[ { "sample_id": "MMMRD_P01", "patient_id": "MMMRD_P01", "sample_type": "BM", "analysis_mode": "mm_mrd", "engine_mode": "real_gating_v1_3", "panel_id": "ngf_inspired_2t_8c", "panel_supported": "yes", "anti_cd38_safe": "yes", "anti_cd38_flag": "no", "events_total": 150000, "events_analyzed": 149402, "event_qc_flag": "insufficient", "total_pc_count": 4505, "normal_pc_count": 4488, "aberrant_pc_count": 0, "uncertain_pc_count": 17, "clonality_call": "polyclonal_or_non_informative", "clonality_method": "unresolved", "standard_clonality_call": "polyclonal_or_non_informative", "rescued_clonality_call": "not_attempted", "rescue_subset_count": 0, "mrd_burden": 0.0, "mrd_burden_scientific": "0.00e+00", "lod": 0.00013386701650580312, "loq": 0.00033466754126450785, "mrd_status": "not_detected", "hemodilution_flag": "adequate", "research_only_flag": "yes", "warnings": [ "Real gating v1.3 active: rule-based plasma-cell gating, sample-adaptive aberrancy scoring, and robust T2 clonality rescue.", "Current v1 uses independent T1 and T2 compartment logic; no advanced multi-tube cell-by-cell fusion yet.", "Clonality not confidently resolved on T2 with current v1.3 thresholds.", "Low-count non-clonal aberrant-like events were suppressed by the v1.1 noise floor." ], "tube_panel_details": { "T1": { "present": true, "resolved_markers": [ "CD117", "CD138", "CD19", "CD27", "CD38", "CD45", "CD56", "CD81", "FSC-A", "FSC-H", "SSC-A", "SSC-H", "Time" ], "missing_required_markers": [] }, "T2": { "present": true, "resolved_markers": [ "CD117", "CD138", "CD19", "CD38_multiE", "CD45", "CD56", "FSC-A", "FSC-H", "SSC-A", "SSC-H", "Time", "cyIgK", "cyIgL" ], "missing_required_markers": [] } }, "source_files": [ "MMMRD_P01_T1_surface.fcs", "MMMRD_P01_T2_cytoplasmic.fcs" ], "gating_thresholds": { "t1_pc": { "cd138": 2.9788403511047363, "cd38": 5.828839302062988 }, "t1_aberrancy": { "CD19_low": 4.7913594245910645, "CD56_high": 3.563232898712158, "CD27_low": 5.909111976623535, "CD81_low": 5.740654945373535, "CD117_high": 3.933603048324585, "active_aberrant_score_min": 3 }, "t2_clonality": { "CD19_low": 4.78153657913208, "CD56_high": 3.565589427947998, "CD117_high": 3.9383938312530518 } }, "t2_clonality_metrics": { "final_method": "unresolved", "pc_like_count": 4502, "aberrant_like_count": 5, "kappa_median": null, "lambda_median": null, "kappa_lambda_ratio": null, "standard_call": "polyclonal_or_non_informative", "standard_kappa_median": null, "standard_lambda_median": null, "standard_kappa_lambda_ratio": null, "standard_aberrant_like_count": 5, "rescued_call": "not_attempted", "rescue_used": false, "rescue_subset_count": 0, "rescue_kappa_median": null, "rescue_lambda_median": null, "rescue_kappa_lambda_ratio": null, "rescue_dominance_fraction": null, "broad_hint_ratio": null }, "plot_files": { "t1_fsc_ssc": "plot_t1_fsc_ssc.png", "t1_cd38_cd138": "plot_t1_cd38_cd138.png", "t1_cd19_cd56": "plot_t1_cd19_cd56.png", "t1_cd27_cd81": "plot_t1_cd27_cd81.png", "t2_cyigk_cyigl": "plot_t2_cyigk_cyigl.png" } }, { "sample_id": "MMMRD_P02", "patient_id": "MMMRD_P02", "sample_type": "BM", "analysis_mode": "mm_mrd", "engine_mode": "real_gating_v1_3", "panel_id": "ngf_inspired_2t_8c", "panel_supported": "yes", "anti_cd38_safe": "yes", "anti_cd38_flag": "no", "events_total": 150000, "events_analyzed": 149402, "event_qc_flag": "insufficient", "total_pc_count": 4520, "normal_pc_count": 4492, "aberrant_pc_count": 15, "uncertain_pc_count": 13, "clonality_call": "kappa_restricted", "clonality_method": "standard_t2", "standard_clonality_call": "kappa_restricted", "rescued_clonality_call": "not_needed", "rescue_subset_count": 0, "mrd_burden": 0.00010040026237935235, "mrd_burden_scientific": "1.00e-04", "lod": 0.00013386701650580312, "loq": 0.00033466754126450785, "mrd_status": "trace_below_lod", "hemodilution_flag": "adequate", "research_only_flag": "yes", "warnings": [ "Real gating v1.3 active: rule-based plasma-cell gating, sample-adaptive aberrancy scoring, and robust T2 clonality rescue.", "Current v1 uses independent T1 and T2 compartment logic; no advanced multi-tube cell-by-cell fusion yet." ], "tube_panel_details": { "T1": { "present": true, "resolved_markers": [ "CD117", "CD138", "CD19", "CD27", "CD38", "CD45", "CD56", "CD81", "FSC-A", "FSC-H", "SSC-A", "SSC-H", "Time" ], "missing_required_markers": [] }, "T2": { "present": true, "resolved_markers": [ "CD117", "CD138", "CD19", "CD38_multiE", "CD45", "CD56", "FSC-A", "FSC-H", "SSC-A", "SSC-H", "Time", "cyIgK", "cyIgL" ], "missing_required_markers": [] } }, "source_files": [ "MMMRD_P02_T1_surface.fcs", "MMMRD_P02_T2_cytoplasmic.fcs" ], "gating_thresholds": { "t1_pc": { "cd138": 2.969743490219116, "cd38": 5.831982135772705 }, "t1_aberrancy": { "CD19_low": 4.71513032913208, "CD56_high": 3.5809426307678223, "CD27_low": 5.894771099090576, "CD81_low": 5.742241859436035, "CD117_high": 3.9687845706939697, "active_aberrant_score_min": 3 }, "t2_clonality": { "CD19_low": 4.781110763549805, "CD56_high": 3.57828688621521, "CD117_high": 3.9720187187194824 } }, "t2_clonality_metrics": { "final_method": "standard_t2", "pc_like_count": 4520, "aberrant_like_count": 19, "kappa_median": 6.225533485412598, "lambda_median": 1.9592362642288208, "kappa_lambda_ratio": 3.1775291329317596, "standard_call": "kappa_restricted", "standard_kappa_median": 6.225533485412598, "standard_lambda_median": 1.9592362642288208, "standard_kappa_lambda_ratio": 3.1775291329317596, "standard_aberrant_like_count": 19, "rescued_call": "not_needed", "rescue_used": false, "rescue_subset_count": 0, "rescue_kappa_median": null, "rescue_lambda_median": null, "rescue_kappa_lambda_ratio": null, "rescue_dominance_fraction": null, "broad_hint_ratio": null }, "plot_files": { "t1_fsc_ssc": "plot_t1_fsc_ssc.png", "t1_cd38_cd138": "plot_t1_cd38_cd138.png", "t1_cd19_cd56": "plot_t1_cd19_cd56.png", "t1_cd27_cd81": "plot_t1_cd27_cd81.png", "t2_cyigk_cyigl": "plot_t2_cyigk_cyigl.png" } }, { "sample_id": "MMMRD_P03", "patient_id": "MMMRD_P03", "sample_type": "BM", "analysis_mode": "mm_mrd", "engine_mode": "real_gating_v1_3", "panel_id": "ngf_inspired_2t_8c", "panel_supported": "yes", "anti_cd38_safe": "yes", "anti_cd38_flag": "no", "events_total": 150000, "events_analyzed": 149401, "event_qc_flag": "insufficient", "total_pc_count": 4651, "normal_pc_count": 4516, "aberrant_pc_count": 103, "uncertain_pc_count": 32, "clonality_call": "lambda_restricted", "clonality_method": "standard_t2", "standard_clonality_call": "lambda_restricted", "rescued_clonality_call": "not_needed", "rescue_subset_count": 0, "mrd_burden": 0.0006894197495331357, "mrd_burden_scientific": "6.89e-04", "lod": 0.00013386791253070594, "loq": 0.0003346697813267649, "mrd_status": "quantifiable", "hemodilution_flag": "adequate", "research_only_flag": "yes", "warnings": [ "Real gating v1.3 active: rule-based plasma-cell gating, sample-adaptive aberrancy scoring, and robust T2 clonality rescue.", "Current v1 uses independent T1 and T2 compartment logic; no advanced multi-tube cell-by-cell fusion yet." ], "tube_panel_details": { "T1": { "present": true, "resolved_markers": [ "CD117", "CD138", "CD19", "CD27", "CD38", "CD45", "CD56", "CD81", "FSC-A", "FSC-H", "SSC-A", "SSC-H", "Time" ], "missing_required_markers": [] }, "T2": { "present": true, "resolved_markers": [ "CD117", "CD138", "CD19", "CD38_multiE", "CD45", "CD56", "FSC-A", "FSC-H", "SSC-A", "SSC-H", "Time", "cyIgK", "cyIgL" ], "missing_required_markers": [] } }, "source_files": [ "MMMRD_P03_T1_surface.fcs", "MMMRD_P03_T2_cytoplasmic.fcs" ], "gating_thresholds": { "t1_pc": { "cd138": 2.9891998767852783, "cd38": 5.836400985717773 }, "t1_aberrancy": { "CD19_low": 2.747753858566284, "CD56_high": 5.746771335601807, "CD27_low": 3.354973077774048, "CD81_low": 3.5615408420562744, "CD117_high": 5.389584064483643, "active_aberrant_score_min": 3 }, "t2_clonality": { "CD19_low": 2.683398962020874, "CD56_high": 5.774266242980957, "CD117_high": 5.400656700134277 } }, "t2_clonality_metrics": { "final_method": "standard_t2", "pc_like_count": 4655, "aberrant_like_count": 99, "kappa_median": 1.3729467391967773, "lambda_median": 6.294308185577393, "kappa_lambda_ratio": 0.21812508707750008, "standard_call": "lambda_restricted", "standard_kappa_median": 1.3729467391967773, "standard_lambda_median": 6.294308185577393, "standard_kappa_lambda_ratio": 0.21812508707750008, "standard_aberrant_like_count": 99, "rescued_call": "not_needed", "rescue_used": false, "rescue_subset_count": 0, "rescue_kappa_median": null, "rescue_lambda_median": null, "rescue_kappa_lambda_ratio": null, "rescue_dominance_fraction": null, "broad_hint_ratio": null }, "plot_files": { "t1_fsc_ssc": "plot_t1_fsc_ssc.png", "t1_cd38_cd138": "plot_t1_cd38_cd138.png", "t1_cd19_cd56": "plot_t1_cd19_cd56.png", "t1_cd27_cd81": "plot_t1_cd27_cd81.png", "t2_cyigk_cyigl": "plot_t2_cyigk_cyigl.png" } }, { "sample_id": "MMMRD_P04", "patient_id": "MMMRD_P04", "sample_type": "BM", "analysis_mode": "mm_mrd", "engine_mode": "real_gating_v1_3", "panel_id": "ngf_inspired_2t_8c", "panel_supported": "yes", "anti_cd38_safe": "yes", "anti_cd38_flag": "no", "events_total": 150000, "events_analyzed": 149401, "event_qc_flag": "insufficient", "total_pc_count": 2834, "normal_pc_count": 2749, "aberrant_pc_count": 7, "uncertain_pc_count": 78, "clonality_call": "kappa_restricted", "clonality_method": "rescued_t2", "standard_clonality_call": "polyclonal_or_non_informative", "rescued_clonality_call": "kappa_restricted", "rescue_subset_count": 3, "mrd_burden": 4.685376938574708e-05, "mrd_burden_scientific": "4.69e-05", "lod": 0.00013386791253070594, "loq": 0.0003346697813267649, "mrd_status": "trace_below_lod", "hemodilution_flag": "suboptimal_hemodiluted", "research_only_flag": "yes", "warnings": [ "Real gating v1.3 active: rule-based plasma-cell gating, sample-adaptive aberrancy scoring, and robust T2 clonality rescue.", "Current v1 uses independent T1 and T2 compartment logic; no advanced multi-tube cell-by-cell fusion yet.", "T2 clonality rescue accepted on a high-stringency subset (n=3, dominance=1.00).", "Hemodilution-aware stricter aberrancy threshold applied (score >= 4)." ], "tube_panel_details": { "T1": { "present": true, "resolved_markers": [ "CD117", "CD138", "CD19", "CD27", "CD38", "CD45", "CD56", "CD81", "FSC-A", "FSC-H", "SSC-A", "SSC-H", "Time" ], "missing_required_markers": [] }, "T2": { "present": true, "resolved_markers": [ "CD117", "CD138", "CD19", "CD38_multiE", "CD45", "CD56", "FSC-A", "FSC-H", "SSC-A", "SSC-H", "Time", "cyIgK", "cyIgL" ], "missing_required_markers": [] } }, "source_files": [ "MMMRD_P04_T1_surface.fcs", "MMMRD_P04_T2_cytoplasmic.fcs" ], "gating_thresholds": { "t1_pc": { "cd138": 2.915301561355591, "cd38": 3.934506893157959 }, "t1_aberrancy": { "CD19_low": 1.9204885959625244, "CD56_high": 3.6509275436401367, "CD27_low": 2.567922592163086, "CD81_low": 2.8005659580230713, "CD117_high": 4.549912452697754, "active_aberrant_score_min": 4 }, "t2_clonality": { "CD19_low": 1.841288685798645, "CD56_high": 3.5820505619049072, "CD117_high": 5.274420738220215, "rescue_score_min": 3, "rescue_min_events": 3, "rescue_ratio_kappa_min": 4.0, "rescue_ratio_lambda_max": 0.25, "rescue_min_dominance_fraction": 0.85, "rescue_hint_ratio_kappa_min": 1.2, "rescue_hint_ratio_lambda_max": 0.83 } }, "t2_clonality_metrics": { "final_method": "rescued_t2", "pc_like_count": 2829, "aberrant_like_count": 30, "kappa_median": 6.2971272468566895, "lambda_median": 1.4410463571548462, "kappa_lambda_ratio": 4.369826720538539, "standard_call": "polyclonal_or_non_informative", "standard_kappa_median": 2.7142550945281982, "standard_lambda_median": 1.756158471107483, "standard_kappa_lambda_ratio": 1.5455629965179152, "standard_aberrant_like_count": 30, "rescued_call": "kappa_restricted", "rescue_used": true, "rescue_subset_count": 3, "rescue_kappa_median": 6.2971272468566895, "rescue_lambda_median": 1.4410463571548462, "rescue_kappa_lambda_ratio": 4.369826720538539, "rescue_dominance_fraction": 1.0, "broad_hint_ratio": 1.5455629965179152 }, "plot_files": { "t1_fsc_ssc": "plot_t1_fsc_ssc.png", "t1_cd38_cd138": "plot_t1_cd38_cd138.png", "t1_cd19_cd56": "plot_t1_cd19_cd56.png", "t1_cd27_cd81": "plot_t1_cd27_cd81.png", "t2_cyigk_cyigl": "plot_t2_cyigk_cyigl.png" } }, { "sample_id": "MMMRD_P05", "patient_id": "MMMRD_P05", "sample_type": "BM", "analysis_mode": "mm_mrd", "engine_mode": "real_gating_v1_3", "panel_id": "ngf_inspired_2t_8c", "panel_supported": "yes", "anti_cd38_safe": "conditional", "anti_cd38_flag": "possible", "events_total": 150000, "events_analyzed": 149401, "event_qc_flag": "insufficient", "total_pc_count": 4557, "normal_pc_count": 4485, "aberrant_pc_count": 59, "uncertain_pc_count": 13, "clonality_call": "kappa_restricted", "clonality_method": "standard_t2", "standard_clonality_call": "kappa_restricted", "rescued_clonality_call": "not_needed", "rescue_subset_count": 0, "mrd_burden": 0.0003949103419655826, "mrd_burden_scientific": "3.95e-04", "lod": 0.00013386791253070594, "loq": 0.0003346697813267649, "mrd_status": "quantifiable", "hemodilution_flag": "adequate", "research_only_flag": "yes", "warnings": [ "Possible anti-CD38 interference: use CD138/multiparametric fallback, not CD38 alone", "Real gating v1.3 active: rule-based plasma-cell gating, sample-adaptive aberrancy scoring, and robust T2 clonality rescue.", "Current v1 uses independent T1 and T2 compartment logic; no advanced multi-tube cell-by-cell fusion yet." ], "tube_panel_details": { "T1": { "present": true, "resolved_markers": [ "CD117", "CD138", "CD19", "CD27", "CD38", "CD45", "CD56", "CD81", "FSC-A", "FSC-H", "SSC-A", "SSC-H", "Time" ], "missing_required_markers": [] }, "T2": { "present": true, "resolved_markers": [ "CD117", "CD138", "CD19", "CD38_multiE", "CD45", "CD56", "FSC-A", "FSC-H", "SSC-A", "SSC-H", "Time", "cyIgK", "cyIgL" ], "missing_required_markers": [] } }, "source_files": [ "MMMRD_P05_T1_surface.fcs", "MMMRD_P05_T2_cytoplasmic.fcs" ], "gating_thresholds": { "t1_pc": { "cd138": 2.980004072189331, "cd38": 5.529473304748535 }, "t1_aberrancy": { "CD19_low": 4.5729899406433105, "CD56_high": 3.692601203918457, "CD27_low": 5.7331953048706055, "CD81_low": 5.643423080444336, "CD117_high": 4.072819709777832, "active_aberrant_score_min": 3 }, "t2_clonality": { "CD19_low": 4.569450378417969, "CD56_high": 3.6418259143829346, "CD117_high": 4.051454067230225 } }, "t2_clonality_metrics": { "final_method": "standard_t2", "pc_like_count": 4549, "aberrant_like_count": 54, "kappa_median": 6.308446407318115, "lambda_median": 1.372253656387329, "kappa_lambda_ratio": 4.597139734927968, "standard_call": "kappa_restricted", "standard_kappa_median": 6.308446407318115, "standard_lambda_median": 1.372253656387329, "standard_kappa_lambda_ratio": 4.597139734927968, "standard_aberrant_like_count": 54, "rescued_call": "not_needed", "rescue_used": false, "rescue_subset_count": 0, "rescue_kappa_median": null, "rescue_lambda_median": null, "rescue_kappa_lambda_ratio": null, "rescue_dominance_fraction": null, "broad_hint_ratio": null }, "plot_files": { "t1_fsc_ssc": "plot_t1_fsc_ssc.png", "t1_cd38_cd138": "plot_t1_cd38_cd138.png", "t1_cd19_cd56": "plot_t1_cd19_cd56.png", "t1_cd27_cd81": "plot_t1_cd27_cd81.png", "t2_cyigk_cyigl": "plot_t2_cyigk_cyigl.png" } } ]