diff --git a/src/pages/studyView/StudyViewPageStore.ts b/src/pages/studyView/StudyViewPageStore.ts
index 1dce27ca2eb..684e9b2b0ba 100644
--- a/src/pages/studyView/StudyViewPageStore.ts
+++ b/src/pages/studyView/StudyViewPageStore.ts
@@ -88,6 +88,8 @@ import {
     getFilteredAndCompressedDataIntervalFilters,
     getUniqueKeyFromMolecularProfileIds,
     getMolecularProfileIdsFromUniqueKey,
+    getClinicalDataBySamples,
+    updateSavedUserPreferenceChartIds,
 } from './StudyViewUtils';
 import MobxPromise from 'mobxpromise';
 import { SingleGeneQuery } from 'shared/lib/oql/oql-parser';
@@ -2198,62 +2200,6 @@ export class StudyViewPageStore {
         return this.clinicalDataBinPromises[uniqueKey];
     }
 
-    private async getClinicalDataBySamples(samples: Sample[]) {
-        let clinicalData: {
-            [sampleId: string]: { [attributeId: string]: string };
-        } = {};
-
-        let sampleClinicalData = await defaultClient.fetchClinicalDataUsingPOST(
-            {
-                clinicalDataType: 'SAMPLE',
-                clinicalDataMultiStudyFilter: {
-                    identifiers: _.map(samples, sample => {
-                        return {
-                            entityId: sample.sampleId,
-                            studyId: sample.studyId,
-                        };
-                    }),
-                } as ClinicalDataMultiStudyFilter,
-            }
-        );
-
-        _.forEach(sampleClinicalData, item => {
-            clinicalData[item.uniqueSampleKey] = {
-                ...(clinicalData[item.uniqueSampleKey] || {}),
-                [item.clinicalAttributeId]: item.value,
-            };
-        });
-
-        let patientClinicalData = await defaultClient.fetchClinicalDataUsingPOST(
-            {
-                clinicalDataType: ClinicalDataTypeEnum.PATIENT,
-                clinicalDataMultiStudyFilter: {
-                    identifiers: _.map(samples, sample => {
-                        return {
-                            entityId: sample.patientId,
-                            studyId: sample.studyId,
-                        };
-                    }),
-                } as ClinicalDataMultiStudyFilter,
-            }
-        );
-
-        const patientSamplesMap = _.groupBy(
-            samples,
-            sample => sample.uniquePatientKey
-        );
-
-        _.forEach(patientClinicalData, item => {
-            (patientSamplesMap[item.uniquePatientKey] || []).forEach(sample => {
-                clinicalData[sample.uniqueSampleKey] = {
-                    ...(clinicalData[sample.uniqueSampleKey] || {}),
-                    [item.clinicalAttributeId]: item.value,
-                };
-            });
-        });
-        return clinicalData;
-    }
-
     readonly molecularProfiles = remoteData<MolecularProfile[]>({
         await: () => [this.queriedPhysicalStudyIds],
         invoke: async () => {
@@ -3198,7 +3144,9 @@ export class StudyViewPageStore {
                     toJS(this.studyIds)
                 );
                 if (userSettings) {
-                    return userSettings.chartSettings || [];
+                    return updateSavedUserPreferenceChartIds(
+                        userSettings.chartSettings
+                    );
                 }
             }
             return [];
@@ -4734,9 +4682,7 @@ export class StudyViewPageStore {
         invoke: async () => {
             let sampleClinicalDataMap: {
                 [attributeId: string]: { [attributeId: string]: string };
-            } = await this.getClinicalDataBySamples(
-                this.selectedSamples.result
-            );
+            } = await getClinicalDataBySamples(this.selectedSamples.result);
             return _.reduce(
                 this.selectedSamples.result,
                 (acc, next) => {
@@ -4998,7 +4944,7 @@ export class StudyViewPageStore {
 
     @autobind
     public async getDownloadDataPromise() {
-        let sampleClinicalDataMap = await this.getClinicalDataBySamples(
+        let sampleClinicalDataMap = await getClinicalDataBySamples(
             this.selectedSamples.result
         );
 
diff --git a/src/pages/studyView/StudyViewUtils.spec.ts b/src/pages/studyView/StudyViewUtils.spec.ts
index 5d4551afe39..2a84df25123 100644
--- a/src/pages/studyView/StudyViewUtils.spec.ts
+++ b/src/pages/studyView/StudyViewUtils.spec.ts
@@ -54,6 +54,7 @@ import {
     getBinName,
     getGroupedClinicalDataByBins,
     getFilteredAndCompressedDataIntervalFilters,
+    updateSavedUserPreferenceChartIds,
 } from 'pages/studyView/StudyViewUtils';
 import {
     DataBin,
@@ -82,6 +83,7 @@ import {
 } from 'shared/lib/Colors';
 import { IStudyViewDensityScatterPlotDatum } from './charts/scatterPlot/StudyViewDensityScatterPlot';
 import { shallow } from 'enzyme';
+import { ChartUserSetting } from './StudyViewPageStore';
 
 describe('StudyViewUtils', () => {
     const emptyStudyViewFilter: StudyViewFilter = {
@@ -3328,4 +3330,62 @@ describe('StudyViewUtils', () => {
             );
         });
     });
+
+    describe('updateChartIds', () => {
+        const chartSetting1: ChartUserSetting = {
+            id: 'SAMPLE_CANCER_TYPE',
+            chartType: 'PIE_CHART',
+            layout: {
+                x: 0,
+                y: 0,
+                w: 1,
+                h: 1,
+            },
+            patientAttribute: false,
+        };
+        const chartSetting2: ChartUserSetting = {
+            id: 'SAMPLE_SAMPLE_TYPE',
+            chartType: 'PIE_CHART',
+            layout: {
+                x: 0,
+                y: 0,
+                w: 1,
+                h: 1,
+            },
+            patientAttribute: false,
+        };
+
+        it('should return correct chart settings', () => {
+            assert.deepEqual(
+                updateSavedUserPreferenceChartIds([chartSetting1]),
+                [{ ...chartSetting1, id: 'CANCER_TYPE' }]
+            );
+            assert.deepEqual(
+                updateSavedUserPreferenceChartIds([
+                    { ...chartSetting1, id: 'CANCER_TYPE' },
+                ]),
+                [{ ...chartSetting1, id: 'CANCER_TYPE' }]
+            );
+            assert.deepEqual(
+                updateSavedUserPreferenceChartIds([
+                    chartSetting1,
+                    chartSetting2,
+                ]),
+                [
+                    { ...chartSetting1, id: 'CANCER_TYPE' },
+                    { ...chartSetting2, id: 'SAMPLE_TYPE' },
+                ]
+            );
+            assert.deepEqual(
+                updateSavedUserPreferenceChartIds([
+                    { ...chartSetting1, id: 'CANCER_TYPE' },
+                    { ...chartSetting2, id: 'SAMPLE_TYPE' },
+                ]),
+                [
+                    { ...chartSetting1, id: 'CANCER_TYPE' },
+                    { ...chartSetting2, id: 'SAMPLE_TYPE' },
+                ]
+            );
+        });
+    });
 });
diff --git a/src/pages/studyView/StudyViewUtils.tsx b/src/pages/studyView/StudyViewUtils.tsx
index a9324525b73..c348ecf9f52 100644
--- a/src/pages/studyView/StudyViewUtils.tsx
+++ b/src/pages/studyView/StudyViewUtils.tsx
@@ -16,6 +16,7 @@ import {
     PatientIdentifier,
     Sample,
     ClinicalData,
+    ClinicalDataMultiStudyFilter,
 } from 'shared/api/generated/CBioPortalAPI';
 import * as React from 'react';
 import { buildCBioPortalPageUrl } from '../../shared/api/urls';
@@ -2417,3 +2418,103 @@ export function getFilteredAndCompressedDataIntervalFilters(
             : undefined;
     return { start, end } as any;
 }
+
+export async function getClinicalDataBySamples(samples: Sample[]) {
+    let clinicalData: {
+        [sampleId: string]: { [attributeId: string]: string };
+    } = {};
+
+    let sampleClinicalData = await defaultClient.fetchClinicalDataUsingPOST({
+        clinicalDataType: 'SAMPLE',
+        clinicalDataMultiStudyFilter: {
+            identifiers: _.map(samples, sample => {
+                return {
+                    entityId: sample.sampleId,
+                    studyId: sample.studyId,
+                };
+            }),
+        } as ClinicalDataMultiStudyFilter,
+    });
+
+    _.forEach(sampleClinicalData, item => {
+        clinicalData[item.uniqueSampleKey] = {
+            ...(clinicalData[item.uniqueSampleKey] || {}),
+            [item.clinicalAttributeId]: item.value,
+        };
+    });
+
+    let patientClinicalData = await defaultClient.fetchClinicalDataUsingPOST({
+        clinicalDataType: ClinicalDataTypeEnum.PATIENT,
+        clinicalDataMultiStudyFilter: {
+            identifiers: _.map(samples, sample => {
+                return {
+                    entityId: sample.patientId,
+                    studyId: sample.studyId,
+                };
+            }),
+        } as ClinicalDataMultiStudyFilter,
+    });
+
+    const patientSamplesMap = _.groupBy(
+        samples,
+        sample => sample.uniquePatientKey
+    );
+
+    _.forEach(patientClinicalData, item => {
+        (patientSamplesMap[item.uniquePatientKey] || []).forEach(sample => {
+            clinicalData[sample.uniqueSampleKey] = {
+                ...(clinicalData[sample.uniqueSampleKey] || {}),
+                [item.clinicalAttributeId]: item.value,
+            };
+        });
+    });
+    return clinicalData;
+}
+
+export function updateSavedUserPreferenceChartIds(
+    chartSettings: ChartUserSetting[]
+): ChartUserSetting[] {
+    const customChartRegex = /^CUSTOM_FILTERS_\d+/i;
+    const chartIdWithDataTypeRegex = /^(?:PATIENT_|SAMPLE_)([a-zA-Z0-9_]+)/i;
+    let numberOfClinicalAttributeCharts = 0;
+    let numberOfChartRequiringUpdates = 0;
+    const specialChartKeySet = _.reduce(
+        UniqueKey,
+        (acc, next) => {
+            acc[next] = true;
+            return acc;
+        },
+        {} as { [id: string]: boolean }
+    );
+
+    chartSettings.forEach(chartSetting => {
+        let customChartmatch = chartSetting.id.match(customChartRegex);
+        if (
+            !customChartmatch &&
+            specialChartKeySet[chartSetting.id] === undefined
+        ) {
+            numberOfClinicalAttributeCharts++;
+            let match = chartSetting.id.match(chartIdWithDataTypeRegex);
+            if (!!match) {
+                numberOfChartRequiringUpdates++;
+            }
+        }
+    });
+
+    // Some of the clinical attributes id contains SAMPLE_ or PATIENT_ prefix. Updating them would not show those charts.
+    // Only way is to check if the chart ids requires update is to see if the
+    // number of clinical attribute charts shown is same as the number of chart ids requiring updates
+    if (numberOfClinicalAttributeCharts === numberOfChartRequiringUpdates) {
+        return chartSettings.map(chartSetting => {
+            let match = chartSetting.id.match(chartIdWithDataTypeRegex);
+            if (!!match) {
+                return {
+                    ...chartSetting,
+                    id: match[1],
+                };
+            }
+            return chartSetting;
+        });
+    }
+    return chartSettings;
+}