{
  "metadata": {
    "name": "Dr. Shahadat Hossain",
    "cr_no": "329314",
    "age_sex": "42 years/ Male",
    "referred_doctor": "Dr. Vineet Talwar",
    "sample_type": "Tumor Tissue (FFPE block) – B/14502/25 (1-3)",
    "diagnosis": "Penile squamous cell carcinoma",
    "tumor_fraction": "60%",
    "order_no": "",
    "order_date": "13-07-2026",
    "receiving_date": "18-07-2026",
    "reporting_date": "26-08-2026",
    "lab_id": "2026234-2031"
  },
  "report_information": {
    "panel_title": "All Comprehensive 550 NGS Panel"
  },
  "clinical_content": {
    "sections": [
      {
        "heading": "Report Highlights",
        "order": 1,
        "page": 1,
        "source_lines": [
          55
        ],
        "children": [
          {
            "heading": "GENOMIC BIOMARKER FINDINGS",
            "order": 2,
            "content": "Variants detected:\n1. SNV/MNV/Microindels\n2. Copy number alterations\n3. Gene Rearrangements (by RNA Sequencing)\nNo clinically significant fusions detected",
            "page": 1,
            "source_lines": [
              56,
              57,
              58,
              62,
              64,
              66
            ],
            "children": [
              {
                "kind": "list_item",
                "content": "TP53 p.(Leu265del)",
                "page": 1,
                "order": 3
              },
              {
                "kind": "list_item",
                "content": "MDM2 amplification",
                "page": 1,
                "order": 4
              }
            ]
          },
          {
            "heading": "COMPOSITE BIOMARKER FINDINGS",
            "order": 5,
            "content": "Microsatellite Stability Status\n2.5 (MSS)\nTumor Mutation Burden\n5.69 mutations/mb (low)",
            "page": 1,
            "source_lines": [
              68,
              69,
              71,
              72,
              74
            ]
          },
          {
            "heading": "DNA Sequence Variants",
            "order": 6,
            "page": 1,
            "source_lines": [
              76
            ],
            "children": [
              {
                "kind": "table",
                "headers": [
                  "Gene",
                  "Transcript",
                  "Genomic Locus",
                  "Coding DNA change",
                  "Amino Acid Change",
                  "Variant Allele Frequency (%)",
                  "Variant Type",
                  "Clinical Significance"
                ],
                "rows": [
                  [
                    "TP53",
                    "NM_000546.6",
                    "chr17:7577143",
                    "c.792_794delACT",
                    "p.(Leu265del)",
                    "18.95",
                    "in-frame deletion",
                    "Strong"
                  ]
                ],
                "order": 7
              },
              {
                "heading": "Genomic Assembly",
                "order": 8,
                "content": "GrCH 37(hg19)",
                "page": 1,
                "source_lines": [
                  97
                ]
              }
            ]
          },
          {
            "heading": "Copy Number Variants",
            "order": 9,
            "content": "Copy number summary:MDM2 amplification may promote tumor growth through suppression of the p53 pathway.\nReport Summary:MDM2 amplification and a rare TP53p.L265del variant were identified, suggesting p53 pathway\ndysregulation.\nMutation Signature in this Sample:",
            "page": 1,
            "source_lines": [
              99,
              106,
              108,
              109,
              180
            ],
            "children": [
              {
                "kind": "table",
                "headers": [
                  "Gene",
                  "Genomic Locus",
                  "Copy number"
                ],
                "rows": [
                  [
                    "MDM2",
                    "chr12:69202958",
                    "10.42"
                  ]
                ],
                "order": 10
              }
            ]
          },
          {
            "heading": "Clinical Significance",
            "order": 11,
            "content": "Variant",
            "page": 2,
            "source_lines": [
              179,
              166
            ],
            "children": [
              {
                "heading": "Pathogenic Contribution",
                "order": 12,
                "content": "This likely oncogenic variant affects the DNA binding domain. The DNA-binding domain (DBD) of TP53 allows\nfor contact with target DNA sequences to transactivate downstream genes. Mutations in the DBD result in\nconformational changes of the protein, altering contact of TP53 with its target DNA sequences and thereby\naltering transcriptional function (PMID:8023157, 11900253). Given that TP53 directs the transcription of\nproteins that enable apoptosis, the inactivation of TP53 results in cells harboring damaged DNA and overall\ngenomic instability (PMID:11900253, 11900253).",
                "page": 2,
                "source_lines": [
                  167,
                  168,
                  169,
                  170,
                  171,
                  172,
                  173
                ]
              },
              {
                "heading": "Predictive/Therapeutic Significance",
                "order": 13,
                "content": "There are no FDA-approved or NCCN-compendium listed treatments specifically for patients with TP53\naltered penile cancer.",
                "page": 2,
                "source_lines": [
                  175,
                  176,
                  177
                ]
              },
              {
                "heading": "Prognostic Significance",
                "order": 14,
                "content": "TP53 alterations are generally associated with adverse outcomes in many cancers; however, no prognostic\ndata exist for this variant specifically in penile cancer.",
                "page": 3,
                "source_lines": [
                  233,
                  234,
                  235
                ]
              },
              {
                "heading": "Diagnostic Significance",
                "order": 15,
                "content": "Somatic TP53 alterations are observed in various solid tumor malignancies and therefore, carries no\ndiagnostic significance in isolation.",
                "page": 3,
                "source_lines": [
                  237,
                  238,
                  239
                ],
                "children": [
                  {
                    "heading": "Additional Note",
                    "order": 16,
                    "content": "Report highlights were conveyed to Dr. Talwar on August 12, 2026, 4:10 pm. Sample DNA passed QC, sample\nRNA was rerun twice but did not pass QC.",
                    "page": 3,
                    "source_lines": [
                      241,
                      242
                    ]
                  }
                ]
              }
            ]
          },
          {
            "heading": "Assay Information and Methodology",
            "order": 17,
            "content": "The assay utilizing a minimum of 20ng of DNA and 20ng of RNA at 500X coverage provides an analytical sensitivity of more than equal to 5\npercent for DNA-based genetic alteration.\nVariants of strong and potential clinical significance are only reported in somatic panels.",
            "page": 3,
            "source_lines": [
              244,
              396,
              397,
              400
            ],
            "children": [
              {
                "heading": "Test Description",
                "order": 18,
                "content": "- Oncomine Comprehensive Assay Plus is a targeted, next-generation sequencing (NGS) assay that provides a comprehensive genomic\nprofiling solution appropriate for formalin-fixed paraffin-embedded (FFPE) tissues. The assay allows concurrent analysis of DNA and RNA to\nsimultaneously detect multiple biomarkers associated with targeted and immune checkpoint research, including comprehensive targets that are relevant\nin cancer, in a single workflow. The assay is run on Ion Torrent S5 Plus platform using a Ion 550 chip.",
                "page": 3,
                "source_lines": [
                  247,
                  248,
                  249,
                  250
                ]
              },
              {
                "heading": "Gene Analyzed for SNVs and Indels",
                "order": 19,
                "content": "ABL1, ABL2, ACVR1,AKT1, AKT2,AKT3, ALK, AR, ARAF, ATP1A1, AURKA, AURKC, AXL, BCL2,BCL2L12,BCL6, BCR,\nBMP5, BRAF, BTK, CACNA1D, CARD11, CBL, CCND1, CCND2,CCND3, CCNE1, CD79B, CDK4, CDK6,CHD4,CSF1R, CTNNB1,CUL1,CYSLTR2 DDR2, DGCR8,\nDROSHA, E2F1, EGFR, IF1AX, EPAS1, ERBB2, ERBB3, ERBB4,ESR1,EZH2,FAM135B,FGF7,FGFR1,FGFR2, FGFR3, FGFR4, FLT3, FLT4, FOXA1, FOXL2, FOXO1,\nGATA2, GLI1, GNA11, GNAQ, GNAS, H3F3A, H3F3B,HIF1A,HIST1H2BD,HIST1H3B, HRAS, IDH1, IDH2, IKBKB, IL6ST, IL7R, IRF4, IRS4, KDR, KIT, KLF4, KLF5,\nKNSTRN, KRAS, MAGOH,MAP2K1, MAP2K2,MAPK1, MAX, MDM4, MECOM, MED12, MEF2B, MET, MITF, MPL, MTOR, MYC, MYCN, MYD88, MYOD1,\nNFE2L2,NRAS, NSD2, NT5C2,NTRK1, NTRK2, NTRK3, NUP93, PAX5, PCBP1, PDGFRA, PDGFRB, PIK3C2B, PIK3CA, PIK3CB, PIK3CD, PIK3CG,PIK 3R2, PIM1,\nPLCG1,PPP2R1A, PPP6C, PRKACA, PTPN11, PTPRD, PXDNL, RAC1, RAF1, RARA, RET, RGS7, RHEB, RHOA, RICTOR, RIT1,ROS1, RPL10,SETBP1, SF3B1, SIX1,\nSIX2, SLCO1B3, SMC1A, SMO,SNCAIP, SOS1, SOX2, SPOP, SRC, SRSF2, STAT3, STAT5B, STAT6,TAF1, TERT,TGFBR1, TOP1, TPMT, TRRAP, TSHR, U2AF1,\nUSP8, WAS, XPO1, ZNF217, ZNF429.",
                "page": 3,
                "source_lines": [
                  253,
                  254,
                  255,
                  256,
                  257,
                  258,
                  259,
                  260,
                  261
                ]
              },
              {
                "heading": "Genes Analyzed for Full Exons",
                "order": 20,
                "content": "ABRAXAS1, ACVR1B, ACVR2A, ADAMTS12, ADAMTS2, AMER1, APC, ARHGAP35, ARID1A,ARID1B,ARID2, ARID5B, ASXL1,\nASXL2, ATM, ATR, ATRX, AXIN1, AXIN2, B2M, BAP1, BARD1, BCOR, BLM, BMPR2, BRCA1, BRCA2, BRIP1, CALR,CASP8, CBFB, CD274, CD276, CDC73, CDH1,\nCDH10, CDK12, CDKN1A, CDKN1B, CDKN2A, CDKN2B, CDKN2C, CHEK1,CHEK2, CIC,CIITA, CREBBP, CSMD3, CTCF, CTLA4, CUL3, CUL4A, CUL4B, CYLD,\nCYP2C9, CYP2D6, DAXX, DDX3X, DICER1, DNMT3A,DOCK3, DPYD,DSC1, DSC3, ELF3, ENO1 , EP300, EPCAM, EPHA2, ERAP1, ERAP2, ERCC2, ERCC4, ERCC5,\nERRFI1, ETV6, FANCA, FANCC,FANCD2,FANCE, FANCF, FANCG, FANCI, FANCL, FANCM, FAS, FAT1, FBXW7, FUBP1, GATA3, GNA13, GPS2, HDAC 2, HDAC9,\nHLA-A,HLA-B,HNF1A, ID3, INPP4B, JAK1, JAK2, JAK3, KDM5C, KDM6A, KEAP1, KLHL13, KMT2A, KMT2B, KMT2C, KMT2D, LARP4B, LATS1,LATS2,MAP2K4,\nMAP2K7, MAP3K1, MAP3K4, MAPK8, MEN1, MGA, MLH1, MLH3, MRE11, MSH2, MSH3, MSH6, MTAP, MTUS2,MUTYH , NBN,NCOR1, NF1, NF2, NOTCH1,\nNOTCH2, NOTCH3, NOTCH4, PALB2, PARP1, PARP2, PARP3, PARP 4, PBRM1, PDCD1,PDCD1LG2, PDIA3,PGD, PHF6, PIK3R1, PMS1, PMS2, POLD1,\nPOLE,POT1, PPM1D, PPP2R2A, PRDM1, PRDM9, PRKAR1A, PSMB10,PSMB8, PSMB9,PTCH1, PTEN, PTPRT, RAD50, RAD51, RAD51B, RAD51C, RAD51D,\nRAD52, RAD54L, RASA1, RASA2, RB1, RBM10, RECQL4,RNASEH2A,RNASEH2B, RNASEH2C, RNF43, RPA1, RPL22, RPL5, RUNX1, RUNX1T1, SDHA, SDHB,\nSDHC, SDHD, SETD2, SLX4, SMAD2,SMAD4,SMARCA4, SMARCB1, SOCS1, SOX9, SPEN, STAG2, STAT1, STK11, SUFU, TAP1, TAP2, TBX3, TCF7L2 , TET2,\nTGFBR2,TMEM132D,TNFAIP3, TNFRSF14, TP53, TP63, TPP2, TSC1, TSC2, UGT1A1, USP9X, VHL, WT1, XRCC2, XRCC3, ZBTB20, ZFHX3,ZMYM3, ZRSR2.",
                "page": 3,
                "source_lines": [
                  264,
                  265,
                  266,
                  267,
                  268,
                  269,
                  270,
                  271,
                  272,
                  273,
                  274,
                  275
                ]
              },
              {
                "heading": "Gene Analyzed for CNAs",
                "order": 21,
                "content": "ABCB1, ABL1, ABL2, ABRAXAS1, ACVR1B, ACVR2A, ADAMTS12, ADAMTS2, AKT1, AKT2, AKT3, ALK,AMER1,APC, AR, ARAF,\nARHGAP35, ARID1A, ARID1B, ARID2, ARID5B, ASXL1, ASXL2, ATM, ATR, ATRX, AURKA, AURKC, AXIN1, AXIN2,AXL,B2M, BAP1, BARD1, BCL2, BCL2L12,\nBCL6, BCOR, BLM, BMPR2, BRAF, BRCA1, BRCA2, BRIP1, CARD11, CASP8, CBFB, CBL,CCND1,CCND2, CCND3, CCNE1, CD274, CD276, CDC73, CDH1, CDH10,\nCDK12, CDK4, CDK6, CDKN1A, CDKN1B, CDKN2A, CDKN2B,CDKN2C,CHD4, CHEK1, CHEK2, CIC, CREBBP, CSMD3, CTCF, CTLA4, CTNND2, CUL3, CUL4A,\nCUL4B, CYLD, CYP2C9, DAXX, DDR1,DDR2, DDX3X,DICER1, DNMT3A, DOCK3, DPYD, DSC1, DSC3, EGFR, EIF1AX, ELF3, EMSY, ENO1, EP300, EPCAM, EPHA2,\nERAP1,ERAP2, ERBB2, ERBB3, ERBB4, ERCC2, ERCC4, ERRFI1, ESR1, ETV6, EZH2, FAM135B, FANCA, FANCC, FANCD2, FANCE, FANCF,FANCG,FANCI, FANCL,\nFANCM, FAT1, FBXW7, FGF19, FGF23, FGF3, FGF4, FGF9, FGFR1, FGFR2, FGFR3, FGFR4, FLT3, FLT4, FOXA1,FUBP1,FYN, GATA2, GATA3, GLI3, GNA13,\nGNAS, GPS2, H3F3A, H3F3B, HDAC2, HDAC9, HLA-A, HLA-B, HNF1A, IDH2, IGF1R, IKBKB,IL7R,INPP4B, JAK1, JAK2, JAK3, KDM5C, KDM6A, KDR, KEAP1, KIT,\nKLF5, KMT2A, KMT2B, KMT2C, KMT2D, KRAS, LARP4B, LATS1,LATS2, MAGOH, MAP2K1, MAP2K4, MAP2K7, MAP3K1, MAP3K4 , MAPK1, MAPK8, MAX,\nMCL1, MDM2, MDM4, MECOM,MEF2B,MEN1, MET, MGA, MITF, MLH1, MLH3, MPL, MRE11, MSH2, MSH3, MSH6, MTAP, MTOR, MUTYH, MYC, MYCL,\nMYCN, MYD88,NBN,NCOR1,NF1, NF2, NFE2L2,NOTCH1, NOTCH2, NOTCH3NOTCH4,NRAS, NTRK1, NTRK3,PALB2,PARP1, PARP2, PARP3,PARP4,PBRM1,\nPCBP1, PDCD1,,PDCD1LG2,,PDGFRA, PDGFRB, PDIA3, PGD, PHF6, PIK3C2B, PIK3CA, PIK3CB, PIK3R1, PIK3R2, PIM1,PLCG1,PMS1, PMS2, POLD1, POLE,\nPOT1, PPM1D, PPP2R1A, PPP2R2A, PPP6C, PRDM1, PRDM9, PRKACA, PRKAR1A, PTCH1, PTEN,PTPN11,PTPRT, PXDNL , RAC1, RAD50, RAD51, RAD51B,\nRAD51C, RAD51D, RAD52, RAD54L, RAF1, RARA, RASA1, RASA2, RB1, RBM10,RECQL4,RET, RHEB, RICTOR, RIT1, RNASEH2A, RNASEH2B, RNF43, ROS1,\nRPA1, RPS6KB1, RPTOR, RUNX1, SDHA, SDHB, SDHD,SETBP1,SETD2, SF3B1, SLCO1B3, SLX4, SMAD2, SMAD 4, SMARCA4, SMARCB1, SMC1A, SMO, SOX9,\nSPEN, SPOP, SRC, STAG2,STAT3, STAT6,STK11, SUFU, TAP1, TAP2, TBX3, TCF7L2, TERT, TET2, TGFBR2, TNFAIP3, TNFRSF14, TOP1, TP53, TP63, TPMT,\nTPP2,TSC1, TSC2,U2AF1, USP8, USP9X, VHL, WT1, XPO1, XRCC2, XRCC3, YAP1, YES1, ZFHX3, ZMYM3, ZNF217,ZNF429,ZRSR2",
                "page": 3,
                "source_lines": [
                  278,
                  279,
                  280,
                  281,
                  282,
                  283,
                  284,
                  285,
                  286,
                  287,
                  288,
                  289,
                  343,
                  344,
                  345,
                  346,
                  347
                ]
              },
              {
                "heading": "Genes Analyzed for Rearrangements",
                "order": 22,
                "content": "AKT2, ALK, AR, AXL, BRAF, BRCA1, BRCA2, CDKN2A, EGFR, ERBB2, ERBB4, ERG, ESR1,ETV1,ETV4, ETV5, FGFR1,\nFGFR2, FGFR3, FGR, FLT3, JAK2, KRAS, MDM4, MET, MYB, MYBL1, NF1, NOTCH1, NOTCH4, NRG1, NTRK1,NTRK2,NTRK3, NUTM1, PDGFRA, PDGFRB,\nPIK3CA, PPARG, PRKACA, PRKACB, PTEN, RAD51B, RAF1, RB1, RELA, RET, ROS1, RSPO2,RSPO3,TERT.\nThe assay utilizes FusionSync Technology and covers >1,300 isoforms across 49 fusion drivers. This enables highly sensitive and robust detection of\nknown fusions and novel combinations of known fusion partners. The exon-tiling imbalance approach simultaneously enables detection of novel fusions\nwith key fusion driver genes, such as ALK, FGFR2, NTRK1, NTRK2, NTRK3,and RET.",
                "page": 4,
                "source_lines": [
                  350,
                  351,
                  352,
                  355,
                  356,
                  357
                ]
              },
              {
                "heading": "Genes Analyzed for HRR pathway",
                "order": 23,
                "content": "ABRAXAS1 ATM ATR BAP1 BARD1 BLM BRCA1 BRCA2 BRIP1 CDK12 CHEK1 CHEK2 FANCA FANCC FANCD2 FANCE\nFANCF FANCG FANCI FANCL FANCM MRE11 NBN PALB2 PARP1 PARP2 PARP3 POLD1 POLE PPP2R2A PTEN RAD50 RAD51 RAD51B RAD51C RAD51D RAD52\nRAD54L RNASEH2A RNASEH2B RNASEH2C RPA1 SLX4 TP53 XRCC2 XRCC3",
                "page": 4,
                "source_lines": [
                  360,
                  361,
                  362
                ]
              },
              {
                "heading": "Genes Analyzed only for TMB",
                "order": 24,
                "content": "A1CF, ACSM2B, ADAM18, ANO4, ARMC4, BRINP3, C6, C8A, C8B, CANX, CASR,CD163,CNTN6, CNTNAP4, CNTNAP5,\nCOL11A1, DCAF4L2, DCDC1, GALNT17, GPR158, GRID2, HCN1, HLA-C, KCND2, KCNH7, KEL,KIR3DL1,KRTAP2-1, KRTAP6-2, LRRC7, MARCO, NLRC5, NOL4,\nNRXN1, NYAP2, OR10G8, OR2G6, OR2L13, OR2L2, OR2L8, OR2M3,OR2T3,OR2T33, OR2T4, OR2W3, OR4A15, OR4C15, OR4C6, OR4M1, OR4M2, OR5D18,\nOR5F1, OR5L1, OR5L2, OR6F1, OR8H2, OR8I2,OR8U1,ORC4, PAK5, PCDH17, PDE1A, PDE1C, PLXDC2, POM121L12, PPFIA2, RBP3, REG1A, REG1B, REG3A,\nREG3G, RPTN, RUNDC3B,SH3RF2,SLC15A2, SLC8A1, SYT10, SYT16, TAPBP, TPTE, TRHDE, TRIM48, TRIM51, ZIM3, ZNF479, ZNF536",
                "page": 4,
                "source_lines": [
                  365,
                  366,
                  367,
                  368,
                  369
                ]
              },
              {
                "heading": "Loci Analyzed for MSI status",
                "order": 25,
                "content": "76 different loci are scored.A cut of >18 is considered to confer the microsatellite instability (MSI-High) status",
                "page": 4,
                "source_lines": [
                  372
                ]
              },
              {
                "heading": "Genomic Instability Metric",
                "order": 26,
                "content": "The Oncomine Comprehensive Assay Plus measures genomic scarring with the genomic instability metric (GIM). GIM is a\nnumeric value between 0 and 100 that summarizes unbalanced copy number changes using genomic segmentation. The Oncomine Comprehensive\nAssay Plus uses heterozygous population SNPs to determine the ploidy levels of genomic segments. The genomic segmentation is then used to infer\ntumor cellularity, loss of heterozygosity (LOH) for each segment, and the GIM This is analogous to the homologous recombination deficiency score, and\na cut off of >16 is considered significant for ovarian cancer.",
                "page": 4,
                "source_lines": [
                  375,
                  376,
                  377,
                  378,
                  379
                ]
              },
              {
                "heading": "Quality Metrics",
                "order": 27,
                "metrics": {
                  "DNA": {
                    "status": "PASSED",
                    "Mean depth of coverage": "2089x",
                    "Uniformity": "96.06%"
                  },
                  "RNA": {
                    "status": "FAILED",
                    "Total mapped fusion reads": "N/A (pool imbalance with low fusion reads in replicate runs)"
                  }
                },
                "page": 4,
                "source_lines": [
                  382,
                  384,
                  386,
                  388,
                  391,
                  393
                ]
              },
              {
                "heading": "Disclaimer",
                "order": 28,
                "content": "The information in this report does not constitute a treatment recommendation or recommendation to not use any specific therapeutic agent,\nand it should not be interpreted as treatment advice. Decisions concerning patient care and treatment rest solely within the discretion of the patient's\ntreating physician",
                "page": 4,
                "source_lines": [
                  403,
                  404,
                  405
                ]
              }
            ]
          }
        ]
      }
    ]
  },
  "authorization": {
    "performed_by": "Amit Negi Scientist A\nMolecular Diagnostics",
    "reviewed_by": "Dr. Sayak Ghatak\nSenior Consultant\nMolecular Diagnostics",
    "approved_by": "Dr. Anurag Mehta\nPrincipal Director Laboratory Services\nRajiv Gandhi Cancer Institute & Research Centre.\nRohini, New Delhi."
  },
  "processing": {
    "source_file": "/app/uploads/29379_ALL COMPREHENSIVE NGS PANEL (550 GENES TMB MSI).pdf",
    "content_hash": "50185b8fbca1263afc9069288bb64fd5d12ab63503e71cbf01e331cd8246bace",
    "processed_at": "2026-09-14T07:18:28.031159+00:00",
    "pipeline_version": "1.0.0",
    "pipeline_name": "molecular",
    "pages": 4,
    "sections_detected": 1,
    "warnings_count": 2,
    "skipped_image_blocks": 5,
    "skipped_figure_lines": 0,
    "content_coverage": 0.9957,
    "validation_status": "PASSED",
    "validation_failures": [],
    "validation_warnings": [],
    "header_layout": "B"
  }
}