Description

This set of tracks shows the genomic positions of probes and targets from a full suite of in-solution-capture target enrichment exome kits for Next Generation Sequencing (NGS) applications. Also known as exome sequencing or whole exome sequencing (WES), this technique allows high-throughput parallel sequencing of all exons (e.g., coding regions of genes which affect protein function), constituting about 1% of the human genome, or approximately 30 million base pairs.

The tracks are intended to show the major differences in target genomic regions between the different exome capture kits from the major players in the NGS sequencing market: Illumina Inc., Roche NimbleGen Inc., Agilent Technologies Inc., MGI Tech, Twist Bioscience, and Integrated DNA Technologies Inc..

Display Conventions and Configuration

Items are shaded according to manufacturing company:

• IDT (Integrated DNA Technologies)
• Twist Biosciences
• MGI Tech (Beijing Genomics Institute)
• Roche NimbleGen
• Agilent Technologies
• Illumina

Tracks labeled as Probes (P) indicate the footprint of the oligonucleotide probes mapped to the human genome. This is the technically relevant targeted region by the assay. However, the sequenced region will be bigger than this since flanking sequences are sequenced as well. Tracks labeled as Target Regions (T) indicate the genomic regions targeted by the assay. This is the biologically relevant target region. Not all targeted regions will necessarily be sequenced perfectly; there might be some capture bias at certain locations. The Target Regions are those normally used for coverage analysis.

Note that most exome probesets are available on hg19 only. If you are working with hg38 and cannot find a particular probeset there, try to go to hg19, configure the same track, and see if it exists there. If you cannot find an array, do not hesitate to send us an email with the name of the manufacturer website with the probe file. If an array is available on hg19 but not on hg38 and you need it for your work, we can lift the locations. Our mailing list can be reached at genome@soe.ucsc.edu.

Methods

The capture of the genomic regions of interest using in-solution capture, is achieved through the hybridization of a set of probes (oligonucleotides) with a sample of fragmented genomic DNA in a solution environment. The probes hybridize selectively to the genomic regions of interest which, after a process of exclusion of the non-selective DNA material, can be pulled down and sequenced, enabling selective DNA sequencing of the genomic regions of interest (e.g., exons). In-solution capture sequencing is a sensitive method to detect single nucleotide variants, insertions and deletions, and copy number variations.

Data Access

The raw data can be explored interactively with the Table Browser or cross-referenced with Data Integrator. The data can be accessed from scripts through our API, with track names found in the Table Schema page for each subtrack after "Primary Table:".

For downloading the data, the annotations are stored in bigBed files that can be accessed at our download directory. Regional or the whole genome text annotations can be obtained using our utility bigBedToBed. Instructions for downloading utilities can be found here.

Credits

Thanks to Illumina (U.S.), Roche NimbleGen, Inc. (U.S.), Agilent Technologies (U.S.), MGI Tech (Beijing Genomics Institute, China), Twist Bioscience (U.S.), and Integrated DNA Technologies (IDT), Inc. (U.S.) for making these data available and to Tiana Pereira, Pranav Muthuraman, Began Nguy and Anna Benet-Pages for enginering these tracks.