diff --git a/src/main/java/org/mskcc/cbio/portal/scripts/GeneticAlterationIncrementalImporter.java b/src/main/java/org/mskcc/cbio/portal/scripts/GeneticAlterationIncrementalImporter.java
index b78c1f78..91a9b8e8 100644
--- a/src/main/java/org/mskcc/cbio/portal/scripts/GeneticAlterationIncrementalImporter.java
+++ b/src/main/java/org/mskcc/cbio/portal/scripts/GeneticAlterationIncrementalImporter.java
@@ -12,6 +12,7 @@
 import java.util.HashSet;
 import java.util.List;
 import java.util.Map;
+import java.util.Set;
 
 public class GeneticAlterationIncrementalImporter extends GeneticAlterationImporter {
 
@@ -58,7 +59,8 @@ public void initialise() {
             });
             // add all new sample ids at the end
             this.orderedSampleList = new ArrayList<>(savedOrderedSampleList);
-            List<Integer> newSampleIds = this.fileOrderedSampleList.stream().filter(sampleId -> !savedOrderedSampleList.contains(sampleId)).toList();
+            Set<Integer> savedSampleSet = new HashSet<>(savedOrderedSampleList);
+            List<Integer> newSampleIds = this.fileOrderedSampleList.stream().filter(sampleId -> !savedSampleSet.contains(sampleId)).toList();
             this.orderedSampleList.addAll(newSampleIds);
             DaoGeneticProfileSamples.deleteAllSamplesInGeneticProfile(this.geneticProfileId);
             this.storeOrderedSampleList();