This cutting-edge technology utilizes a single tube of stable DNA oligos to capture all exons in solution, comes with a simple, scalable workflow, and includes built-in controls to evaluate capture performance. With 2.1 million DNA probes, which are empirically optimized, SeqCap EZ Exome Library delivers a high level of performance and substantial savings on sequencing. Compared with other exon enrichment methods, significantly fewer sequencing runs are required to achieve the same or better SNP detections; consequently, researchers can save on total budget, or include more samples in the study.

Better Coverage with Less Sequencing

• Greater coverage and uniformity using 2.1 million optimized DNA probes (>10 probes/exon on average).
• Saves on sequencing compared to other methods.

Easy and Scalable Workflow

• Target the exome using a single tube of stable DNA oligos.
• Capture up to 96 samples in a microplate with a truly scalable workflow.
• Set up the enrichment reaction with fewer steps and minimize evaporation with 47°C hybridization.

Built-in Controls to Evaluate Capture Performance

• Measure enrichment success before sequencing.

Table 1

Sequencing Output	1 Lane	2 Lanes	4 Lanes
Total Sequence (Gb)	1.2	2.8	5.5
Total Number of Reads (million)*	15.2	35.5	69.2
% read on Target	60.8%	60.2%	61.9%
% Target Base Covered by 1+ Reads	96.4%	97.5%	98.2%
% Target Base Covered by 5+ Reads	86.0%	92.9%	96.3%
% Target Base Covered by 10+ Reads	70.7%	86.3%	93.6%
Detection Rate for Known Heterozygous SNPs in Exon Targets (6318)	88.8%	95.4%	97.9%
Detection Rate for Known Homozygous SNPs in Exon Targets (4787)	94.3%	96.3%	97.3%
* This is total number of raw sequence reads (paired-end 2x40 base reads). The reads are filtered for uniquely mapped reads for downstream SNP analysis.

Table 1. SNPs are readily detected by targeted sequencing on samples prepared by SeqCap EZ Exome. HapMap sample NA12762 was used in this experiment, and the sequencing data was analyzed with Short Oligonucleotide Alignment Package (SOAP).

Figure 1

Figure 1. SeqCap EZ Exome provides better coverage with less sequencing compared to another exome enrichment method. The 10+ coverage plots are more relevant for experiments aimed at discovering novel and rare SNPs because multiple reads (at least 8 or 10 reads) are needed to detect a heterozygous SNP reliably. Coverage for SeqCap EZ Exome is from the same data set as shown in Table 1.

Catalog Number	Pack Size	Name
05977215001	4	SeqCap EZ Human Exome Library SR, 4 reactions
05977223001	48	SeqCap EZ Human Exome Library SR, 48 reactions
05933374001	4	SeqCap EZ Human Exome Library LR, 4 reactions
05933382001	48	SeqCap EZ Human Exome Library LR, 48 reactions
The design targets 180,000 coding exons (from CCDS database) and ~550 miRNA exons (from miRBase). SeqCap EZ Human Exome Library SR is optimized for short read sequencing. SeqCap EZ Human Exome Library LR is optimized for long read sequencing with the 454 Sequencing System.

General Documents

• NimbleGen Sequence Capture
  Brochure (PDF Format 2MB)
• NimbleGen Array Capture Outperforms Two Target-Enrichment Methods in ABRF Research Group Comparison
  Reprint - GenomeWeb InSequence (PDF Format 107KB)
• Comparison of Enrichment Technologies for Targeted Resequencing of Custom Regions
  Technical Note (PDF Format 552KB)
• Sequence Capture Custom Designs: Guide to Submitting Your Target Sequence
  User’s Guide (PDF Format 906KB)

SeqCap EZ Exome Documents

• SeqCap EZ Exome Library & 454 GS FLX Titanium Series
  Sales Flyer (PDF Format 1.5MB)
• SeqCap EZ Exome Library LR
  User’s Guide (PDF Format 712KB)
• SeqCap EZ Exome for Short Read Sequencing
  Sales Flyer (PDF Format 1.1MB)
• SeqCap EZ Exome Library SR (Version 1.2)
  User’s Guide (PDF Format 1.4MB)

Delivery Workflow Documents

• NimbleGen 454 Optimized Sequence Capture 385K Arrays
  Sales Flyer (PDF Format 473KB)
• NimbleGen Sequence Capture 2.1M Human Exome Array
  Sales Flyer (PDF Format 977KB)
• NimbleGen Sequence Capture 385K Version 2.0 Arrays: Custom Human Arrays for Delivery
  Sales Flyer (PDF Format 309KB)
• NimbleGen Sequence Capture 2.1M and 385K Arrays: Equipment and Reagent Requirements
  Sales Flyer (PDF Format 247KB)
• NimbleGen Arrays User’s Guide: 454 Optimized Sequence Capture Array Delivery (Version 1.1)
  User’s Guide (PDF Format 1.3MB)
• NimbleGen Arrays User’s Guide: Sequence Capture Array Delivery (Version 3.2)
  User’s Guide (PDF Format 3.4MB)
• 2.1M Human Exome Annotation Files
  Annotation Files (ZIP Format 8.7MB)
  What files are included in this download?

Service Workflow Documents

• NimbleGen Sequence Capture - Full Service Solution
  Sales Flyer (PDF Format 275KB)
• NimbleGen Services User’s Guide: Sequence Capture Service (Version 3.0)
  User’s Guide (PDF Format 2.2MB)
• NimbleGen Sequence Capture 2.1M Human Exome Array
  Sales Flyer (PDF Format 977KB)

For a complete listing of literature covering all Roche NimbleGen products and services please visit our literature page.

Hide All Topics     Show All Topics

Experimental Design

Can I send my gDNA samples to a service provider for genomic enrichment in my area? Roche NimbleGen is currently establishing certified service providers (CSP) globally. Please click here to check for available CSPs in your area. How much total sequence can I capture on your NimbleGen Sequence Capture 2.1M and 385K custom arrays? The maximum amount of sequence that our current NimbleGen Sequence Capture 2.1M arrays can capture is 30Mb. Our 385K arrays can capture up to 5Mb. What organisms does Roche NimbleGen currently accept for NimbleGen Sequence Capture service? At this time, we are only accepting genomic DNA from human through full service. In principle this method should work with any species where a sequenced genome is available, and we continue to work on developing and evaluating optimized protocols for both services as well as products that will enable capture of targeted DNA from other species. If you are interested in developing your own protocol for use of NimbleGen products or services with other species, we strongly recommend performing initial pilot studies before embarking on large-scale projects. What level of training does Roche NimbleGen provide for Sequence Capture Array delivery? Customers interested in being trained on the Sequence Capture protocol can take part in a 3 day on-site customer workshop conducted by our certified trainers. For more details contact your local Roche NimbleGen Sales representative. Can I perform Sequence Capture on organisms other than human using Array Delivery? Performing Sequence Capture on other organisms can be done by ordering Sequence Capture arrays for delivery. However, Roche NimbleGen does not support the use of these arrays for Sequence Capture. QC tests must be developed by the researcher to ensure a successful capture. What types of sequence are researchers typically capturing when applying this technology to their research? The types of sequences that researchers are capturing typically fall into two distinct categories: discontiguous and contiguous. Examples of discontiguous regions include exons, promoters, and enhancers. A classic example of a contiguous region would be a disease associated region (DAR), such as the BRCA1 locus, in which you could look at different intervals sequence coverage around the gene. Why should I use NimbleGen Sequence Capture microarrays instead of various PCR methods as a preparative tool for next-generation sequencing? The severe costs, performance limitations, and extensive amount of labor required for large-scale PCR experiments makes taking full advantage of the capacity of next-generation sequencers virtually impossible. With NimbleGen Sequence Capture arrays, you can reduce the complexity of your genome in a matter of weeks all while saving considerable time and money. Are there any publications demonstrating the reproducibility and robustness of NimbleGen Sequence Capture technology? Yes, there are an ever-increasing number of publications. Click here to view the list of current publications citing the use of NimbleGen Sequence Capture technology.

Array Design

How do I generate a target sequence list of coordinates for a custom design? Roche NimbleGen provides a guide for generating and submitting target sequences for your custom design. Click here to find out more. How do I go about designing a custom NimbleGen Sequence Capture array? Once you place an order, you will complete our Design Specification form indicating what regions (chromosome, tiling start position, and tiling stop position) you would like tiled on the array. Once our Bioinformatics scientists have designed the array, they will send it to you for approval. What human genome build is Roche NimbleGen using to design a Sequence Capture custom array? We are using the HG18 build. Will I be able to design a custom NimbleGen Sequence Capture array that targets repetitive regions? No, at this time we are only designing probes that cover unique regions of the human genome. What genomic database is acceptable for submitting my design coordinates? At this time we are only accepting genomic coordinates for custom design using the UCSC database. Who owns the designs for the sequence capture arrays? The design that we create for each NimbleGen Sequence Capture array - whether that array is delivered to customers for their own use or we use it in performing a service for the customer - is proprietary to and the property of Roche NimbleGen. Can I re-use NimbleGen Sequence Capture arrays? No, we do not recommend re-use at this time.

Sample Requirements

What are the sample requirements for a NimbleGen Sequence Capture 385K or HD2 Exome full service experiment? We require at least 21μg human genomic DNA at a concentration of 250-500ng/μl per array. The A260/A280 ratio should be at least 1.8 And the A260/A230 ratio should be at least 1.9. Also, the genomic DNA should not show a smear when analyzed on a bioanalyzer. What if my submitted genomic DNA samples are less then required? If your samples do not meet our QC requirements you will be contacted by Roche NimbleGen for replacement samples. Do you accept whole-genome amplified genomic DNA? No, at this time we are only accepting unamplified genomic DNA.

Deliverables

After the Roche NimbleGen Service Lab captures my desired sequences, what do I get back? You will receive 6μg of amplified DNA (by LM-PCR), which can be used directly for next-generation, high-throughput sequencing. What types of QC information and supporting data files will I receive after my sequences are captured? You will receive a report on sequence capture yield and the level of enrichment. Also included are a list of regions targeted by the array design (.gff and .bed), a coverage summary.txt file showing coverage of the design by probes, and a User's Guide that describes how to sequence the captured DNA using the 454 Genome Sequencer FLX Instrument and either GS FLX Standard series kits or GS FLX Titanium Series kits. GFF files can be anaylyzed with Roche NimbleGen SignalMap software. A free, 30-day demo version of SignalMap software is available for download. Will the Array Delivery User’s Guide that is optimized for human Sequence Capture be publically available for capture of other organisms (for empirical protocol development)? Yes, the User’s Guide (Version 3.2) is available for download from the Sequence Capture homepage.

Downstream Applications

What regions can be captured by this technology? These can be any regions in the genome, either contiguous, such as disease associated regions, or non-contiguous, such as exons of a candidate gene panel. Please note that, in our technology development efforts, we currently only design probes against unique parts of the genome, although some repetitive regions can be captured by the array and sequenced with long reads from 454 Genome Sequencer FLX technology if they flank unique regions. The total size of captured regions per array can vary from a few hundred kilobases to 30Mb using 385K and 2.1M arrays. For more information on the current technology status, please see: Direct selection of human genomic loci by microarray hybridization (Nat Methods. 2007 Nov;4(11):903-5). Will this technology be compatible with all next-generation sequencing platforms? The Roche NimbleGen Sequence Capture method yields the highest quality results when used in conjunction with a sequencing technology that can deliver sequence read lengths in excess of 400bp because long reads enable comprehensive variant detection. To supply our customers with an affordable, high-quality solution, we have been working closely with 454 Life Sciences, to develop, test, validate, and optimize protocols for obtaining enriched DNA that can be directly and easily integrated into the workflow of the 454 Genome Sequencer FLX Instrument. The 454 Genome Sequencer FLX Instrument with GS FLX Titanium Kits delivers read lengths of 400bp (500MB raw sequence per PTP) and is the most appropriate sequencing technology for the NimbleGen Sequence Capture solution. Other early customers are working on modified protocols to enable use of NimbleGen Sequence Capture arrays and reagents with other sequencing platforms; however, these protocols have not been internally validated by Roche NimbleGen. What is the advantage of using this technology? For most studies that require resequencing of large regions of the genome, this technology will clearly offer significant benefits in terms of cost and time, particularly when compared with multiplex and/or long-range PCR. Please contact your local Roche NimbleGen sales representative for a quote.

Future Developments

Is Roche NimbleGen optimizing their Sequence Capture technology with any of the next-generation sequencing platforms? Yes, we are currently developing 385K Sequence Capture products that use a protocol optimized for the 454 GS FLX Instrument using GS FLX Titanium Series Kits. This provides a seamless transition from capture into sequencing since no library preparation needs to be performed after array capture. Captured fragments are ready to go into the emPCR Amplification step.

		Contact Information
Email	*
First Name	*
Last Name	*
Organization	*
Department
Address Line 1	*
Address Line 2
City	*
State/Province	*
ZIP/Postal Code	*
Country	*	United States Albania Algeria American Samoa Andorra Angola Anguilla Antarctica Antigua And Barbuda Argentina Armenia Aruba Australia Austria Azerbaijan Bahamas, The Bahrain Bangladesh Barbados Belarus Belgium Belize Benin Bermuda Bhutan Bolivia Bosnia and Herzegovina Botswana Bouvet Island Brazil British Indian Ocean Territory Brunei Bulgaria Burkina Faso Burundi Cambodia Cameroon Canada Cape Verde Cayman Islands Central African Republic Chad Chile China Christmas Island Cocos (Keeling) Islands Colombia Comoros Congo Congo, Democractic Republic of the Cook Islands Costa Rica Cote D'Ivoire (Ivory Coast) Croatia (Hrvatska) Cuba Cyprus Czech Republic Denmark Djibouti Dominica Dominican Republic East Timor Ecuador Egypt El Salvador Equatorial Guinea Eritrea Estonia Ethiopia Falkland Islands (Islas Malvinas) Faroe Islands Fiji Islands Finland France French Guiana French Polynesia French Southern Territories Gabon Gambia, The Georgia Germany Ghana Gibraltar Greece Greenland Grenada Guadeloupe Guam Guatemala Guinea Guinea-Bissau Guyana Haiti Heard and McDonald Islands Honduras Hong Kong S.A.R. Hungary Iceland India Indonesia Iran Iraq Ireland Israel Italy Jamaica Japan Jordan Kazakhstan Kenya Kiribati Korea Korea, North Kuwait Kyrgyzstan Laos Latvia Lebanon Lesotho Liberia Libya Liechtenstein Lithuania Luxembourg Macau S.A.R. Macedonia, Former Yugoslav Republic of Madagascar Malawi Malaysia Maldives Mali Malta Marshall Islands Martinique Mauritania Mauritius Mayotte Mexico Micronesia Moldova Monaco Mongolia Montserrat Morocco Mozambique Myanmar Namibia Nauru Nepal Netherlands Antilles Netherlands, The New Caledonia New Zealand Nicaragua Niger Nigeria Niue Norfolk Island Northern Mariana Islands Norway Oman Pakistan Palau Panama Papua new Guinea Paraguay Peru Philippines Pitcairn Island Poland Portugal Puerto Rico Qatar Reunion Romania Russia Rwanda Saint Helena Saint Kitts And Nevis Saint Lucia Saint Pierre and Miquelon Saint Vincent And The Grenadines Samoa San Marino Sao Tome and Principe Saudi Arabia Senegal Seychelles Sierra Leone Singapore Slovakia Slovenia Solomon Islands Somalia South Africa South Georgia And The South Sandwich Islands Spain Sri Lanka Sudan Suriname Svalbard And Jan Mayen Islands Swaziland Sweden Switzerland Syria Taiwan Tajikistan Tanzania Thailand Togo Tokelau Tonga Trinidad And Tobago Tunisia Turkey Turkmenistan Turks And Caicos Islands Tuvalu Uganda Ukraine United Arab Emirates United Kingdom United States United States Minor Outlying Islands Uruguay Uzbekistan Vanuatu Vatican City State (Holy See) Venezuela Vietnam Virgin Islands (British) Virgin Islands (US) Wallis And Futuna Islands Yemen Zambia Zimbabwe
Phone	*
		Experiment Details
Product Interest	*	SeqCap EZ Exome Library LR (Long Read) SeqCap EZ Exome Library SR (Short Read) Sequence Capture Human Exome 2.1M Array Sequence Capture Human Custom 2.1M Array 454 Optimized Sequence Capture 385K Array Sequence Capture 385K Array
Workflow	*	Delivery Service
Cumulative Targeted Regions (Mb)	*
Array Format	*	2.1M (between 5MB and 30MB) 385K (less than 5MB)
Number of Samples	*
Sequencing Platform	*
Additional information about your experiment.
		Other Information
Where did you hear about us?		Advertisement Conference or Tradeshow Direct Mail Publication or Press Release Seminar Web Word of Mouth or Colleague Recommendation Sales Person Called Me
Promo Code
	*	Required field.