Our NGS Panel Details

Please note: For all of the assays detailed below, sequence data (from the specified regions) will only be assessed for the presence of unique coding variants contained within version 79 of the COSMIC database. Any variants outside of this designation are not routinely assessed or reported.

For details of our legacy NGS panels, including previous revisions of MGP-4, click here

MGP-4 version 5

Our ‘Flexible’ Targeted Therapies Panel – assessing Hotspots, Copy Number Gains and Gene Fusions

This is our  entirely bespoke Multi-Gene Panel (MGP), intended to help guide the use of targeted anti-cancer therapies in common solid tumours. Launched in mid-2020, following extensive validation and ISO15189 accreditation, we were able to replace all of our preceding panels (MGP-1,2 & 3) with this very robust, sensitive and highly informative solution. MGP-4 is also very cost effective, providing as much clinically actionable information as many larger and considerably more expensive panels.

It is available in a fully flexible format, with service users able to choose only the DNA component (for hot-spot variants & copy number gains- CNGs), only the RNA component (for gene fusions), or both DNA/RNA combined. With combined testing, both components can be requested ‘upfront’ to save time, or alternatively with an option to reflex to RNA analysis only if the DNA based analysis proves uninformative, thus saving money and potentially precious tissue.

MGP-4 combines the highest utility targets from our previous three panels and also allows formal* reporting of copy number gains (CNGs) in relevant genes and suitable samples. However, please note that relative tumour content requirements are higher for CNG reporting (>20%) than for hotpots (>5%).

*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 Gains (MGP-4DNA)

SNV – A single nucleotide variant; Small Indel – An Insertion, deletion or substitution of between 1 and 50 nucleotides; Copy Number Gains (>4 fold in >20% tumour samples)  are detected via proprietary in house analysis pipeline and are indicative only.

z

Gene RefSeq Transcript Exons Codons
AKT1 NM_001382430.1 4, 5, 12 17-50, 65-93, 322-373
ALK NM_004304.3 22, 23, 24, 25 1151-1171, 1173-1214, 1216-1247, 1249-1275
BRAF NM_004333.6 11, 12, 14, 15, 16 450-477, 479-494, 566-589, 582-611, 623-659
CCNE1 NM_001238.4 3, 4, 6, 7, 8, 11 12-37, 42-60, 110-137, 167-195, 204-235, 319-333
CDK4 NM_000075.4 2, 6 8-49, 212-224
CDK6 NM_001145306.2 5 180-215
CDKN2A NM_000077.5 1, 2, 3 13-39, 51-88, 98-139, 154-157
CTNNB1 NM_001904.4 3 13-50
CXCR4 NM_003467.3 1 315-354
EGFR† NM_005228.5 3, 7, 12, 15, 17, 18, 19, 20, 21 85-125, 282-296, 474-499, 583-625, 641-671, 696-725, 729-761, 762-799, 814-823, 827-865
ERBB2† NM_004448.4 8, 12, 14, 16, 17 ,18 ,19, 20, 21, 22, 24, 25 302-326, 472-501, 557-579, 634-648, 650-679, 718-736, 737-760, 770-797, 832-870, 884-903, 969-990, 1007-1048
ESR1 NM_000125.4 3, 4, 5, 7, 8 233-253, 300-339, 367-384, 458-481, 533-574
FBXW7 NM_001349798.2 7, 10, 11, 12, 13 256-287, 379-402, 435-472, 479-508, 567-593
FGFR1 NM_023110.3 3, 4, 8, 10, 12, 14, 17 44-79, 121-147, 315-356, 439-476, 529-554, 640-659, 730-758
FGFR2 NM_000141.5 3, 5, 7, 9, 12, 14, 16 71-113, 179-204, 251-269, 284-313, 363-395, 527-557, 647-662, 715-731
FGFR3 NM_000142.5 7, 9, 13, 15, 16 248-260, 369-412, 559-590, 654-662, 690-721
GNA11 NM_002067.4 4, 5 166-196, 206-240
GNAQ NM_002072.5 2, 4, 5 60-99, 164-201, 203-223
GNAS NM_000516.7 8, 9 196-218, 221-239
HRAS NM_005343.4 2, 3, 4 6-33, 45-86, 107-139
IDH1 NM_005896.4 4 101-138
IDH2 NM_002168.4 4 162-178
KIT† NM_000222.3 9, 10, 11, 13, 14, 15, 17 488-513, 517-549, 550-588, 629-663, 665-687, 715-727, 788-826
KRAS† NM_004985.5 2, 3, 4, 5 6-37, 38-65, 113-150, 151-175
MAP2K1 NM_002755.4 2, 3, 4 44-81, 98-135, 191-226
MET*† NM_000245.4 2, 9, 11, 13, 14, 15, 16, 19, 20, 21
+5′ & 3′ Flanking regions of exon 14
152-191, 345-383, 751-754, 844-879, 969-980, 982-994, 1009-1027, 1029-1052, 1106-1131, 1234-1274, 1289-1328, 1331-1369
MTOR NM_004958.4 30, 39, 40, 43, 44, 47, 53 1449-1498, 1789-1811, 1872-1904, 1971-1996, 2012-2040, 2187-2220, 2394-2433
MYD88 NM_002468.5 3, 4, 5 185-211, 216-234, 247-255
NRAS NM_002524.5 2, 3, 4 1-21, 43-68, 113-149
NTRK1 NM_002529.4 14, 15 554-597, 645-674
NTRK3 NM_001012338.3 16, 17
PDGFRA NM_006206.6 12, 14, 15, 18 552-584, 644-667, 669-701, 835-854
PIK3CA† NM_006218.4 2, 3, 5, 6, 8, 10, 12, 14, 19, 21 23-57, 78-108, 119-137, 312-351, 354-381, 418-443, 452-468, 533-554, 585-627, 694-729, 896-924, 1020-1059
POLD1 NM_002691.4 8, 10, 12, 13, 17 283-323, 380-414, 462-498, 499-549, 670-716
POLE NM_006231.4 9, 11, 12, 13, 14, 19, 31, 32, 34, 41 268-303, 341-368, 370-408, 410-453, 454-491, 689-724, 1272-1315, 1346-1383, 1434-1460, 1852-1889
PTEN NM_000314.8 1, 2, 3, 4, 5, 6, 7, 8, 9 1-26, 28-46, 56-69, 79-84, 86-106, 123-158, 165-181, 213-234, 283-299, 313-342, 343-353
RET NM_020975.6 3, 6, 10, 11, 13, 14, 15, 16 114-120, 356-387, 610-626, 628-634, 665-706, 763-797, 799-817, 831-869, 876-910, 911-925
ROS1 NM_02944.3 37, 38, 40 1981-2001, 2003-2036, 2082-2122
SMAD4 NM_005359.6 2, 3, 6, 9, 10, 11, 12 18-58, 110-139, 224-254, 336-374, 385-424, 443-478, 484-511, 526-553
STK11 NM_000455.5 1, 4, 5, 6, 7, 8 27-57, 162-189, 206-235, 269-287, 291-306, 318-359
TP53 NM_000546.6 2, 3, 4, 5, 6, 7, 8, 9, 10, 11 1-18, 27-32, 53-94, 108-125, 138-180, 188-222, 225-251, 262-302, 308-331, 332-343, 356-366

 

*including selected DNA variants which have been associated with MET exon 14 skipping
†Validated for assessment of copy number gain. Not assessable in samples with <20% tumour.

Fusions (MGP-4RNA)

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

‡Validated for detection of inter- or intra-genic rearrangement events

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_202758.5 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

MGP-5

Our Homologous Recombination Deficiency Panel

This is our latest Multi-Gene Panel (MGP), offering comprehensive sequencing of the full coding region of 15 key genes (see below) involved in the homologous recombination repair pathway. This is intended to help guide the use of therapies such as PARPi inhibitors in certain tumour types (e.g. Breast, Prostate, Ovarian, Pancreatic)  which may exhibit homologous recombination deficiencies. Please note: 1) This test does not provide a measure of genomic instability.

SNVs & Small Indels

SNV – A single nucleotide variant; Small Indel – An Insertion, deletion or substitution of between 1 and 50 nucleotides
Gene RefSeq Transcript
ATM NM_000051.4
BARD1 NM_000465.4
BRCA1 NM_007294.4
BRCA2 NM_000059.4
BRIP1 NM_032043.3
CDK12 NM_016507.4
CHEK2 NM_007194.4
FANCD2 NM_001018115.3
MRE11 NM_005591.4
NBN NM_002485.5
PALB2 NM_024675.4
PPP2R2A NM_002717.4
RAD51B NM_133510.4
RAD54L NM_003579.4
TP53 NM_000546.6