Tumor : HCC1187 Normal : HCC-1187BL
Project : Cell_lines
Key terms
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- All somatic
- All PASS-filtered calls by the NYGC pipeline
- Low confidence
- All somatic calls that were only called by one caller
- High confidence
SNVs/Indels: All somatic calls that were either called by two or more callers, or called by one caller and validated by Lancet or Manta SV calls
SVs: All somatic called by two or more callers, or called by one caller with either additional support from nearby CNV changepoints or split-read support from SplazerS
- CancerGeneCensus (CGC)
- High confidence variants that overlap genes listed in the Tier 1 Cancer Gene Census list from COSMIC. In B-Allele Frequency plots CGC gene variants with AF >= 1% in 1000G or gnomAD are excluded
Caller agreement
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Upset plots showing agreement between callers
* NOTE: Lancet is only run on exonic regions, and also in validation mode to confirm variants called by 1 caller
VAF distribution
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Variant allele frequency distribution of High confidence SNVs
Variant Profile
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SV: High confidence SV calls
CNV: Amplification: log2 > 0.2, Deletion: log2 < -0.235
BAF: B-Allele Frequency is the allele frequency of germline, heterozygous SNVs in the tumor sample
VAF: Variant allele frequency of High confidence SNVs
Intermutation distance: Distance between High confidence SNVs
Circos plot
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Circos tracks from inner to outer. A: Inter-chromosomal translocations B: Cytogenetic ideogram C: Inversions D: Deletions E: Amplifications F: Somatic SNVs/INDELs positions (y-axis indicates VAF) G: CNV deletions (y-axis indicates log2) H: CNV amplifications (y-axis indicates log2)
High impact SNVs/INDELs
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High impact, High confidence, SNVs/INDELs in Tier 1 Cancer Census Genes. The variant is assumed to have high (disruptive) impact in the protein, probably causing protein truncation, loss of function or triggering nonsense mediated decay. See Variant effect predictor (VEP) documentation for description of variant consequences
| Gene | Protein change | Coordinates | Variant classification | CosmicID | Cosmic count | VAF |
|---|---|---|---|---|---|---|
| BAP1 | p.Q261* | chr3:52406255 | stop_gained&splice_region_variant | COSM50881 | 5 | 100.0 |
Moderate impact SNVs/INDELs
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Moderate impact, High confidence, SNVs/INDELs in Tier 1 Cancer Census Genes. Moderate variants are non-disruptive variants that might change protein effectiveness. See Variant effect predictor (VEP) documentation for description of variant consequences
| Gene | Protein change | Coordinates | Variant classification | CosmicID | Cosmic count | VAF | PolyPhen | FATHMM SOMATIC | SIFT |
|---|---|---|---|---|---|---|---|---|---|
| NUP98 | p.G1652V | chr11:3679672 | missense_variant | COSM22094 | 2 | 98.08 | probably_damaging | deleterious | |
| SPEN | p.R1488I | chr1:15930703 | missense_variant | COSM22675 | 2 | 62.50 | probably_damaging | PASSENGER/OTHER(-0.56) | deleterious |
| MYH9 | p.H1401del | chr22:36292127 | inframe_deletion | COSM32605 | 1 | 100.00 | |||
| TP53 | p.G108del | chr17:7676044 | inframe_deletion | COSM13119 | 3 | 98.57 |
SVs
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SVs with either the left or right disrupted section overlapping at least one Tier 1 CGC
| Coordinates1 | Coordinates2 | Type | DisruptL | DisruptR |
|---|---|---|---|---|
| chrX:77602700-77602701 | chrX:77603722-77603723 | DEL | ATRX | ATRX |
| chr2:221633792-221633793 | chr2:222290638-222290639 | DUP | PAX3 | |
| chr6:41234532-41234533 | chr6:41719688-41719689 | DUP | TREML4 | TFEB |
| chr8:107973150-107973151 | chr8:107974357-107974358 | DEL | RSPO2 | RSPO2 |
| chr12:11730208-11730209 | chr12:11760929-11760930 | DUP | ETV6 | ETV6 |
| chr13:48375134-48375135 | chr13:48378608-48378609 | DEL | RB1 | RB1 |
| chr14:68302189-68302190 | chr14:68621145-68621146 | DUP | RAD51B | RAD51B |
| chr19:18743352-18743353 | chr19:18809683-18809684 | DUP | CRTC1 |
CNV amplifications
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CNV amplifications overlapping at least one Tier 1 CGC
| Coordinates | Size (Kb) | Log2 | Tier1 CGC | Tier2 CGC | Cytoband |
|---|---|---|---|---|---|
| chr1:143268055-152269317 | 9001.26 | 1.56 | MLLT11, BCL9, ARNT, PDE4DIP | chr1q21.1-q21.3 | |
| chr6:41330046-42280534 | 950.49 | 1.53 | TFEB, CCND3 | chr6p21.1 | |
| chr10:77999459-82676186 | 4676.73 | 1.22 | NUTM2B | chr10q22.3-q23.1 | |
| chr10:1549131-22502952 | 20953.82 | 0.90 | KLF6, GATA3, MLLT10 | chr10p15.3-p12.2 | |
| chr8:142901154-145078494 | 2177.34 | 0.89 | RECQL4 | chr8q24.3 | |
| chr1:117039160-122510058 | 5470.90 | 0.68 | FAM46C, NOTCH2 | chr1p13.1-p11.1 | |
| chr10:71740919-77999458 | 6258.54 | 0.64 | KAT6B | chr10q22.1-q22.3 | |
| chr6:5740656-41330045 | 35589.39 | 0.63 | HIST1H3B, HIST1H4I, HLA-A, POU5F1, DAXX, PIM1, DEK, TRIM27, HMGA1, FANCE, SRSF3 | CDKN1A | chr6p25.1-p21.1 |
| chr1:31088920-83995849 | 52906.93 | 0.62 | MYCL, TAL1, JUN, LCK, SFPQ, CSF3R, MPL, MUTYH, STIL, CDKN2C, FUBP1, JAK1, EPS15 | THRAP3 | chr1p35.2-p31.1 |
| chr7:16339-149545816 | 149529.48 | 0.61 | HOXA11, HOXA13, CARD11, PMS2, RAC1, ETV1, HNRNPA2B1, HOXA9, SFRP4, SBDS, POT1, SMO, EZH2, EGFR, HIP1, CDK6, TRRAP, CUX1, MET, CREB3L2, TRIM24, BRAF, SND1, IKZF1 | FKBP9, ZNF479, KIAA1549, FAM131B, JAZF1, ELN, GRM3, AKAP9, CNTNAP2 | chr7p22.3-q36.1 |
| chr20:6218413-32713333 | 26494.92 | 0.61 | ASXL1 | CRNKL1 | chr20p12.3-q11.21 |
| chr18:10814016-55692428 | 44878.41 | 0.60 | SMAD2, SMAD4, SS18, SETBP1, ZNF521 | DCC | chr18p11.22-q21.2 |
| chr19:5824139-37270966 | 31446.83 | 0.59 | KEAP1, LYL1, CEBPA, MLLT1, CALR, PRKACA, DNAJB1, BRD4, TPM4, JAK3, CCNE1, DNM2, SMARCA4, ELL, CRTC1 | CD209, MUC16, ZNF429, VAV1, CEP89, LSM14A | chr19p13.3-q13.12 |
| chr12:41087-28617172 | 28576.08 | 0.58 | CDKN1B, KDM5A, CCND2, CHD4, ZNF384, KRAS, ETV6, ETNK1, PPFIBP1, ERC1 | PTPN6 | chr12p13.33-p11.22 |
| chr6:89830-1864356 | 1774.53 | 0.57 | IRF4 | chr6p25.3 | |
| chr14:68302168-68621129 | 318.96 | 0.56 | RAD51B | chr14q24.1 | |
| chrX:94069101-123576326 | 29507.22 | 0.55 | IRS4, BTK | SEPT6 | chrXq21.32-q25 |
| chr19:50944419-58607515 | 7663.10 | 0.55 | PPP2R1A, ZNF331, CNOT3 | TFPT | chr19q13.41-q13.43 |
| chrX:52040692-53248308 | 1207.62 | 0.53 | SSX2, KDM5C | chrXp11.22 | |
| chr1:152269318-248946322 | 96677.00 | 0.52 | SLC45A3, TPM3, LMNA, PRCC, NTRK1, FCRL4, FCGR2B, DDR2, PRRX1, ABL2, TPR, MDM4, ELK4, H3F3A, FH, SDHC, CDC73, PTPRC, MUC1, PBX1 | S100A7, ELF3, AKT3, RGS7 | chr1q21.3-q44 |
| chr8:126449872-127768744 | 1318.87 | 0.40 | MYC | chr8q24.21 | |
| chr13:102801718-114354111 | 11552.39 | 0.38 | ERCC5 | chr13q33.1-q34 | |
| chr11:10460501-78421457 | 67960.96 | 0.32 | MYOD1, FANCF, MEN1, WT1, LMO2, CREB3L1, DDB2, SDHAF2, CCND1, NUMA1, EXT2 | CLP1, FEN1, MALAT1, CTNND1 | chr11p15.4-q14.1 |
| chr11:5558212-9130419 | 3572.21 | 0.31 | LMO1 | chr11p15.4 | |
| chr11:90936583-135076522 | 44139.94 | 0.31 | SDHD, KCNJ5, BIRC3, POU2AF1, PAFAH1B2, DDX6, BCL9L, MAML2, ATM, DDX10, ZBTB16, CBL, ARHGEF12, FLI1, KMT2A | FAT3, FOXR1 | chr11q14.3-q25 |
| chr10:22502953-71740918 | 49237.96 | 0.22 | NCOA4, ABI1, KIF5B, PRF1, RET, CCDC6, TET1 | A1CF, ZEB1 | chr10p12.2-q22.1 |
| chr1:114927902-117039159 | 2111.26 | 0.20 | ATP1A1 | chr1p13.2-p13.1 | |
| chr5:11484-46502194 | 46490.71 | 0.20 | SDHA, TERT, IL7R, LIFR, DROSHA | CDH10, CTNND2 | chr5p15.33-p11 |
CNV deletions
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CNV deletions overlapping at least one Tier 1 CGC
| Coordinates | Size (Kb) | Log2 | Tier1 CGC | Tier2 CGC | Cytoband |
|---|---|---|---|---|---|
| chrX:10446-27188681 | 27178.24 | -1.36 | P2RY8, CRLF2, ZRSR2 | EIF1AX | chrXp22.33-p21.3 |
| chr1:97547227-114927901 | 17380.67 | -1.35 | RBM15, NRAS, TRIM33 | chr1p21.3-p13.2 | |
| chr11:128355-5558211 | 5429.86 | -0.64 | HRAS, NUP98, CARS | chr11p15.5-p15.4 | |
| chr11:78421458-90936582 | 12515.12 | -0.63 | PICALM | EED | chr11q14.1-q14.3 |
| chr14:18263373-39133588 | 20870.22 | -0.57 | NKX2-1, FOXA1, CCNB1IP1 | ARHGAP5, BAZ1A | chr14q11.2-q21.1 |
| chr14:41200381-63236251 | 22035.87 | -0.55 | SIX1, NIN, KTN1, HIF1A | chr14q21.1-q23.2 | |
| chr14:64374267-68302167 | 3927.90 | -0.53 | MAX, RAD51B, GPHN | chr14q23.3-q24.1 | |
| chrX:27188682-52040691 | 24852.01 | -0.44 | SSX1, WAS, BCOR, DDX3X, SSX4, GATA1, TFE3, KDM6A, RBM10 | ARAF, FAM47C | chrXp21.3-p11.22 |
| chr7:149545817-159335873 | 9790.06 | -0.41 | KMT2C | MNX1 | chr7q36.1-q36.3 |
| chr15:17083473-34410561 | 17327.09 | -0.41 | NUTM1 | chr15p11.2-q14 | |
| chr18:55692429-80263172 | 24570.74 | -0.41 | KDSR, BCL2, MALT1 | chr18q21.2-q23 | |
| chr15:85513790-90138915 | 4625.12 | -0.40 | IDH2, NTRK3 | POLG | chr15q25.3-q26.1 |
| chr12:131344273-133264924 | 1920.65 | -0.40 | POLE | chr12q24.33 | |
| chr10:82676187-133787316 | 51111.13 | -0.40 | TLX1, NUTM2A, NFKB2, BMPR1A, PTEN, FAS, SUFU, NT5C2, TCF7L2, FGFR2 | CYP2C8, CPEB3, VTI1A, KIAA1598, MGMT | chr10q23.1-q26.3 |
| chr6:149655901-170740360 | 21084.46 | -0.39 | EZR, FGFR1OP, ARID1B, QKI, MLLT4, ESR1 | chr6q25.1-q27 | |
| chrX:123576327-156030795 | 32454.47 | -0.39 | RPL10, MTCP1, STAG2, ELF4, PHF6, ATP2B3, GPC3, BCORL1 | DCAF12L2, FLNA | chrXq25-q28 |
| chr22:10514978-50808368 | 40293.39 | -0.39 | APOBEC3B, LZTR1, MAPK1, SMARCB1, EWSR1, ZNF278, PDGFB, MKL1, CLTCL1, BCR, MN1, CHEK2, NF2, MYH9, EP300 | SEPT5, DGCR8, ZNRF3, ISX | chr22p11.2-q13.33 |
| chr20:32713334-64334067 | 31620.73 | -0.39 | MAFB, SRC, TOP1, SDC4, SALL4, GNAS, SS18L1, PTK6, PLCG1, NFATC2, PTPRT | chr20q11.21-q13.33 | |
| chr19:90733-5824138 | 5733.40 | -0.39 | FSTL3, STK11, TCF3, GNA11, MAP2K2, SH3GL1 | chr19p13.3 | |
| chr16:10005-12896986 | 12886.98 | -0.39 | TRAF7, SOCS1, RMI2, TNFRSF17, AXIN1, TSC2, CREBBP, GRIN2A, CIITA | RUNDC2A, NTHL1 | chr16p13.3-p13.12 |
| chr15:90290295-101981087 | 11690.79 | -0.38 | FES, BLM, CRTC3 | CHD2 | chr15q26.1-q26.3 |
| chr2:11340611-32953080 | 21612.47 | -0.38 | MYCN, C2orf44, NCOA1, DNMT3A, ALK | ASXL2, BIRC6 | chr2p25.1-p22.3 |
| chr1:11072310-30937957 | 19865.65 | -0.38 | PAX7, MTOR, SPEN, SDHB, ARID1A | ID3, MDS2, CASP9, PRDM2, ARHGEF10L | chr1p36.22-p35.2 |
| chr3:10565956-129572182 | 119006.23 | -0.38 | MYD88, BAP1, PPARG, RAF1, MLH1, CTNNB1, RHOA, MITF, TFG, GATA2, RPN1, CNBP, XPC, TGFBR2, SETD2, PBRM1, CACNA1D, FOXP1, CBLB, POLQ, FHIT | CCR4, NCKIPSD, FBLN2, ROBO2, EPHA3 | chr3p25.3-q22.1 |
| chr2:222290576-242183395 | 19892.82 | -0.38 | ACKR3, ACSL3, PAX3 | CUL3 | chr2q36.1-q37.3 |
| chr17:168977-39261864 | 39092.89 | -0.38 | TP53, YWHAE, USP6, PER1, FLCN, TAF15, MLLT6, LASP1, RABEP1, GAS7, MAP2K4, NCOR1, NF1, SUZ12 | SPECC1 | chr17p13.3-q12 |
| chr16:30065417-90226217 | 60160.80 | -0.37 | FUS, MAF, CYLD, HERPUD1, CDH11, CBFB, CBFA2T3, CTCF, CDH1, ZFHX3, FANCA | RFWD3 | chr16p11.2-q24.3 |
| chr2:33018158-53970246 | 20952.09 | -0.37 | EPAS1, MSH6, FBXO11, STRN, EML4, MSH2 | SIX2 | chr2p22.3-p16.2 |
| chr15:72152244-84936396 | 12784.15 | -0.37 | PML | chr15q23-q25.3 | |
| chr3:129701072-198139690 | 68438.62 | -0.37 | FOXL2, SOX2, EIF4A2, MECOM, TBL1XR1, PIK3CA, ETV5, BCL6, PIK3CB, ATR, WWTR1, MLF1, MAP3K13, LPP, TP63 | GMPS, MUC4, TFRC, STAG1, IGF2BP2, MB21D2 | chr3q22.1-q29 |
| chr2:67038352-165996671 | 98958.32 | -0.37 | CXCR4, DCTN1, TMEM127, RANBP2, ACVR1, ERCC3, AFF3, PAX8, LRP1B, ACVR2A | PCBP1, RGPD3 | chr2p14-q24.3 |
| chr4:13868012-136871289 | 123003.28 | -0.37 | RHOH, SLC34A2, PHOX2B, FIP1L1, KIT, KDR, IL2, PDGFRA, PTPN13, RAP1GDS1, TET2, LEF1, FAT4, AFF1 | TEC, CHIC2, N4BP2 | chr4p15.33-q28.3 |
| chr12:34655818-128424712 | 93768.89 | -0.36 | HOXC13, HOXC11, NAB2, DDIT3, CDK4, BTG1, TBX3, COL2A1, KMT2D, SMARCD1, ATF1, STAT6, LRIG3, WIF1, PTPRB, SH2B3, ARID2, ERBB3, HMGA2, MDM2, PTPN11, HNF1A, BCL7A, CLIP1, NCOR2 | GLI1, SETD1B, PRPF40B, NACA, USP44, ZCCHC8, CHST11, ALDH2 | chr12p11.1-q24.32 |
| chr6:42280535-78257462 | 35976.93 | -0.36 | NFKBIE, HSP90AB1 | BMP5 | chr6p21.1-q14.1 |
| chr2:55078447-66780863 | 11702.42 | -0.36 | BCL11A, REL, XPO1 | chr2p16.1-p14 | |
| chr6:78326602-134006347 | 55679.75 | -0.36 | PRDM1, FOXO3, ROS1, GOPC, RSPO3, PTPRK | CCNC, EPHA7 | chr6q14.1-q23.2 |
| chr4:145584969-190066290 | 44481.32 | -0.36 | FBXW7, FAT1 | CASP3 | chr4q31.21-q35.2 |
| chr17:39350015-83247341 | 43897.33 | -0.35 | H3F3B, SRSF2, CANT1, CDK12, RARA, ETV4, SPOP, RNF43, PPM1D, CD79B, DDX5, PRKAR1A, ASPSCR1, ERBB2, SMARCE1, STAT5B, STAT3, BRCA1, COL1A1, HLF, MSI2, CLTC, BRIP1, AXIN2, RNF213 | CCR7, KAT7, SEPT9 | chr17q12-q25.3 |
| chr2:166087602-221633776 | 55546.17 | -0.35 | HOXD13, HOXD11, FEV, NFE2L2, CASP8, CREB1, IDH1, BARD1, ATIC, SF3B1, ERBB4 | CD28, COL3A1, ITGAV, PMS1 | chr2q24.3-q36.1 |
| chr1:83995850-97547226 | 13551.38 | -0.35 | BCL10, RPL5 | chr1p31.1-p21.3 | |
| chr15:34526120-71887858 | 37361.74 | -0.34 | BUB1B, B2M, CASC5, USP8, TCF12, MAP2K1, MYO5A, SMAD3 | KNSTRN | chr15q14-q23 |
| chr5:46502195-181449255 | 134947.06 | -0.34 | MAP3K1, APC, PDGFRB, CD74, ITK, NPM1, FGFR4, IL6ST, PIK3R1, AFF4, ARHGAP26, EBF1, TLX3, FLT4, NSD1 | RAD17, PWWP2A, ACSL6, CSF1R | chr5p11-q35.3 |
| chr6:134216593-149186361 | 14969.77 | -0.34 | MYB, TNFAIP3 | BCLAF1, ECT2L | chr6q23.2-q25.1 |
HLA-typing : OptiType
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HLA class I allele (see HLA nomenclature) prediction from OptiType run on normal samples.| HLA-A | HLA-B | HLA-C |
|---|---|---|
| A*31:01 | B*08:01 | C*03:04 |
| A*01:01 | B*40:01 | C*07:01 |
HLA-typing: Kourami
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HLA class I and HLA class II alleles prediction from Kourami, run on normal samples. Kourami provides the output in “G” resolution whenever “G” grouping information is available
| HLA-A | HLA-B | HLA-C | DQA1 | DQB1 | DRB1 |
|---|---|---|---|---|---|
| A*01:01:01G | B*08:01:01G | C*03:04:01G | DQA1*01:01:01G | DQB1*05:01:01G | DRB1*01:01:01G |
| A*31:01:02G | B*40:01:01G | C*07:01:01G | DQA1*05:01:01G | DQB1*02:01:01G | DRB1*03:01:01G |
MSI status
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MSI status derived using Step-Wise Difference metrics from MANTIS
| MSI Status | MSI Score | Threshold |
|---|---|---|
| Stable | 0.2097 | 0.4 |
Mutational signatures
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Mutational profile and COSMIC signatures v2 for the tumor sample as determined by deconstructSigs
| Signature | Contribution |
|---|---|
| 3 | 0.26 |
| 5 | 0.17 |
| 16 | 0.14 |
| 9 | 0.08 |
| 1 | 0.06 |
| 8 | 0.06 |