SeqCap EZ Exome v3

Product Overview

The SeqCap EZ Human Exome Kit v3.0, as part of the SeqCap EZ Enrichment System, enables enrichment of the whole exome. This kit captures 64 Mb of target.

Description Catalog Number Pack Size
SeqCap EZ Exome Kit v3.0 06465684001 4 Reactions
SeqCap EZ Exome Kit v3.0 06465692001 48 Reactions

Please Contact Us for ordering and questions

NEW! SeqCap EZ HyperCap Workflow User's Guide v1.0

The SeqCap EZ system can now be used with the SeqCap EZ HyperCap Workflow. The HyperCap workflow provides an integrated, application-specific approach for efficient, streamlined and automatable targeted sequencing solution. It combines high-efficiency KAPA Hyper Prep and KAPA HyperPlus Library Preparation Kits with performance-optimized SeqCap EZ capture protocol.

For life science research only. Not for use in diagnostic procedures.


Product Description

The SeqCap EZ Exome Kit v3.0 product covers more than 20,000 genes in the human genome. All the genome coordinates are based on human genome build GRCh37 (hg19). 

More than two million oligonucleotide DNA probes capture the target regions. Because the flanking regions of some coding exons and miRNAs are also covered by probes, the total size of the regions covered by probes is 64 Mb.

Benefits

  • Achieve the most comprehensive coverage of 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.
  • Experience the highest target enrichment efficiency: The NimbleGen Sequence Capture advanced design algorithm coupled with 2.1 million long oligonucleotide probes delivers superior target enrichment performance to discover more variants, including both single nucleotide variants and indels. See Nature Biotechnology article for a detailed comparison of target enrichment methods.
  • Maximize variant discovery while minimizing sequencing costs: Reduce the sequencing output needed to verify mutations potentially responsible for disease.

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 Roche NimbleGen products:

  • SeqCap EZ Human Exome Kit v3.0, 4 Reactions (Catalog No. 06465684001)
  • SeqCap EZ Human Exome Kit v3.0, 48 Reactions (Catalog No. 06465692001)
 
 
 
Overview
 
The SeqCap EZ Exome Kit v3.0 product covers more than 20,000 genes in the human genome. The following sources provided information about the genes:
  • 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

All the genome coordinates were based on human genome build GRCh37 (hg19).

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, Roche NimbleGen extended the target region to 100 bp.

More than two million long oligonucleotide DNA probes were designed to capture the target regions. Because the flanking regions of some coding exons and miRNAs are also covered by probes, the total size of the regions covered by probes is 64 Mb.

 

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 Roche NimbleGen 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 probes (“Probe_Coverage”), and the percentage of primary target bases with estimated sequencing coverage for typical results (“Estimated_Coverage”).

Download Design Files

Demo Data

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

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