Resource Files

Mostly distributed as a BaseSpace Project and an ICA Bundle

Product files to support the analysis of samples prepared with the Illumina FFPE DNA Prep with Exome 2.5 Enrichment are predominately distributed as a BaseSpace Project and an ICA Bundle. Please reach out to your local sales representative to get access. Note that these product files are considered early access and will be superseded by official resource files published on the DRAGEN Resources page.

Target BED

If no spike-in probes were included in enrichment, download from Illumina DNA Prep with Exome 2.5 BED files for hg19 or hg39 reference genomes. If other spike-in probes were included in enrichment, use a BED file of the combined coverage areas, ie., Exome 2.5 Plus Panel and the custom panel. The requirements of a BED file are defined here.

Systematic noise files

Systematic noise files are considered essential for reducing false positive calls in Tumor-Only workflows, and they are also effective at improving precision in Tumor-Normal workflows. The normal samples used to generate the systematic noise file should match as closely as possible the sequencer, sample type, and library prep of the tumor samples.

Prebuilt

Prebuilt systematic noise BED files can be downloaded on DRAGEN Resources. The WES_*_v2.0.0_systematic_noise.snv.bed.gz noise files are built from a mixture of FF (fresh-frozen) and FFPE samples, with a mix of TruSeq PCR prep and Nextera prep.

Custom

For instructions on how to build your own systematic noise file using internally-sequenced normal samples, see Custom Systematic Noise Files.

CNV - Somatic pipelines

A Panel of normals (PONs) is used for calling gene amplification in tumor samples. Provided in the BSSH project/ICA bundle are the individual target.counts files (i.e. one per normal sample) and combined target.count files. The PON was generated from 45 FFPE benign adjacent samples from different tissue types and from male and female donors. Libraries were sequenced on the NovaSeq 6000 sequencing system. Current supported builds include hg19 and hg39, both target.counts and gc-corrected.target.counts.

MSI - Reference directory of normals

To be used when enabling the biomarker Microsatellite Instability (MSI) in Tumor-only mode. This is a reference directory containing the miscrosatellite repeat distribution in a collection of 44 FFPE normals (.dist files) sequenced on the NovaSeq 6000 sequencing system. Currently, hg19 is the only supported builds but will be expanded to hg38 soon. Alternatively, see the DRAGEN manual for instructions on how to generate your own.

MSI - Microsatellite sites

To be used when enabling the biomarker Microsatellite Instability (MSI). A list of microsatellite sites from which to calculate instability. Currently, hg19 is the only supported builds but will be expanded to hg38 soon. Note that this list is a subset of the sites in the WES microsatellite list provided on the DRAGEN product files in May 2024.