• 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.

Figure 1

Figure 1: Comparison of SeqCap EZ Exome Library v3 design with two other products. For the databases shown, SeqCap EZ Exome v3 targets more exons and miRNAs compared to both Agilent and Illumina products.

Figure 2

Figure 2: SeqCap EZ Exome Library v3 coverage of coding bases. Coverage comparison of a NimbleGen SeqCap EZ Human Exome v3.0 capture sequenced using Illumina 2x76 bp reads versus an Agilent SureSelect Human All Exon 50 Mb capture using Ilumina 2x100 bp reads. Despite the larger 64 Mb design of the SeqCap EZ Exome v3.0, significantly less sequencing is required to obtain 10X coverage of 90% of targeted bases compared to the Agilent product.

Roche NimbleGen offers SeqCap EZ Library as a solution-based method for target enrichment.

Sequence Capture Protocols

1. Genomic DNA: SeqCap EZ Oligo pool is made against target regions in the genome.
2. Library Preparation: Standard shot-gun sequencing library is made from genomic DNA.
3. Hybridization: The sequencing library is hybridized to the SeqCap EZ Oligo pool.
4. Bead Capture: Streptavidin beads are used to pull down the complex of capture oligos and genomic DNA fragments.
5. Washing: Unbound fragments are removed by washing.
6. Amplification: Enriched fragment pool is amplified by PCR.
7. Enrichment QC: The success of enrichment is measured by qPCR at control loci.
8. Sequencing-Ready DNA: The end product is a sequencing library enriched for target regions, ready for high throughput sequencing.

Download the complete 3-file set!

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

Overview

The SeqCap EZ Exome Library 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

The folder contains these three files:

• SeqCap_EZ_Exome_v3_primary.bed: This file contains primary target intervals along with associated annotation IDs in BED format.
• SeqCap_EZ_Exome_v3_capture.bed: This file contains capture target intervals along with associated annotation IDs in BED format. The coordinates listed here correspond to locations where capture probes were actually designed and placed. If an exon was originally targeted for capture, but probes could not be placed in that region (for example, due to highly repetitive sequences), then the coordinates would be included in the SeqCap_EZ_Exome_v3_primary.bed file but not included in the SeqCap_EZ_Exome_v3_capture.bed file. Annotations provided in this file assume a 100 bp theoretical padding surrounding the capture targets.
  • Annotation provided in the BED file is derived from Ensemble Genes (version 64) and includes IDs for RefSeq, CCDS, Ensembl, Vega, miRBase along with the associated gene_name for each interval.
  • The BED file can be used to create a custom annotation track for display in the UCSC Genome browser (http://genome.ucsc.edu).
• SeqCap_EZ_Exome_v3.gff: This file contains both primary target and capture target intervals in GFF format.
  • The GFF files can be opened using SignalMap software from Roche NimbleGen.

Download the complete 3-file set!

Use SeqCap EZ Hybridization and Wash Kits to perform hybridization and wash steps in sequence capture protocols using NimbleGen SeqCap EZ products. The kits are available in handy 24 and 96 reaction pack sizes.

Description	Catalog Number	Pack Size	Kit Capacity	Compatible Applications	Ordering*
SeqCap EZ Hybridization and Wash Kits	05634261001	1 Kit	24 Reactions	SeqCap EZ Library
	05634253001	1 Kit	96 Reactions
* Availability of products varies from country to country.

Brochures and Sales Flyers

• NimbleGen Sequence Capture
  Brochure (PDF Format 3.9MB)
• SeqCap EZ Human Exome Library v3.0
  Sales Flyer (PDF Format 943KB)

User Guides

• NEW! NimbleGen SeqCap EZ Library LR User's Guide (Version 2.0)
  For use with SeqCap EZ Exome and SeqCap EZ Choice (long read sequencing protocol)
  User’s Guide (PDF Format 1.4MB)
• NEW! NimbleGen SeqCap EZ Library SR User's Guide (Version 3.0)
  For use with SeqCap EZ Exome and SeqCap EZ Choice (short read sequencing protocol)
  User’s Guide (PDF Format 1.5MB)
• Reference Guide to Your Custom SeqCap EZ Oligos
  For use with SeqCap EZ Exome and SeqCap EZ Choice (short read sequencing protocol)
  Reference Guide (PDF Format 590KB)

Downloads

• SeqCap EZ Human Exome Library v3.0
  Design and Annotation Files (ZIP Format 9.6MB)
  What files are included in this download?
• SeqCap EZ Human Exome Library v2.0
  Design and Annotation Files (ZIP Format 12.8MB)
  What files are included in this download?

Application & Technical Notes

• NEW! Multiplex Sequence Capture for Targeted Resequencing of Candidate Gene Panels in Cancer
  Application Note (PDF Format 308KB)
• SeqCap EZ Human Exome Library v2.0: Performance Evaluation
  Technical Note (PDF Format 954KB)