Contrived and Cell Line Sample Considerations

Using cell lines or contrived samples for validation or as positive controls may result in inconsistent or unusual results depending on how the samples were constructed. Illumina recommends using commercial controls only for the variant class they are intended for. For example, if the sample is contrived for CNVs but not explicitly for SNV, MSI, TMB, or fusions, we would not recommend using this sample for validation or as a positive control for SNV, MSI, TMB, or fusions.

Demo Data for Commercial Controls

Illumina has provided demo data of some common commercial controls on BaseSpace Sequence Hub on various flow cells:

• TSO 500 ctDNA v2: 1.5B (NovaSeq X)

• TSO 500 ctDNA v2: 10B (NovaSeq X)

• TSO 500 ctDNA v2: S2 (NovaSeq 6000)

• TSO 500 v1: NextSeq 550

Known Limitations with Commercial Controls

TSO 500 ctDNA v2

Product Name	Variant Class	Description	SW Version Impacted
Seraseq ctDNA Complete Mutation Mix AF0.5%; Material Number 0710-0531	Small Variants	Low recall on Deletion chr17 41245586 CT>C due to a high noise region adjacent to a homoploymer. Under review to be addressed in the future SW versions.	All
Seraseq ctDNA Complete Mutation Mix AF0.5%; Material Number 0710-0531	TMB	Not recommended for TMB validation due to many small variants having VAF close to the TMB limit of detection. Small changes in preparation and dilution result in large changes in TMB scores (behavior not observed in clinical samples).	All
Twist cfDNA Pan-Cancer Reference Standard v2	Fusions	False negatives due to a known issue on high efficiently libraries.	Resolved 2.6.1+
Seraseq ctDNA Reference Material v2 (multiple VAF)	Fusions	False negatives due to a known issue on high efficiently libraries.	Resolved 2.6.1+

TSO 500 v1 and v2

Product Name	Variant Class	Description	SW Version Impacted
Seraseq® FFPE BRCA1/2 LGR Reference Material Material Number 0730-0564	BRCA LR	Not recommended for LR validation due to 1) high level of noise 2) method of contriving resulting in some artifacts. We have found Seraseq BRCA 1/2 Exon Deletions DNA Mix Material Number 0730-0570 to work well.	All