diff --git a/src/main/java/org/cbioportal/persistence/StudyViewRepository.java b/src/main/java/org/cbioportal/persistence/StudyViewRepository.java
index 3888850473c..a05f09da29c 100644
--- a/src/main/java/org/cbioportal/persistence/StudyViewRepository.java
+++ b/src/main/java/org/cbioportal/persistence/StudyViewRepository.java
@@ -54,15 +54,15 @@ public interface StudyViewRepository {
     
     int getSampleProfileCountWithoutPanelData(StudyViewFilter studyViewFilter, String alterationType, List<CustomSampleIdentifier> customDataSamples);
     
-    List<ClinicalEventTypeCount> getClinicalEventTypeCounts(StudyViewFilter studyViewFilter);
+    List<ClinicalEventTypeCount> getClinicalEventTypeCounts(StudyViewFilter studyViewFilter, List<CustomSampleIdentifier> customDataSamples);
     
-    List<PatientTreatment> getPatientTreatments(StudyViewFilter studyViewFilter);
+    List<PatientTreatment> getPatientTreatments(StudyViewFilter studyViewFilter, List<CustomSampleIdentifier> customDataSamples);
 
-    int getTotalPatientTreatmentCount(StudyViewFilter studyViewFilter);
+    int getTotalPatientTreatmentCount(StudyViewFilter studyViewFilter, List<CustomSampleIdentifier> customDataSamples);
     
-    List<SampleTreatment> getSampleTreatments(StudyViewFilter studyViewFilter);
+    List<SampleTreatment> getSampleTreatments(StudyViewFilter studyViewFilter, List<CustomSampleIdentifier> customDataSamples);
 
-    int getTotalSampleTreatmentCount(StudyViewFilter studyViewFilter);
+    int getTotalSampleTreatmentCount(StudyViewFilter studyViewFilter, List<CustomSampleIdentifier> customDataSamples);
 
     List<GenomicDataCountItem> getCNACounts(StudyViewFilter studyViewFilter, List<GenomicDataFilter> genomicDataFilters);
 
diff --git a/src/main/java/org/cbioportal/persistence/mybatisclickhouse/StudyViewMapper.java b/src/main/java/org/cbioportal/persistence/mybatisclickhouse/StudyViewMapper.java
index 117ce7dcf7e..e0aec7ca2c2 100644
--- a/src/main/java/org/cbioportal/persistence/mybatisclickhouse/StudyViewMapper.java
+++ b/src/main/java/org/cbioportal/persistence/mybatisclickhouse/StudyViewMapper.java
@@ -59,12 +59,12 @@ List<ClinicalDataCount> getClinicalDataCounts(StudyViewFilter studyViewFilter, C
     
     int getSampleProfileCountWithoutPanelData(StudyViewFilter studyViewFilter, CategorizedClinicalDataCountFilter categorizedClinicalDataCountFilter, boolean applyPatientIdFilters, String alterationType, List<CustomSampleIdentifier> customDataSamples);
 
-    List<ClinicalEventTypeCount> getClinicalEventTypeCounts(StudyViewFilter studyViewFilter, CategorizedClinicalDataCountFilter categorizedClinicalDataCountFilter, boolean applyPatientIdFilters);
+    List<ClinicalEventTypeCount> getClinicalEventTypeCounts(StudyViewFilter studyViewFilter, CategorizedClinicalDataCountFilter categorizedClinicalDataCountFilter, boolean applyPatientIdFilters, List<CustomSampleIdentifier> customDataSamples);
     
-    List<PatientTreatment> getPatientTreatments(StudyViewFilter studyViewFilter, CategorizedClinicalDataCountFilter categorizedClinicalDataCountFilter, boolean applyPatientIdFilters);
-    int getPatientTreatmentCounts(StudyViewFilter studyViewFilter, CategorizedClinicalDataCountFilter categorizedClinicalDataCountFilter, boolean applyPatientIdFilters);
-    List<SampleTreatment> getSampleTreatmentCounts(StudyViewFilter studyViewFilter, CategorizedClinicalDataCountFilter categorizedClinicalDataCountFilter, boolean applyPatientIdFilters);
-    int getTotalSampleTreatmentCounts(StudyViewFilter studyViewFilter, CategorizedClinicalDataCountFilter categorizedClinicalDataCountFilter, boolean applyPatientIdFilters);
+    List<PatientTreatment> getPatientTreatments(StudyViewFilter studyViewFilter, CategorizedClinicalDataCountFilter categorizedClinicalDataCountFilter, boolean applyPatientIdFilters, List<CustomSampleIdentifier> customDataSamples);
+    int getPatientTreatmentCounts(StudyViewFilter studyViewFilter, CategorizedClinicalDataCountFilter categorizedClinicalDataCountFilter, boolean applyPatientIdFilters, List<CustomSampleIdentifier> customDataSamples);
+    List<SampleTreatment> getSampleTreatmentCounts(StudyViewFilter studyViewFilter, CategorizedClinicalDataCountFilter categorizedClinicalDataCountFilter, boolean applyPatientIdFilters, List<CustomSampleIdentifier> customDataSamples);
+    int getTotalSampleTreatmentCounts(StudyViewFilter studyViewFilter, CategorizedClinicalDataCountFilter categorizedClinicalDataCountFilter, boolean applyPatientIdFilters, List<CustomSampleIdentifier> customDataSamples);
 
     List<GenomicDataCountItem> getCNACounts(StudyViewFilter studyViewFilter, CategorizedClinicalDataCountFilter categorizedClinicalDataCountFilter, List<GenomicDataFilter> genomicDataFilters);
 
diff --git a/src/main/java/org/cbioportal/persistence/mybatisclickhouse/StudyViewMyBatisRepository.java b/src/main/java/org/cbioportal/persistence/mybatisclickhouse/StudyViewMyBatisRepository.java
index 8c327625d5c..14a923130a2 100644
--- a/src/main/java/org/cbioportal/persistence/mybatisclickhouse/StudyViewMyBatisRepository.java
+++ b/src/main/java/org/cbioportal/persistence/mybatisclickhouse/StudyViewMyBatisRepository.java
@@ -205,37 +205,37 @@ public int getSampleProfileCountWithoutPanelData(StudyViewFilter studyViewFilter
 
 
     @Override
-    public List<ClinicalEventTypeCount> getClinicalEventTypeCounts(StudyViewFilter studyViewFilter) {
+    public List<ClinicalEventTypeCount> getClinicalEventTypeCounts(StudyViewFilter studyViewFilter, List<CustomSampleIdentifier> customDataSamples) {
         CategorizedClinicalDataCountFilter categorizedClinicalDataCountFilter = extractClinicalDataCountFilters(studyViewFilter);
         return mapper.getClinicalEventTypeCounts(studyViewFilter, categorizedClinicalDataCountFilter,
-            shouldApplyPatientIdFilters(studyViewFilter,categorizedClinicalDataCountFilter));
+            shouldApplyPatientIdFilters(studyViewFilter,categorizedClinicalDataCountFilter), customDataSamples);
     }
 
     @Override
-    public List<PatientTreatment> getPatientTreatments(StudyViewFilter studyViewFilter) {
+    public List<PatientTreatment> getPatientTreatments(StudyViewFilter studyViewFilter, List<CustomSampleIdentifier> customDataSamples) {
         CategorizedClinicalDataCountFilter categorizedClinicalDataCountFilter = extractClinicalDataCountFilters(studyViewFilter);
-        return mapper.getPatientTreatments(studyViewFilter, categorizedClinicalDataCountFilter, shouldApplyPatientIdFilters(studyViewFilter, categorizedClinicalDataCountFilter));
+        return mapper.getPatientTreatments(studyViewFilter, categorizedClinicalDataCountFilter, shouldApplyPatientIdFilters(studyViewFilter, categorizedClinicalDataCountFilter), customDataSamples);
     }
     
     @Override
-    public int getTotalPatientTreatmentCount(StudyViewFilter studyViewFilter) {
+    public int getTotalPatientTreatmentCount(StudyViewFilter studyViewFilter, List<CustomSampleIdentifier> customDataSamples) {
         CategorizedClinicalDataCountFilter categorizedClinicalDataCountFilter = extractClinicalDataCountFilters(studyViewFilter);
        return mapper.getPatientTreatmentCounts(studyViewFilter, categorizedClinicalDataCountFilter, 
-            shouldApplyPatientIdFilters(studyViewFilter, categorizedClinicalDataCountFilter));
+            shouldApplyPatientIdFilters(studyViewFilter, categorizedClinicalDataCountFilter), customDataSamples);
     }
 
     @Override
-    public List<SampleTreatment> getSampleTreatments(StudyViewFilter studyViewFilter) {
+    public List<SampleTreatment> getSampleTreatments(StudyViewFilter studyViewFilter, List<CustomSampleIdentifier> customDataSamples) {
         CategorizedClinicalDataCountFilter categorizedClinicalDataCountFilter = extractClinicalDataCountFilters(studyViewFilter);
         return mapper.getSampleTreatmentCounts(studyViewFilter, categorizedClinicalDataCountFilter,
-            shouldApplyPatientIdFilters(studyViewFilter, categorizedClinicalDataCountFilter));
+            shouldApplyPatientIdFilters(studyViewFilter, categorizedClinicalDataCountFilter), customDataSamples);
     }
 
     @Override
-    public int getTotalSampleTreatmentCount(StudyViewFilter studyViewFilter) {
+    public int getTotalSampleTreatmentCount(StudyViewFilter studyViewFilter, List<CustomSampleIdentifier> customDataSamples) {
         CategorizedClinicalDataCountFilter categorizedClinicalDataCountFilter = extractClinicalDataCountFilters(studyViewFilter);
         return mapper.getTotalSampleTreatmentCounts(studyViewFilter, categorizedClinicalDataCountFilter,
-            shouldApplyPatientIdFilters(studyViewFilter, categorizedClinicalDataCountFilter));
+            shouldApplyPatientIdFilters(studyViewFilter, categorizedClinicalDataCountFilter), customDataSamples);
     }
 
     private void buildClinicalAttributeNameMap() {
diff --git a/src/main/java/org/cbioportal/service/impl/StudyViewColumnarServiceImpl.java b/src/main/java/org/cbioportal/service/impl/StudyViewColumnarServiceImpl.java
index d70c3b218ae..57b6d546aa2 100644
--- a/src/main/java/org/cbioportal/service/impl/StudyViewColumnarServiceImpl.java
+++ b/src/main/java/org/cbioportal/service/impl/StudyViewColumnarServiceImpl.java
@@ -71,17 +71,20 @@ public List<GenomicDataCount> getMolecularProfileSampleCounts(StudyViewFilter st
 
     @Override
     public List<ClinicalEventTypeCount> getClinicalEventTypeCounts(StudyViewFilter studyViewFilter) {
-        return studyViewRepository.getClinicalEventTypeCounts(studyViewFilter);
+        List<CustomSampleIdentifier> customDataSamples = customDataFilterUtil.extractCustomDataSamples(studyViewFilter);
+        return studyViewRepository.getClinicalEventTypeCounts(studyViewFilter, customDataSamples);
     }
 
     @Override
     public PatientTreatmentReport getPatientTreatmentReport(StudyViewFilter studyViewFilter) {
-        return treatmentCountReportService.getPatientTreatmentReport(studyViewFilter);
+        List<CustomSampleIdentifier> customDataSamples = customDataFilterUtil.extractCustomDataSamples(studyViewFilter);
+        return treatmentCountReportService.getPatientTreatmentReport(studyViewFilter, customDataSamples);
     }
 
     @Override
     public SampleTreatmentReport getSampleTreatmentReport(StudyViewFilter studyViewFilter) {
-        return treatmentCountReportService.getSampleTreatmentReport(studyViewFilter);
+        List<CustomSampleIdentifier> customDataSamples = customDataFilterUtil.extractCustomDataSamples(studyViewFilter);
+        return treatmentCountReportService.getSampleTreatmentReport(studyViewFilter, customDataSamples);
     }
 
     public List<CopyNumberCountByGene> getCnaGenes(StudyViewFilter studyViewFilter) {
diff --git a/src/main/java/org/cbioportal/service/treatment/TreatmentCountReportService.java b/src/main/java/org/cbioportal/service/treatment/TreatmentCountReportService.java
index 5c275fefc26..27e3c8a210c 100644
--- a/src/main/java/org/cbioportal/service/treatment/TreatmentCountReportService.java
+++ b/src/main/java/org/cbioportal/service/treatment/TreatmentCountReportService.java
@@ -2,9 +2,12 @@
 
 import org.cbioportal.model.PatientTreatmentReport;
 import org.cbioportal.model.SampleTreatmentReport;
+import org.cbioportal.web.parameter.CustomSampleIdentifier;
 import org.cbioportal.web.parameter.StudyViewFilter;
 
+import java.util.List;
+
 public interface TreatmentCountReportService {
-    PatientTreatmentReport getPatientTreatmentReport(StudyViewFilter studyViewFilter);
-    SampleTreatmentReport getSampleTreatmentReport(StudyViewFilter studyViewFilter);
+    PatientTreatmentReport getPatientTreatmentReport(StudyViewFilter studyViewFilter, List<CustomSampleIdentifier> customDataSamples);
+    SampleTreatmentReport getSampleTreatmentReport(StudyViewFilter studyViewFilter, List<CustomSampleIdentifier> customDataSamples);
 }
diff --git a/src/main/java/org/cbioportal/service/treatment/TreatmentCountReportServiceImpl.java b/src/main/java/org/cbioportal/service/treatment/TreatmentCountReportServiceImpl.java
index 8af2139a814..0820cefdadf 100644
--- a/src/main/java/org/cbioportal/service/treatment/TreatmentCountReportServiceImpl.java
+++ b/src/main/java/org/cbioportal/service/treatment/TreatmentCountReportServiceImpl.java
@@ -5,10 +5,12 @@
 import org.cbioportal.model.SampleTreatmentRow;
 import org.cbioportal.model.TemporalRelation;
 import org.cbioportal.persistence.StudyViewRepository;
+import org.cbioportal.web.parameter.CustomSampleIdentifier;
 import org.cbioportal.web.parameter.StudyViewFilter;
 import org.springframework.beans.factory.annotation.Autowired;
 import org.springframework.stereotype.Service;
 
+import java.util.List;
 import java.util.Set;
 import java.util.stream.Stream;
 
@@ -23,22 +25,22 @@ public TreatmentCountReportServiceImpl(StudyViewRepository studyViewRepository)
     }
 
     @Override
-    public PatientTreatmentReport getPatientTreatmentReport(StudyViewFilter studyViewFilter) {
-        var patientTreatments = studyViewRepository.getPatientTreatments(studyViewFilter);
-        var totalPatientTreatmentCount = studyViewRepository.getTotalPatientTreatmentCount(studyViewFilter);
+    public PatientTreatmentReport getPatientTreatmentReport(StudyViewFilter studyViewFilter, List<CustomSampleIdentifier> customDataSamples) {
+        var patientTreatments = studyViewRepository.getPatientTreatments(studyViewFilter, customDataSamples);
+        var totalPatientTreatmentCount = studyViewRepository.getTotalPatientTreatmentCount(studyViewFilter, customDataSamples);
         return new PatientTreatmentReport(totalPatientTreatmentCount, 0, patientTreatments);
     }
 
     @Override
-    public SampleTreatmentReport getSampleTreatmentReport(StudyViewFilter studyViewFilter) {
-        var sampleTreatments = studyViewRepository.getSampleTreatments(studyViewFilter)
+    public SampleTreatmentReport getSampleTreatmentReport(StudyViewFilter studyViewFilter, List<CustomSampleIdentifier> customDataSamples) {
+        var sampleTreatments = studyViewRepository.getSampleTreatments(studyViewFilter, customDataSamples)
             .stream()
             .flatMap(sampleTreatment -> 
                 Stream.of(new SampleTreatmentRow(TemporalRelation.Pre, sampleTreatment.treatment(), sampleTreatment.preSampleCount(), Set.of()),
                     new SampleTreatmentRow(TemporalRelation.Post, sampleTreatment.treatment(), sampleTreatment.postSampleCount(), Set.of() ))
                     )
             .toList();
-        var totalSampleTreatmentCount = studyViewRepository.getTotalSampleTreatmentCount(studyViewFilter);
+        var totalSampleTreatmentCount = studyViewRepository.getTotalSampleTreatmentCount(studyViewFilter, customDataSamples);
         return new SampleTreatmentReport(totalSampleTreatmentCount, sampleTreatments);
     }
     
diff --git a/src/test/java/org/cbioportal/persistence/mybatisclickhouse/StudyViewMapperTest.java b/src/test/java/org/cbioportal/persistence/mybatisclickhouse/StudyViewMapperTest.java
index 7159eb8c38b..73cea7c75c3 100644
--- a/src/test/java/org/cbioportal/persistence/mybatisclickhouse/StudyViewMapperTest.java
+++ b/src/test/java/org/cbioportal/persistence/mybatisclickhouse/StudyViewMapperTest.java
@@ -135,7 +135,7 @@ public void getClinicalEventTypeCounts() {
        studyViewFilter.setStudyIds(List.of(STUDY_TCGA_PUB));
 
        var clinicalEventTypeCounts = studyViewMapper.getClinicalEventTypeCounts(studyViewFilter,
-           CategorizedClinicalDataCountFilter.getBuilder().build(), false);
+           CategorizedClinicalDataCountFilter.getBuilder().build(), false, null);
 
        assertEquals(4, clinicalEventTypeCounts.size());
        
@@ -152,7 +152,7 @@ public void getClinicalEventTypeCounts() {
        studyViewFilter.setClinicalEventFilters(List.of(dataFilter));
 
        clinicalEventTypeCounts = studyViewMapper.getClinicalEventTypeCounts(studyViewFilter,
-           CategorizedClinicalDataCountFilter.getBuilder().build(), true);
+           CategorizedClinicalDataCountFilter.getBuilder().build(), true, null);
        
        assertEquals(3, clinicalEventTypeCounts.size());
        
@@ -169,10 +169,10 @@ public void getPatientTreatmentReportCounts() {
        
        
        var patientTreatmentCounts = studyViewMapper.getPatientTreatmentCounts(studyViewFilter,
-           CategorizedClinicalDataCountFilter.getBuilder().build(), false );
+           CategorizedClinicalDataCountFilter.getBuilder().build(), false, null );
        
        var patientTreatments = studyViewMapper.getPatientTreatments(studyViewFilter,
-           CategorizedClinicalDataCountFilter.getBuilder().build(), false );
+           CategorizedClinicalDataCountFilter.getBuilder().build(), false, null );
        
        assertEquals(1, patientTreatmentCounts);
        assertEquals("madeupanib", patientTreatments.getFirst().treatment());
@@ -188,10 +188,10 @@ public void getPatientTreatmentReportCounts() {
        studyViewFilter.setPatientTreatmentFilters(andedPatientTreatmentFilters);
 
        patientTreatmentCounts = studyViewMapper.getPatientTreatmentCounts(studyViewFilter,
-           CategorizedClinicalDataCountFilter.getBuilder().build(), true );
+           CategorizedClinicalDataCountFilter.getBuilder().build(), true, null );
 
        patientTreatments = studyViewMapper.getPatientTreatments(studyViewFilter,
-           CategorizedClinicalDataCountFilter.getBuilder().build(), true );
+           CategorizedClinicalDataCountFilter.getBuilder().build(), true, null );
 
        assertEquals(1, patientTreatmentCounts);
        assertEquals("madeupanib", patientTreatments.getFirst().treatment());
@@ -205,10 +205,10 @@ public void getSampleTreatmentCounts() {
 
 
         var totalSampleTreatmentCount = studyViewMapper.getTotalSampleTreatmentCounts(studyViewFilter,
-            CategorizedClinicalDataCountFilter.getBuilder().build(), false );
+            CategorizedClinicalDataCountFilter.getBuilder().build(), false, null );
 
         var sampleTreatmentCounts = studyViewMapper.getSampleTreatmentCounts(studyViewFilter,
-            CategorizedClinicalDataCountFilter.getBuilder().build(), false );
+            CategorizedClinicalDataCountFilter.getBuilder().build(), false, null );
 
         assertEquals(1, totalSampleTreatmentCount);
         assertEquals("madeupanib", sampleTreatmentCounts.getFirst().treatment());
@@ -227,10 +227,10 @@ public void getSampleTreatmentCounts() {
         studyViewFilter.setSampleTreatmentFilters(andedSampleTreatmentFilters);
 
         totalSampleTreatmentCount = studyViewMapper.getTotalSampleTreatmentCounts(studyViewFilter,
-            CategorizedClinicalDataCountFilter.getBuilder().build(), false );
+            CategorizedClinicalDataCountFilter.getBuilder().build(), false, null );
 
         sampleTreatmentCounts = studyViewMapper.getSampleTreatmentCounts(studyViewFilter,
-            CategorizedClinicalDataCountFilter.getBuilder().build(), false );
+            CategorizedClinicalDataCountFilter.getBuilder().build(), false, null );
 
         assertEquals(0, totalSampleTreatmentCount);
         assertEquals(0, sampleTreatmentCounts.size());