Exome Probesets Track Settings
 
Exome Capture Probesets and Targeted Region   (All Mapping and Sequencing tracks)

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 IDT xGen V2 P  IDT - xGen Exome Research Panel V2 Probes   Schema 
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 IDT xGen V2 T  IDT - xGen Exome Research Panel V2 Target Regions   Schema 
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 KAPA Hyper P  Roche - KAPA HyperExome Capture Probe Footprint   Schema 
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 KAPA Hyper T  Roche - KAPA HyperExome Primary Target Regions   Schema 
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 SeqCap EZ Med P  Roche - SeqCap EZ MedExome Capture Probe Footprint   Schema 
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 SeqCap EZ Med T  Roche - SeqCap EZ MedExome Empirical Target Regions   Schema 
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 SeqCap EZ Med+Mito P  Roche - SeqCap EZ MedExome + Mito Capture Probe Footprint   Schema 
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 SeqCap EZ Med+Mito T  Roche - SeqCap EZ MedExome + Mito Empirical Target Regions   Schema 
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 SureSel. Clinical V2 P  Agilent - SureSelect Clinical Research Exome V2 Covered by Probes   Schema 
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 SureSel. Clinical V2 T  Agilent - SureSelect Clinical Research Exome V2 Target Regions   Schema 
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 SureSel. Focused P  Agilent - SureSelect Focused Exome Covered by Probes   Schema 
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 SureSel. Focused T  Agilent - SureSelect Focused Exome Target Regions   Schema 
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 SureSel. V4+UTR P  Agilent - SureSelect All Exon V4 + UTRs Covered by Probes   Schema 
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 SureSel. V4+UTR T  Agilent - SureSelect All Exon V4 + UTRs Target Regions   Schema 
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 SureSel. V5+UTR P  Agilent - SureSelect All Exon V5 + UTRs Covered by Probes   Schema 
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 SureSel. V5+UTR T  Agilent - SureSelect All Exon V5 + UTRs Target Regions   Schema 
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 SureSel. V6 +UTR T  Agilent - SureSelect All Exon V6 + UTR r2 Target Regions   Schema 
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 SureSel. V6 P  Agilent - SureSelect All Exon V6 r2 Covered by Probes   Schema 
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 SureSel. V6 T  Agilent - SureSelect All Exon V6 r2 Target Regions   Schema 
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 SureSel. V6+COSMIC P  Agilent - SureSelect All Exon V6 + COSMIC r2 Covered by Probes   Schema 
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 SureSel. V6+COSMIC T  Agilent - SureSelect All Exon V6 + COSMIC r2 Target Regions   Schema 
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 SureSel. V6+UTR P  Agilent - SureSelect All Exon V6 + UTR r2 Covered by Probes   Schema 
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 SureSel. V7 P  Agilent - SureSelect All Exon V7 Covered by Probes   Schema 
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 SureSel. V7 T  Agilent - SureSelect All Exon V7 Target Regions   Schema 
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 Twist Compr. T  Twist - Comprehensive Exome Panel Target Regions   Schema 
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 Twist Core T  Twist - Bioscience - Core Exome Panel Target Regions   Schema 
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 Twist RefSeq T  Twist - RefSeq Exome Panel Target Regions   Schema 
    

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.

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.

Kit Targeted Region Databases Used for Design Year of Release
IDT - xGen Exome Research Panel V1.0 39 Mb Coding sequences from RefSeq (19,396 genes) 2015
IDT - xGen Exome Research Panel V2.0 34 Mb Coding sequences from RefSeq 109 (19,433 genes) 2020
Twist - RefSeq Exome Panel 3.6 Mb Curated subset of protein coding genes from CCDS N/A
Twist - Core Exome Panel 33 Mb Protein coding genes from CCDS N/A
Twist - Comprehensive Exome Panel 36.8 Mb Protein coding genes from RefSeq, CCDS, and GENCODE 2020
MGI - Easy Exome Capture V4 59 Mb CCDS, GENCODE, RefSeq, and miRBase N/A
MGI - Easy Exome Capture V5 69 Mb CCDS, GENCODE, RefSeq, miRBase, and MGI Clinical Database N/A
Agilent - SureSelect Clinical Research Exome 54 Mb Disease-associated regions from OMIM, HGMD, and ClinVar 2014
Agilent - SureSelect Clinical Research Exome V2 63.7 Mb Disease-associated regions from OMIM, HGMD, ClinVar, and ACMG 2017
Agilent - SureSelect Focused Exome 12 Mb Disease-associated regions from HGMD, OMIM and ClinVar 2016
Agilent - SureSelect All Exon V4 51 Mb Coding regions from CCDS, RefSeq, and GENCODE v6, miRBase v17, TCGA v6, and UCSC known genes 2011
Agilent - SureSelect All Exon V4 + UTRs 71 Mb Coding regions and 5' and 3' UTR sequences from CCDS, RefSeq, and GENCODE v6, regions from miRBase v17, TCGA v6, and UCSC known genes 2011
Agilent - SureSelect All Exon V5 50 Mb Coding regions from Refseq, GENCODE, UCSC, TCGA, CCDS, and miRBase (21.522 genes) 2012
Agilent - SureSelect All Exon V5 + UTRs 74 Mb Coding regions and 5' and 3' UTR sequences from Refseq, GENCODE, UCSC, TCGA, CCDS, and miRBase (21.522 genes) 2012
Agilent - SureSelect All Exon V6 r2 60 Mb Coding regions from RefSeq, CCDS, GENCODE, HGMD, and OMIM 2016
Agilent - SureSelect All Exon V6 + COSMIC r2 66 Mb Coding regions from RefSeq, CCDS, GENCODE, HGMD, and OMIM, and targets from both TCGA and COSMIC 2016
Agilent - SureSelect All Exon V6 + UTR r2 75 Mb Coding regions and 5' and 3' UTR sequences from RefSeq, GENCODE, CCDS, and UCSC known genes,and miRNAs and lncRNA sequences 2016
Agilent - SureSelect All Exon V7 35.7 Mb Coding regions from RefSeq, CCDS, GENCODE, and UCSC known genes 2018
Roche - KAPA HyperExome 43Mb Coding regions from CCDS, RefSeq, Ensembl, GENCODE,and variants from ClinVar 2020
Roche - SeqCap EZ Exome V3 64 Mb Coding regions from RefSeq RefGene CDS, CCDS, and miRBase v14 databases, plus coverage of 97% Vega, 97% Gencode, and 99% Ensembl 2018
Roche - SeqCap EZ Exome V3 + UTR 92 Mb Coding sequences from RefSeq RefGene, CCDS, and miRBase v14, plus coverage of 97% Vega, 97% Gencode, and 99% Ensembl and UTRs from RefSeq RefGene table from UCSC GRCh37/hg19 March 2012 and Ensembl (GRCh37 v64) 2018
Roche - SeqCap EZ MedExome 47 Mb Coding sequences from CCDS 17, RefSeq, Ensembl 76, VEGA 56, GENCODE 20, miRBase 21, and disease-associated regions from GeneTests, ClinVar, and based on customer input 2014
Roche - SeqCap EZ MedExome + Mito 47 Mb Coding sequences and mitochondrial genes from CCDS 17, RefSeq, Ensembl 76, VEGA 56, GENCODE 20 and miRBase 21, disease-associated regions from GeneTests, ClinVar, and based on customer input 2014
Illumina - Nextera DNA Exome V1.2 45 Mb Coding regions from RefSeq, CCDS, Ensembl, and GENCODE v19 2015
Illumina - Nextera Rapid Capture Exome 37 Mb 212,158 targeted exonic regions with start and stop chromosome locations in GRCh37/hg19 2013
Illumina - Nextera Rapid Capture Exome V1.2 37 Mb Coding regions from RefSeq, CCDS, Ensembl, and GENCODE v12 2014
Illumina - Nextera Rapid Capture Expanded Exome 66 Mb Coding regions from RefSeq, CCDS, Ensembl, and GENCODE v12 2013
Illumina - TruSeq DNA Exome V1.2 45 Mb Coding regions from RefSeq, CCDS, and Ensembl 2017
Illumina - TruSeq Rapid Exome V1.2 45 Mb Coding regions from RefSeq, CCDS, Ensembl, and GENECODE v19 2015
Illumina - TruSight ONE V1.1 12 Mb Coding regions of 6700 genes from HGMD, OMIM, and GeneTest 2017
Illumina - TruSight Exome 7 Mb Disease-causing mutations as curated by HGMD 2017
Illumina - AmpliSeq Exome Panel N/A CCDS coding regions 2019

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.