Performance comparison of exome dna sequencing technologies pdf

Comparison of exome and genome sequencing technologies for the complete capture. There are multiple targeted sequencing methods available, but none has been systematically investigated and compared. Comparison of three nextgeneration sequencing platforms. Performance comparison of four commercial human wholeexome. Dna sequencing ontarget percentage comparison in contrast, library preparation kits from other vendors showed lower % ontarget results. Institute of technology, solna, sweden, tomtebodavagen 23a, se17165 solna.

Jun 09, 2014 distinctive features of four exome capture technologies. The technique which made this new era a reality was sanger sequencing. Nextera exome enrichment kit illumina sequencing and. Library preparation for wholeexome sequencing is a critical step serving the enrichment of the regions of interest. Pdf performance comparison of exome dna sequencing. Dna sequencing technologies generate sequencing data that are big, sparse, and heterogeneous. Singlenucleotide polymorphism snp sequencing services. The advent of next generation sequencing ngs technology has revolutionized the knowledge of cancer genomics becoming a valuable tool to characterize the molecular landscape of cancer genomes in.

We evaluated four commercially available customtargeted dna technologies for nextgeneration sequencing with respect to ontarget. In recent years, whole exome sequencing wes, which allows detection of 85% of diseasecausing variants, has been used to compare tumor and normal dna to allow the identification. Comparison of variant calls from whole genome and whole exome. The kit from vendor e performed the best among them, producing a consistent % ontarget of 6571%, which is as much as 1015% lower than what was achieved using the agilent sureselectxt hs kit. Targeted sequencing uses deep sequencing to detect known and novel variants within your region of interest. Representative variations derived from the real data detected uniquely by each. It is now possible to analyze the genomic dna of individuals using whole genome sequencing wgs and exome sequencing exomeseq, and these strategies have become. Comparisons among six different library preparation kits. Over 90% of human wholegenome sequencing has been performed using instruments from two companies, illumina and complete genomics. Comparison of exome and genome sequencing technologies for the complete. Comparison of solutionbased exome capture methods for. Comparison of aligners simulated exome data percentage correct. Sep, 2017 exome sequencing is the sequencing of the complete set of exons or coding dna regions present in an organism whereas rna sequencing is the sequencing procedure of ribonucleic acids rna.

Advance your genomic research using targeted resequencing. Comparison of nextgeneration sequencing systems by bgi. Performance comparison of snp detection tools with illumina. It is now possible to analyze the genomic dna of individuals using whole genome sequencing wgs and exome sequencing exomeseq, and these strategies have become popular for basic 4, 5 and. To investigate the ffpe specimen suitability for ngs analysis and to establish. Ngs technologies have many applications such as dna sequencing and assembly to determine an unknown genome without any preparation or search for variations among genome samples, rna sequencing 26,27, to analyze gene expression and to predominantly identify dna regions of dna binding proteins, for example, transcription factors etc. Comparison of custom capture for targeted nextgeneration. An earlier performance comparison of whole exome sequencing wes technologies and whole genome sequencing wgs platforms, which assessed the impacts of these platforms on the. Alka malhotra, susan levine, diane allinghamhawkins genetic test evaluation program, winifred s hayes, inc. Wholegenome sequencing is more powerful than wholeexome. Deep sequencing of patient genomes for disease diagnosis. Dna sequencing technologies ideally should be fast, accurate, easytooperate, and cheap. Whole exome sequencing by highthroughput sequencing of targetenriched genomic dna exomeseq has become common in basic and translational research as a means of interrogating the interpretable. This page lists the different dna sequencing services.

Article pdf available in nature biotechnology 2910. Here, we systematically evaluate the performance of ampliseq and sureselect. Several published studies have concentrated on comparing the performance of. Comparison of whole exome capture products coverage. Performance comparison of wholegenome sequencing platforms. The global analysis of protein coding regions in genomes of interest by whole exome sequencing is a widely used application. Shows the performance of all tested exome capture libraries. There are considerable differences between the four exome capture technologies, as shown in table 1. Dewey fe, grove me, pan c, goldstein ba, bernstein ja, chaib h, merker jd, goldfeder. For ion proton, there are only two exome library preparation methods available, ampliseq and. The global analysis of protein coding regions in genomes of interest by.

Performance comparison of snp detection tools with. Sep 25, 2011 it is now possible to analyze the genomic dna of individuals using whole genome sequencing and exome sequencing 1,2,3, and these strategies have become popular for basic 4,5 and translational 6,7. Systematic dissection of biases in wholeexome and wholegenome. Apr 01, 20 next generation sequencing refers to the advancement of sequencing technologies that allowed for significant improvements in quantity, speed, and cost of generating sequencing data. Difference between exome and rna sequencing compare the. Whole exome sequencing by highthroughput sequencing of targetenriched genomic dna exome seq has become common in basic and translational research as a means of interrogating the interpretable part of the human genome at relatively low cost. Concurrently, metagenomic sequencing mgs is rapidly emerging as a tool for interrogating complex samples that defy conventional analyses. Exome sequencing involves the capture of rna coding regions by hybridizing genomic dna to oligonucleotide probes baits on beads that collectively cover the human. Next generation sequencing refers to the advancement of sequencing technologies that allowed for significant improvements in quantity, speed, and cost of generating sequencing data. Comprehensive comparison of three commercial human wholeexome capture platforms comprehensive comparison of three commercial human wholeexome capture platforms. The introduction of benchtop sequencers has made adoption of whole genome sequencing possible for a broader community of researchers than ever before. Targeted next generation sequencing allows you to sequence specific areas of the genome for indepth analyses more rapidly and costeffectively than whole genome sequencing wgs.

Performance comparison of exome dna sequencing technologies. Evaluation of hybridization capture versus amplicon. Computational analysis of next generation sequencing data and. Each of these machines shared similar performance on throughput, accuracy and cost in comparison to sanger and so after. Exome capture comparison study stanford comparison to whole genome sequencing clark et al.

Recently, ampliconbased methods were designed to simplify preparation and utilize smaller dna inputs. Oct 22, 2018 whole exome sequencing wes is an efficient strategy to selectively sequence the coding regions exons of a genome, typically human, to discover rare or common variants associated with a disorder or phenotype 1, 2. This paper presents a comparison of three major commercial exome sequencing platforms from agilent, illumina and nimblegen applied to the same human blood sample. Frontiers evaluation of the performance of ampliseq and. Next generation dna sequencing technologies are rapidly transforming the. Library preparation for whole exome sequencing is a critical step serving the enrichment of the regions of interest. Whole exome sequencing for cancer is there evidence of clinical utility.

Comparison of three nextgeneration sequencing platforms for. Performance comparison of four exome capture systems for. Targeted next generation sequencing integrated dna technologies. Exome sequencing samples were collected for two current mainstream technologies. An earlier performance comparison of whole exome sequencing wes technologies and whole genome sequencing wgs platforms, which assessed the impacts of these platforms on the quality of variant detection, either applied snp array data from matched samples of an exome seq dataset, or used a series of evaluation criteria. Illumina truseq and nextera technologies are identical in many characteristics, except that nextera uses transposomes for fragmentation, whereas truseq fragments the dna by ultrasonication. Dna sequencing technologies could help biologists and health care providers in a broad range of applications such as molecular cloning, breeding, finding pathogenic genes, and comparative and evolution studies. Key difference exome vs rna sequencing nucleic acid sequencing is the technique which determines the order of nucleotides in a particular fragment of dna or rna of an organism. Karczewski, rong chen, ghia euskirchen, atul butte, michael snyder. Recent developments in deep nextgeneration sequencing technologies are significantly impacting medical research. Initial strategies for exome enrichment utilized a. These libraries were enriched either as 8plex suppliers x, r, and a or 12plex idt captures. Dec 18, 2011 over 90% of human wholegenome sequencing has been performed using instruments from two companies, illumina and complete genomics.

Performance comparison of two commercial human wholeexome. With fast development and wide applications of nextgeneration sequencing ngs technologies, genomic sequence information is within reach to aid the achievement of goals to decode life. Variant annotation and working with wholeexome data one sample produces 100k variants one hundred samples gives rise to 600k or more. Initial strategies for exome enrichment utilized a hybridizationbased capture approach. Performance comparison of two commercial human whole. For ion proton, there are only two exome library preparation methods available, ampliseq and sureselect. Sample dna fragmentation illumina library preparation exome enrichment cluster generation sequencing and basecalling sequence read alignment variation detection. This paper presents a comparison of three major commercial exome sequencing platforms from agilent. The streamlined, automationfriendly workflow combines library preparation and exome enrichment steps. Karczewski, rong chen, ghia euskirchen, atul butte, michael snyder supplementary figure 1. Full text whole exome sequencing for cancer is there. Exome capture technology, nextgeneration sequencing, coverage. Many technologies for exome capture are commercially available. The nextera exome enrichment kit provides a fast, simple method for isolating the human exome.

Exome sequencing, also known as whole exome sequencing wes, is a genomic technique for sequencing all of the proteincoding regions of genes in a genome known as the exome. Regions covered amount of sequencing to be done exome seq observes important variants missed by a typical wgs experiment these lessons extend to all target enrichment experiments. This technology can produce accurate, longer reads without the artifacts and biases associated with the amplification process in other sequencing methods and the exome capture stage of wes shin et al. Computational analysis of next generation sequencing data. This results in the rapid development of various data protocols and bioinformatics tools for handling. Pdf performance comparison of exome dna sequencing technologies. Clark mj, chen r, lam hy, karczewski kj, chen r, euskirchen g, butte aj, snyder m 2011 performance comparison of exome dna sequencing technologies. We compared wholeexome sequencing wes and wholegenome sequencing. It is now possible to analyze the genomic dna of individuals using whole genome sequencing and exome sequencing 1,2,3, and these strategies have become popular for basic 4,5 and translational 6,7. It is now possible to analyze the genomic dna of individuals using whole genome sequencing wgs and exome sequencing exomeseq, and. It is now possible to analyze the genomic dna of individuals using whole genome sequencing and exome sequencing 1,2,3, and these strategies have become popular for basic 4,5 and. Performance comparison of exome dna sequencing technologies article pdf available in nature biotechnology 2910. Massively parallel signature sequencing as a highthroughput sequencing technology was introduced following the completion of the human genome sequence with the aim of addressing the efficiency. Whole genome sequencing wgs services singlenucleotide polymorphism snp sequencing services whole exome sequencing is the middle ground between these two types, where a large amount of genes are sequenced, but only those that produce meaningful differences important for practical purposes, which is only 1% of the whole genome.

Dewey fe, grove me, pan c, goldstein ba, bernstein ja, chaib h, merker jd, goldfeder rl, enns gm, david sp, pakdaman n, ormond ke, et al. Dna libraries were created from 100 ng of human genomic dna coriell using xgen stubby adapter and unique dual index i primer pairs with the lotus dna library prep kit. Regions covered amount of sequencing to be done exomeseq observes important variants. In addition, nextgeneration sequencers are increasingly being used in clinical or related settings, for. Comparison of exome and genome sequencing technologies for. In 2004 first parallelized version of 454 pyrosequencing instrument was commercialize. Performance comparison of exome dna sequencing technologies in nature biotechnology 2011. The streamlined, automationfriendly workflow combines library preparation and exome enrichment steps, and can be easily completed in 2. Comparison with a large database of diseaserelated variants 29, 30 classified 456 agilent, 369 nimblegen and 467 illumina exome sequencingspecific snvs as associated with human diseases. Performance comparison of four exome capture systems for deep. Comparison of custom capture for targeted nextgeneration dna. To investigate the ffpe specimen suitability for ngs analysis and to establish the performance of two solutionbased exome capture technologies, we compared the whole exome sequencing wes data of gdna. Dna libraries were created from 100 ng of human genomic dna coriell using xgen stubby adapter and unique dual index i primer pairs.

Distinctive features of four exome capture technologies. A comparison of enrichment technologies michael james clark, rui chen, hugo lam, konrad j. This is the key difference between exome and rna sequencing. Although of major interest, a comparison of the two methods is hitherto missing in the literature. Whole exome sequencing wes is an efficient strategy to selectively sequence the coding regions exons of a genome, typically human, to discover rare or common variants associated with a. It is now possible to analyze the genomic dna of individuals using whole genome sequencing wgs and exome sequencing exome seq, and these strategies have become popular for basic 4, 5 and translational 611 research. Continuous advancement in sequencing technologies increases the throughput of dna sequencing, while at the same time contributes sharply to. There are several differences between the available platforms, which are constantly being updated and improved. Several published studies have concentrated on comparing the performance of different exome capture technologies, or comparison between.