Illumina FFPE DNA Prep with Exome 2.5 Enrichment

llumina FFPE DNA Prep with Exome 2.5 Enrichment is part of an integrated whole-exome sequencing (WES) Tumor-Normal workflow to deliver variant calling and biomarker analysis in low-input formalin-fixed paraffin-embedded (FFPE) samples. This page provides software user guides to Illumina's cloud-based and on-premise solutions for the data analysis of this library preparation kit.

The software performs the following workflows to analyze sequencing data.

• DNA Mapping and Aligning

• Somatic Small Variant (SNV) Caller

• Copy Number Variant (CNV) Caller

• Tumor Mutational Burden (TMB)

• Variant annotation

Notes on additional biomarkers:

Microsatellite Instability (MSI) is under development. With current software versions, it is recommended to run the tumor sample in Tumor/Only mode for highest performance of this biomarker. See the Additional Information page on MSI for detailed instructions.

Homologous Recombination Deficiency (HRD) is also under development, and performance improvements are expected with the release of upcoming software versions.

Structural Variant (SV) Caller results have not been evaluated for accuracy. Calculations for SV can add significant runtime to the analysis.