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Error detection in chemical array fabricationRelated Patent Categories: Chemistry: Molecular Biology And Microbiology, Measuring Or Testing Process Involving Enzymes Or Micro-organisms; Composition Or Test Strip Therefore; Processes Of Forming Such Composition Or Test Strip, Involving Nucleic AcidError detection in chemical array fabrication description/claimsThe Patent Description & Claims data below is from USPTO Patent Application 20050287586, Error detection in chemical array fabrication. Brief Patent Description - Full Patent Description - Patent Application Claims
FIELD OF THE INVENTION [0001] This invention relates to arrays, particularly polynucleotide arrays such as DNA arrays, which are useful in diagnostic, screening, gene expression analysis, and other applications. BACKGROUND OF THE INVENTION [0002] In the following discussion and throughout the present application, no cited reference is admitted to be prior art to the present application. [0003] Polynucleotide arrays (such as DNA or RNA arrays), are known and are used, for example, as diagnostic or screening tools. Such arrays include regions of usually different sequence polynucleotides arranged in a predetermined configuration on a substrate. These regions (sometimes referenced as "features") are positioned at respective locations ("addresses") on the substrate. The arrays, when exposed to a sample, will exhibit an observed binding pattern. This binding pattern can be detected upon interrogating the array. For example all polynucleotide targets (for example, DNA) in the sample can be labeled with a suitable label (such as a fluorescent compound), and the fluorescence pattern on the array accurately observed following exposure to the sample. Assuming that the different sequence polynucleotides were correctly deposited in accordance with the predetermined configuration, then the observed binding pattern will be indicative of the presence and/or concentration of one or more polynucleotide components of the sample. [0004] Biopolymer arrays can be fabricated by depositing previously obtained biopolymers (such as from synthesis or natural sources) onto a substrate, or by in situ synthesis methods. Methods of depositing obtained biopolymers include loading then touching a pin or capillary to a surface, such as described in U.S. Pat. No. 5,807,522 or deposition by firing from a pulse jet such as an inkjet head, such as described in U.S. Pat. No. 6,180,351, PCT publications WO 95/25116 and WO 98/41531, and elsewhere. Such a deposition method can be regarded as forming each feature by one cycle of attachment (that is, there is only one cycle at each feature during which the previously obtained biopolymer is attached to the substrate). For in situ fabrication methods, multiple different reagent droplets are deposited by pulse jet or other means at a given target location in order to form the final feature (hence a probe of the feature is synthesized on the array substrate). The in situ fabrication methods include those described in U.S. Pat. No. 5,449,754 for synthesizing peptide arrays, and in U.S. Pat. No. 6,180,351 and WO 98/41531 and the references cited therein for polynucleotides, and may also use pulse jets for depositing reagents. The in situ method for fabricating a polynucleotide array typically follows, at each of the multiple different addresses at which features are to be formed, the same conventional iterative sequence used in forming polynucleotides from nucleoside reagents on a support by means of known chemistry. This iterative sequence can be considered as multiple ones of the following attachment cycle at each feature to be formed: (a) coupling an activated selected nucleoside (a monomeric unit) through a phosphite linkage to a functionalized support in the first iteration, or a nucleoside bound to the substrate (i.e. the nucleoside-modified substrate) in subsequent iterations; (b) optionally, blocking unreacted hydroxyl groups on the substrate bound nucleoside (sometimes referenced as "capping"); (c) oxidizing the phosphite linkage of step (a) to form a phosphate linkage; and (d) removing the protecting group ("deprotection") from the now substrate bound nucleoside coupled in step (a), to generate a reactive site for the next cycle of these steps. The coupling can be performed by depositing drops of an activator and phosphoramidite at the specific desired feature locations for the array. Capping, oxidation and deprotection can be accomplished by treating the entire substrate ("flooding") with a layer of the appropriate reagent. The functionalized support (in the first cycle) or deprotected coupled nucleoside (in subsequent cycles) provides a substrate bound moiety with a linking group for forming the phosphite linkage with a next nucleoside to be coupled in step (a). Final deprotection of nucleoside bases can be accomplished using alkaline conditions such as ammonium hydroxide, in another flooding procedure in a known manner. Conventionally, a single pulse jet or other dispenser is assigned to deposit a single monomeric unit. [0005] The foregoing chemistry of the synthesis of polynucleotides is described in detail, for example, in Caruthers, Science 230: 281-285, 1985; Itakura et al., Ann. Rev. Biochem. 53: 323-356; Hunkapillar et al., Nature 310: 105-110, 1984; and in "Synthesis of Oligonucleotide Derivatives in Design and Targeted Reaction of Oligonucleotide Derivatives", CRC Press, Boca Raton, Fla., pages 100 et seq., U.S. Pat. No. 4,458,066, U.S. Pat. No. 4,500,707, U.S. Pat. No. 5,153,319, U.S. Pat. No. 5,869,643, EP 0294196, and elsewhere The phosphoramidite and phosphite triester approaches are most broadly used, but other approaches include the phosphodiester approach, the phosphotriester approach and the H-phosphonate approach. The substrates are typically functionalized to bond to the first deposited monomer. Suitable techniques for functionalizing substrates with such linking moieties are described, for example, in Southern, E. M., Maskos, U. and Elder, J. K., Genomics, 13, 1007-1017, 1992. [0006] In the case of array fabrication, different monomers and activator may be deposited at different addresses on the substrate during any one cycle so that the different features of the completed array will have different desired biopolymer sequences. One or more intermediate further steps may be required in each cycle, such as the conventional oxidation, capping and washing steps in the case of in situ fabrication of polynucleotide arrays (again, these steps may be performed in flooding procedure). [0007] In array fabrication, the quantities of polynucleotide available are usually very small and expensive. Additionally, sample quantities available for testing are usually also very small and it is therefore desirable to simultaneously test the same sample against a large number of different probes on an array. These conditions require use of arrays with large numbers of very small, closely spaced features. It is important in such arrays that features actually be present, that they are put down as accurately as possible in the desired target pattern, are of the correct size, and that the DNA is uniformly coated within the feature. If any of these conditions are not met within a reasonable tolerance, the results obtained from a given array may be unreliable and misleading. This of course can have serious consequences to diagnostic, screening, gene expression analysis or other purposes for which the array is being used. [0008] However, in any system used to fabricate arrays with the required small features, there is inevitably some degree of error, either fixed (and hence repeated) and/or random. In the case of both the deposition of previously obtained biopolymers, but particularly in the in situ fabrication method, drop deposition errors may occur from cycle to cycle and may be different from different cycles or may be the same. For example, one or more drop dispensers may exhibit an error (that is, a malfunction) during particular cycles or may have a same malfunction over multiple cycles. Such malfunctions include errors in firing (that is, "misfiring" which includes not dispensing a drop at all or dispensing an incorrect drop volume) as well as trajectory errors (that is, the dispenser fires a drop on an unexpected error due, for example, to an error in nozzle construction). [0009] It would be desirable then to provide a means by which drop dispenser errors during any array fabrication method, can be identified. SUMMARY OF THE INVENTION [0010] The present invention realizes that drop dispenser errors may be evaluated by detecting (such as by imaging) one or more drops deposited by the dispenser onto the substrate during array fabrication. However, the present invention further realizes that multiple dispensers may deposit drops at a same feature over one or more same cycles. In this situation, while a first drop deposited by a first dispenser on a substrate location may be detected, it is difficult to detect a second and subsequent drops deposited at the same location by different dispensers. This is so in the case since where different dispensers dispense drops to the same location during a same cycle, the second and subsequent drops mix with the first drop previously deposited on the substrate and it may be difficult to then evaluate whether the second or subsequent drops were actually deposited or of correct volume and location (that is, it may be difficult to evaluate whether the second and subsequent drop dispensers are in error). Other factors may also make such an evaluation difficult. Even in the case where only one drop is dispensed by a dispenser during each of multiple cycles, with different drops being dispensed by different dispensers at the same location over multiple cycles, it may become difficult to detect later drops. For example, changes in surface properties of the substrate may occur as a result of one or more reagents (such as an activated phosphoramidite) being applied to the same location over the many cycles. In this case, the feature location on the substrate becomes more hydrophilic than the hydrophobic starting substrate surface. In such a situation even though a dispenser may dispense a drop slightly off from a target location (for example 20 .mu.m off the center of a feature) the droplet may still migrate to the center because it prefers the hydrophilic region, and the resulting array is fine. Thus, it may be useful to evaluate the results from the detecting based on what cycle they are from in order to estimate their impact. A same deposition error (for example, the 20 .mu.m error mentioned) at earlier cycles in the start of a feature synthesis will likely be of more concern than at later cycles. [0011] The present invention then, provides in a method of forming an addressable array of chemical moieties on a substrate. The method includes for each of multiple locations (sometimes referenced as "feature locations") on the substrate, depositing a reagent drop set during a cycle so as to attach a corresponding moiety for that location. The foregoing is repeated as required, until the addressable array is formed. In any event, for each of multiple locations, a multi-dispenser drop group is deposited over one or more cycles for a corresponding feature location which group includes drops which are deposited from different dispensers. By "over" in this context is meant in one cycle, or as a result of multiple cycles (for example, two dispenser one dispenses one drop and dispenser two dispenses another drop at the same location) The method additionally includes depositing and detecting drops at respective separate locations (sometimes referenced as "test locations") on the substrate from different dispensers which deposit a multi-dispenser drop group. [0012] The present invention also provides a method of forming multiple addressable arrays of chemical moieties on a substrate, in which for each array, for each of multiple feature locations on the substrate a reagent drop set is deposited during a cycle so as to attach a corresponding moiety for that location. This step is repeated if required until the addressable array is formed. Multiple dispensers are used to dispense drops to form the array. The method additionally includes depositing and detecting drops from the different dispensers at respective separate locations on the substrate, wherein the drops are deposited at a separate test pattern area between arrays. In this case, the number of test locations of the test pattern area during any one cycle may be less than one quarter (or even less than one-tenth or one-twentieth) the number of locations in the smallest of the arrays which the test pattern area is between. Also, the number of locations of the test pattern area during any one cycle may be such as to not be greater than ten times (or not greater than five or two times, and may even be the same as) the number of the dispensers used to form an array during any one cycle. The test pattern area may be the same area through which the substrate is later cut or otherwise separated to provide multiple portions of the substrate each with one or more fabricated arrays thereon. [0013] The method may be used for forming an addressable array of polymers on the substrate. In this case, the reagent drop set deposited during a cycle attaches a monomeric unit of the corresponding polymer for that feature location. However, a method of the present invention could also be used [0014] A method of the present invention may (by "may" throughout this application is meant "optionally") include the possibility of not independently detecting drops of a drop group at a corresponding feature location at which such group is deposited, for one or more or all such feature locations receiving a drop group. Alternatively, or additionally, a method of the present invention may include the referenced separate test locations in a test pattern area which is separate from (that is, distinguishable from) the array. [0015] A method of the present invention may use a multi-dispenser drop group which has a drop including an attachment moiety which becomes attached at a feature location at which the group is deposited but which does not become attached at test location. For example, the attachment moiety may be one which will become attached at the feature location upon activation by an activator. Another drop of the group may include the activator moiety. In the foregoing example, the attachment moiety and activator are deposited at separate test locations. Results from the detecting (such as an image) may be evaluated for a dispenser error. When an error is detected, the array may be discarded or an attempt made to correct such error (such as by depositing further drops to correct the error), or the results used for other purposes. Also, drops of a multi-dispenser drop group may, but need not, contact one another. For example, in the attachment moiety and activator combination already mentioned, drops of each will typically be deposited in a same cycle and so will contact one another. However, particularly where the multi-dispenser drop group is over multiple cycles, a drop of the group deposited in one cycle may already have been removed from the corresponding feature location before a drop of the group in another cycle contacts that same feature location. [0016] The present invention further provides an apparatus which an execute a method of the present invention. Such an apparatus may include a deposition system having multiple dispensers each of which can dispense a reagent drop, as well as a transport system to move at least one of the deposition system or the substrate. A drop detector may further be present, as well as a process which controls the deposition system and the transport system such that a method of the present application may be performed. The present invention also provides a computer program product which can execute any one or more methods of the present invention. Optionally, the present invention may further provide for exposing the array to a sample, and reading the array following the exposure and optionally processing results of the interrogation. The result of an array reading (whether processed or not) may be forwarded for receipt at a remote location. [0017] The various aspects of the present invention can provide any one or more of the following and/or other useful benefits. For example, a dispenser error which could result in a feature error during an in situ or any array fabrication method, can be detected. This allows an opportunity to identify and discard possibly defect arrays or an opportunity to attempt to correct the defect. BRIEF DESCRIPTION OF THE DRAWINGS [0018] FIG. 1 illustrates a substrate carrying multiple arrays, such as may be fabricated by methods of the present invention; [0019] FIG. 2 is an enlarged view of a portion of FIG. 1 showing multiple ideal spots or features; [0020] FIG. 3 is an enlarged illustration of a portion of the substrate in FIG. 2; Continue reading about Error detection in chemical array fabrication... Full patent description for Error detection in chemical array fabrication Brief Patent Description - Full Patent Description - Patent Application Claims Click on the above for other options relating to this Error detection in chemical array fabrication patent application. ###  How KEYWORD MONITOR works... a FREE service from FreshPatents1. Sign up (takes 30 seconds). 2. Fill in the keywords to be monitored. 3. Each week you receive an email with patent applications related to your keywords. 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