SeqCap Shared Designs

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SeqCap Shared Designs

Shared designs makes it simple to access pre designed NGS panels from researchers around the world. These custom target enrichment designs were developed and shared by researchers like you. Built upon our empirically optimized probe design algorithms, this continuously expanding collection features designs made to suit the specific/specialized needs of demanding applications including oncology, human genetics, agriculture and other research applications.

The designs are the result of combining the design expertise of Roche with the scientific experience of expert researchers in various fields. If you would like to share your design on this page, please contact your local sales representative.

New Designs

We are pleased to announce  a new Inherited Disease Panel. This panel was designed and curated by researchers at the Dallas Children’s Hospital and covers over 4,100 genes.

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

Human Designs

SeqCap EZ Exome v2.0 Design
  • 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 Choice XL
Design Name: 110208_HG19_CCDS_exome_V2_1_5_EZ
Reference #: IRN# 4000016420

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Inherited Disease Panel
  • Organism: Human
  • Genome Build: HG38
  • Design Files: IDP Design
  • Demo Data: available, please contact your local Roche office
  • Collaborator: Dallas Children's Hospital
  • 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 Dallas Children's Hospital. Total design size (hg38) is 9.0 Mb primary target and 11.8 Mb capture target.

 

Ordering Information

Product Name: SeqCap EZ Choice XL
Design Name: 150803_HG38_IDP2_REZ_HX3
Reference #: IRN# 4000024240

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Comprehensive Cancer Design
  • SeqCap EZ Design: Comprehensive Cancer Design
  • Organism: Human
  • Genome Build: HG19
  • Design File: Comprehensive Cancer Design (362 KB .zip)
  • Collaborator: Roche NimbleGen
  • 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.

Publications/Information

Comprehensive Cancer Design Flyer

Ordering Information

Product Name: SeqCap EZ Choice Library
Design Name: 120522_HG19_Onco_R_EZ
Reference #: 4000007080

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Neurology Panel Design
  • SeqCap EZ Design: Neurology Panel Design
  • Organism: Human
  • Genome Build: HG19
  • Design File: Neurology Panel Design (154 KB .zip)
  • Collaborator: Roche NimbleGen
  • 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.

Publications/Information

Neurology Panel Design Flyer

Ordering Information

Product Name: SeqCap EZ Choice Library
Design Name: 120522_HG19_Neuro_R_EZ
Reference #: 4000007090

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50 Mb Human UTR Design
  • SeqCap EZ Design: 50 Mb Human UTR Design
  • Organism: Human
  • Genome Build: HG19
  • Design File: 50 Mb Human UTR Design (5.4Mb .zip)
  • Collaborator: Roche NimbleGen
  • 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.

Publications/Information

SeqCap EZ Exome +UTR Flyer

Ordering Information

Product Name: SeqCap EZ Choice XL Library
Design Name: 120501_HG19_RefSeq_Ensembl_UTRs_EZ_HX1
Reference #: 4000007100

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Human MHC Design
  • SeqCap EZ Design: Human MHC Design
  • Organism: Human
  • Genome Build: HG19
  • Design File: Human MHC Design (271 KB .zip)
  • Collaborator: Roche NimbleGen/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.

Publications/Information

Press Release
Technical Note: Capturing Complex Human Genetic Variations using the GS FLX+ System

Ordering Information

Product Name: SeqCap EZ Choice Library
Design Name: 110729_HG19_MHC_L2R_D03_EZ
Reference #: 9999042755

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Mitochondrial Genome Design
  • SeqCap EZ Design: Mitochondrial Genome Design
  • Organism: Human
  • Genome Build: HG38
  • Design Files: 
  • Collaborator: Roche NimbleGen
  • Specifications/Details: This is a 16 Kb capture design that targets the entire mitochondrial genome. The design is based on hg 38 annotation source.

Publications/Information

Tech Note: How To Target the Mitochondrial Genome with MedExome?

Ordering Information

Product Name: SeqCap EZ Developer 
Design Name: 140910_GRCh38_chrM_v1_EZ
Reference #: IRN# 4000021490

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Non-Human Designs

Switchgrass Exome Design
  • 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

Nucleotide polymorphism and copy number variant detection using exome capture and next-generation sequencing in the polyploid grass Panicum virgatum
The Plant Journal, (2014), 79, 993-1008

Ordering Information

Product Name: SeqCap EZ Developer
Design Name: 120911_Switchgrass_GLBRC_R_EZ_HX1
Reference #: IRN 4000021240

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Maize Exome Design
  • SeqCap EZ Design: Maize Exome
  • Organism: Maize
  • Genome Build: Maize (B73 and Mo17)
  • 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

Webinar - Efficient SNP Discovery for Crop Genomes through Exome Sequencing

Ordering Information

Product Name: SeqCap EZ Developer Library
Design Name: 130614_Maize_ISU_RNG_Zeaome_EZ_HX1
Reference #: 4000020170

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Barley Exome Design
  • SeqCap EZ Design: Barley Exome
  • Organism: Barley
  • Genome Build: Hordeum vulgare (various), see provided file barley_mapping_sequence.fa
  • Design File: Barley Exome Design (42 MB .zip)
  • Collaborator: Wheat Barley Exome Consortium (WBEC)
  • Specifications/Details: The Barley Exome design is a consortium derived design, based on the mRNA coding exome from multiple sources with a total design size of 88.6 Mb. 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

Barley whole exome capture: a tool for genomic research in the genus Hordeum and beyond
A physical, genetic and functional sequence assembly of the barley genome
Webinar - Efficient SNP Discovery for Crop Genomes through Exome Sequencing

Ordering Information

Design Name: 120426_Barley_BEC_D04

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Wheat Exome Design
  • 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

Webinar - Efficient SNP Discovery for Crop Genomes through Exome Sequencing

Ordering Information

Design Name: 120426_Wheat_WEC_D02

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Soy Exome Design
  • 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

Soybean Exome Capture-Technical Note

Ordering Information

Product Name: SeqCap EZ Developer Library
Design Name: 120403_Gmax_Exome_EZ_HX1
Reference #: 4000007450

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Mouse Exome Design
  • 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

Mutation discovery in mice by whole exome sequencing.
Massively parallel sequencing of the mouse exome to accurately identify rare, induced mutations: an immediate source for thousands of new mouse models.

Ordering Information

Product Name: SeqCap EZ Developer Library
Design Name: 110624_MM9_Exome L2R_D02_EZ_HX1
Reference #: 9999042611

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Pig Exome Design
  • 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

Design and development of exome capture sequencing for the domestic pig (Sus scrofa)

Ordering Information

Product Name: SeqCap EZ Developer Library
Design Name: 130104_Sscr_10_2_MW_EZ_HX1
Reference #: 4000017630

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Canine Exome Design
  • SeqCap EZ Design: Canine Exome
  • Organism: Canis familiaris
  • Genome Build: CanFam3.1
  • Collaborators: Bart Broeckx, Christophe Hitte, Thomas Derrien, Jessica Nieuwerburgh, Dieter Deforce
  • Specifications/Details: The Canine Exome design combines the exons of the CanFam 3.1 Ensembl annotation, more recently discovered protein coding exons and a variety of non-coding RNA regions (microRNAs, long non-coding RNAs and antisense transcripts), leading to a total size of approximately 152 Mb. This design originated from a collaboration between Ghent University, Université Rennes1, Broad Institute of MIT, Harvard University and Uppsala University. For additional information, see Broeckx et al. (2015).

Publications / Information

Improved canine exome designs, featuring ncRNAs and increased coverage of protein coding genes

Development and performance of a targeted whole exome sequencing enrichment kit for the dog (Canis Familiaris Build 3.1)

Ordering Information

Product Name: SeqCap EZ Developer
Design Name: 140702_canFam3_exomeplus_BB_EZ_HX1
Reference #: IRN 4000022470 

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