public HER2AmplificationResult(PanelSetOrderCollection panelSetOrderCollection, HER2AnalysisSummary.HER2AnalysisSummaryTestOrder panelSetOrder) { Her2AmplificationByIHC.Her2AmplificationByIHCTest her2AmplificationByIHCTest = new Her2AmplificationByIHC.Her2AmplificationByIHCTest(); HER2AmplificationRecount.HER2AmplificationRecountTest her2AmplificationRecountTest = new HER2AmplificationRecount.HER2AmplificationRecountTest(); this.m_HER2AnalysisSummaryTestOrder = panelSetOrder; this.m_Indicator = this.m_HER2AnalysisSummaryTestOrder.Indicator; this.m_AverageHer2Chr17SignalAsDouble = this.m_HER2AnalysisSummaryTestOrder.AverageHer2Chr17SignalAsDouble; this.m_AverageHer2NeuSignal = this.m_HER2AnalysisSummaryTestOrder.AverageHer2NeuSignal; this.m_IsHer2AmplificationByIHCRequired = true; if (panelSetOrderCollection.Exists(her2AmplificationByIHCTest.PanelSetId) == true) { this.m_IsHer2AmplificationByIHCOrdered = true; this.m_PanelSetOrderHer2AmplificationByIHC = (Her2AmplificationByIHC.PanelSetOrderHer2AmplificationByIHC)panelSetOrderCollection.GetPanelSetOrder(her2AmplificationByIHCTest.PanelSetId); if (this.m_PanelSetOrderHer2AmplificationByIHC.Final == true) { if (this.m_PanelSetOrderHer2AmplificationByIHC.Score == "2+") { this.m_IsHER2AmplificationRecountRequired = true; } } } if (panelSetOrderCollection.Exists(her2AmplificationRecountTest.PanelSetId) == true) { this.m_IsHER2AmplificationRecountOrdered = true; this.m_HER2AmplificationRecountTestOrder = (HER2AmplificationRecount.HER2AmplificationRecountTestOrder)panelSetOrderCollection.GetPanelSetOrder(her2AmplificationRecountTest.PanelSetId); } }
public HER2AmplificationResultGroup3Breast(PanelSetOrderCollection panelSetOrderCollection, HER2AnalysisSummary.HER2AnalysisSummaryTestOrder panelSetOrder) : base(panelSetOrderCollection, panelSetOrder) { this.m_InterpretiveComment = "There are insufficient data on the efficacy of human epidermal growth factor receptor 2 (HER2)-targeted " + "therapy in cases with a HER2 ratio of < 2.0 in the absence of protein overexpression because such patients were not eligible " + "for the first generation of adjuvant trastuzumab clinical trials. When concurrent immunohistochemistry (IHC) results are " + "negative (0 or 1+), it is recommended that the specimen be considered HER2 negative."; }
public override void SetStatus(PanelSetOrderCollection panelSetOrderCollection) { if (panelSetOrderCollection.HasPanelSetBeenOrdered(this.PanelSet.PanelSetId) == false) { this.m_Ordered = false; this.m_StatusMessage = "Not Ordered"; } else { YellowstonePathology.Business.Test.PanelSetOrder panelSetOrder = panelSetOrderCollection.GetPanelSetOrder(this.PanelSet.PanelSetId); this.m_Ordered = true; this.m_OrderDate = panelSetOrder.OrderDate; if (panelSetOrder.Final == false) { this.m_StatusMessage = "Not Finalized"; } else { this.m_StatusMessage = "Finaled"; this.m_ResultIsFinal = true; this.m_ResultFinalDate = panelSetOrder.FinalDate; } } }
public HER2AmplificationResultCollection(PanelSetOrderCollection panelSetOrderCollection, HER2AmplificationByISHTestOrder panelSetOrder) { this.Add(new HER2AmplificationResultGroup1Breast(panelSetOrderCollection, panelSetOrder)); this.Add(new HER2AmplificationResultGroup2Breast(panelSetOrderCollection, panelSetOrder)); this.Add(new HER2AmplificationResultGroup3Breast(panelSetOrderCollection, panelSetOrder)); this.Add(new HER2AmplificationResultGroup4Breast(panelSetOrderCollection, panelSetOrder)); this.Add(new HER2AmplificationResultGroup5Breast(panelSetOrderCollection, panelSetOrder)); this.Add(new HER2AmplificationResultGastric(panelSetOrderCollection, panelSetOrder)); }
public HER2AmplificationResultGroup4Breast(PanelSetOrderCollection panelSetOrderCollection, HER2AnalysisSummary.HER2AnalysisSummaryTestOrder panelSetOrder) : base(panelSetOrderCollection, panelSetOrder) { this.m_InterpretiveComment = "It is uncertain whether patients with an average of ≥ 4.0 and < 6.0 human epidermal growth factor 2 " + "receptor(HER2) signals per cell and HER2 / chromosome enumeration probe 17(CEP17) ratio of < 2.0 benefit from HER2 - " + "targeted therapy in the absence of protein overexpression(immunohistochemistry[IHC] 3 +). If the specimen test result is " + "close to the in situ hybridization (ISH)ratio threshold for positive, there is a higher likelihood that repeat testing will " + "result in different results by chance alone. Therefore, when IHC results are not 3 + positive, it is recommended that the " + "sample be considered HER2 negative without additional testing on the same specimen."; }
public HER2AmplificationResultGastric(PanelSetOrderCollection panelSetOrderCollection, HER2AmplificationByISHTestOrder panelSetOrder) : base(panelSetOrderCollection, panelSetOrder) { this.m_InterpretiveComment = "Human epidermal growth factor receptor 2 gene (HER2) is amplified in up to 25% of gastric cancers, " + "particularly those that arise at the gastroesophageal junction. Amplification of the HER2 gene in gastric tumors is associated with " + "a worse prognosis and is also predictive of response to chemotherapeutic agents. Dual in situ hybridization (ISH) studies for HER2 " + "amplification were performed on the submitted sample, in accordance with ASCO/CAP guidelines." + Environment.NewLine + Environment.NewLine + "For this patient, the HER2:Chr17 ratio was *RATIO*. A total of *CELLSCOUNTED* nuclei were examined. Therefore, HER2 status is *HER2STATUS*."; this.m_ReportReference = "Gravalos, C. et al., HER2 in gastric cancer: a new prognostic factor and a novel therapeutic target. Ann " + "Oncology 2008, 19:1523-1529."; }
public HER2AmplificationResultGroup2Breast(PanelSetOrderCollection panelSetOrderCollection, HER2AnalysisSummary.HER2AnalysisSummaryTestOrder panelSetOrder) : base(panelSetOrderCollection, panelSetOrder) { this.m_InterpretiveComment = "Evidence is limited on the efficacy of human epidermal growth factor 2 (HER2)-targeted therapy in the " + "small subset of cases with a HER2/chromosome enumeration probe 17 (CEP17) ratio ≥ 2.0 and an average HER2 copy number " + "of < 4.0 per cell. In the first generation of adjuvant trastuzumab trials, patients in this subgroup who were randomly " + "assigned to the trastuzumab arm did not seem to derive an improvement in disease-free or overall survival, but there were " + "too few such cases to draw definitive conclusions. Immunohistochemistry (IHC) expression for HER2 should be used to " + "complement in situ hybridization (ISH) and define HER2 status. If the IHC result is not 3+ positive, it is recommended " + "that the specimen be considered HER2 negative because of the low HER2 copy number by ISH and the lack of protein expression."; }
public override void SetStatus(PanelSetOrderCollection panelSetOrderCollection) { this.m_ReflexTestingPlanStepCollection.Clear(); InvasiveBreastPanelStep1 step1 = new InvasiveBreastPanelStep1(); step1.Walk(panelSetOrderCollection, this); InvasiveBreastPanelStep2 step2 = new InvasiveBreastPanelStep2(); step2.Walk(panelSetOrderCollection, this); InvasiveBreastPanelStep3 step3 = new InvasiveBreastPanelStep3(); step3.Walk(panelSetOrderCollection, this); }
public override void Walk(PanelSetOrderCollection panelSetOrderCollection, YellowstonePathology.Business.Test.ReflexTesting.ReflexTestingPlan reflexTestingPlan) { reflexTestingPlan.ReflexTestingPlanStepCollection.Add(this); this.SetStatus(panelSetOrderCollection); reflexTestingPlan.StatusMessage += System.Environment.NewLine; if (panelSetOrderCollection.HasTestBeenOrdered(this.m_Test.TestId) == true) { reflexTestingPlan.StatusMessage += "Progesterone Receptor, Semi-quantitative has been ordered."; } else { reflexTestingPlan.StatusMessage += "Progesterone Receptor, Semi-quantitative has not been ordered."; } }
public override void Walk(PanelSetOrderCollection panelSetOrderCollection, YellowstonePathology.Business.Test.ReflexTesting.ReflexTestingPlan reflexTestingPlan) { reflexTestingPlan.ReflexTestingPlanStepCollection.Add(this); this.SetStatus(panelSetOrderCollection); reflexTestingPlan.StatusMessage += System.Environment.NewLine; if (panelSetOrderCollection.HasTestBeenOrdered(this.m_Test.TestId) == true) { reflexTestingPlan.StatusMessage += "Estrogen Receptor, Semi-quantitative has been ordered."; } else { reflexTestingPlan.StatusMessage += "Estrogen Receptor, Semi-quantitative has not been ordered."; } }
public override void SetStatus(PanelSetOrderCollection panelSetOrderCollection) { if (panelSetOrderCollection.HasTestBeenOrdered(this.m_Test.TestId) == false) { this.m_Ordered = false; this.m_StatusMessage = "Not Ordered"; } else { YellowstonePathology.Business.Test.Model.TestOrder testOrder = panelSetOrderCollection.GetTestOrderByTestId(this.m_Test.TestId); YellowstonePathology.Business.Test.PanelOrder panelOrder = panelSetOrderCollection.GetPanelOrderByTestOrderId(testOrder.TestOrderId); this.m_Ordered = true; this.m_OrderDate = panelOrder.OrderTime; this.m_StatusMessage = "Test has been ordered"; } }
public override void Walk(PanelSetOrderCollection panelSetOrderCollection, YellowstonePathology.Business.Test.ReflexTesting.ReflexTestingPlan reflexTestingPlan) { reflexTestingPlan.ReflexTestingPlanStepCollection.Add(this); this.SetStatus(panelSetOrderCollection); if (this.Ordered == true) { if (this.ResultIsFinal == true) { reflexTestingPlan.StatusMessage = "HER2 is finalized."; } else { reflexTestingPlan.StatusMessage = "HER2 is not finalized."; } } else { reflexTestingPlan.StatusMessage = "HER2 has not been ordered."; } }
public void SetResults(PanelSetOrderCollection panelSetOrderCollection) { StringBuilder interpretation = new StringBuilder(); StringBuilder method = new StringBuilder(); StringBuilder references = new StringBuilder(); YellowstonePathology.Business.Test.PDL122C3.PDL122C3Test pdl122C3Test = new PDL122C3.PDL122C3Test(); YellowstonePathology.Business.Test.EGFRMutationAnalysis.EGFRMutationAnalysisTest egfrMutationAnalysisTest = new YellowstonePathology.Business.Test.EGFRMutationAnalysis.EGFRMutationAnalysisTest(); YellowstonePathology.Business.Test.ROS1ByFISH.ROS1ByFISHTest ros1ByfishTest = new ROS1ByFISH.ROS1ByFISHTest(); YellowstonePathology.Business.Test.ALKForNSCLCByFISH.ALKForNSCLCByFISHTest alkTest = new ALKForNSCLCByFISH.ALKForNSCLCByFISHTest(); YellowstonePathology.Business.Test.BRAFMutationAnalysis.BRAFMutationAnalysisTest brafTest = new BRAFMutationAnalysis.BRAFMutationAnalysisTest(); YellowstonePathology.Business.Test.PDL1SP142.PDL1SP142Test pdl1SP142Test = new PDL1SP142.PDL1SP142Test(); YellowstonePathology.Business.PanelSet.Model.PanelSetALKRetired panelSetALKRetired = new PanelSet.Model.PanelSetALKRetired(); if (panelSetOrderCollection.Exists(egfrMutationAnalysisTest.PanelSetId) == true) { Test.EGFRMutationAnalysis.EGFRMutationAnalysisTestOrder egfrMutationAnalysisTestOrder = (EGFRMutationAnalysis.EGFRMutationAnalysisTestOrder)panelSetOrderCollection.GetPanelSetOrder(egfrMutationAnalysisTest.PanelSetId); interpretation.AppendLine("EGFR: " + egfrMutationAnalysisTestOrder.Interpretation); references.AppendLine("EGFR: " + egfrMutationAnalysisTestOrder.ReportReferences); method.AppendLine("EGFR: " + egfrMutationAnalysisTestOrder.Method); this.m_EGFRMutationAnalysisResult = egfrMutationAnalysisTestOrder.Result; this.m_EGFRMutationAnalysisComment = egfrMutationAnalysisTestOrder.Comment; } if (panelSetOrderCollection.Exists(alkTest.PanelSetId) == true) { Test.ALKForNSCLCByFISH.ALKForNSCLCByFISHTestOrder alkTestOrder = (ALKForNSCLCByFISH.ALKForNSCLCByFISHTestOrder)panelSetOrderCollection.GetPanelSetOrder(alkTest.PanelSetId); references.AppendLine(); references.AppendLine("ALK: " + alkTestOrder.ReportReferences); interpretation.AppendLine(); interpretation.AppendLine("ALK: " + alkTestOrder.Interpretation); method.AppendLine(); method.AppendLine("ALK: " + alkTestOrder.Method); this.m_ALKForNSCLCByFISHResult = alkTestOrder.Result; } else if (panelSetOrderCollection.Exists(panelSetALKRetired.PanelSetId) == true) { YellowstonePathology.Business.Test.ALKForNSCLCByFISH.ALKForNSCLCByFISHTestOrderReportedSeparately alkForNSCLCByFISHTestOrderReportedSeparately = new YellowstonePathology.Business.Test.ALKForNSCLCByFISH.ALKForNSCLCByFISHTestOrderReportedSeparately(); this.m_ALKForNSCLCByFISHResult = alkForNSCLCByFISHTestOrderReportedSeparately.Result; } if (panelSetOrderCollection.Exists(ros1ByfishTest.PanelSetId) == true) { Test.ROS1ByFISH.ROS1ByFISHTestOrder ros1ByFISHTestOrder = (ROS1ByFISH.ROS1ByFISHTestOrder)panelSetOrderCollection.GetPanelSetOrder(ros1ByfishTest.PanelSetId); interpretation.AppendLine(); interpretation.AppendLine("ROS1: " + ros1ByFISHTestOrder.Interpretation); method.AppendLine(); method.AppendLine("ROS1: " + ros1ByFISHTestOrder.Method); this.m_ROS1ByFISHResult = ros1ByFISHTestOrder.Result; } if (panelSetOrderCollection.Exists(pdl1SP142Test.PanelSetId) == true) { Test.PDL1SP142.PDL1SP142TestOrder pdl1SP142TestOrder = (PDL1SP142.PDL1SP142TestOrder)panelSetOrderCollection.GetPanelSetOrder(pdl1SP142Test.PanelSetId); interpretation.AppendLine(); interpretation.AppendLine(pdl1SP142TestOrder.PanelSetName + ": " + pdl1SP142TestOrder.Interpretation); method.AppendLine(); method.AppendLine(pdl1SP142TestOrder.PanelSetName + ": " + pdl1SP142TestOrder.Method); this.m_PDL1SP142Result = pdl1SP142TestOrder.Result; this.m_PDL1SP142StainPercent = pdl1SP142TestOrder.StainPercent; } if (panelSetOrderCollection.Exists(pdl122C3Test.PanelSetId) == true) { Test.PDL122C3.PDL122C3TestOrder pdl122C3TestOrder = (PDL122C3.PDL122C3TestOrder)panelSetOrderCollection.GetPanelSetOrder(pdl122C3Test.PanelSetId); interpretation.AppendLine(); interpretation.AppendLine(pdl122C3TestOrder.PanelSetName + ": " + pdl122C3TestOrder.Interpretation); method.AppendLine(); method.AppendLine(pdl122C3TestOrder.PanelSetName + ": " + pdl122C3TestOrder.Method); this.m_PDL122C3Result = pdl122C3TestOrder.Result; } if (panelSetOrderCollection.Exists(brafTest.PanelSetId) == true) { Test.BRAFMutationAnalysis.BRAFMutationAnalysisTestOrder brafTestOrder = (BRAFMutationAnalysis.BRAFMutationAnalysisTestOrder)panelSetOrderCollection.GetPanelSetOrder(brafTest.PanelSetId); interpretation.AppendLine(); interpretation.AppendLine(brafTestOrder.PanelSetName + ": " + brafTestOrder.Interpretation); method.AppendLine(); method.AppendLine(brafTestOrder.PanelSetName + ": " + brafTestOrder.Method); this.m_BRAFMutationAnalysisResult = brafTestOrder.Result; } char[] lineFeedCharacters = { '\r', '\n' }; this.Interpretation = interpretation.ToString().TrimEnd(lineFeedCharacters); this.Method = method.ToString().TrimEnd(lineFeedCharacters); this.ReportReferences = references.ToString().TrimEnd(lineFeedCharacters); this.NotifyPropertyChanged(string.Empty); }
public HER2AmplificationResultGroup5Breast(PanelSetOrderCollection panelSetOrderCollection, HER2AmplificationByISHTestOrder panelSetOrder) : base(panelSetOrderCollection, panelSetOrder) { }
public virtual void Walk(PanelSetOrderCollection panelSetOrderCollection, ReflexTestingPlan reflexTestingPlan) { throw new Exception("Not implemented here."); }
public virtual void SetStatus(PanelSetOrderCollection panelSetOrderCollection) { throw new Exception("Not implemented here."); }
public HER2AmplificationResultBreast(PanelSetOrderCollection panelSetOrderCollection, HER2AnalysisSummary.HER2AnalysisSummaryTestOrder panelSetOrder) : base(panelSetOrderCollection, panelSetOrder) { this.m_ReportReference = "Wolff AC, Hammond MEH, Hicks DG, et al. Recommendations for Human Epidermal Growth Factor Receptor 2 Testing in " + "Breast Cancer. Arch Pathol Lab Med. doi: 10.5858/arpa.2013-0953-SA."; }
public HER2AmplificationResultCollection(PanelSetOrderCollection panelSetOrderCollection, HER2AnalysisSummary.HER2AnalysisSummaryTestOrder panelSetOrder) { this.Add(new HER2AmplificationResultGroup2Breast(panelSetOrderCollection, panelSetOrder)); this.Add(new HER2AmplificationResultGroup3Breast(panelSetOrderCollection, panelSetOrder)); this.Add(new HER2AmplificationResultGroup4Breast(panelSetOrderCollection, panelSetOrder)); }