{ "metadata": { "name": "MRS. ARCHANA SHARMA", "cr_no": "391520", "age_sex": "47Y/Female", "referred_doctor": "Dr. ULLAS BATRA", "sample_type": "Peripheral Blood", "diagnosis": "Breast Cancer", "tumor_fraction": "", "order_no": "", "order_date": "11.08.2026", "receiving_date": "11.08.2026", "reporting_date": "27.08.2026", "lab_id": "2026223-1672" }, "report_information": { "panel_title": "The assay utilizing a minimum of 10ng of DNA at 30X coverage." }, "clinical_content": { "sections": [ { "heading": "Report Highlights", "order": 1, "content": "Variant Detected:", "page": 1, "source_lines": [ 61, 64 ], "children": [ { "kind": "list_item", "content": "Pathogenic variant in BRCA1 p.(Glu730Thrfs*5)", "page": 1, "order": 2 }, { "heading": "DNA Sequence Variants", "order": 3, "page": 1, "source_lines": [ 66 ], "children": [ { "kind": "table", "headers": [ "Gene", "Transcript", "Genomic Locus", "Coding DNA change", "Amino Acid Change", "Zygosity", "Variant Allele Frequency", "Variant Type", "Clinical Significance" ], "rows": [ [ "BRCA1", "NM_007294.4", "chr17:41245347", "c.2188_2201del", "p.(Glu730Thrfs*5)", "Heterozygous", "65%", "Frameshift deletion", "Pathogenic" ] ], "order": 4 }, { "heading": "Genomic Assembly", "order": 5, "content": "GrCH 37(hg19)", "page": 1, "source_lines": [ 93 ] }, { "heading": "Clinical Significance", "order": 6, "page": 1, "source_lines": [ 56 ], "children": [ { "heading": "Variant:BRCA1 p.(Glu730Thrfs*5)", "order": 7, "page": 1, "source_lines": [ 95 ], "children": [ { "heading": "Interpretation", "order": 8, "content": "BRCA1 p.(Glu730Thrfs*5) is a truncating frameshift variant predicted to result in loss of BRCA1 protein function. Loss-of-\nfunction variants in BRCA1 are an established pathogenic mechanism (PMID:20104584). The variant is absent from\npopulation databases (gnomAD) and has been reported in individuals with BRCA1-related clinical features (PMID:\n10923033, 21520333). Accordingly, this variant is classified as Pathogenicon Clinvar database.\nClinical Significance\nThis finding is clinically actionable and has implications for cancer risk assessment, surveillance, and management.\nGenetic counseling is strongly recommended.", "page": 1, "source_lines": [ 96, 97, 98, 99, 100, 102, 103, 104 ] }, { "heading": "Additional note", "order": 9, "content": "Germline cascade testing is recommended for at-risk family members to assess for the presence of the BRCA1\n(NM_007294.4): c.2188_2201del p.(Glu730Thrfs*5) pathogenic variant.\nReport highlights were conveyed to Dr. Ullas Batra’s clinical team (Tannu) on 26/08/2026, 02:50 pm.", "page": 1, "source_lines": [ 106, 107, 108 ] } ] } ] } ] }, { "heading": "Assay Information and Methodology", "order": 10, "content": "Clinical Exome Sequencing for Germline Mutation\nassociated with hereditary disease research, plus the ClinVar pathogenic and likely pathogenic variants content. It is a DNA\nbased panel which interrogates for single nucleotide variants, insertions and deletions (InDels) in the 3332 genes\nencompassed by the probes employed in this panel. It follows a hybrid capture based target enrichment, and the libraries\nare sequenced on Illumina NextSeq 1000 using a P1 flow cell with a 2*150bp paired end sequencing, with a minimum depth\nof 30x for germline sequencing.\nfiltered and called in accordance with ACMG guidelines for reporting germline variants", "page": 1, "source_lines": [ 110, 55, 113, 169, 170, 171, 172, 175 ], "children": [ { "kind": "list_item", "content": "Test Description. - The KAPA HyperCap Heredity Panel is a 10 Mb capture target panel covering 3332 genes strongly", "page": 1, "order": 11 }, { "kind": "list_item", "content": "The raw data obtained was preprocessed and processed using custom bioinformatics pipeline (Geneyx). The variants were", "page": 2, "order": 12 }, { "kind": "list_item", "content": "Variant of uncertain significance are reported and periodically followed up every six months.", "page": 2, "order": 13 }, { "kind": "list_item", "content": "All ACMG specified inherited cancer genes are included and examined.", "page": 2, "order": 14 }, { "heading": "Quality Metrics", "order": 15, "metrics": { "DNA": { "status": "PASSED", "Mean depth of coverage": "122x" } }, "page": 2, "source_lines": [ 182, 185, 188 ] }, { "heading": "Disclaimer", "order": 16, "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": 2, "source_lines": [ 194, 195, 196 ] } ] } ] } ] }, "authorization": { "performed_by": "Mamta Arya Scientist C\nAmit Negi Scientist A\nAkaash Kumar Scientist B\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/29387_CLINICAL EXOME SEQUENCING.pdf", "content_hash": "438456cefb4708526cefc2d752b24f107d43c11348d3522bacc4fd6c91c83532", "processed_at": "2026-09-12T11:51:53.981114+00:00", "pipeline_version": "1.0.0", "pipeline_name": "molecular", "pages": 2, "sections_detected": 1, "warnings_count": 2, "skipped_image_blocks": 2, "skipped_figure_lines": 0, "content_coverage": 0.9951, "validation_status": "PASSED", "validation_failures": [], "validation_warnings": [], "header_layout": "B" } }