{ "metadata": { "name": "MR. SHREEJAL SHAH", "cr_no": "394220", "age_sex": "16Y/Male", "referred_doctor": "Dr. DINESH BHURANI", "sample_type": "Peripheral Blood", "diagnosis": "B-cell Lineage Acute Lymphoblastic Leukemia", "tumor_fraction": "", "order_no": "", "order_date": "01.08.2026", "receiving_date": "01.08.2026", "reporting_date": "26.08.2026", "lab_id": "2026213-1830" }, "report_information": { "panel_title": "Archer FusionPlex Acute lymphoblastic leukemia (ALL) Panel" }, "clinical_content": { "sections": [ { "heading": "_preamble", "order": 1, "content": "BLAST/TLC: 31%/ 2410 per cumm (Peripheral Smear 1824/26)", "page": 1, "source_lines": [ 61 ] }, { "heading": "Report Highlights", "order": 2, "content": "Alteration detected", "page": 1, "source_lines": [ 64 ], "children": [ { "kind": "list_item", "content": "ETV6::RUNX1 fusion", "page": 1, "order": 3 }, { "kind": "list_item", "content": "P2RY8::CRLF2 fusion", "page": 1, "order": 4 }, { "heading": "RNA Sequence Variants", "order": 5, "page": 1, "source_lines": [ 85 ], "children": [ { "kind": "table", "headers": [ "Fusion", "Breakpoint", "Reading Frame", "Supporting Reads", "Unique Start", "Reads per" ], "rows": [ [ "Detected", "", "", "", "Sites", "million/Reads %" ], [ "ETV6::RUNX1", "chr12:12022903-chr21:36265260", "In-Frame", "89", "199", "9.04" ], [ "P2RY8::CRLF2", "chrX:1655814-chrX:1331529", "In-Frame", "7", "7", "0.22" ] ], "order": 6 }, { "heading": "Genomic Assembly", "order": 7, "content": "GrCH 37(hg19)", "page": 1, "source_lines": [ 68 ] } ] }, { "heading": "Interpretation Summary", "order": 8, "content": "In this ETV6::RUNX1 fusion-positive ALL,P2RY8::CRLF2 fusion was detected at a low level (7 supporting reads; 0.22%). Given the\nlow supporting read count, this finding may represent a minor/subclonal leukemic population and should be interpreted with\ncaution. Orthogonal confirmation by an independent method, preferably FISH for CRLF2 rearrangement, is recommended. Rare\ncases of co-existence of ETV6::RUNX1 and P2RY8::CRLF2 have been reported; however, available evidence is insufficient to establish\nthis combination as an independently high-risk molecular profile. (PMIDs:33890726, 40089289) Therefore, the clinical and\nprognostic significance of a low-level P2RY8::CRLF2 clone in the setting of concomitant ETV6::RUNX1 fusion remains uncertain.", "page": 1, "source_lines": [ 70, 71, 72, 73, 74, 75, 76 ] }, { "heading": "Clinical Significance", "order": 9, "page": 1, "source_lines": [ 111 ], "children": [ { "heading": "Variant:ETV6::RUNX1 fusion", "order": 10, "page": 1, "source_lines": [ 78 ], "children": [ { "heading": "Pathogenic Contribution", "order": 11, "content": "ETV6::RUNX1 fusion is an established oncogenic alteration recurrently observed in B-acute lymphoblastic leukemia and is\ngenerally associated with favorable prognosis (PMID:7780150, 8609706). The fusion protein retains RUNX1 DNA-binding\nactivity but recruits ETV6-mediated transcriptional repression/HDAC complexes, resulting in repression of RUNX1 target\ngenes (PMID:15156184, 11001911, 28299659).ETV6::RUNX1 promotes leukemic cell self-renewal and survival (PMID:\n18202291, 16044150).", "page": 1, "source_lines": [ 79, 80, 81, 82, 83, 84 ] }, { "heading": "Predictive/Therapeutic Significance", "order": 12, "content": "There are no FDA-approved or NCCN-compendium listed treatments specifically for patients with ETV6-RUNX1 fusion-", "page": 2, "source_lines": [ 171, 172 ] }, { "heading": "Prognostic Significance", "order": 13, "content": "ETV6::RUNX1 is a favorable prognostic abnormality in pediatric B-ALL, associated with excellent treatment response and\nsuperior event-free and overall survival. However, prognosis remains influenced by clinical risk factors and, most\nimportantly, early MRD response, with delayed/persistent MRD associated with inferior outcomes even within this\nfavorable molecular subgroup [PMID:39316653;27506214;DOI: 10.3389/fonc.2021.797194].", "page": 2, "source_lines": [ 175, 176, 177, 178, 179 ] } ] }, { "heading": "Variant:P2RY8::CRLF2 fusion", "order": 15, "page": 2, "source_lines": [ 184 ], "children": [ { "heading": "Pathogenic Contribution", "order": 16, "content": "P2RY8::CRLF2 is an oncogenic fusion resulting from an interstitial deletion of the pseudoautosomal region of\nXp22.3/Yp11.3. It leads to CRLF2 overexpression and activation of downstream signaling, contributing to leukemogenesis\nin B-cell ALL. (PMIDs:19641190, 20139093, 22150304)", "page": 2, "source_lines": [ 185, 186, 187, 188 ] }, { "heading": "Predictive/Therapeutic Significance", "order": 17, "content": "There are no FDA-approved or NCCN-compendium listed treatments specifically for patients with P2RY8-CRLF2 fusion-", "page": 2, "source_lines": [ 190, 191 ] }, { "heading": "Prognostic Significance", "order": 18, "content": "P2RY8::CRLF2 has been associated with adverse outcomes in pediatric B-ALL; however, its prognostic significance is\nheterogeneous and may depend on the molecular subtype,CRLF2 expression level, and treatment response/MRD.\nImportantly, the presence of P2RY8::CRLF2 does not invariably result in high CRLF2 expression. (PMID:38023153)\nTherefore, the prognostic significance of P2RY8::CRLF2 should not be inferred from the fusion alone and should be\ninterpreted in conjunction with the overall molecular profile and MRD response.", "page": 2, "source_lines": [ 194, 195, 196, 197, 198, 199 ] }, { "heading": "Diagnostic Significance", "order": 19, "content": "P2RY8::CRLF2 is a defining molecular alteration of B-lymphoblastic leukemia/lymphoma, BCR::ABL1-like (Ph-like) subtype,", "page": 2, "source_lines": [ 200, 201 ] } ] } ] }, { "heading": "Assay Information and Methodology", "order": 20, "content": "RIN/DV200%:6.7/95.18%\no\nTotal unique fragments:473,448\no\nOn Target %:98.9%\no\nRNA QC Status: PASS\nTotal RNA unique fragments: 287,028\nAverage Unique RNA Start Sites per GSP2:113.82\nAverage Unique RNA Start Sites per GSP2 Control: 179.62\no\nDNA QC Status: PASS\nTotal DNA unique fragments: 84,835\nAverage Unique DNA Start Sites per GSP2:78.44\nAverage Unique DNA Start Sites per GSP2 Control: 80\nAnalytical Sensitivity and Limitations:Assay performance may be affected by tumor cellularity, RNA quality, specimen preservation, and fusion\ntranscript expression levels. A negative result does not exclude the presence of alterations outside assay coverage or below the validated limit of\ndetection.", "page": 2, "source_lines": [ 205, 291, 292, 293, 294, 295, 297, 298, 300, 302, 304, 307, 308, 310, 312, 314, 317, 318, 319 ], "children": [ { "heading": "Test Description", "order": 21, "content": "– This customized panel is a targeted next-generation sequencing (NGS)-based RNA fusion assay utilizing the Archer FusionPlex ALL\nPanel for detection of clinically relevant gene fusions and rearrangements associated with lymphoid malignancies using 506 GSPs targeting 81 genes.\nThe assay employs Anchored Multiplex PCR (AMP™) technology for identification of both known and novel fusion partners from formalin-fixed paraffin-\nembedded (FFPE) tumor tissue TNA (Total Nucleic Acid)/RNA.\nGenes Analyzed for Rearrangements/SNVs– ABL1, ABL2, AICDA, BCL11B, BCL2, BCL6, BCR, BLNK, BRAF, CD274, CHD1, CREBBP, CRLF2, CSF1R, CTLA4,\nDNM2, DNTT, EBF1, EPOR, ETV6, EZH2, FBXW7, FGFR1, FLT3, HOXA10, HOXA9, IDH1, IDH2, IKZF1, IKZF2, IKZF3, IL7R, IRF4, IRF8, JAK1, JAK2, JAK3, KDM6A,\nKLF2, KMT2A, KRAS, LMO1, LYL1, MLLT4, MPL, MYC, NF1, NOTCH1, NRAS, NT5C2, NTRK3, NUP214, NUP98, P2RY8, PAG1, PAX5, PBX1, PDCD1, PDCD1LG2,\nPDGFRA, PDGFRB, PICALM, PTK2B, PTPN11, RAG1, RAG2, RUNX1, SEMA6A, SETD2, SH2B3, SOX11, STAT3, STAT5B, STIL, TAL1, TCF3, TLX1, TLX3, TYK2,\nWT1, ZCCHC7\nThe assay utilizes a minimum input of 20 ng total nucleic acid (TNA), and libraries are sequenced to a minimum depth of 1.5 million reads. Sequencing\ndata are processed and analyzed using Archer Analysis Pipeline version 7.5.1 for detection and reporting of gene fusions, rearrangements, and single\nnucleotide variants (SNVs).\nVariants of strong and potential clinical significance are only reported in somatic panels.", "page": 2, "source_lines": [ 208, 209, 210, 211, 273, 274, 275, 276, 277, 280, 281, 282, 285 ] }, { "heading": "Disclaimer", "order": 23, "content": "The information in this report does not constitute a treatment recommendation or recommendation to not use any specific therapeutic agent, and\nit should not be interpreted as treatment advice. Decisions concerning patient care and treatment rest solely within the discretion of the patient's treating\nphysician.", "page": 3, "source_lines": [ 321, 322, 323 ] } ] } ] } ] }, "authorization": { "performed_by": "Mamta Arya Scientist C\nAmit Negi Scientist A\nMolecular Diagnostics", "reviewed_by": "Dr Rushali Saxena\nAttending consultant, Pathology", "approved_by": "Dr. Anurag Mehta\nPrincipal Director Laboratory Services\nRajiv Gandhi Cancer Institute & Research Centre.\nRohini, New Delhi." }, "processing": { "source_file": "/app/uploads/29385_TranSeq ALL NGS.pdf", "content_hash": "66b33913ff870c60255d739abfe2ea01f0164c4f07d7c5b431b7855e25f37d9b", "processed_at": "2026-09-12T10:55:09.770485+00:00", "pipeline_version": "1.0.0", "pipeline_name": "molecular", "pages": 3, "sections_detected": 2, "warnings_count": 1, "skipped_image_blocks": 3, "skipped_figure_lines": 0, "content_coverage": 0.9989, "validation_status": "PASSED", "validation_failures": [], "validation_warnings": [], "header_layout": "B" } }