Demo Data
Last updated
Last updated
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:
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.
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.
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.
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.
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.
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.
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.
