# Demo Data

Demo Data is available on BSSH with the Project name "NovaSeq6000/NovaSeqX: Illumina FFPE DNA Prep with Exome 2.5 Enrichment - Demo Data" and on ICA with the Bundle name "Illumina FFPE DNA Prep with Exome 2.5 Enrichment - Demo Data".

Data includes 14 samples, or seven Tumor/Normal pairs:

1. SNV-tumor-AF10-NovaSeq6K & SNV-normal-NovaSeq6K: Seracare Seraseq Tumor Mutation DNA Mix v2 AF10 and Seraseq WT (DNA/RNA) Reference Material. Samples with known truth variants at expected Variant Allele frequency at 10%, sequenced on the NovaSeq6000 Sequencing System.
2. SNV-tumor-AF5-NovaSeqX & SNV-normal-NovaSeqX: Seracare Seraseq Tumor Mutation DNA Mix v2 AF5 and Seraseq WT (DNA/RNA) Reference Material. Seracare Reference Material diluted to expected Variant Allele frequency at 5%, sequenced on the NovaSeqX Sequencing System.
3. CNV-tumor-NovaSeq6K & CNV-normal-NovaSeq6K: Seracare Seraseq Solid Tumor CNV Mix +3 Copies and Seraseq WT (DNA/RNA) Reference Material. Sample with known CNV events at expected duplication events with fold change at 3x, sequenced on the NovaSeq6000 Sequencing System.
4. FFPE-tumor-21706-NovaSeq6K & FFPE-normal-21707-NovaSeq6K: clinical formalin-fixed paraffin-embedded (FFPE) tumor sample 21706 and benign adjacent tissue sample 21707. FFPE samples sequenced on the NovaSeq6000 Sequencing System.
5. FFPE-tumor-21706-NovaSeqX & FFPE-normal-21707-NovaSeqX: clinical formalin-fixed paraffin-embedded (FFPE) tumor sample 21706 and benign adjacent tissue sample 21707. FFPE samples sequenced on the NovaSeqX Sequencing System.
6. FFPE-tumor-12293-exome-NovaSeq6K & FFPE-normal-12294-exome-NovaSeq6K: FFPE tumor sample 12293 and benign adjacent tissue sample 12294, enriched with the Twist Exome v2.5 panel. FFPE samples sequenced on the NovaSeq6000 Sequencing System.
7. FFPE-tumor-12293-exome-plus-spike-NovaSeq6K & FFPE-normal-12294-exome-plus-spike-NovaSeq6K: FFPE tumor sample 12293 and benign adjacent tissue sample 12294, enriched with the Twist Exome v2.5 panel and a custom spike-in panel. FFPE samples sequenced on the NovaSeq6000 Sequencing System.

Sample pair #7 (FFPE 12293/12294 enriched with and without a custom spike-in panel) was not included in variant calling because a systematic noise file and a Panel of Normals were not available for these combined covered regions. The pre-built WES systematic noise file based on the exome region (without spike-in) can be used, but precision in the custom spike-in areas may be reduced. The pre-built PON target counts based on the exome region (without spike-in) can be used, but CNV events may be inaccurate. Differences in coverage can seen by viewing the bam files.

<figure><img src="https://1307232601-files.gitbook.io/~/files/v0/b/gitbook-x-prod.appspot.com/o/spaces%2F5SraS7nvevahPiUwFnmm%2Fuploads%2Fgit-blob-448d8d7a7c27d8c946465329db9af5c86da5e148%2FScreenshot%202025-03-14%20at%2010.51.20%E2%80%AFAM.png?alt=media" alt=""><figcaption><p>Demo Data in BaseSpace Sequence Hub</p></figcaption></figure>