diff --git a/src/main/java/org/cbioportal/persistence/StudyViewRepository.java b/src/main/java/org/cbioportal/persistence/StudyViewRepository.java
index 1c93f3ef57d..cc2b2629a58 100644
--- a/src/main/java/org/cbioportal/persistence/StudyViewRepository.java
+++ b/src/main/java/org/cbioportal/persistence/StudyViewRepository.java
@@ -38,7 +38,7 @@ public interface StudyViewRepository {
 
     List<CaseListDataCount> getCaseListDataCounts(StudyViewFilter studyViewFilter);
 
-    Map<String, AlterationCountByGene> getTotalProfiledCounts(StudyViewFilter studyViewFilter, String alterationType);
+    Map<String, Integer> getTotalProfiledCounts(StudyViewFilter studyViewFilter, String alterationType);
     
     int getFilteredSamplesCount(StudyViewFilter studyViewFilter);
     
@@ -46,5 +46,7 @@ public interface StudyViewRepository {
     
     int getTotalProfiledCountsByAlterationType(StudyViewFilter studyViewFilter, String alterationType);
     
+    int getSampleProfileCountWithoutPanelData(StudyViewFilter studyViewFilter, String alterationType);
+    
     List<ClinicalEventTypeCount> getClinicalEventTypeCounts(StudyViewFilter studyViewFilter);
 }
diff --git a/src/main/java/org/cbioportal/persistence/mybatisclickhouse/StudyViewMapper.java b/src/main/java/org/cbioportal/persistence/mybatisclickhouse/StudyViewMapper.java
index 0e762a1d07a..a249333641e 100644
--- a/src/main/java/org/cbioportal/persistence/mybatisclickhouse/StudyViewMapper.java
+++ b/src/main/java/org/cbioportal/persistence/mybatisclickhouse/StudyViewMapper.java
@@ -44,14 +44,15 @@ List<ClinicalDataCount> getClinicalDataCounts(StudyViewFilter studyViewFilter, C
     
     List<ClinicalData> getPatientClinicalDataFromStudyViewFilter(StudyViewFilter studyViewFilter, CategorizedClinicalDataCountFilter categorizedClinicalDataCountFilter, boolean applyPatientIdFilters, List<String> attributeIds);
     
-    @MapKey("hugoGeneSymbol")
-    Map<String, AlterationCountByGene> getTotalProfiledCounts(StudyViewFilter studyViewFilter, CategorizedClinicalDataCountFilter categorizedClinicalDataCountFilter, boolean applyPatientIdFilters, String alterationType);
+    List<AlterationCountByGene> getTotalProfiledCounts(StudyViewFilter studyViewFilter, CategorizedClinicalDataCountFilter categorizedClinicalDataCountFilter, boolean applyPatientIdFilters, String alterationType);
     
     int getFilteredSamplesCount(StudyViewFilter studyViewFilter, CategorizedClinicalDataCountFilter categorizedClinicalDataCountFilter, boolean applyPatientIdFilters);
     
     List<GenePanelToGene> getMatchingGenePanelIds(StudyViewFilter studyViewFilter, CategorizedClinicalDataCountFilter categorizedClinicalDataCountFilter, boolean applyPatientIdFilters, String alterationType);
     
     int getTotalProfiledCountByAlterationType(StudyViewFilter studyViewFilter, CategorizedClinicalDataCountFilter categorizedClinicalDataCountFilter, boolean applyPatientIdFilters, String alterationType);
+    
+    int getSampleProfileCountWithoutPanelData(StudyViewFilter studyViewFilter, CategorizedClinicalDataCountFilter categorizedClinicalDataCountFilter, boolean applyPatientIdFilters, String alterationType);
 
     List<ClinicalEventTypeCount> getClinicalEventTypeCounts(StudyViewFilter studyViewFilter, CategorizedClinicalDataCountFilter categorizedClinicalDataCountFilter, boolean applyPatientIdFilters);
 }
diff --git a/src/main/java/org/cbioportal/persistence/mybatisclickhouse/StudyViewMyBatisRepository.java b/src/main/java/org/cbioportal/persistence/mybatisclickhouse/StudyViewMyBatisRepository.java
index a0709db0e78..1690ba82a8b 100644
--- a/src/main/java/org/cbioportal/persistence/mybatisclickhouse/StudyViewMyBatisRepository.java
+++ b/src/main/java/org/cbioportal/persistence/mybatisclickhouse/StudyViewMyBatisRepository.java
@@ -132,10 +132,13 @@ public List<ClinicalData> getPatientClinicalData(StudyViewFilter studyViewFilter
     }
     
     @Override
-    public Map<String, AlterationCountByGene> getTotalProfiledCounts(StudyViewFilter studyViewFilter, String alterationType) {
+    public Map<String, Integer> getTotalProfiledCounts(StudyViewFilter studyViewFilter, String alterationType) {
         CategorizedClinicalDataCountFilter categorizedClinicalDataCountFilter = extractClinicalDataCountFilters(studyViewFilter);
         return mapper.getTotalProfiledCounts(studyViewFilter, categorizedClinicalDataCountFilter,
-            shouldApplyPatientIdFilters(studyViewFilter,categorizedClinicalDataCountFilter), alterationType);
+            shouldApplyPatientIdFilters(studyViewFilter,categorizedClinicalDataCountFilter), alterationType)
+            .stream()
+            .collect(Collectors.groupingBy(AlterationCountByGene::getHugoGeneSymbol,
+                Collectors.mapping(AlterationCountByGene::getNumberOfProfiledCases, Collectors.summingInt(Integer::intValue))));
     }
 
     @Override
@@ -162,6 +165,14 @@ public int getTotalProfiledCountsByAlterationType(StudyViewFilter studyViewFilte
            shouldApplyPatientIdFilters(studyViewFilter,categorizedClinicalDataCountFilter), alterationType); 
     }
 
+    @Override
+    public int getSampleProfileCountWithoutPanelData(StudyViewFilter studyViewFilter, String alterationType) {
+        CategorizedClinicalDataCountFilter categorizedClinicalDataCountFilter = extractClinicalDataCountFilters(studyViewFilter);
+        return mapper.getSampleProfileCountWithoutPanelData(studyViewFilter, categorizedClinicalDataCountFilter,
+            shouldApplyPatientIdFilters(studyViewFilter,categorizedClinicalDataCountFilter), alterationType);
+    }
+
+
     @Override
     public List<ClinicalEventTypeCount> getClinicalEventTypeCounts(StudyViewFilter studyViewFilter) {
         CategorizedClinicalDataCountFilter categorizedClinicalDataCountFilter = extractClinicalDataCountFilters(studyViewFilter);
diff --git a/src/main/java/org/cbioportal/service/impl/AlterationCountServiceImpl.java b/src/main/java/org/cbioportal/service/impl/AlterationCountServiceImpl.java
index 29f94f0fd0f..a8aa0dbe723 100644
--- a/src/main/java/org/cbioportal/service/impl/AlterationCountServiceImpl.java
+++ b/src/main/java/org/cbioportal/service/impl/AlterationCountServiceImpl.java
@@ -273,37 +273,28 @@ public List<AlterationCountByGene> getStructuralVariantGenes(StudyViewFilter stu
     private < T extends AlterationCountByGene> List<T> populateAlterationCounts(@NonNull List<T> alterationCounts,
                                                                                 @NonNull StudyViewFilter studyViewFilter,
                                                                                 @NonNull AlterationType alterationType) {
-        var updatedAlterationCounts = alterationCounts.stream().map(SerializationUtils::clone).toList();
-        var profiledCountsMap = studyViewRepository.getTotalProfiledCounts(studyViewFilter,
-            alterationType.toString());
-        var profiledCountWithoutGenePanelData = studyViewRepository.getTotalProfiledCountsByAlterationType(studyViewFilter, alterationType.toString());
-        var matchingGenePanelIdsMap = studyViewRepository.getMatchingGenePanelIds(studyViewFilter, alterationType.toString());
+        final int profiledCountWithoutGenePanelData = studyViewRepository.getTotalProfiledCountsByAlterationType(studyViewFilter, alterationType.toString());
+        var profiledCountsMap = studyViewRepository.getTotalProfiledCounts(studyViewFilter, alterationType.toString());
+        final var matchingGenePanelIdsMap = studyViewRepository.getMatchingGenePanelIds(studyViewFilter, alterationType.toString());
+        final int sampleProfileCountWithoutGenePanelData = studyViewRepository.getSampleProfileCountWithoutPanelData(studyViewFilter, alterationType.toString());
 
-        updatedAlterationCounts.parallelStream()
+        alterationCounts.parallelStream()
             .forEach(alterationCountByGene ->  {
                 String hugoGeneSymbol = alterationCountByGene.getHugoGeneSymbol();
                 Set<String> matchingGenePanelIds = matchingGenePanelIdsMap.get(hugoGeneSymbol) != null ?
                     matchingGenePanelIdsMap.get(hugoGeneSymbol) : Collections.emptySet();
-
-                int totalProfiledCount = getTotalProfiledCount(hugoGeneSymbol,
-                    profiledCountsMap, profiledCountWithoutGenePanelData, matchingGenePanelIds);
+                
+                int totalProfiledCount = hasGenePanelData(matchingGenePanelIds) 
+                    ? profiledCountsMap.getOrDefault(hugoGeneSymbol, 0) + sampleProfileCountWithoutGenePanelData
+                    : profiledCountWithoutGenePanelData;
 
                 alterationCountByGene.setNumberOfProfiledCases(totalProfiledCount);
 
                 alterationCountByGene.setMatchingGenePanelIds(matchingGenePanelIds);
             }); 
-        return updatedAlterationCounts;
+        return alterationCounts;
     }
 
-    private int getTotalProfiledCount(@NonNull String hugoGeneSymbol, @NonNull Map<String, AlterationCountByGene> profiledCountsMap,
-                                      int profiledCountWithoutGenePanelData, @NonNull Set<String> matchingGenePanelIds) {
-        int totalProfiledCount = profiledCountWithoutGenePanelData;
-        
-        if (hasGenePanelData(matchingGenePanelIds) && profiledCountsMap.containsKey(hugoGeneSymbol)) {
-                totalProfiledCount  = profiledCountsMap.get(hugoGeneSymbol).getNumberOfProfiledCases();
-        }
-        return totalProfiledCount;
-    }
     
     private boolean hasGenePanelData(@NonNull Set<String> matchingGenePanelIds) {
         return matchingGenePanelIds.contains(WHOLE_EXOME_SEQUENCING) 
diff --git a/src/main/resources/db-scripts/clickhouse/clickhouse.sql b/src/main/resources/db-scripts/clickhouse/clickhouse.sql
index 5cad1670464..3c4b42cbc1f 100644
--- a/src/main/resources/db-scripts/clickhouse/clickhouse.sql
+++ b/src/main/resources/db-scripts/clickhouse/clickhouse.sql
@@ -47,7 +47,7 @@ SELECT
     'WES' AS gene_panel_id,
     gene.hugo_gene_symbol AS gene
 FROM gene
-WHERE gene.entrez_gene_id > 0;
+WHERE gene.entrez_gene_id > 0 AND gene.type = 'protein-coding';
 
 CREATE TABLE sample_derived
 (
diff --git a/src/main/resources/org/cbioportal/persistence/mybatisclickhouse/StudyViewMapper.xml b/src/main/resources/org/cbioportal/persistence/mybatisclickhouse/StudyViewMapper.xml
index 576c5b7378b..e4e226be8c2 100644
--- a/src/main/resources/org/cbioportal/persistence/mybatisclickhouse/StudyViewMapper.xml
+++ b/src/main/resources/org/cbioportal/persistence/mybatisclickhouse/StudyViewMapper.xml
@@ -232,15 +232,22 @@
         JOIN cancer_study cs on cs.cancer_study_id = cam.cancer_study_id
     </select>
 
-    <!-- Grab Total Profiled Counts -->
-    <select id="getTotalProfiledCounts">
-        SELECT
+    <!-- Grab Total Profiled Counts. Currently, this query filters out all samples associated with a Gene Panel WES before
+    doing a join on gene_panel_to_gene_derived table. This is to prevent unnecessary stress on the db. For every sample
+    associated with a gene panel WES we multiply that row by the number of genes in the gene table. This could be greater
+    than 20K genes. This can create a huge join table that can slow down CH tremendously. 
+    We compute the WES counts by using the query getSampleProfileCountWithoutPanelData and adding this value to the 
+    totalProfiled Count per gene in java.
+     -->
+    <select id="getTotalProfiledCounts" resultType="org.cbioportal.model.AlterationCountByGene">
+        SELECT 
         gene as hugoGeneSymbol,
         COUNT(*) as numberOfProfiledCases
         FROM sample_to_gene_panel_derived stgp
             INNER JOIN gene_panel_to_gene_derived gptg on stgp.gene_panel_id = gptg.gene_panel_id 
         <where>
-            stgp.alteration_type = '${alterationType}' 
+            stgp.alteration_type = '${alterationType}'
+            AND stgp.gene_panel_id != 'WES'
             AND
             <include refid="applyStudyViewFilter">
                 <property name="filter_type" value="'SAMPLE_ID_ONLY'"/>
@@ -248,7 +255,18 @@
         </where>
         GROUP BY gptg.gene;
     </select>
-
+    
+    <select id="getSampleProfileCountWithoutPanelData" resultType="int">
+       SELECT COUNT(*)
+        FROM sample_to_gene_panel_derived
+        <where>
+            alteration_type = '${alterationType}' AND gene_panel_id = 'WES'
+            AND
+            <include refid="applyStudyViewFilter">
+                <property name="filter_type" value="'SAMPLE_ID_ONLY'"/>
+            </include>
+        </where>
+    </select>
     <!-- Helper query to get counts for totalProfiledCount when no genePanel data is available. 
     When no genePanel data is available we assume the whole genome was sequenced AKA WES (Whole Exome Sequencing). If this 
     is the case we use the current sample count from the cohort as the totalProfiledCount -->
diff --git a/src/test/java/org/cbioportal/persistence/mybatisclickhouse/StudyViewMapperTest.java b/src/test/java/org/cbioportal/persistence/mybatisclickhouse/StudyViewMapperTest.java
index f8019f72e54..0a6279ae937 100644
--- a/src/test/java/org/cbioportal/persistence/mybatisclickhouse/StudyViewMapperTest.java
+++ b/src/test/java/org/cbioportal/persistence/mybatisclickhouse/StudyViewMapperTest.java
@@ -114,8 +114,9 @@ public void getTotalProfiledCountsByGene() {
        
        assertEquals(3, totalProfiledCountsMap.size());
        
-       var akt2TotalProfiledCounts = totalProfiledCountsMap.get("akt2");
-       assertEquals(4, akt2TotalProfiledCounts.getNumberOfProfiledCases().intValue());
+       var akt2TotalProfiledCounts = totalProfiledCountsMap.stream().filter(c -> c.getHugoGeneSymbol().equals("akt2")).findFirst();
+       assertTrue(akt2TotalProfiledCounts.isPresent());
+       assertEquals(4, akt2TotalProfiledCounts.get().getNumberOfProfiledCases().intValue());
    } 
    
    @Test