Table 4.
9p24.1 Amplified Renal Cell Carcinomas: Molecular Profiling
| Case Identifier | Sequencing Platform | ¶Tumor Mutation Burden (mutations/ Megabase | Mutations | Copy Number Changes | Structural Variants |
|---|---|---|---|---|---|
| Case 1 (Discovery Cohort) | MSK-IMPACT (468 gene panel) | 2.6 (Purity: 24%) | PTEN p.X212_splice, FOXO1 p.F14L, TP53 p.G334W | CEBPA/JAK2/PD-L1/PDL-2 Amplified | - |
| Case 2 (Discovery Cohort) | MSK-IMPACT (410 gene panel) | 2.0 (Purity: 33%) | MYOD1 p.R203C, RASA1 p.H1021Y |
CDKN2Ap16INK4A/CDKN2Ap14 ARF/ CDKN2B Loss
PTPRD/JAK2/PD-L1 Amplified |
- |
| Case 3 (Discovery Cohort & Casuscelli et al) | MSK-IMPACT (341 gene panel) | 2.2 (Purity: 38%) | TP53 p.R196X, PTEN p.Y346C | CRKL/JAK2/PD-L1 Amplified | - |
| Case 4 (Discovery Cohort) | MSK-IMPACT (468 gene panel) | 5.3 (Purity: 45%) | TRAF7 p.R641H, ANKRD11 p.R82Q, MST1R p.G231D, PDGFRA p.L686V, PARK2 p.R334C, RAC1 p.N111T | 3p Loss, JAK2/PD-L1/PDL-2 Amplified | - |
| Case 5 (Discovery Cohort) | MSK-IMPACT (410 gene panel) | 7.9 (Purity: 27%) |
TP53 p.C135Y, AXIN1 p.A552P, DNMT3A p.A84T, NTRK1 p.A612T, NTRK1 p.G643D, VHL p.L169*, PBRM1 splice variant c.2567+1G>C, SPEN splice variant c.1043A>T |
JAK2/PD-L1 Amplified | - |
| Case 6 (TCGA-BP-4983) | Whole exome sequencing | - | SETD2 p. P2288Ifs*22, ASXL1 p.E997*, SPEN p.V1129I, TRAF7 p.R524Q, ACAN p.V94M, AMPH p.K112N, CACNA1E p.G310W, CHAD p.A94V CYLC1 p.L110F, CYP2B6 p.T303I | JAK2/PD-L1/PDL-2 Amplified | Fusions with genes on 9p24.1 (DOCK8-JAK2 & CD274-KANK1) in the setting of 9p24.1 Amplification (including JAK2/PDL1/ PDL-2) |
| Case 7 (Validation Cohort) | None | - | - | - | - |
| Case 8 (Validation Cohort) | None | - | - | - | - |
| Case 9 (Validation Cohort) | None | - | - | - | - |
| Case 10 (Validation Cohort) | None | - | - | - | - |
| Case 11 (TCGA-CZ-5468) | Whole exome sequencing | - | APC p.A1884S, INPP4A p.L202W, MUTYH p.T490Pfs*67, AGO2 p.P484A, AGO2 p.M483I, CDK12 p.L649R, ABCA4 p.R152*, ABCA4 p.Q2104H, BCHE p.W550R, CDH7 p.L605H | 3p Loss & JAK2/PD-L1/PDL-2 Amplified | - |
| Case 12 (TCGA-B8-4143) | Whole exome sequencing | - | BAP1 p.Y627*, DICER1 p.E731*, BRAF p.N49I, SMO p.A235T, SOX9 p.D444E, AMPD1 p.K375*, RCBTB2 p.Y299F, CHRM5 p.W271*, GALC p.K628T, GNAT2 p.D103G | JAK2 Amplification | - |
| Case 13 (Casuscelli et al) | Whole exome sequencing | - | BARD1 p.L359_P365del, BLM p.R15C, NOTCH3 p.G2081V, NTRK2 p.P204H, KMT2D p.A2620T, SOCS1 p.Q210H | TBX3 Loss, MYC/NBN/SPOP/ PD-L1 Amplified | - |
TCGA: The Cancer Genome Atlas; MSK-IMPACT: Memorial Sloan Kettering-Integrated Mutation Profiling of Actionable Cancer Targets.
¶
Average TMB for RCCs in the MSK Clinical Sequencing Cohort=3.0mt/MB. Tumor purity predictions based on FACETS. FACETS: Algorithm involving allele-specific copy number analysis from next generation sequencing data, Nucleic Acids Res. 2016 Sep 19;44(16):e131.