GenapSys Cancer Panel Sample Data Set

A pan-cancer panel library was generated using the Oncospan Reference Standard (HD827) obtained from Horizon Discovery. The reference standard is composed of DNA from multiple cell lines and contains 386 variants across 152 key cancer genes. The allele frequencies range from 1% to 100%. Hybrid capture-based enrichment was done using IDT Pan Cancer panel V1.5 (800 kb region, 127 genes) and sequencing was carried out using the GenapSys™ Sequencer. The sequencing data was then down-sampled to coverage levels of 1000x, 500x, 200x, and 100x. Sequencing reads were aligned to the hg38 reference genome using BWA MEM (v0.7.17). The variants were called using Google's DeepVariant trained on GenapSys sequencing data.

For variant calling analysis and results, see our Variant Calling Application Note

The following files are included in the download:

  • Oncospan_IDT_Cancer_Panel_37212.fastq.gz: The GenapSys Oncospan sequencing data.
  • IDT_xgen_pan_cancer_panel_coding_exons_HG38.bed: This is the IDT xGen Cancer Panel Targets bed file limited to coding exon regions.
  • SNV_Oncospan_GenapSys_IDT_CancerPanel_CodingExonRegions.vcf: The variants (SNVs) with allele frequency>~2% were called using GenapSys variant caller based on Vardict.