SeqCap EZ HGSC VCRome

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Product Overview


Description

Catalog Number

Pack Size
SeqCap EZ HGSC VCRome

06465587001

12 Reactions

SeqCap EZ HGSC VCRome

06465668001

48 Reactions
SeqCap EZ HGSC VCRome

06465676001

96 Reactions

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

Please Contact Us for ordering and questions


Product Description

SeqCap EZ HGSC VCRome was designed by scientists at the Human Genome Sequencing Center (HGSC) at the Baylor College of Medicine in Houston, TX as a clinical research exome. The HGSC scientists worked with NimbleGen R&D scientists to optimize capture performance through empirical rebalancing. The name comes from the primary coding sequence (CDS) annotation sources which were Vega, CCDS, and RefSeq. Also included are miRNAs from miRBase. The design covers 23,585 genes and 189,028 non-overlapping exons (July 2014 Ensembl annotation). Design files are included for both the hg18 and hg19 genome assemblies. Total design size is 45.1 Mb capture target.

Benefits

  • Trust one of the most heavily validated exomes: VCRome has been successfully used with tens of thousands of research subject samples on a yearly basis.
  • Achieve maximal multiplexing efficiency with the focused design: At 45.2Mb capture target size, with optimized uniformity, VCRome is one of the most efficient exome designs, enabling high coverage with maximal multiplexing capability.
  • Enjoy best-in-class performance: On-target rate and coverage enable best usage of your sequencing capacity, well suited for medical or clinical research.

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 HGSC VCRome, 12 Reactions (Catalog No. 06 465 587 001)
  • SeqCap EZ HGSC VCRome, 48 Reactions (Catalog No. 06 465 668 001)
  • SeqCap EZ HGSC VCRome, 96 Reactions (Catalog No. 06 465 676 001)

Download the complete set (18 MB .zip)

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:

  • HGSC_VCRome_v2.1_hg18_primary_targets.bed: This file contains the design primary target (unpadded) in hg18 coordinates. Gene annotation is not provided.
  • HGSC_VCRome_v2.1_hg18_capture_targets.bed: This file contains coordinates showing the probe footprint with no padding in hg18 coordinates.
  • HGSC_VCRome_v2.1_hg18_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”). This file is only provided based on hg18 coordinates.
  • HGSC_VCRome_v2.1_hg19_primary_targets.bed: This file contains the design primary target (unpadded) in hg19 coordinates and gene annotation in the 4th column.
  • HGSC_VCRome_v2.1_hg19_capture_targets.bed: This file contains coordinates showing the probe footprint with no padding in hg19 coordinates.
  • HGSC_VCRome_v2.1_hg19_UCSCBrowser.bed: This file is for viewing target coordinates in the UCSC Genome Browser. This file is only provided based on hg19 coordinates.
  • HGSC_VCRome_v2.1_hg19_gene_list.txt: This file contains a list of gene names and symbols from multiple annotation sources (see file header). This file is only provided based on hg19 coordinates.

Download design files

Demo Data

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

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