Also, an embodiment of a method for correcting an error associated with phasic synchrony of sequence data generated from a population of substantially identical copies of a template molecule is described that comprises a detecting a signal generated in response to an incorporation of one or more nucleotides in a sequencing reaction; b generating a value for the signal; c incorporating the value into a representation associated with a sequence of a template molecule; d repeating steps a - c for each sequence position of the template molecule; e correcting each value for the phasic synchrony error in the representation using a first parameter and a second parameter; and f generating a corrected representation using the corrected values.
Additionally, an embodiment of a system for correcting an error associated with phasic synchrony of sequence data generated from a population of substantially identical copies of a template molecule is described that comprises a computer with program code stored for execution thereon that performs a method that comprises a generating a value for a signal detected in response to an incorporation of one or more nucleotides in a.
Even further, an embodiment of a system for correcting error associated with phasic synchrony of sequence data generated from a population of substantially identical copies of a template molecule is described that comprises a computer with program code stored for execution thereon that performs a method that comprises a generating a value for a signal detected in response to an incorporation of one or more nucleotides in a sequencing reaction; b incorporating the value into a representation associated with a sequence of a template molecule; c repeating steps a - b for each sequence position of the template molecule; d correcting each value for the phasic synchrony error in the representation using a first parameter and a second parameter; and e generating a corrected representation using the corrected values.
The advantages achieved by embodiments of the present invention include but are not limited to: a the quality of the sequence data is increased, resulting in lesser depth of sequence coverage being required to achieve a desired level of accuracy of the consensus sequence; b the useful sequence read length is extended, which means that more high- quality sequence data can be obtained from a single run; c because the useful sequence read length is extended, fewer runs will be needed to achieve a given depth of sequence coverage; d because the useful sequence read length is extended, fewer sequences are needed to assemble a sequence contig spanning a given region; and e the resulting increased read lengths facilitate the assembly of overlapping reads, particularly in repetitive sequence regions.
The above and further features will be more clearly appreciated from the following detailed description when taken in conjunction with the accompanying drawings. In the drawings, like reference numerals indicate like structures, elements, or method steps and the leftmost digit of a reference numeral indicates the number of the figure in which the references element first appears for example, element appears first in Figure 1. All of these conventions, however, are intended to be typical or illustrative, rather than limiting.
Figure 1 is a simplified graphical representation of one embodiment of a mathematical model for converting a "perfect" theoretical flowgram to a "dirty" observed flowgram;. Figure 2 is a simplified graphical representation of one embodiment of an inversion of the mapping model of Figure 1 ; Fig. Embodiments of the presently described invention are based, at least in part, upon the discovery that a theoretical or "perfect" flowgram can be converted into a real life observed "dirty" flowgram by a mathematical model of IE and CF.
The term "flowgram" as used herein generally refers to a representation of sequencing data generated from a sequencing run that may, for instance, include a graph representation of the sequencing data. For example, a perfect or theoretical flowgram represents data from generated from a sequencing run that has no error from the CAFIE mechanisms described above or other types of background error.
Along the same lines a dirty or observed flowgram represents data generated from a sequencing run that includes the CAFIE and background error factors. In the present example, some or all of the error factors may be accurately approximated and applied to the perfect flowgram model to provide a representation of real data obtained from an actual sequencing run. Importantly, the presently described invention is also based, at least in part, upon the discovery that an inversion of the mathematical model described above can serve to approximate a perfect theoretical flowgram from a dirty observed flowgram.
Thus, continuing the example from above an approximation of error may be applied to actual sequencing data represented in an observed flowgram resulting in a perfect or substantially perfect theoretical flowgram representation of the actual sequence data with all or substantially all of the error factors removed. Those of ordinary skill in the related art will appreciate that the accurate removal of error from data provides for a more efficient and accurate interpretation of said data.
Thus, for instance, removing error from data generated in a sequencing run results in more accurate production of calls identifying each nucleic acid species in a sequence generated from a. Some embodiments of the presently described invention include systems and' methods for analyzing data generated from SBS sequencing runs on a sequencing apparatus. Some examples of SBS apparatus and methods may employ what may be referred to as a pyrophosphate based sequencing approach that may, for instance, comprise one or more of a detection device such as a charge coupled device CCD camera, a microfluidics chamber, a sample cartridge holder, or a pump and flow valves.
Taking the example of pyrophosphate based sequencing, embodiments of an apparatus may use chemiluminescence as the detection method, which for pyrophosphate sequencing produces an inherently low level of background noise. In the present example, the sample cartridge holder for sequencing may include what is referred to as a "picotiterplate" formed from a fiber optics faceplate that is acid-etched to yield hundreds of thousands of very small wells each enabled to hold a population of substantially identical template molecules.
In some embodiments, each population of substantially identical template molecule may be disposed upon a solid substrate such as a bead, each of which may be disposed in one of said wells. Continuing with the present example, an apparatus may include a reagent delivery element for providing fluid reagents to the picotiterplate holders, as well as a CCD type detection device enabled to collect photons emitted from each well on the picotiterplate.
Further, the systems and methods of the presently described embodiments of the invention may include implementation on a computer readable medium stored for execution on a computer system. For example, several embodiments are described in detail below to process and correct error in signals detected using SBS systems and methods implementable on computer systems. A computer may include any type of computer platform such as a workstation, a personal computer, a server, or any other present or future computer.
Computers typically include known components such as a processor, an operating system, system memory, memory storage devices, input-output controllers, input-output devices, and display devices. It will be understood by those of ordinary skill in the relevant art that there are many possible configurations and components of a computer and may also include cache memory, a data backup unit, and many other devices.
An interface controller may also be included that may comprise any of a variety of known or future software programs for providing input and output interfaces. For example, interfaces may include what are generally referred to as "Graphical User Interfaces" often referred to as GUI's that provide one or more graphical representations to a user. Interfaces are typically enabled to accept user inputs using means of selection or input known to those of ordinary skill in the related art.
In the same or alternative embodiments, applications on a computer may employ an interface that includes what are referred to as "command line interfaces" often referred to as CLI's. CLI's typically provide a text based interaction between an application and a user. Typically, command line interfaces present output and receive input as lines of text through display devices.
For example, some implementations may include what are referred to as a "shell" such as Unix Shells known to those of ordinary skill in the related art, or Microsoft Windows Powershell that employs object-oriented type programming architectures such as the Microsoft. NET framework. Those of ordinary skill in the related art will appreciate that interfaces may include one or more GUI's, CLI' s or a combination thereof. For example, a multi-core architecture typically comprises two or more processor "execution cores". In the present example each execution core may perform as an independent processor that enables parallel execution of multiple threads.
In addition, those of ordinary skill in the related will appreciate that a processor may be configured in what is generally referred to as 32 or 64 bit architectures, or other architectural configurations now known or that may be developed in the future. An operating system interfaces with firmware and hardware in a well-known manner, and facilitates the processor in coordinating and executing the functions of various computer programs that may be written in a variety of programming languages. An operating system, typically in cooperation with a processor, coordinates and executes functions of the other components of a computer.
An operating system also provides scheduling, input-output control, file and data management, memory management, and communication control and related services, all in accordance with known techniques. System memory may include any of a variety of known or future memory storage devices. Examples include any commonly available random access memory RAM , magnetic medium such as a resident hard disk or tape, an optical medium such as a read and write compact disc, or other memory storage device.
Memory storage devices may include any of a variety of known or future devices, including a compact disk drive, a tape drive, a removable hard disk drive, USB or flash drive, or a diskette drive. Any of these program storage media, or others now in use or that may later be developed, may be considered a computer program product. In some embodiments, a computer program product is described comprising- a computer usable medium having control logic computer software program, including program code stored therein.
The control logic, when executed by a processor,. In other embodiments, some functions are implemented primarily in hardware using, for example, a hardware state machine. Implementation of the hardware state machine so as to perform the functions described herein will be apparent to those skilled in the relevant arts. Input-output controllers could include any of a variety of known devices for accepting and processing information from a user, whether a human or a machine, whether local or remote.
Such devices include, for example, modem cards, wireless cards, network interface cards, sound cards, or other types of controllers for any of a variety of known input devices. Output controllers could include controllers for any of a variety of known display devices for presenting information to a user, whether a human or a machine, whether local or remote. In the presently described embodiment, the functional elements of a computer communicate with each other via a system bus.
Some embodiments of a computer may communicate with some functional elements using network or other types of remote communications. Also a computer may include one or more library files, experiment data files, and an internet client stored in system memory. For example, experiment data could include data related to one or more experiments or assays such as detected signal values, or other values associated with one or more SBS experiments or processes. Additionally, an internet client may include an application enabled to accesses a remote service on another computer using a network and may for instance comprise what are generally referred to as "Web Browsers".
Also, in the same or other embodiments an internet client may include, or could be an element of, specialized software applications enabled to access remote information via a network such as a data processing application for SBS applications. A network may include one or more of the many various types of networks well known to those of ordinary skill in the art.
A network may include a network comprising a worldwide system of interconnected computer networks that is commonly referred to as the internet, or could also include various intranet architectures. For example, firewalls may comprise hardware or software elements or some combination thereof and are typically designed to enforce security policies put in place by users, such as for instance network administrators, etc. Examples of SBS embodiments typically employ serial or iterative cycles of nucleotide species addition to the template molecules described above.
These cycles are also referred to herein as "flows". For example, in each flow either one of the four nucleotide species, A, G, C or T is presented e. Continuing with the present example, a flow may include a nucleotide specie complementary to the nucleotide specie in the template molecule at the sequence position immediately adjacent to the 3' end of the nascent molecule being synthesized, where the nucleotide specie will be incorporated into the nascent molecule. After each iteration of a flow of a nucleotide specie, a wash method is implemented to remove the unincorporated excess of the nucleotide specie and reagents.
Upon completion of the washing stage, the next iteration of a flow presents another nucleotide specie, or mix of nucleotide species, to the template-polymerase complex. In some embodiments a "flow cycle" may refer the addition of four nucleotide species either iteratively or in parallel where for instance one flow cycle includes the addition of all four nucleotide species.
When charted on a flowgram, a value for the detected light or other signal for each flow may be about zero indicating a nucleotide specie in the flow was not complementary to the nucleotide specie in the template at the next sequence position and thus not incorporated , or about one indicating incorporation of exactly one nucleotide specie complementary to the nucleotide specie in the template was detected , or about an integer greater than one indicating incorporation of 2 or more copies of the nucleotide specie presented in the flow complementary two consecutive nucleotide specie in the template were detected.
As described above, a theoretical outcome for an iterative series of flows results in a signal from each flow that should be either exactly zero, or an integer and represented in a perfect flowgram. Through various experimental variations that include CF and IE mechanisms, the actual detected signals tend to fluctuate around these expected theoretical values by varying amounts.
The detected signals that include this variation are represented as a dirty or observed flowgram. The terms flowgram and pyrogram are used interchangeably herein. The terms "perfect flowgram", "clean flowgram" and "theoretical flowgram" are used interchangeably herein. The terms "dirty flowgram", "real-life flowgram" and "observed flowgram" are used interchangeably herein. Further, as used herein, a "read" generally refers to the entire sequence data obtained from a single nucleic acid template molecule or a population of a plurality of substantially identical copies of the template molecule.
A "nascent molecule" generally refers to a DNA strand which is being extended by the template-dependent DNA polymerase by incorporation of nucleotide species which are complementary to the corresponding nucleotide species in the template molecule. The term "completion efficiency" as used herein generally refers to the percentage of nascent molecules that are properly extended during a given flow.
The term "incomplete extension rate" as used herein generally refers to the ratio of the number of nascent molecules that fail to be properly extended over the number of all nascent molecules. Some embodiments of the presently described invention correct the detected signals of each flow to account for the CF and IE mechanisms described above.
For example, one aspect of the invention includes calculating the extent of phasic synchronism loss for any known sequence, assuming given levels of CF and IE. Furthermore, an IE rate of no greater than 0. Table 1. It will be understood that the values presented in Table 1 are for the purposes of illustration only and should not be considered limiting.
Those of ordinary skill will appreciate that several factors may contribute to variability of values such as the genomic or reference sequences and other parameters used to formulate predictions. As described above, correction of CF and IE is desirable because the loss of phasic synchronism has a cumulative effect over the read length and degrades the quality of a read as read length increases.
In one embodiment of the presently described invention, values representing both CF and IE are assumed to be substantially constant across the entire read of a substantially identical template molecule population, such as for instance a population of template molecules residing within a single well of a picotiterplate system.
This permits numerical correction of each sequence position across the entire read using two simple parameters "incomplete extension" and "carry forward" without any a priori knowledge of the actual sequence of the template molecule. The system and methods of the presently described embodiments of the invention are useful in determining, and correcting for, the amounts of CF and IE occurring in a population of template molecules.
For example, embodiments of-the invention correct the signal value detected from each flow for each population of substantially identical template molecules residing in each well to account for CF and IE. Embodiments of the present invention model the lack of phasic synchronism as a nonlinear mapping: Equation 1 :.
A model for such a mapping formula can be generated by, for example, analyzing the errors that are introduced to an observed flowgram q by sequencing a " polynucleotide template molecule having a known sequence. An illustrative. For example on the left hand side of Figure 1, theoretical flowgram is an illustrative representation of a theoretical perfect or ideal flowgram p , that shows an idealized signal strength value depicted in brackets next to its associated nucleotide specie.
Each idealized value of theoretical flowgram is an integer or zero. On the right hand side of Figure 1, observed flowgram is an illustrative representation of a detected signal strength value from an observed or simulated dirty flowgram q.
WO2013138685A1 - Systems and methods for assessing of biological samples - Google Patents
Similarly, each signal strength value in flowgram is depicted in brackets next to its associated nucleotide specie. Also on the right hand side of Figure 1 is flow that provides a representative number representing the iterative flow sequence associated with a nucleotide specie and signal values e. For instance, flow 1 as illustrated in Figure 1 is associated with the "C" nucleotide specie introduced in said iteration of flow and a corresponds to a signal value for both theoretical flowgram and observed flowgram In the example of Figure 1 the differences in signal strength values between theoretical flowgram and observed flowgram for the each flow iteration is indicative, at least in part, of a loss of phasic synchronicity.
For instance, the signal values represented in observed flowgram are not integers, rather each are typically. Mapping model represented as "M", may be estimated using known values for parameters Parameters may be employed to estimate mapping model and convert the signal values of the theoretical flowgram p into the observed values q In the present example, the error value represented by mapping model accumulates with each iteration of flow , and grows exponentially.
Continuing the example from above, the error represented by the error value may in theory grow exponentially with each flow. For instance, the phasicaly synchronized sequencing reactions associated with each population of substantially identical template molecules become three different phasicaly synchronized sub-populations after a flow iteration.
The sub-populations include: a first sub-population of phasicaly synchronized reactions where the nucleotide specie in the flow is properly incorporated at the appropriate sequence position relative to the template molecules e. In the present. Those of ordinary skill in the related art will appreciate that at an rc-th flow iteration, there will be 3" populations of phasicaly. Further continuing the example from above, Figure 2 provides an illustrative representation of an inversion of mapping model that is represented in Figure 2 as inversion mapping model For instance, by estimating the correct values for parameters e.
Those of ordinary skill in the related art will appreciate that the signal values represented in Figures 1 and 2 are provided for the purposes of illustration only and that a broad range of signal values are possible. Thus they should not be considered as limiting. Some embodiments of the invention execute the inverted mapping in two consecutive- stages, i and ii outlined below:.
The mapping model carries out these calculations flow-by-flow e. Figure 3a provides an illustrative example of models employed for matrix calculations. For example as will be described in greater detail below, forward matrix model may be employed to derive inverse matrix model In the present example, performing matrix calculations using inverse matrix model may be employed to derive estimations for parameters For instance, various values for parameters may be applied in the matrix calculations and evaluated for the degree of fit to observed flowgram Typically, parameters that provide the best fit to observed flowgram q are determined to be good estimates for actual values of parameters Further, Fig.
Each row associated with an iteration of flow of the matrix records the operations and results of recursive stages i, ii for each nucleotide specie flow. Equation 1 and the recursive stages i, ii can be rewritten as a matrix-array operation: Equation 2 :. The inverse form of Equation 2 gives the inverse mapping, converting the "dirty" observed flowgram q back to theoretical flowgram p Equation 3 :. An iterative method is used solve the inverse Equation 3 , illustrated as inverse matrix model in Figure 3a, to obtain the theoretical flowgram p for each read. Similar to Figure 3b, Figure 4a provides an illustrative example of an inverse matrix calculation using inverse matrix model In such an implementation, the binary encoding of a flowgram p' encodes a value "1" when the flowgram value p is greater than 0.
Alternatively, some implementations may employ a threshold value in the range between 0 and 1, such as 0. Thus, the "dirty" observed flowgram q can be inverted back to the clean "perfect" theoretical flowgram p through. In many implementations, a single iteration of flowgram inversion can generally suffice, hi some implementations it may be desirable to perform, 2, 3, or more iterations of flowgram inversion where the accuracy of the flowgram representation may be improved with each iteration, particularly for longer read lengths, until convergence of the calculation on a solution with a desired quality.
GATA 8 , — Bains, W. A novel method for nucleic acid sequence determination. Jett, J. High-speed DNA sequencing: an approach based upon fluorescence detection of single molecules. Tawfik, D. Man-made cell-like compartments for molecular evolution. Nature Biotechnol. Ghadessy, F. Directed evolution of polymerase function by compartmentalized self-replication. USA 98 , — Dressman, D. Transforming single DNA molecules into fluorescent magnetic particles for detection and enumeration of genetic variations.
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Correspondence to Jonathan M. This file contains Supplementary Figures S1-S11 that illustrate various experimental, data processing and modelling results pertinent to the sequencing technology described in the paper. DOC kb. This file includes Supplementary Tables S1-S4 with model results and sequencing statistics for a number of runs performed with the instrument described in the paper. DOC 87 kb. This file includes detailed methods and materials for the sequencing technology described in the paper, and detailed description of data processing and bioinformatics algorithms.
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Advanced search. Skip to main content. A Corrigendum to this article was published on 26 January A Corrigendum to this article was published on 04 May Abstract The proliferation of large-scale DNA-sequencing projects in recent years has driven a search for alternative methods to reduce time and cost. Main DNA sequencing has markedly changed the nature of biomedical research and medicine. Emulsion-based sample preparation We generate random libraries of DNA fragments by shearing an entire genome and isolating single DNA molecules by limiting dilution Supplementary Methods.
Figure 1: Sample preparation. Full size image.
WOA1 - Systems and methods for assessing of biological samples - Google Patents
Sequencing in fabricated picolitre-sized reaction vessels We perform sequencing by synthesis simultaneously in open wells of a fibre-optic slide using a modified pyrosequencing protocol that is designed to take advantage of the small scale of the wells. Figure 2: Sequencing instrument. Base calling of individual reads Nucleotide incorporation is detected by the associated release of inorganic pyrophosphate and the generation of photons 5 , Figure 3: Flowgram of a bases read from an M.
Table 1 Summary of sequencing statistics for test fragments Full size table. High-quality reads and consensus accuracy Before base calling or aligning reads, we select high-quality reads without relying on a priori knowledge of the genome or template being sequenced Supplementary Methods. Mycoplasma genitalium Mycoplasma genomic DNA was fragmented and prepared into a sequencing library as described above.
Table 2 Summary statistics for M. Combined with the low maximum specific growth rate of anammox bacteria and stringent operational conditions, the practical application of anammox fell far behind the research progress. Many efforts have been made on the development of a marketable product. Here, we would like to mention the Paques BV Balk, The Netherlands for its unremitting efforts on the practical application of anammox process. Early in , Van Dongen et al. The combined SHARON-anammox system could work stably over long periods, and the authors predicted that the combination process was readyfor full-scale implementation.
Based on constant and successful study, in , the first full-scale granular anammox reactor was accomplished at the wastewater treatment plant of Waterboard Hollandse Delta in Rotterdam, The Netherland [9,65]. This stands for the start of the commercial application of anammox process, exhibiting to be another milestone. The first full-scale 70 m3 reactor was directly scaled up fold from lab-scale experiment. The reactor was initially inoculated with nitrifying sludge and a total amount of 9. Even with the addition of anammox sludge, the start-up took 3.
Several reasons caused the long start-up time, besides the low growth rates of anammox microorganisms. Most important is that there was no anammox seed sludge available to inoculate the first full-scale reactor, and delay was caused by technical issues such as operational and temperature problems , as the first full-scale reactor was directly scaled up from lab scale, skipping the pilot phase. This first full-scale reactor on the other hand had a pilot plant character. Another four anammox plants were built before , three in Europe and one in Asia Table 3.
The third reactor, part of a plant for the treatment of the effluent of a potato factory, exhibited a largest ammonium load rate. Japan built the first full-scale Asian anammox reactor at a semiconductor plant. In , Paques Environmental Technology Shanghai released the news that an agreement had been reached to build world's largest anammox based.
Anammox process was designed to have a capacity for conversion of 11 tons of nitrogen per day almost ten times larger than the largest plant built before The two-step combination of anammox and internal circulation IC reactors will be the sixth full-scale application of anammox. Since , anammox experienced huge development.
Another 11 anammox plants were implemented by Paques, seven of which are located in China. As the world's biggest developing market, China contributes significantly towards commercialization of anammox process. Thanks to the experience from the established anammox plants, the start-up time of the marketable plant became shorter and shorter. This could be another milestone. The second reactor started up in 1 year and it took 2 months for the start-up of the first Asian plant.
All these emphasize on anammox process becoming a commercial technique. The discovery of the green process, anammox, brings revolutionary changes to conventional biological nitrogen removal. Playing an important part in the biological nitrogen cycle, this unique process makes great contribution to our environment and economy. Anammox development experienced several important points: laboratory culture based on basal medium, full-scale reactor system implementation, and extensive engineering applications. Although starting up the reactor from scratch is universal, inoculation with highly enriched anammox sludge is more feasible.
Currently, at least 30 full-scale anammox systems are operational. Thus, application of anammox process offers an attractive alternative to current wastewater treatment systems for ammonia-nitrogen removal. Development of anammox process from laboratory to commercialization was reviewed. There were three milestones: basal medium, first plant, and extensive applications.
Seeding with enriched anammox sludge is more feasible than starting from scratch. Over 30 full-scale anammox plants are in operation around the world. Anammox eventually becomes the priority choice for ammonium wastewater treatment. The authors gratefully acknowledge the support from the National Natural Science Foundation of China nos. Shiskowski and D. Mavinic, "Biological treatment of a high ammonia leachate: influence of external carbon during initial startup," Water Research, vol.
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