 5, 6, 7, 8, 10 1-20, 67-114, 150-186, 126-138, 188-221, 225-257, 262-306, 332-366

MGP-2 (50 Gene panel, on ISO Scope)

SNVs & Small Indels

SNV – A single nucleotide variant; Small Indel – An Insertion, deletion or substitution of between 1 and 50 nucleotides
Gene RefSeq Transcript Exons Codons
ABL1 NM_005157.5 4, 5, 6, 7 230-261, 275-280, 314-360, 380-412
AKT1 NM_001014432.1 4, 7 17-52, 154-182
ALK NM_004304.3 23, 25 1173-1204, 1269-1277
APC NM_000038.5 16 861-891, 1090-1126, 1284-1326, 1342-1385, 1426-1471, 1483-1524, 1543-1582
ATM NM_000051.3 8, 9, 12, 17, 26, 34, 35, 36, 39, 50, 54, 55, 56, 59, 61, 63 326-355, 408-411, 602-627, 833-866, 1293-1324, 1675-1708, 1727-1757, 1790-1815, 1925-1950, 2437-2453, 2647-2669, 2682-2711, 2718-2736, 2865-2890, 2932-2950, 2997-3026, 3041-3057
BRAF NM_004333.4 11, 15 439-472, 582-609
CDH1 NM_004360.4 3, 8, 9 63-96, 337-375, 380-409
CDKN2A NM_000077.4 2 51-91, 98-140
CSF1R NM_005211.3 7, 22 298-318, 954-973
CTNNB1 NM_001904.3 3 9-48
EGFR NM_005228.3 3, 7, 15, 18, 19, 20, 21 94-123, 279-296, 575-601, 693-726, 729-761, 763-799, 803-823, 854-875
ERBB2 NM_004448.2 19, 20, 24 753-769, 770-797, 839-882
ERBB4 NM_005235.2 3, 4, 6, 7, 8, 9, 15, 23 135-140, 167-185, 226-247, 254-290, 296-323, 334-368, 578-622, 917-947
EZH2 NM_004456.4 16 626-649
FBXW7 NM_033632.3 5, 8, 9, 10, 11 261-287, 377-402, 434-472, 478-508, 567-597
FGFR1 NM_023110.2 4, 7 121-149, 250-275
FGFR2 NM_000141.4 7, 9, 12 295-313, 363-399, 542-557
FGFR3 NM_000142.4 7, 9, 14, 16, 18 248-277, 367-402, 631-653, 689-719, 772-807
FLT3 NM_004119.2 11, 14, 16, 20 438-467, 569-609, 663-684, 828-847
GNA11 NM_002067.4 5 203-220
GNAQ NM_002072.4 5 206-246
GNAS NM_000516.5 8, 9 196-219, 221-239
HNF1A NM_000545.6 3, 4 192-221, 250-283
HRAS NM_001130442.1 2, 3 5-35, 41-83
IDH1 NM_005896.3 4 100-136
IDH2 NM_002168.3 4 133-176
JAK2 NM_004972.3 14 602-621
JAK3 NM_000215.3 4, 13, 16 128-140, 568-580, 707-733
KDR NM_002253.2 6, 7, 11, 19, 21, 26, 27, 30, 30 245-266, 267-291, 472-479, 873-893, 960-988, 1136-1155, 1191-1220, 1284-1311, 1322-1357
KIT NM_000222.2 2, 9, 10, 11, 13, 14, 15, 17, 18 24-59, 495-513, 526-549, 550-589, 628-661, 665-686, 715-724, 803-828, 832-860
KRAS NM_004985.4 2, 3, 4 5-37, 38-66, 114-150
MET NM_001127500.1 2, 11, 14, 16, 19 159-188, 339-378, 815-859, 982-1014, 1106-1131, 1244-1274
MLH1 NM_000249.3 12 373-415
MPL NM_000537.2 10 502-521
NOTCH1 NM_017617.3 26, 27, 34 1566-1602, 1674-1680, 2435-2476
NPM1 NM_002520.6 11 283-295
NRAS NM_002524.3 2, 3, 4 3-31, 41-69, 121-150
PDGFRA NM_006206.5 12, 14, 15, 18 552-583, 644-667, 672-710, 819-854
PIK3CA NM_006218.2 2, 5, 7, 8, 10, 14, 19, 21 51-90, 107-117, 315-351, 390-417, 418-422, 449-468, 522-550, 676-720, 898-924, 1017-1051, 1063-1069
PTEN NM_000314.4 1, 3, 5, 6, 7, 8 1-25, 56-69, 99-136, 165-184, 213-218, 230-267, 280-302, 312-342
PTPN11 NM_002834.4 3, 13 47-82, 485-528
RB1 NM_000321.2 4, 6, 10, 11, 14, 17, 18, 20, 21, 22 130-159, 196-202, 314-345, 351-366, 453-463, 548-565, 566-582, 656-691, 703-724, 743-770
RET NM_020975.4 10, 11, 13, 15, 16 607-626, 628-656, 763-787, 876-910, 911-924
SMAD4 NM_005359.5 3, 4, 5, 6, 8, 9, 10, 11, 12 98-136, 143-146, 165-202, 241-262, 307-318, 326-365, 384-426, 444-473, 494-533
SMARCB1 NM_003073.4 2, 4, 5, 9 36-72, 144-166, 168-206, 374-386
SMO NM_005631.4 3, 5, 6, 9, 11 186-228, 308-335, 392-419, 510-543, 608-645
SRC NM_005417.4 14 499-533
STK11 NM_000455.4 1, 4, 5, 6, 8 22-64, 156-184, 192-207, 254-286, 319-361
TP53 NM_000546.5 2, 4, 5, 5, 6, 7, 8, 10 1-20, 67-114, 126-138, 150-186, 188-221, 225-257, 262-306, 332-366
VHL NM_000551.3 1, 2, 3 78-108, 115-150, 156-174

MGP-3 (Combined hotspot & fusion test)

On ISO scope for hotspots & validated for ALK, ROS1, RET & NTRK1/3 Fusions)

SNVs & Small Indels

SNV – A single nucleotide variant; Small Indel – An Insertion, deletion or substitution of between 1 and 50 nucleotides
Gene RefSeq Transcript Exons Codons
AKT1 NM_001014432.1 3 17-51
ALK NM_004304.3 21, 22, 23, 24, 25 1121-1150, 1151-1171, 1173-1214, 1216-1247, 1252-1277
AR NM_000044.4 6, 8 788-816, 870-890
BRAF NM_004333.4 11, 15 451-477, 582-610
CDK4 NM_000075.3 2 14-49
CTNNB1 NM_001904.3 3 10-47
DDR2 NM_001014796.1 5 93-134
EGFR NM_005228.3 3, 7, 12, 15, 18, 19, 20, 21 115-140, 298-314, 491-517, 593-618, 713-743, 747-778, 780-817, 845-883
ERBB2 NM_004448.2 8, 17, 18, 19, 20, 21, 22 301-326, 662-690, 703-735, 753-768, 770-796, 840-881, 884-904
ERBB3 NM_001982.3 2, 3, 6, 8, 9 47-77, 87-119, 205-243, 292-311, 330-369
ERBB4 NM_005235.2 18 694-713
ESR1 NM_001122742.1 9 533-571
FGFR2 NM_000141.4 7, 8, 9, 12, 14 251-274, 314-348, 363-398, 546-557, 631-662
FGFR3 NM_00142.1 7, 9, 14, 16 247-276, 368-401, 632-652, 691-718
GNA11 NM_002067.4 4, 5 168-201, 203-219
GNAQ NM_002072.4 4, 5 166-195, 206-245
HRAS NM_001130442.1 2, 3 9-25, 43-81
IDH1 NM_005896.3 4 101-134
IDH2 NM_002168.3 4 134-175
JAK1 NM_002227.3 14, 15, 16 638-662, 686-705, 706-742
JAK2 NM_004972.3 14 604-621
JAK3 NM_000215.3 11, 12, 15 484-507, 524-567, 641-681
KIT NM_000222.2 8, 9, 11, 13, 17 412-433, 495-513, 550-587, 628-660, 792-828
KRAS NM_004985.4 2, 3, 4 10-37, 38-65, 114-149
MAP2K1 NM_002755.3 2, 3, 6 44-81, 106-144, 191-225
MAP2K2 NM_030662.3 2 32-67
MET NM_001127500.1 14, 15, 16, 19 1000-1027, 1081-1104, 1106-1131, 1247-1273
MTOR NM_004985.3 30, 39, 40, 43, 43, 47, 53 1457-1489, 1789-1810, 1872-1904, 1971-1979, 1999-2011, 2187-2220, 2394-2433
NRAS NM_002524.3 2, 3, 4 9-30, 43-68, 113-149
PDGFRA NM_006206.5 12, 14, 18 552-583, 645-667, 820-854
PIK3CA NM_0062.18.2 2, 2, 5, 6, 8, 8, 10, 14, 19, 21 50-60, 105-113, 317-350, 354-378, 418-433, 450-468, 533-554, 692-729, 899-923, 1018-1050
RAF1 NM_002880.3 7, 12 246-273, 407-441
RET NM_020975.4 10, 11, 13, 15, 16 609-626, 628-654, 763-785, 876-910, 911-923
ROS1 NM_002944.2 36, 38 1901-1939, 1962-1995
SMO NM_005631.4 4, 6, 8, 9 358-399, 486-511, 547-582, 605-635

 

Fusions

Fusion – A hybrid of two separate genes (caused by translocations, interstitial deletions, or chromosomal inversions)
Gene Partner Genes
ABL1 EML1
AKT3 MAGI3
ALK A2M, ACTG2, ATIC, C2orf44, CARS, CLIP4, CLTC, DCTN1, EML4, GTF2IRD1, HIP1, KIF5B, KLC1, MEMO1, NCOA1, PRKAR1A, PTPN3, RANBP2, SEC31L1_SEC31A, SMEK2, STRN, TFG, TPM1, TPM3, TPM4, TPR, TRAF1, VCL
AXL MBIP
BRAF AGTRAP, AKAP9, CDC27, FAM131B, FCHSD1, KIAA1549, PAPSS1, SLC45A3, SND1, TAX1BP1, TRIM24
EGFR EGFR (Exon 2-7 Skipping)
ERBB2 WIPF2
ERG SLC45A3, TMPRSS2
ETV1 TMPRSS2
ETV4 TMPRSS2
ETV5 TMPRSS2
FGFR1 BAG4, ERLIN2, TACC1
FGFR2 AFF3, BICC1, CASP7, CIT, KIAA1967_CCAR2, MGEA5, OFD1, TACC3, SLC45A3
FGFR3 AES, BAIAP2L1, ELAVL3, TACC3
MET BAIAP2L1, C8orf34, CAPZA2, OXR1, PTPRZ1, TFG, TPR
MET (Exon 14 Skipping)
NTRK1 BCAN, CD74, CEL, DYNC2H1, IRF2BP2, LMNA, MPRIP, NFASC, RNF213, SQSTM1, SSBP2, TFG, TPM3, TPR
NTRK2 AFAP1, AGBL4, NACC2, QKI, SQSTM1, TRIM24, VCL
NTRK3 BTBD1, COX5A, ETV6
PDGFRA SCAF11
PPARG PAX8
RAF1 B4GALT1, ESRP1
RET ACBD5, AFAP1, AKAP13, CCDC6, CUX1, ERC1, ERC1_ELKS, FKBP15, GOLGA5, HOOK3, KIAA1468, KIF5B, KTN1, NCOA4, NCOA4_ELE1, PCM1, PRKAR1A, RUFY2, SPECC1L, TBL1XR1, TRIM24, TRIM27, TRIM33
ROS1 CCDC6, CD74, CEP85L, CLIP1, CLTC, ERC1, EZR, GOPC, HLA_A, KDELR2, KIAA1598, LRIG3, MSN, MYO5A, PPFIBP1, PWWP2A, SDC4, SLC34A2, TFG, TPM3, ZCCHC8

 

MGP-4 (‘Flexible’ Hotspot, CNVs and Fusion Test – Under development)

This is our bespoke new panel, which is currently in it’s final validation stages. We intend to make this available in a fully flexible format with users able to choose DNA (hotspots/CNVs) only, RNA (fusions) only or DNA/RNA combined, either with both requested ‘upfront’ to save time, or with the option to do DNA first and then reflex straight to RNA if the DNA based analysis was uninformative, thus saving money and potentially precious tissue.

This panel combines the highest utility targets from our previous three panels and will also allow formal* reporting of copy number gains (CNGs) in relevant genes and suitable samples (please note that relative tumour content requirements will be higher for CNVs (~30% TBC) than for hotpots (>5%).

Because of the high utility, flexibility and cost effectiveness of this panel, we are intending to withdraw all 3 preceding panels after it’s full implementation. We will of course be consulting you, our users, on this, before making any final decisions, so please look out for our 2019 user survey which will be sent out this summer. Although should you wish to contact us directly about this or indeed any aspect of our current and planned future service provision, we would be very happy to hear from you.

*CNGs have previously been reported, but only as incidental findings, requiring appropriate confirmation before being used for clinical decision making.

SNVs, Small Indels & Copy Number Aberrations

SNV – A single nucleotide variant; Small Indel – An Insertion, deletion or substitution of between 1 and 50 nucleotides; Copy Number Aberrations are detected via proprietary in house analysis pipeline and are indicative only.
Gene RefSeq Transcript Exons Codons
AKT1 NM_001014432.1 4 17-50
ALK NM_004304.3 Intron 22-23, 23, 25 1173-1204, 1249-1275
BRAF NM_004333.4 11, 15 450-477, 582-611
CDKN2A NM_000077.4 Intron 0-1, 1, 2, Intron 2-3, 3 13-39, 51-88, 98-139
CTNNB1 NM_001904.3 3 13-50
EGFR NM_005228.3 3, Intron 5-6, 7, 12, 15, 18, 19, 20, 21 85-125, 282-296, 474-499, 583-625, 696-725, 729-761, 767-799, 814-823, 827-865
ERBB2 NM_004448.3 8, 12, 14, 17 ,18 ,19, 20, 21, 22, 24 302-326, 472-501, 557-579, 650-679, 718-736, 737-760, 770-797, 832-870, 884-903, 969-990, 1007-1048
FBXW7 NM_033632.3 5, 8, 9, 10, 11 256-287, 379-402, 435-472, 479-508, 567-593
GNA11 NM_002067.4 4, 5 166-196, 206-240
GNAQ NM_002072.4 2, 4, 5 60-99, 164-201, 203-223
HRAS NM_001130442.2 2, 3, 4 6-33, 45-86, 107-139
IDH1 NM_005896.3 4 101-138
IDH2 NM_002168.3 4 162-178
KIT NM_000222.2 9, 10, 11, 13, 14, 15, 17 488-513, 517-549, 550-588, 629-663, 665-687, 715-727, 788-826
KRAS NM_004985.4 Intron 1-2, 2, Intron 2-3, 3, 4, Intron 4-5, 5 7-37, 38-65, 113-150, 151-175
MAP2K1 NM_002755.3 2, 3, 6 44-81, 98-135, 191-226
MET NM_001127500.2 Intron 1-2, 2, 9, 11, 13, 14, 15, 16, 19, 20, 21 152-191, 345-383, 751-754, 844-879, 969-980, 982-994, 1009-1027, 1029-1052, 1106-1131, 1234-1274, 1289-1328, 1331-1369
MYD88 NM_002468.4 3, 4, 5 198-224, 229-247, 260-268
NRAS NM_002524.4 2, 3, 4 2-21, 43-68, 122-150
PDGFRA NM_006206.5 12, 14, 15, 18 552-584, 644-667, 669-701, 835-854
PIK3CA NM_006218.3 2, 3, 5, 8, 10, 14, 21 23-57, 78-108, 119-137, 312-351, 418-443, 533-554, 694-729, 1020-1059
PTEN NM_000314.6 1, 2, 3, 4, 5, 6, 7, 8, 9 2-26, 28-46, 56-69, 79-84, 86-106, 123-158, 165-181, 213-234, 283-299, 313-342, 343-353
RET NM_020975.4 3, 10, 11, 13, 15, 16 114-120, 610-626, 628-636, 665-706, 763-785, 872-904, 911-925
SMAD4 NM_005359.5 2, 3, 6, 9, 10, 11, 12 18-58, 110-139, 224-254, 336-374, 385-424, 443-478, 484-511, 526-553
SMARCA4 NM_001128844.1 6, 18, 20, 27, 35 255-284, 814-832, 903-942, 1183-1211, 1227-1258, 1595-1634
STK11 NM_000455.4 1, 4, 5, 6, 7, 8 27-57, 162-189, 206-235, 269-287, 291-306, 318-359
TP53 NM_000546.5 2, 3, 4, 5, 6, 7, 8, 9, 10, Intron 10-11 2-18, 27-32, 53-94, 108-125, 138-180, 188-222, 225-251, 262-302, 308-331, 332-343, 356-366

 

The following genes are included for potential ‘future proofing’. These will NOT be analysed or reported routinely until further notice.

Gene RefSeq Transcript Exons Codons
DPYD NM_000110.3 Intron 10-11, 11, 13, 14, Intron 14-15, 22 386-427, 530-569, 630-635, 932-969
ENOSF1 NM_017512.5 Intron 10-11
G6PD NM_000402.4 4, 5, 7 92-119, 149-182, 246-261
TPMT NM_000367.4 4, 6, Intron 8-9 79-82, 146-164
UGT1A1 NM_000463.2 Intron 0-1, 1 65-106

Fusions

Fusion – A hybrid of two separate genes (caused by translocations, interstitial deletions, or chromosomal inversions)
Gene Partners
ABL1 A2M, ACBD5, ACTG2, AFAP1, AGBL4, AGTRAP, AKAP13, AKAP9, ATIC, AXL, B4GALT1, BAG4, BAIAP2L1, BCAN, BTBD1, C2orf44, C8orf34, CAPZA2, CARS, CCDC6, CD74, CDC27, CEL, CEP85L, CLIP1, CLIP4, CLTC, COX5A, CUX1, DCTN1, EGFR, EML1, EML4, ERC1, ERLIN2, ESRP1, ETV6, EZR, FAM131B, FCHSD1, FGFR1, FGFR2, FGFR3, FKBP15, GOLGA5, GOPC, GTF2IRD1, HIP1, HLA_A, HOOK3, IRF2BP2, KDELR2, KIAA1468, KIAA1549, KIAA1598, KIF5B, KLC1, KTN1, LMNA, LRIG3, MAGI3, MEMO1, MET, MPRIP, MSN, MYO5A, NACC2, NCOA1, NCOA4, NFASC, NTRK1, OXR1, PAPSS1, PAX8, PCM1, PPFIBP1, PRKAR1A, PTPN3, PTPRZ1, PWWP2A, QKI, RANBP2, RNF213, RUFY2, SCAF11, SDC4, SEC31A, SLC34A2, SLC45A3, SMEK2, SND1, SPECC1L, SQSTM1, SSBP2, STRN, TAX1BP1, TBL1XR1, TFG, TMPRSS2, TPM1, TPM3, TPM4, TPR, TRAF1, TRIM24, TRIM27, TRIM33, VCL, WIPF2, ZCCHC8
ABL1
AES
AFF3
AKT3
ALK
BAIAP2L1
BICC1
BRAF
CASP7
CIT
DYNC2H1
EGFR
ELAVL3
ERBB2
ERG
ETV1
ETV4
ETV5
FGFR1
FGFR2
CCAR2
MBIP
MET
MGEA5
NTRK1
NTRK2
NTRK3
OFD1
PDGFRA
PPARG
RAF1
RET
ROS1
TACC1
TACC3

 

Internal Gene Rearrangements

Rearrangements within a gene resulting in an abnormal transcript
Gene Alias Description
EGFR EGFRvIII
EGFR-EGFR.E1E8
Rearrangement resulting in the loss of exons 2 through 7
MET MET Exon14 Skipping
MET-MET.M13M15
Rearrangement resulting in the loss of exon 14