Sequence capture is used to enrich genomic regions of interest, thereby reducing the sequencing depth (and cost) needed to obtain a given coverage level. Capture baits are oligonucleotides that are used to pull-down complementary DNA through hybridization. Both custom and pre-designed capture baits are available from several vendors (listed in the Vendor Options tab), for a variety of applications.
Exome sequencing is a common application of sequence capture that enriches for exons, the coding region of expressed genes. As an example, the human exome constitutes about 1% of the total genome size. A variety of pre-defined exome panels, or expanded exome panels, are available from Agilent, Roche (NimbleGen), and Illumina, as detailed in the Vendor Options tab.
The SeqCap Epi workflow from Roche (NimbleGen) is available to capture DNA for methylation analysis. Following library creation, DNA is bisulfite treated and then amplified before capture. The capture probes are designed to target both methylated and unmethylated DNA, allowing for downstream analysis of epigenetic modifications in large genomic regions or whole exomes.
While many off-the-shelf options exist, it is often desirable or necessary to develop a custom capture for a specific target or organism. We have significant experience working with vendors to develop baits for these custom projects. We can coordinate and carry-out your entire project, from the design phase through data delivery. Please inquire.
Sequence capture projects include two costs:
In the Pricing tab, we show the costs for the first portion using workflows from Agilent, Roche (NimbleGen), or IDT. For the additional costs associated with baits, please inquire.
Contact Ben Auch: firstname.lastname@example.org.
|Seq-Cap Library Creation: Agilent/NimbleGen/IDT.|
|Very High Scale.||49-any||sample||$102.91||$121.34|
There are more bait options offered by vendors than we can list here. Please contact us for more information.
Please contact email@example.com for project specifications.
Once project details are finalized, complete appropriate submission form for submitting samples or submitting client-made libraries and email to firstname.lastname@example.org.
Samples should be frozen and shipped on dry ice in a 96-well plate. We recommend using plate tape to seal the wells. Place the plate inside of a plastic bag prior to placing on dry ice. Please give advance notice of submission date and time so staff can be prepared to receive samples. If shipping samples from outside the University of Minnesota, ship via express shipping carrier on dry ice to the address below:
1-202 Nils Hasselmo Hall (Minneapolis campus)
1-210 Cancer & Cardiovascular Research Building (Minneapolis campus)
20 Snyder Hall (St. Paul campus)
Please send the tracking information to email@example.com.
University of Minnesota Genomics Center
1475 Gortner Avenue
28 Snyder Hall
St. Paul, MN 55108
Sequence capture projects are considered custom projects and not subject to standard turnaround times. Please contact Ben Auch firstname.lastname@example.org to inquire about availability and estimated turnaround for specific projects.
|Species||Array Name||Product Design|
|SeqCap EZ System|
|Human||SeqCap EZ MedExome Enrichment Kit||is a 47Mb whole exome enrichment design that targets the latest genomic annotation GRCh38/hg38. The product provides comprehensive sequencing coverage of medically-relevant regions and protein coding regions|
|Human||SeqCap EZ Human Exome Enrichment Kit v3.0||is a 64Mb sequence capture design that enables the discovery of more coding variants. It is based on the human genome build GRCh37/hg19. SeqCap EZ Exome Plus configuration provides you with a 64 Mb exome capture with the ability to add up to 50 Mb of your custom targets.|
|Human||SeqCap EZ Human Exome Enrichment Kit v2.0||The SeqCap EZ Human Exome Kit v2.0, as part of the SeqCap EZ Enrichment System, enables enrichment of the whole exome. This kit captures 44.1 Mb of target.|
|Human||SeqCap EZ Exome +UTR Enrichment Kit||The SeqCap EZ Human Exome + UTR Kit, as part of the SeqCap EZ Enrichment System, enables enrichment of 64 Mb of coding exons and miRNA regions, plus 32 Mb of untranslated regions (UTRs).|
|Human||SeqCap EZ Exome Plus Enrichment Kit||The SeqCap EZ Exome Plus Kit, as part of the SeqCap EZ Enrichment System, enables enrichment of 64 Mb of coding exons and miRNA regions, plus up to 200 Mb of custom targets.|
|Human||SeqCap HGSC VCRome||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.|
|SeqCap EZ Design|
|Human||Comprehensive Cancer Design||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.|
|Human||Neurology Panel Design||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.|
|Human||50 Mb Human UTR Design||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.|
|Human||Human MHC Design||Targets the MHC region (3.37Mb), 1.6Mb of regions surrounding the MHC, and 8 known haplotypes with a total design of 4.97Mb.|
|Human||Mitochondrial Genome Design||This is a 16 Kb capture design that targets the entire mitochondrial genome. The design is based on hg 38 annotation source.|
|Switchgrass||Switchgrass Exome Design||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|
|Maize||Maize Exome Design||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.|
|Barley||Barley Exome Design||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.|
|Wheat||Wheat Exome Design||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.|
|Soy||Soy Exome Design||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.|
|Mouse||Mouse Exome Design||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.|
|Pig||Pig Exome Design||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 ÒexomeÓ 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.|
|Canine||Canine Exome Design||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, IGDR-CNRS (UniversitŽ Rennes), Broad Institute of MIT and Harvard and Uppsala University. For additional information, see Broeckx et al. (2015).|
|Product||Description||Number of Reactions||URL|
|OneSeq||OneSeq Constitutional Research Panel: Comprised of 300 kb functional copy number resolution genome-wide, with higher resolution of 25-50 kb in disease-associated ClinGen regions, copy-neutral LOH as small as 5 Mb, PLUS gene targets from the SureSelect Focused Exome panel. Coding sequence data and copy number variants in one capture with 7Gb of sequencing providing deep and comprehensive coverage: >95% at 20x.||16 or 96||http://www.genomics.agilent.com/en/OneSeq-DNA-Target-Enrichment-Baits-NEW-/Constitutional-Research-Panel/?cid=AG-PT-194&tabId=AG-PR-1330|
|SureSelect XT||The SureSelectXT Reagent Kit enables post-capture pooling of enriched sequencing-ready libraries. This protocol enables the generation of libraries from either standard 3ug sample input, providing the highest complexity libraries, or lower 200ng input providing compatibility with samples of limited availability. With one library per capture, maximal efficiency and complexity is enabled providing deep coverage of regions of interest facilitating confident variant calling.||16 or 96||http://www.genomics.agilent.com/en/SureSelect-DNA-Library-Preps/SureSelectXT-Reagent-Kits/?cid=AG-PT-177&tabId=AG-PR-1302|
|SureSelect QXT||The SureSelectQXT Reagent Kit is a combined shearing-free transposase-based library prep and target enrichment solution that enables a 90-minute hybridization step, the fastest in the market, resulting in sequencing-ready libraries in less than a day. This highly streamlined protocol which requires only 3.5 hrs of hands-on time. With one library per capture, the generation of high quality sequencing-ready libraries from only 50 ng sample input is enabled providing faster time-to-answers.||16 or 96||http://www.genomics.agilent.com/en/SureSelect-DNA-Library-Preps/SureSelectQXT-Reagent-Kits/?cid=AG-PT-177&tabId=AG-PR-1303|
|SureSelect XT2||The SureSelectXT2 Reagent Kit enables pooling of DNA libraries prior to capture resulting in a streamlined protocol requiring less hands-on time: 8 precapture libraries into 1 exome capture, 16 libraries into 1 custom capture. This protocol enables the generation of sequencing-ready libraries from either standard 1 ug sample input, providing libraries of good complexity, or lower 100 ng input providing compatibility with samples of limited availability.||16 or 96||http://www.genomics.agilent.com/en/SureSelect-DNA-Library-Preps/SureSelectXT2-Reagent-Kits/?cid=AG-PT-177&tabId=AG-PR-1301|
|RNA - SureSelect||agilent’s SureSelect Strand Specific RNA Library Preparation Kit is the highest sensitivity, strand-specific method for preparing libraries for mRNA or targeted RNA-seq, enabling a greater understanding of gene regulation.||16 or 96||http://www.genomics.agilent.com/en/SureSelect-Gene-Regulation-/RNA-Seq/?cid=AG-PT-178&tabId=prod170017|