diff --git a/src/main/java/org/cbioportal/persistence/helper/StudyViewFilterHelper.java b/src/main/java/org/cbioportal/persistence/helper/StudyViewFilterHelper.java
index d10d85d98c4..2a06b059d42 100644
--- a/src/main/java/org/cbioportal/persistence/helper/StudyViewFilterHelper.java
+++ b/src/main/java/org/cbioportal/persistence/helper/StudyViewFilterHelper.java
@@ -63,11 +63,7 @@ private CategorizedGenericAssayDataCountFilter extractGenericAssayDataCountFilte
 
         CategorizedGenericAssayDataCountFilter.Builder builder = CategorizedGenericAssayDataCountFilter.getBuilder();
 
-        // TODO: Support patient level profiles and data filtering
-        List<String> sampleCategoricalProfileTypes = genericAssayProfilesMap.get(DataSource.SAMPLE)
-            .stream().filter(profile -> profile.getDatatype().equals("CATEGORICAL") || profile.getDatatype().equals("BINARY"))
-            .map(profile -> profile.getStableId().replace(profile.getCancerStudyIdentifier() + "_", ""))
-            .toList();
+        // TODO: Support data filtering
         List<String> sampleNumericalProfileTypes = genericAssayProfilesMap.get(DataSource.SAMPLE)
             .stream().filter(profile -> profile.getDatatype().equals("LIMIT-VALUE"))
             .map(profile -> profile.getStableId().replace(profile.getCancerStudyIdentifier() + "_", ""))
@@ -75,9 +71,21 @@ private CategorizedGenericAssayDataCountFilter extractGenericAssayDataCountFilte
         builder.setSampleNumericalGenericAssayDataFilters(studyViewFilter.getGenericAssayDataFilters().stream()
             .filter(genericAssayDataFilter -> sampleNumericalProfileTypes.contains(genericAssayDataFilter.getProfileType()))
             .toList());
+        List<String> sampleCategoricalProfileTypes = genericAssayProfilesMap.get(DataSource.SAMPLE)
+            .stream().filter(profile -> profile.getDatatype().equals("CATEGORICAL") || profile.getDatatype().equals("BINARY"))
+            .map(profile -> profile.getStableId().replace(profile.getCancerStudyIdentifier() + "_", ""))
+            .toList();
         builder.setSampleCategoricalGenericAssayDataFilters(studyViewFilter.getGenericAssayDataFilters().stream()
             .filter(genericAssayDataFilter -> sampleCategoricalProfileTypes.contains(genericAssayDataFilter.getProfileType()))
             .toList());
+        // Patient level profiles only have CATEGORICAL datatype for now
+        List<String> patientCategoricalProfileTypes = genericAssayProfilesMap.get(DataSource.PATIENT)
+            .stream().filter(profile -> profile.getDatatype().equals("CATEGORICAL"))
+            .map(profile -> profile.getStableId().replace(profile.getCancerStudyIdentifier() + "_", ""))
+            .toList();
+        builder.setPatientCategoricalGenericAssayDataFilters(studyViewFilter.getGenericAssayDataFilters().stream()
+            .filter(genericAssayDataFilter -> patientCategoricalProfileTypes.contains(genericAssayDataFilter.getProfileType()))
+            .toList());
         return builder.build();
     }
 
diff --git a/src/main/resources/org/cbioportal/persistence/mybatisclickhouse/StudyViewFilterMapper.xml b/src/main/resources/org/cbioportal/persistence/mybatisclickhouse/StudyViewFilterMapper.xml
index f4388cf4260..09c20012147 100644
--- a/src/main/resources/org/cbioportal/persistence/mybatisclickhouse/StudyViewFilterMapper.xml
+++ b/src/main/resources/org/cbioportal/persistence/mybatisclickhouse/StudyViewFilterMapper.xml
@@ -138,7 +138,6 @@
                 <include refid="applySampleTreatmentFilter"/>
             </if>
             <!-- Apply Genomic Data Filter -->
-            <!-- TODO: add patient level data filtering -->
             <if test="studyViewFilterHelper.studyViewFilter.genomicDataFilters != null and !studyViewFilterHelper.studyViewFilter.genomicDataFilters.isEmpty()">
                 <foreach item="genomicDataFilter" collection="studyViewFilterHelper.studyViewFilter.genomicDataFilters" open="INTERSECT" separator="INTERSECT">
                     (
@@ -154,25 +153,9 @@
                 </foreach>
             </if>
             <!-- Apply Generic Assay Data Filter -->
-            <if test="studyViewFilterHelper.categorizedGenericAssayDataCountFilter.getSampleNumericalGenericAssayDataFilters() != null and !studyViewFilterHelper.categorizedGenericAssayDataCountFilter.getSampleNumericalGenericAssayDataFilters().isEmpty()">
-                <foreach item="genericAssayDataFilter" collection="studyViewFilterHelper.categorizedGenericAssayDataCountFilter.getSampleNumericalGenericAssayDataFilters()" open="INTERSECT" separator="INTERSECT">
-                    (
-                    <include refid="numericalGenericAssayDataFilter">
-                        <property name="unique_id" value="sample_unique_id"/>
-                        <property name="table_name" value="generic_assay_data_derived"/>
-                    </include>
-                    )
-                </foreach>
-            </if>
-            <if test="studyViewFilterHelper.categorizedGenericAssayDataCountFilter.getSampleCategoricalGenericAssayDataFilters() != null and !studyViewFilterHelper.categorizedGenericAssayDataCountFilter.getSampleCategoricalGenericAssayDataFilters().isEmpty()">
-                <foreach item="genericAssayDataFilter" collection="studyViewFilterHelper.categorizedGenericAssayDataCountFilter.getSampleCategoricalGenericAssayDataFilters()" open="INTERSECT" separator="INTERSECT">
-                    <include refid="categoricalGenericAssayDataCountFilter">
-                        <property name="unique_id" value="sample_unique_id"/>
-                        <property name="table_name" value="generic_assay_data_derived"/>
-                    </include>
-                </foreach>
-            </if>
-            
+            <if test="studyViewFilterHelper.studyViewFilter.genericAssayDataFilters != null and !studyViewFilterHelper.studyViewFilter.genericAssayDataFilters.isEmpty()">
+                <include refid="applyGenericAssayDataFilter"/>
+            </if>            
             <!-- Apply Clinical Data Filter -->
             <if test="studyViewFilterHelper.studyViewFilter.clinicalDataFilters != null and !studyViewFilterHelper.studyViewFilter.clinicalDataFilters.isEmpty()">
                 <include refid="applyClinicalDataCountFilter"/>
@@ -549,8 +532,39 @@
             </foreach>
     </sql>
 
+    <sql id="applyGenericAssayDataFilter">
+        <if test="studyViewFilterHelper.categorizedGenericAssayDataCountFilter.getSampleNumericalGenericAssayDataFilters() != null and !studyViewFilterHelper.categorizedGenericAssayDataCountFilter.getSampleNumericalGenericAssayDataFilters().isEmpty()">
+            <foreach item="genericAssayDataFilter" collection="studyViewFilterHelper.categorizedGenericAssayDataCountFilter.getSampleNumericalGenericAssayDataFilters()" open="INTERSECT" separator="INTERSECT">
+                (
+                    <include refid="numericalGenericAssayDataFilter">
+                        <property name="type" value="sample"/>
+                    </include>
+                )
+            </foreach>
+        </if>
+        <if test="studyViewFilterHelper.categorizedGenericAssayDataCountFilter.getSampleCategoricalGenericAssayDataFilters() != null and !studyViewFilterHelper.categorizedGenericAssayDataCountFilter.getSampleCategoricalGenericAssayDataFilters().isEmpty()">
+            <foreach item="genericAssayDataFilter" collection="studyViewFilterHelper.categorizedGenericAssayDataCountFilter.getSampleCategoricalGenericAssayDataFilters()" open="INTERSECT" separator="INTERSECT">
+                (
+                    <include refid="categoricalGenericAssayDataCountFilter">
+                        <property name="type" value="sample"/>
+                    </include>
+                )
+            </foreach>
+        </if>
+        -- patient level profile only have categorical for now
+        <if test="studyViewFilterHelper.categorizedGenericAssayDataCountFilter.getPatientCategoricalGenericAssayDataFilters() != null and !studyViewFilterHelper.categorizedGenericAssayDataCountFilter.getPatientCategoricalGenericAssayDataFilters().isEmpty()">
+            <foreach item="genericAssayDataFilter" collection="studyViewFilterHelper.categorizedGenericAssayDataCountFilter.getPatientCategoricalGenericAssayDataFilters()" open="INTERSECT" separator="INTERSECT">
+                (
+                    <include refid="categoricalGenericAssayDataCountFilter">
+                        <property name="type" value="patient"/>
+                    </include>
+                )
+            </foreach>
+        </if>
+    </sql>
+    
     <sql id="selectAllGenericAssays">
-        SELECT sample_unique_id, value, datatype
+        SELECT sample_unique_id, patient_unique_id, value, datatype
         FROM generic_assay_data_derived
         WHERE profile_type = #{genericAssayDataFilter.profileType}
             AND entity_stable_id = #{genericAssayDataFilter.stableId}
@@ -647,10 +661,18 @@
     </sql>
     
     <sql id="categoricalGenericAssayDataCountFilter">
-        SELECT ${unique_id}
+        SELECT sample_unique_id
         FROM sample_derived sd
-        LEFT JOIN (<include refid="selectAllGenericAssays"/>) AS generic_assay_query
-        ON sd.sample_unique_id = generic_assay_query.sample_unique_id 
+            LEFT JOIN (<include refid="selectAllGenericAssays"/>) AS generic_assay_query
+            ON
+            <choose>
+                <when test="'${type}' == 'sample'">
+                    sd.sample_unique_id = generic_assay_query.sample_unique_id
+                </when>
+                <otherwise>
+                    sd.patient_unique_id = generic_assay_query.patient_unique_id
+                </otherwise>
+            </choose>
         <where>
             datatype != 'LIMIT-VALUE' 
             <foreach item="dataFilterValue" collection="genericAssayDataFilter.values" open=" AND ((" separator=") OR (" close="))">
diff --git a/src/main/resources/org/cbioportal/persistence/mybatisclickhouse/StudyViewMapper.xml b/src/main/resources/org/cbioportal/persistence/mybatisclickhouse/StudyViewMapper.xml
index 632c280c88e..178074ec7a3 100644
--- a/src/main/resources/org/cbioportal/persistence/mybatisclickhouse/StudyViewMapper.xml
+++ b/src/main/resources/org/cbioportal/persistence/mybatisclickhouse/StudyViewMapper.xml
@@ -304,12 +304,17 @@
     </select>
     
     <select id="getGenericAssayDataCounts" resultMap="GenericAssayDataCountItemResultMap">
-        <bind name="profileType" value="genericAssayDataFilters[0].profileType"/> 
-        WITH generic_assay_query AS (
+        <bind name="profileType" value="genericAssayDataFilters[0].profileType"/>
+        WITH profile_info AS (
+            SELECT patient_level
+            FROM genetic_profile
+            WHERE stable_id = concat(#{studyViewFilterHelper.studyViewFilter.studyIds[0]}, '_', #{profileType})
+        ),
+        generic_assay_query AS (
             SELECT
                 entity_stable_id AS stableId,
                 value,
-                cast(count(*) AS INTEGER) AS count
+                cast(count(distinct patient_unique_id) AS INTEGER) AS count
             FROM generic_assay_data_derived
             <where>
                 <!-- Table creation in clickhouse.sql has ensured no NA values but extra caution is always appreciated -->
@@ -339,9 +344,17 @@
         <!-- The NA count is specially caculated using total sample count minus non-NA count, therefore 
          these 2 coalesces are here in case the non-NA subquery returned empty results and we need to provide properties needed to construct the target object -->
         SELECT
-        coalesce((SELECT stableId FROM generic_assay_data_sum LIMIT 1), #{genericAssayDataFilters[0].stableId}) as stableId,
-        'NA' as value,
-        cast(((SELECT * FROM (<include refid="getTotalSampleCount"/>)) - coalesce((SELECT gad_count FROM generic_assay_data_sum LIMIT 1), 0)) as INTEGER) as count 
+            coalesce((SELECT stableId FROM generic_assay_data_sum LIMIT 1), #{genericAssayDataFilters[0].stableId}) as stableId,
+            'NA' as value,
+            cast((
+                CASE
+                    WHEN (SELECT patient_level FROM profile_info) = 1 THEN
+                        (SELECT * FROM (<include refid="getTotalPatientCount"/>))
+                    ELSE
+                        (SELECT * FROM (<include refid="getTotalSampleCount"/>))                        
+                END
+                - coalesce((SELECT gad_count FROM generic_assay_data_sum LIMIT 1), 0))
+            as INTEGER) as count 
     </select>
 
     <!-- for /mutation-data-counts/fetch (returns GenomicDataCountItem objects) mutation counts pie chart part -->