Shared Designs

Overview

Target enrichment designs are developed independently, as well as in collaboration with Roche Sequencing Solutions scientists, by researchers around the world. With our dedicated shared designs page, we make it simple to access predesigned next-generation sequencing (NGS) panels.

Custom target enrichment designs shared by researchers across the world, built using our empirically optimized probe design algorithms, are continuously expanding and serve to suit the needs of demanding applications including oncology, human genetics, agriculture and other research applications.

If you would like to share your design on this page, please contact your local sales representative.

Human Genetic Disease

  • Organism: Human
  • Genome Build: HG38
  • Design Files: IDP Design
  • Demo Data: available, please contact your local Roche office
  • Collaborator: Dr. Jason Park
  • Specifications/Details: The SeqCap EZ Inherited Disease Panel covers over 4100 genes and regions associated with inherited disease and was designed in collaboration by scientists at Roche Sequencing and Dr. Jason Park. Total design size (hg38) is 9.0 Mb primary target and 11.8 Mb capture target.
  • Ordering Information:
    Product Name: SeqCap EZ Share Choice XL
    Design Name: 150803_HG38_IDP2_REZ_HX3
    Internal Reference #: 4000024240
  • Material Number:
    24 Rxn: 08332991001
    96 Rxn: 08333009001
    384 Rxn: 08333017001

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  • Organism: Human
  • Genome Build: GRCh37 (hg19)
  • Design Files: SeqCap EZ Exome v2.0 Design
  • Specifications/Details: The SeqCap EZ Exome Kit v2.0 product covers more than 20,000 genes in the human genome. All the genome coordinates were based on human genome build GRCh37 (hg19). The total capture target size is 44.1 Mb. More than two million long oligonucleotide DNA probes were designed to capture a total target size of 44.1 Mb.
  • Ordering Information:
    Product Name: SeqCap EZ Share Choice XL
    Design Name: 110208_HG19_CCDS_exome_V2_1_5_EZ
    Internal Reference #: 4000016420
  • Material Number:
    24 Rxn: 08332991001
    96 Rxn: 08333009001
    384 Rxn: 08333017001

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Oncology

 

  • SeqCap EZ Design: Comprehensive Cancer Design
  • Organism: Human
  • Genome Build: HG19
  • Design File: Comprehensive Cancer Design (362 KB .zip)
  • Specifications/Details: The Comprehensive Cancer Design is a 4Mb design and targets 578 cancer genes. The genes were gathered from the Sanger Institute Cancer Gene Census Database and the NCBI Gene Tests databases.
  • Ordering Information:
    Product Name: SeqCap EZ Share Choice
    Design Name: 120522_HG19_Onco_R_EZ
    Internal Reference #: 4000007080
  • Material Number:
    24 Rxn: 08332967001
    96 Rxn: 08332975001
    384 Rxn: 08332983001

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Virology

  • Organism: Vertebrate Infecting Viruses
  • Genome Build: EMBL Coding Domain Sequence Database release 122 (December 2014)
  • Design Files: VirCapSeq-VERT design (73mb)
  • Collaborator: Dr. Ian Lipkin
  • Publication: 
    Virome Capture Sequencing Enables Sensitive Viral Diagnosis and Comprehensive Virome Analysis
    mBio (2015), e01491-15
  • Specifications/Details: The SeqCap EZ VirCapSeq-VERT Capture Panel covers the genomes of 207 viral taxa known to infect vertebrates (including humans) and enables detection of viral sequences in complex sample types. The panel was designed in collaboration by scientists at Roche Sequencing and Professor Ian Lipkin using a database of 401,716 representative sequences spanning all virus sequence records, excluding bacteriophages. A list of all virus genera known to infect vertebrates was generated from the master species list of the International Committee on Taxonomy of Viruses (ICTV; http://talk.ictvonline.org/files/ictv_documents/m/msl/5208.aspx).
    Through cross-referencing of protein IDs with NCBI taxonomy IDs, a set of 342,438 coding sequence records was identified for the selected virus genera.
  • Ordering Information:
    Product Name: SeqCap EZ Share Developer
    Design Name: 150401_VIR_CIIv1_TB_EZ_HX1
    Internal Reference #: 4000020060
  • Material Number:
    24 Rxn: 08333025001
    96 Rxn: 08333033001
    384 Rxn: 08333050001

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Model Organisms

  • SeqCap EZ Design: Mouse Exome Design
  • Organism: Mouse
  • Genome Build: C57BL/6J, NCBI37, MM9
  • Design File: Mouse Exome Design (10.2 MB .zip)
  • Collaborator: Roche NimbleGen/Mouse Consortium
  • Specifications/Details: The coding sequence selected for the mouse exome probe pool design includes 203,225 exonic regions, including microRNAs, and collectively comprises over 54.3 Mb of target sequence (C57BL/6J, NCBI37/mm9). The design was based on a unified, Mouse Genome Database-curated gene set, consisting of non-redundant gene predictions from the National Center for Biotechnology Information (NCBI), Ensembl and The Vertebrate Genome Annotation (VEGA) database. To manage the size of the probe pool and to avoid non-uniquely mappable regions, we excluded olfactory receptors and pseudogenes from the target sequence. In cases where an exon contained both UTR and coding sequence, the UTR sequence was included in the design.
  • Publications/Information
  • Ordering Information
    Product Name: SeqCap EZ Share Developer
    Design Name: 110624_MM9_Exome L2R_D02_EZ_HX1
    Internal Reference #: 4000032100
  • Material Number:
    24 Rxn: 08333025001
    96 Rxn: 08333033001
    384 Rxn: 08333050001

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  • Ordering Information
    Product Name: SeqCap EZ Share Developer
    Design Name: 140702_canFam3_exomeplus_BB_EZ_HX1
    Internal Reference #: 4000022470 
  • Material Number:
    24 Rxn: 08333025001
    96 Rxn: 08333033001
    384 Rxn: 08333050001

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  • SeqCap EZ Design: Roslin Pig Exome Design Version 1
  • Organism: Sus scrofa (pig)
  • Genome Build: Sscrofa10.2 with additional sequences from GenBank in provided file
  • Design File: Design files are available upon request, please contact your local Roche office for design file information
  • Collaborator: Mick Watson, Edinburgh Genomics, The Roslin Institute, University of Edinburgh
  • Specifications/Details: The Ensembl gene annotations for the pig from release 71 were used as a starting point for the design, corresponding to assembly Sscrofa10.2 and the May 2012 genebuild (patched Oct 2012). The file Sus_scrofa.Sscrofa10.2.71.gtf.gz was downloaded from the Ensembl ftp site, and the lengths of non-overlapping genomic regions corresponding to exons of protein-coding genes were summed. Having found that the pig “exome” is smaller than that of human and mouse, ESTs from build 42 of UniGene Sus scrofa were mapped to the pig genome. The file Ssc.seq.uniq, representing the longest, best quality single sequence from each cluster, was downloaded from the NCBI FTP site, and used as input for NCBI BLASTN. High-scoring segment pairs (HSPs) at least 50 bp in length and >90% identical were chosen; HSPs that mapped more than 200 times in the genome filtered out; and overlapping HSPs merged. The resulting regions summed to 22.5Mb (mega-bases). These regions were merged with the Ensembl gene annotation using BEDTools. The final set of target genomic regions sums to 58.1 Mb.
  • Publications/Information:
  • Ordering Information:
    Product Name: SeqCap EZ Share Developer
    Design Name: 130104_Sscr_10_2_MW_EZ_HX1
    Internal Reference #: 4000017630
  • Material Number:
    24 Rxn: 08333025001
    96 Rxn: 08333033001
    384 Rxn: 08333050001

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Agriculture

  • SeqCap EZ Design: Maize Exome
  • Organism: Maize
  • Genome Build: Maize (B73 and Mo17)
  • Design Files: Design files are available upon request, please contact your local Roche office for design file information
  • Collaborator: Dr. Patrick Schnable and Dr. Nathan Springer
  • Specifications/Details: The Maize Exome design is a collaboration by Roche NimbleGen, Dr. Patrick Schnable (Iowa State University) and Dr. Nathan Springer (University of Minnesota). It is based on a comprehensive collection of 110 Mb of exome content derived from the B73 reference genome and expressed non-B73 sequences identified from the founder inbreds of the NAM population and teosinte via RNA-Seq.
  • Publications/Information:
  • Ordering Information:
    Product Name: SeqCap EZ Share Developer
    Design Name: 130614_Maize_ISU_RNG_Zeaome_EZ_HX1
    Internal Reference #: 4000020170
  • Material Number:
    24 Rxn: 08333025001
    96 Rxn: 08333033001
    384 Rxn: 08333050001

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  • Ordering Information:
    Design Name: 120426_Barley_BEC_D04

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  • SeqCap EZ Design: Wheat Exome
  • Organism: Wheat
  • Genome Build: Triticum aestivum (various), see provided file wheat_mapping_sequence.fa
  • Design File: Wheat Exome Design (43 MB .zip)
  • Collaborator: Wheat Barley Exome Consortium (WBEC)
  • Specifications/Details: The Wheat Exome design is a consortium derived design, comprised of 106.9 Mb of genomic DNA sequence from multiple wheat varieties.The Wheat Barley Exome Consortium is a collaboration of researchers from the University of Liverpool, Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), James Hutton Institute, Kansas State University, University of Minnesota, University of Saskatchewan, and BIOGEMMA.
  • Publications/Information:
  • Ordering Information:
    Design Name: 120426_Wheat_WEC_D02

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  • SeqCap EZ Design: Switchgrass Exome
  • Organism: Switchgrass
  • Genome Build: Two sets of transcripts were used for probe design. The PlantGDB (Duvick et al., 2008) assembly of P. virgatum Sanger-derived expressed sequence tags (Release 181a; 120 524 unique transcripts) and a custom assembly of P. virgatum pyrosequencing-derived transcript sequences downloaded from NCBI (SRR064785-SRR064802).
  • Design File: Switchgrass Exome (17 MB .zip)
  • Collaborator: Shawn Kaeppler and Steph Chow, University of Wisconsin, Madison
  • Specifications/Details: Of the annotated genes, the probe set represents a total of 50,038,805 bp composed of 168,961 exons in 44,873 genes in Release 0 of the AP13 reference genome.
  • Publications:
  • Ordering Information:
    Product Name: SeqCap EZ Share Developer
    Design Name: 120911_Switchgrass_GLBRC_R_EZ_HX1
    Internal Reference #: 4000021240
  • Material Number:
    24 Rxn: 08333025001
    96 Rxn: 08333033001
    384 Rxn: 08333050001

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  • SeqCap EZ Design: Soy Exome Design
  • Organism: Soy
  • Genome Build: Joint Genome Institute
  • Design File: Soy Exome Design (9.9 MB .zip)
  • Collaborator: Roche NimbleGen
  • Specifications/Details: The Soy Exome is an 85.3Mb design that targets 95.3% of the bases associated to the exon of 46,367 soy genes. We recommend the use of SeqCap EZ Developer Reagent (Cat. No.06684335001) for effective enrichment of the soybean exome.
  • Publications/Information:
  • Ordering Information:
    Product Name: SeqCap EZ Share Developer
    Design Name: 120403_Gmax_Exome_EZ_HX1
    Internal Reference #: 4000007450
  • Material Number:
    24 Rxn: 08333025001
    96 Rxn: 08333033001
    384 Rxn: 08333050001

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Metabolic Disease

  • SeqCap Epi Developer XL Design: 131010_HG19_EG_met_EPI
  • Organism: Homo sapiens (human)
  • Genome Build: GRCh37/hg19
  • Design File: McGill_human_disease_methylome.zip (10 Mb .zip)
  • Collaborator: Dr. Elin Grundberg, McGill University and Genome Quebec Innovation Centre, Department of Human Genetics, McGill University, Montreal, Quebec, Canada
  • Specifications/Details: The panel targets 156Mb of sequence spanning ~4.5 million unique CpGs ( ~9 million total CpGs) and ~3 million autosomal SNPs from dbSNP137 allowing researchers to do simultaneous epigenome- and genome wide association studies focusing on metabolic diseases and related traits.
    • The regions targeted by the panel aim to cover the functional methylome including:
      • CpGs contained within low and unmethylated regions identified from large-scale whole-genome bisulfite sequencing data from human adipose tissue and associated with enhancers and promoters, respectively.
      • Additional CpGs located within human adipocyte regulatory elements (H3K4me1 and H3K4me3 marking enhancers and promoters, respectively) profiled by the NIH Roadmap Epigenomics Mapping Consortium.
      • All ~480,000 CpGs from the Illumina 450K array.
    • Of the ~3 million SNPs covered by the panel, the following variants are included:
      • About 30,000 regions covering metabolic disease associated GWAS loci from the NHGRI GWAS catalog (9 January, 2014)
      • About 250,000 highly-informative genome-wide tag SNPs found across diverse world populations from the Illumina HumanCore BeadChip.
  • Ordering Information:
    Product Name: SeqCap Epi Developer XL
    Design Name: 131010_HG19_EG_met_EPI
    Internal Reference #: 4000019550

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  • Ordering Information
    Product Name: SeqCap EZ Share Developer 
  • Design Name: 140910_GRCh38_chrM_v1_EZ
    Internal Reference #: 4000021490
  • Material Number:
    24 Rxn: 08333025001
    96 Rxn: 08333033001
    384 Rxn: 08333050001

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Gene Regulation

  • SeqCap EZ Design: 50 Mb Human UTR Design
  • Organism: Human
  • Genome Build: HG19
  • Design File: 50 Mb Human UTR Design (5.4Mb .zip)
  • Specifications/Details: UTRs are untranslated regions on the 5’ and 3’ side of genes. The 3’ UTR contains regulatory elements that are involved in the control of expression of many genes. This design is a 50Mb capture library targeting these regions.
  • Ordering Information
    Product Name: SeqCap EZ Share Choice XL
    Design Name: 120501_HG19_RefSeq_Ensembl_UTRs_EZ_HX1
    Internal Reference #: 4000007100
  • Material Number:
    24 Rxn: 08332991001
    96 Rxn: 08333009001
    384 Rxn: 08333017001

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Neurology

  • SeqCap EZ Design: Neurology Panel Design
  • Organism: Human
  • Genome Build: HG19
  • Design File: Neurology Panel Design (154 KB .zip)
  • Specifications/Details: The Neurology Panel Design is a 1.5Mb design and targets 256 genes associated with 87 neurological disorders. The genes were gathered from the National Institute of Neurological Disorders and Stroke and NCBI Gene Tests databases.
  • Ordering Information:
    Product Name: SeqCap EZ Share Choice
    Design Name: 120522_HG19_Neuro_R_EZ
    Internal Reference #: 4000007090
  • Material Number:
    24 Rxn: 08332967001
    96 Rxn: 08332975001
    384 Rxn: 08332983001

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MHC/HLA

  • SeqCap EZ Design: Human MHC Design
  • Organism: Human
  • Genome Build: HG19
  • Design File: Human MHC Design (271 KB .zip)
  • Collaborator: BGI
  • Specifications/Details: Targets the MHC region (3.37Mb), 1.6Mb of regions surrounding the MHC, and 8 known haplotypes with a total design of 4.97Mb.
  • Ordering Information
    Product Name: SeqCap EZ Share Choice
    Design Name: 110729_HG19_MHC_L2R_D03_EZ
    Internal Reference #: 4000032110
  • Material Number:
    24 Rxn: 08332967001
    96 Rxn: 08332975001
    384 Rxn: 08332983001

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