Discontinued SeqCap Portfolio

SeqCap EZ Exome Probes v3.0 have been discontinued. Our new KAPA Target Enrichment Portfolio is now available and contains our new KAPA HyperExome, as well as our new custom probes, KAPA HyperChoice and KAPA HyperExplore. For additional questions, please contact your regional sales representative.



An integrated approach to sample preparation, for applications such as whole exome sequencing, encompassing all the steps required to convert a sample to a sequencing-ready library is beneficial in your research considering the precious nature of NGS samples. Therefore, we offer Roche Sample Prep Solutions, from sample collection to library quantification for different sample types and sequencing applications that are provencomplete and simple.

The SeqCap® EZ Human Exome Probes v3.0 enables enrichment of the whole exome and includes the following features:

  • Capture of 64 Mb of total target by 2.1 million oligonucleotide probes
  • Coverage of more than 20,000 genes in the human genome
  • Genome coordinates based on human genome build GRCh37 (hg19) 
  • Coverage of flanking regions of some coding exons and miRNAs by probes

Features and benefits of the SeqCap EZ Human Exome Probes v3.0

  • Comprehensive exome coverage
  • Higher target enrichment efficiency than other options*
  • High variant discovery while minimizing sequencing costs*
  • Ability to integrate with the high efficient HyperCap Workflow, a streamlined and automatable targeted sequencing solution

Product Highlights

More comprehensive exome coverage than other available options

  • Coverage of more coding regions
  • Coverage of genes from RefSeq RefGene CDS, CCDS, and miRBase v14 databases, plus coverage of 97% Vega, 97% Gencode, and 99% Ensembl databases*

Superior target enrichment efficiency and ability to discover more number of variants compared to a competitor product

  • Superior target enrichment performance using the SeqCap advanced design algorithm coupled with 2.1 million long oligonucleotide probes *

Design sources for the SeqCap EZ Exome Probes v3.0

  • NCBI Reference Sequence (RefSeq) RefGene from UCSC (GRCh37_CDS_06092011)
  • CCDS.2 from NCBI GRCh37_20110422
  • Vega (GRCh37_CDS_42)
  • Gencode(GRCh37_CDS_v3C)
  • Ensembl (GRCh37_CDS_v63)
  • miRNAs from miRBase (version 16)
  • miRNAs from snoRNABase (version 3)
  • Customer inputs
For RefSeq genes, only transcripts with an "NM_" prefix were selected, and only protein coding parts of the transcripts were targeted. For exons that are smaller than 100 bp, the target region is extended to 100 bp.

Design Files

The design and annotation files provide information about genomic regions covered by the capture probes and the genes included in these regions. These files were designed for use with the following products:

  • SeqCap EZ Human Exome Probes v3.0, 4 Reactions (Catalog No. 06465684001)
  • SeqCap EZ Human Exome Probes v3.0, 48 Reactions (Catalog No. 06465692001)

Download design files.

File Descriptions

BED files are plain text, tab-delimited files which list genomic coordinates. These files may be used to explore design targets and to assess capture performance within the targeted regions. The first 3 columns are chromosome or sequence name, target start (0-based), and target end (1-based). For selected SeqCap EZ designs, the fourth column of primary and capture target BED files shows associated gene annotation for each genomic region.

BED files can be imported into Microsoft Excel as tab-delimited text or visualized using the SignalMap software.

The following files are included in the downloadable zip file:

  • SeqCap_EZ_Exome_v3_hg19_primary_targets.bed: This file contains the design primary target (unpadded) in hg19 coordinates and gene annotation in the 4th column.
  • SeqCap_EZ_Exome_v3_hg19_capture_targets.bed: This file contains coordinates showing the probe footprint with no padding in hg19 coordinates.
  • SeqCap_EZ_Exome_v3_hg19_UCSCBrowser.bed: This file is for viewing target coordinates in the UCSC Genome Browser.
  • SeqCap_EZ_Exome_v3_hg19_gene_list.txt: This file contains a list of gene names and symbols from multiple annotation sources (see file header).
  • SeqCap_EZ_Exome_v3_hg19_coverage_summary.txt: This file describes the primary target size, the percentage of primary target bases directly covered by one or more probes (“Probe_Coverage”), and the percentage of primary target bases with estimated sequencing coverage for typical results (“Estimated_Coverage”).

Demo Data

Demo data is available for evaluation.Please contact Roche representative for your country. 


*Data on file.