+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 region 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.. +
+ ++Items are shaded according to manufacturing company: +
+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. It's not granted that all targeted regions +will be sequenced perfectly, it might be some capture bias on certain locations. The Target +Regions are those normally used for coverage analysis. +
+ ++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 (e.g. exons) of interest. +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 | +
+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 this data available and to Tiana Pereira, Pranav Muthuraman, Began Nguy and Anna Benet-Pages for enginering this tracks. +
+ + +