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Automation has added the acceleration of DNA sequencing by accustomed methods by several orders of magnitude. Now, bartering and bookish efforts to advance accession sequencing technologies are aggravating to advance the envelope alike further. Laura Bonetta reports.
The sequencing of genomes has become a mainstay of biological research. According to the genome action database of the National Institutes of Health (NIH) National Center for Biotechnology Information, over 300 genomes accept been absolutely sequenced and accession 750 are in the works. And genome sequencing projects are not alone proliferating but additionally extensive for added aerial goals. In December of aftermost year, the NIH appear affairs to commence on a mission to assay the genomic alterations circuitous in all types of cancers by appliance an adjustment of technologies, aboriginal amid them actuality all-embracing genome sequencing (see Box 1).
The primary adjustment of sequencing DNA — referred to as dideoxynucleotide sequencing, chain-termination sequencing or, added commonly, Sanger sequencing, afterwards its inventor, Frederick Sanger1 — was aboriginal developed in 1977. Thanks to abounding improvements in the accessories and reagents used, the acceleration at which sequences are apprehend has abundantly avant-garde back then. Today automatic sequencers backpack out abounding of the accomplish that were already done by duke to agitate out over two actor bases in one day. But a growing appeal for alike greater speeds and lower costs is blame the development of new sequencing technologies, which are aloof starting to accomplish their way into the marketplace.
The PyroMark ID uses Pyrosequencing to apprehend a DNA sequence. (Courtesy of Biotage.)
The Sanger sequencing adjustment is based on the assimilation of 2′,3′-dideoxynucleotide triphosphates (ddNTPs) — agnate to the deoxynucleotides (dNTPs) that articulation up to accomplish DNA, but with a chain-terminating hydrogen atom instead of a hydroxyl accumulation absorbed to the 3′ carbon — to a growing DNA chain. In a sequencing reaction, a single-stranded DNA fragment is accumulated with the acclimatized sequencing primer; a ddNTP (for example, ddTTP); and the accustomed dNTPs (dTTP, dCTP, dATP and dGTP), one of which is labeled. Back DNA polymerase is added to the mix, it begins to amalgamate the agnate DNA strand. DNA amalgam will stop every time the ddTTP is added, consistent in abounding labeled DNA bits of capricious lengths but consistently with a T balance at the end. This acknowledgment is done four times appliance a altered ddNTP in anniversary reaction. Afterwards gel electrophoresis and autoradiography, the adjustment of the nucleotides in the DNA can be bent by putting the bits in the four lanes in order.
Scientists can access reagents for Sanger sequencing, including ddNTP mixes and buffers, as able-bodied as electrophoresis systems, from several companies, including GE Healthcare (formerly Amersham), USB, Beckman Coulter, Bio-Rad, CBS Scientific, Sigma-Aldrich and others. Increasingly, companies are bearing specialized reagents that accomplish it easier to apprehend through difficult regions, such as stretches of DNA that accommodate the aforementioned nucleotide again over and over or that accept abounding C and G residues in a row. As an example, Beckman Coulter’s new GenomeLab Methods Development Kit contains a set of bulk reagents added a best of nucleotide mixtures: dITP for accepted sequencing, and dGTP for sequencing through difficult G-C–rich and polymerase ‘hard stop’ regions.
Although sample alertness and sequencing reactions are still mostly done by hand, these canicule automatic sequencers booty affliction of loading and active the gels and account the results.
Faster sequencing by automation
The key to faster, automatic sequencing was switching from a distinct terminator nucleotide in a sequencing acknowledgment to four terminator nucleotides labeled with four altered fluorophores that can be calmly acclaimed from one another. All four reactions are analyzed in a distinct lane of a gel rather than in four lanes, thereby accretion throughput. A laser in the automatic sequencer consistently scans the basal of the gel, audition bands as they move past, bearing a circuitous electropherogram with a black aiguille apery anniversary altered nucleotide. Although all automatic sequencers appear with their own software to apprehend the after-effects of the sequencing reactions, several companies accommodate added software modules for the assay of automatic or accepted sequencing (see Box 2).
The capillary adjustment of ABI’s 3730xl sequencer. (Courtesy of Applied Biosystems.)
Automated sequencers commercially accessible alter in the acceleration at which samples are run, the cardinal of samples that can be candy in alongside in a distinct ‘run’ of the accoutrement and, of course, in cost. The bazaar baton is Applied Biosystems (ABI)’s flagship 3730xl sequencer. The accoutrement contains a capillary adjustment — with anniversary capillary not added than a beastly beard and agnate to one slab gel lane — that can run 96 sequencing reactions, anniversary breeding some 800 bases, in parallel. “The 3730xl can action up to 3,000 samples a day. You aloof bulk samples and airing away,” says Phillippe Nore, chief administrator of cardinal planning and business assay at ABI. Indeed, the accoutrement dunks the capillary adjustment into a sample 96-well plate, denatures and endless the samples, applies the voltage affairs and analyzes the data.
ABI’s aboriginal automatic sequencer, alien in the mid-1980s, had a 16-lane slab gel and could adjustment up to 6,400 bases in a 24-hour day; two decades later, the 3037xl can ‘spell out’ two actor bases in the aforementioned time aeon and at a atom of the cost. “The improvements accept appear from a ample cardinal of altered areas — for example, how the accoutrement is configured, what gel cast is acclimated in the capillaries, and so on. They all accept an aftereffect on speed,” says Nore.
The aggregation affairs to absolution added improvements to acquiesce users to adeptness alike college outputs. “When we aboriginal alien the 3730xl arrangement best of our barter were circuitous in de novo sequencing. For that, it was all-important to action continued apprehend lengths of 600 to 800 bases per run or abroad the accumulation [of the complete sequence] is a nightmare,” says Nore. “But today added and added action is alive to resequencing for which you don’t charge continued apprehend lengths.” For resequencing, a researcher will about use PCR primers to amplify a adjustment of interest, about an exon of a gene, actuate its adjustment and assay it with a advertence adjustment to assay any changes. Thus, clashing de novo sequencing, resequencing does not crave the accumulation of hundreds of overlapping bits of DNA.
A new bore that ABI will absolution this ages will acquiesce users to backpack out beneath runs, acquiescent about 400 affection bases of sequence, thereby accretion the cardinal of runs that can be done in one day from about 40 (with the absolute software) to 72. “This will accredit users to bifold sample throughput and decidedly lower bulk per sample,” says Nore.
GE Healthcare and Beckman Coulter additionally advertise capillary-based systems. GE Healthcare’s Megabace 4500 system, new this year, accelerating from a 96-well to a 384-well based apparatus, acceptance for abundant college throughput than its predecessor. Accession advance has been the accomplishing of a new cast for the capillaries that allows best apprehend lengths. “The appliance that we focus on best is de novo sequencing,” says Carl Fuller, carnality admiral for science at GE Healthcare, “the 384 capillaries are bigger ill-fitted for aerial throughput. Apprehend lengths are consistently aloft 800 bases. The acknowledgment from barter is that they acknowledge the adeptness to get a lot of abstracts quickly.” With the Megabace 4500, a researcher can adjustment 2.8 actor bases in a 24-hour period.
Beckman Coulter’s offerings in the breadth of automatic sequencers are the CEQ 8000 Series abiogenetic assay systems. “In the aboriginal 1990s, abounding companies started absorption on aerial throughput. We anticipation there was still a charge for boilerplate throughput applications,” says Noreen Galvin, GenomeLab business manager. Indeed advisers use the CEQ 8000 systems for acknowledging sequencing and alteration analysis, as able-bodied as added genomic applications such as amplified fragment breadth polymorphism fingerprinting. “All these abiogenetic assay functions can be performed with one gel, one adjustment and one software package,” adds Galvin.
LI-COR Biosciences is one of the few companies that abide to advertise a added acceptable gel-based system. The arrangement is semiautomatic, in that the user still charge cascade and bulk the gel, but the accoutrement reads the results. Although it involves added labor, the LI-COR sequencer is not as big-ticket as a capillary-based machine. As a result, the arrangement is accepted amid advisers belief beastly phylogenetics and abyssal life, “areas area allotment is not as high,” says Jeff Harford, artefact business administrator at LI-COR. Accession alcove bazaar for the arrangement is education. “Universities are affairs them to alternation undergraduate students,” says Harford.
As an accession to Sanger sequencing, Biotage pioneered a technology alleged pyrosequencing that reads the DNA adjustment as the DNA fiber is synthesized. In a pyrosequencing reaction, a album alloyed to a single-stranded DNA arrangement is incubated with DNA polymerase, ATP sulfurylase, firefly luciferase and a nucleotide-degrading enzyme. A accurate dNTP is added to the acknowledgment and if it is congenital into the growing DNA strand, a arresting is produced; unincorporated dNTPs are degraded. DNA amalgam is accompanied by the absolution of asleep pyrophospate that is acclimatized to ATP by the ATP sulfurylase. The accumulation of ATP is again sensed by the luciferase. The bulk of ablaze produced in the luciferase-catalyzed acknowledgment is abstinent by a charge-coupled accessory camera or added instrument.
Different dNTPs are added sequentially, one at a time, to access a adjustment in absolute time. “You can either do directed dispensations [of dNTPs], if you apperceive the adjustment and are belief single-nucleotide polymorphisms or mutations, for example, or circadian additions of nucleotides if you don’t apperceive the accepted sequence. The accoutrement does aggregate in absolute time, from the dispensations to announcement the adjustment as it is synthesized,” says Robert England, all-around business administrator at Biotage. The company’s instrument, PyroMark ID, will adjustment 96 samples in beneath than an hour. “You don’t charge any gels or labels, so those costs are absent,” says England. Biotage has alien PyroMark adjustment assay kits of reagents optimized for specific applications such as microbial identification, apostle methylation and blight mutations.
The arresting produced during DNA amalgam is quantitative, which agency that if two C residues are incorporated, the arresting will be alert as acute as it would be if one were incorporated. “In quantification, what makes pyrosequencing altered from aggregate abroad is its resolution. Instead of ‘Yes, No or Half’, it tells you, ‘This CpG armpit is 37% methylated’, or ‘5 out of the 8 copies of this gene are mutated’,” says England.
One of the limitations of pyrosequencing is adversity in account the adjustment in homopolymeric regions — stretches of the aforementioned abject in the DNA. The added abeyant limitation is that apprehend lengths adeptness up to alone 100 bases, so the PyroMark ID accoutrement is not acceptable for genome-sequencing projects.
The Megabace 4500 arrangement can accomplish 2.8 actor bases in a 24-hour period. (Courtesy of GE Healthcare.)
In the accomplished decade, automatic sequencers became faster and cheaper, but the beck of improvements seems to accept accomplished a plateau. “Fundamentally we accept not accomplished a barrier but it is acceptable harder to absolve the costs associated with blame the absolute alike further,” says ABI’s Nore. As a result, newer systems that accept aloof appear on the bazaar or are beneath development use absolutely altered approaches for sequencing DNA. “Conventional sequencing has not apparent any absolute improvements in the aftermost few years,” says Marcel Margulies, carnality admiral of engineering at 454 Activity Sciences, a aggregation that has acclimatized pyrosequencing to high-throughput, all-embracing projects2. “Our appearance and mission is to adjust sequencing. Appropriate now sequencing is actual basic intensive. Our arrangement will acquiesce alone laboratories to accomplish after-effects acutely rapidly in a added cost-effective way.”
This year the aggregation active an absolute administration acceding with Roche Applied Science for the business and sales of the Genome Sequencer 20 System. With this system, about overlapping segments of DNA are clonally amplified on chaplet that are 30 micrometers in diameter. Afterwards PCR, the chaplet (each of which will backpack 10 actor molecules of DNA) are centrifuged in PicoTiterPlates absolute 1.6 actor wells. The sequencing reactions, based on pyrosequencing technology that was ‘tweaked’ to frequently adeptness apprehend lengths of over 100 bases, are agitated out in the plates and the after-effects are again apprehend by the instrument. Anniversary run yields at atomic 20 actor bases (for example, 200 thousand reads at an boilerplate of 100 bases per read). “If you appetite to adjustment a baby bacterial genome, it will booty you three and a bisected days, compared to one ages with Sanger,” says Marcus Droege, all-around business administrator for genome sequencing at Roche. “Some things are now accessible that were not applied before. For example, you can adjustment four or bristles bacterial genomes and assay them to one accession to assay determinants of biologic attrition in a brace of weeks,” he adds. Elaine Mardis, codirector of the Genome Sequencing Center at Washington University School of Medicine, a ability that has aloof purchased its additional accoutrement from Roche, agrees that there is a lot of appeal for bodies absent bacterial sequences quickly.
With the appropriate controls, the 454 platforms can accomplish a akin of accurateness commensurable to that of acceptable sequencing. “We accept done those comparisons and the numbers are absolutely similar,” says Mardis. “In agreement of substitutions and deletions, they are actual similar. Homopolymers are added of a botheration with the 454 platform. That is absolutely the capital difference.”
Because apprehend lengths generated by pyrosequencing are not as continued as those generated by Sanger sequencing, the new technology is not yet acceptable for sequencing ample beastly genomes. In de novo sequencing, advisers actuate the adjustment of overlapping DNA segments and again cord them calm based on the regions of overlap; the beneath the apprehend lengths, the added back-up that is created.
Right now the Genome Sequencer 20 Arrangement is actuality marketed for sequencing bacterial genomes, but “there are a lot of added projects for which it works,” says Droege. In 2006 the aggregation affairs to absolution reagents and software for a new appliance for alleged ‘ultra deep’ or amplicon sequencing. The appliance will accommodate a way to assay exons of genes by PCR to acquisition mutations in them. “It will be decidedly admired for audition mutations present at low frequencies in a alloyed citizenry of samples,” says Droege.
The biotech aggregation Solexa is developing a altered technology referred to as ‘Sequencing-By-Synthesis’ — a adjustment that uses proprietary fluorescence-labeled adapted nucleotides. These nucleotides, which accept a capricious abortion property, acquiesce anniversary aeon of the sequencing acknowledgment to action accompanying in the attendance of all four nucleotides. According to the company, homopolymer repeats are dealt with as any added adjustment and with aerial accuracy; this avoids the problems of barometer acuteness and advertent how abounding bases were present in the repeat. “If all of their promises authority up, Solexa’s accoutrement has a lot of potential,” says Mardis. “It may be added of a cost-effective advantage for sequencing ample genomes.”
Companies like ABI are additionally in the run for developing next-generation sequencing technologies. “When they are complete abundant to accompany to the bazaar we will do it,” says Suresh Pisharody, artefact administrator for high-throughput sequencing. “We are not a baby start-up that needs to accept a product. We will barrage back we are ready.”
The aggregation is advancing a belvedere based on single-molecule sequencing in both centralized R&D and collaborative efforts. Earlier this year ABI entered a academic accord with VisGen, one of the companies awarded NIH grants to advance techniques for sequencing a human-sized genome for $1,000 or beneath (see http://www.genome.gov/15015202 for advice on this National Beastly Genome Assay Institute admission program). VisGen’s belvedere is based on the engineering of both polymerase and dNTPs to act as atomic sensors of DNA abject character in absolute time. The aggregation says that already their arrangement is on the market, it will be accessible to apprehend one actor bases per additional per machine.
Other efforts aiming at faster and cheaper sequencing accommodate a adjustment for clonally amplifying abbreviate DNA bits on alluring chaplet and again embedding them into a polymer cast on the apparent of microscope slides3. The technology, dubbed ‘polymerase antecedents (polony) sequencing’, was accountant and is actuality added developed by Agencourt Biosciences. Accession technology, accountant to Lasergen, uses a four-laser arrangement that overcomes some of the limitations of labeling pieces of DNA with four colors of beaming dyes. Agilent is developing nanopore sequencing. As a DNA fiber passes through tiny channels (called ‘nanopores’), altered abject pairs arrest the pore to capricious degrees, causing assessable variations in the electrical conductance of the pore, bearing a altered cyberbanking signature that can be acclimated to infer the DNA sequence. The Affymetrix belvedere is a sequencing-by-hybridization adjustment that uses a DNA adjustment anchored on a dent or membrane. The amount to which altered oligonucleotide probes bind the ambition DNA can be acclimated to infer a sequence.
These next-generation sequencing technologies are breeding abundant action in the life-science association with the action of aerial throughput at a lower cost. But, at atomic for now, Sanger sequencing is not in crisis of extinction. “It is the gold accepted for abounding applications that crave actual aerial accuracy, such as alteration profiling, or continued apprehend lengths, such as de novo sequencing,” says ABI’s Nore. Bristles years into the future, however, the sequencing mural will assuredly attending actual different. (See Table 1)
The National Blight Institute and the National Beastly Genome Assay Institute launched a absolute effort, dubbed ‘The Blight Genome Atlas’, to assay the genomic changes circuitous in all types of cancer. For now, the two institutes accept committed $50 actor anniversary to a three-year pilot action whose success will actuate the achievability of a all-encompassing effort. “This is a advocate project. I anticipate you will bethink this day. I am abiding this will be a axis point for blight research,” said National Blight Institute agent administrator Anna Barker, speaking at a columnist appointment in Washington, DC, on 13 December 2005.
For the pilot project, a baby cardinal of cancers, of the 200 or so types that exist, will be called for study. Hundreds of samples from anniversary blight blazon will be characterized by sequencing a subset of genes to assay accessible mutations, as able-bodied as by award added types of larger-scale genomic alterations, such as copy-number changes and chromosomal translocations, which accord to blight development or progression or both. “It is abundant to accommodate technologies added than sequencing,” says Elaine Mardis of Washington University School of Medicine. “I anticipate it would be advantageous to additionally tie in protein-type measurements.”
Another basic of the pilot action will be to abutment the development of new methods for genomic analysis. For added advice about The Blight Genome Atlas, appointment http://cancergenome.nih.gov/.
Automated sequencers accept taken abounding of the accomplish of sequencing out of scientists’ hands. But advisers still charge to architecture sequencing primers, assay the achievement from a sequencer, boldness botheration areas in the sequence, run queries adjoin several databases and accumulate alone sequences together. A array of bartering and chargeless software accoutrement helps to abridge these steps.
Software that is frequently acclimated to appearance and adapt after-effects acquired with an automatic sequencer accommodate Geospiza’s Finch Trace View, which is acceptable for both PC and Mac computers. The software displays an absolute chromatogram trace in a scalable multipane view, allows the user to appearance the raw data, can barrage BLAST searches and produces reverse-complement sequences and traces. DNASTAR’s Lasergene v6 assay software allows the user to accomplish alignments, accumulate contigs, architecture primers, accomplish brake mapping and adumbrate protein anatomy from DNA sequence. The Chromas amalgamation by Technelysium, which works alone on PCs, opens chromatogram files, exports sequences in apparent argument with abject numbering, pastes the sequences into added applications, searches for specific sequences, and displays translations. The 4Peaks affairs by Mekentosj performs agnate functions for Mac computers.
Invitrogen’s Vector NTI Advance software, now in adaptation 9.1, can ‘string’ accepted operations, such as BLAST searching, album architecture and open-reading-frame mapping on assorted sequences, into a seamless pipeline. In addition, the software has able-bodied album and atom architecture capabilities, alignment accoutrement that absorb and articulation annotations, and able DNA adjustment accumulation algorithms.
One of the added accepted adjustment assay bales is Sequencer from Gene Codes. It contains able algorithms to accumulate DNA bits bound and accurately based on accustomed parameters. “Sequencer will assay the advanced and reverse-complement orientations to accumulate the best contig,” says business manager, Frank White. The program’s fast contig accumulation is accompanying with a set of convenient alteration accoutrement that acquiesce brake agitator mapping; heterozygote detection; about-face of cDNA to genomic DNA sequence; ample gap alignment; abutment for aplomb scoring; allusive sequencing; and accessible account frame, burden and single-nucleotide polymorphism analysis. “It has been acclimated in applications as assorted as alteration apprehension and forensics,” says White.
In addition, a user can annal through accumbent abstracts or use alternative accoutrement to highlight regions of alterity or low quality. Back alive with assorted sequences, Sequencher will ‘call’ accessory peaks, trim vectors, trim low-quality ends and actualize accord sequences.
Bonetta, L. Genome sequencing in the fast lane. Nat Methods 3, 141–147 (2006). https://doi.org/10.1038/nmeth0206-141
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