US20020009394A1 - Automated process line - Google Patents

Automated process line Download PDF

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US20020009394A1
US20020009394A1 US09/285,481 US28548199A US2002009394A1 US 20020009394 A1 US20020009394 A1 US 20020009394A1 US 28548199 A US28548199 A US 28548199A US 2002009394 A1 US2002009394 A1 US 2002009394A1
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data
test
defined
system
mass spectrometer
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Abandoned
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US09/285,481
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Hubert Koster
Ping Yip
Jhobe Steadman
Dirk Reuter
Richard MacDonald
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Sequenom Inc
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Sequenom Inc
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Priority to US09/285,481 priority Critical patent/US20020009394A1/en
Assigned to SEQUENOM, INC. reassignment SEQUENOM, INC. ASSIGNMENT OF ASSIGNORS INTEREST (SEE DOCUMENT FOR DETAILS). Assignors: KOSTER, HUBERT, STEADMAN, JHOBE, YIP, PING, REUTER, DIRK
Assigned to SEQUENOM, INC. reassignment SEQUENOM, INC. ASSIGNMENT OF ASSIGNORS INTEREST (SEE DOCUMENT FOR DETAILS). Assignors: MACDONALD, RICHARD
Publication of US20020009394A1 publication Critical patent/US20020009394A1/en
Application status is Abandoned legal-status Critical

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    • GPHYSICS
    • G01MEASURING; TESTING
    • G01NINVESTIGATING OR ANALYSING MATERIALS BY DETERMINING THEIR CHEMICAL OR PHYSICAL PROPERTIES
    • G01N35/00Automatic analysis not limited to methods or materials provided for in any single one of groups G01N1/00 - G01N33/00; Handling materials therefor
    • G01N35/0099Automatic analysis not limited to methods or materials provided for in any single one of groups G01N1/00 - G01N33/00; Handling materials therefor comprising robots or similar manipulators
    • YGENERAL TAGGING OF NEW TECHNOLOGICAL DEVELOPMENTS; GENERAL TAGGING OF CROSS-SECTIONAL TECHNOLOGIES SPANNING OVER SEVERAL SECTIONS OF THE IPC; TECHNICAL SUBJECTS COVERED BY FORMER USPC CROSS-REFERENCE ART COLLECTIONS [XRACs] AND DIGESTS
    • Y10TECHNICAL SUBJECTS COVERED BY FORMER USPC
    • Y10TTECHNICAL SUBJECTS COVERED BY FORMER US CLASSIFICATION
    • Y10T436/00Chemistry: analytical and immunological testing
    • Y10T436/11Automated chemical analysis
    • YGENERAL TAGGING OF NEW TECHNOLOGICAL DEVELOPMENTS; GENERAL TAGGING OF CROSS-SECTIONAL TECHNOLOGIES SPANNING OVER SEVERAL SECTIONS OF THE IPC; TECHNICAL SUBJECTS COVERED BY FORMER USPC CROSS-REFERENCE ART COLLECTIONS [XRACs] AND DIGESTS
    • Y10TECHNICAL SUBJECTS COVERED BY FORMER USPC
    • Y10TTECHNICAL SUBJECTS COVERED BY FORMER US CLASSIFICATION
    • Y10T436/00Chemistry: analytical and immunological testing
    • Y10T436/11Automated chemical analysis
    • Y10T436/113332Automated chemical analysis with conveyance of sample along a test line in a container or rack
    • YGENERAL TAGGING OF NEW TECHNOLOGICAL DEVELOPMENTS; GENERAL TAGGING OF CROSS-SECTIONAL TECHNOLOGIES SPANNING OVER SEVERAL SECTIONS OF THE IPC; TECHNICAL SUBJECTS COVERED BY FORMER USPC CROSS-REFERENCE ART COLLECTIONS [XRACs] AND DIGESTS
    • Y10TECHNICAL SUBJECTS COVERED BY FORMER USPC
    • Y10TTECHNICAL SUBJECTS COVERED BY FORMER US CLASSIFICATION
    • Y10T436/00Chemistry: analytical and immunological testing
    • Y10T436/20Oxygen containing
    • Y10T436/203332Hydroxyl containing
    • YGENERAL TAGGING OF NEW TECHNOLOGICAL DEVELOPMENTS; GENERAL TAGGING OF CROSS-SECTIONAL TECHNOLOGIES SPANNING OVER SEVERAL SECTIONS OF THE IPC; TECHNICAL SUBJECTS COVERED BY FORMER USPC CROSS-REFERENCE ART COLLECTIONS [XRACs] AND DIGESTS
    • Y10TECHNICAL SUBJECTS COVERED BY FORMER USPC
    • Y10TTECHNICAL SUBJECTS COVERED BY FORMER US CLASSIFICATION
    • Y10T436/00Chemistry: analytical and immunological testing
    • Y10T436/24Nuclear magnetic resonance, electron spin resonance or other spin effects or mass spectrometry
    • YGENERAL TAGGING OF NEW TECHNOLOGICAL DEVELOPMENTS; GENERAL TAGGING OF CROSS-SECTIONAL TECHNOLOGIES SPANNING OVER SEVERAL SECTIONS OF THE IPC; TECHNICAL SUBJECTS COVERED BY FORMER USPC CROSS-REFERENCE ART COLLECTIONS [XRACs] AND DIGESTS
    • Y10TECHNICAL SUBJECTS COVERED BY FORMER USPC
    • Y10TTECHNICAL SUBJECTS COVERED BY FORMER US CLASSIFICATION
    • Y10T436/00Chemistry: analytical and immunological testing
    • Y10T436/25Chemistry: analytical and immunological testing including sample preparation
    • Y10T436/25875Gaseous sample or with change of physical state

Abstract

A fully automated modular analytical system integrates instrumentation to permit analysis of biopolymer samples. The samples include, but are not limited to, all biopolymers, e.g., nucleic acids, proteins, peptides and carbohydrates. The system integrates analytical methods of detection and analysis, e.g., mass spectrometry, radiolabeling, mass tags, chemical tags, fluorescence chemiluminescence, and the like, with robotic technology and automated chemical reaction systems to provide a high-throughput, accurate Automated Process Line (APL).

Description

    BACKGROUND OF THE INVENTION
  • In recent years, developments in the field of life sciences have proceeded at a breathtaking rate. Ground breaking scientific discoveries and advances in such fields as genomics (sequencing and characterization of genetic information and analysis of the relationship between gene activity and cell function) and proteomics (systematic analysis of protein expression in tissues, cells, and biological systems) promise to reshape the fields of medicine, agriculture, and environmental science. The success of these efforts depends, in part, on the development of sophisticated laboratory tools that will automate and expedite the testing and analysis of biological samples. [0001]
  • Current methods of testing typically employ multiple instruments for preparing and analyzing samples and involve multiple manual handling steps and transfers. Such procedures are labor-intensive, time-consuming, and costly and they are susceptible to human error, sample contamination, and loss. After samples have been prepared, they can be subjected to testing procedures that produce data for analysis. Conventional testing procedures often must be performed by an individual laboratory technician, one sample at a time. Laboratory technicians are typically individuals who are most likely trained to operate only a single instrument. Automation will reduce the number of personnel and training necessary to carry out the research. Reliable and accurate automated process and analysis tools are necessary for the benefits of recent scientific discoveries to be fully achieved. [0002]
  • Genomic research is increasing the availability of genomic markers that can be used for the identification of all organisms, including humans. These markers (all genetic loci including SNPs, microsatellites and other noncoding genomic regions) provide a way to not only identify populations but also allow stratification of populations according to their response to drug treatment, resistance to environmental agents, and other factors. Importantly, the identification of the large number of genomic markers has become the driving force behind the development of new automated technologies. [0003]
  • At the forefront of the efforts to develop better analytical tools are efforts to expedite the analysis of complex biochemical structures. For example, robotic devices have been employed to assist in sample preparation and handling. [0004]
  • Such automated sample preparation systems could find application is the areas of: identification and validation of disease-causing genes or drug targets; defining mutations and polymorphisims associated with specific diseases; monitoring gene expression and comparing disease states, cell cycles or other changes; genetic profiling of patients for responsiveness to genomics-based therapies; and genetic profiling of subjects in drug clinical studies to link response with genotype. [0005]
  • The utility of genomic markers to identify and stratify populations is depending on the industry's ability to measure great numbers (100-100,000) of markers in large populations. This approach is extremely limited in terms of time and research costs. Automation of these systems provides advantages such as increasing throughput and accuracy, but miniaturization also is an important consideration in terms of research costs. Accordingly, there is a need to automate processes in which very small volumes are handled, and retain the accuracy of the results to permit their use in high throughput screening protocols and diagnostics. [0006]
  • Therefore it is an object herein to provide automated systems and methods for high-throughput analysis of biological samples, particularly samples of very small volume, for screening, diagnosis and other proceudres. Other objects will become apparent from the following disclosure. [0007]
  • SUMMARY OF THE INVENTION
  • Provided herein is a fully automated modular analytical system that integrates sample preparation, instrumentation, and analysis of biopolymer samples. The samples include, but are not limited to, all biopolymers, e.g., nucleic acids, proteins, peptides, carbohydrates, PNA (peptide nucleic acids), biopolymer (nucleic acid/peptide) analogs, and libraries of combinatorial molecules. The system integrates analytical methods of detection and analysis, e.g., mass spectrometry, radiolabeling, mass tags, chemical tags, fluorescence chemiluminescence, and the like, with robotic technology and automated chemical reaction systems to provide a high-throughput, accurate automated process line (APL). The systems and methods provided herein are particularly suited for handling very small volumes, on the order of milliliters, nanoliters and even smaller picoliter volumes. [0008]
  • In certain embodiments, the analytical system includes one portion that is a contamination-controlled environment, such as a clean room or laminar flow room, and includes a means, such as a transporter, for moving the samples from such environment into a second room or space for further processing. This dual space system permits performance of procedures that require clean room conditions to be automatedly linked to procedures that do not require such conditions. [0009]
  • An integrated system for performing a process line comprising a plurality of processing stations, each of which performs a procedure on a biological sample contained in a reaction vessel; a robotic system that transports the reaction vessel from processing station to processing station; a control system that determines when the procedure at each processing station is complete and, in response, moves the reaction vessel to the next test station, and continuously processes reaction vessels one after another until the control system receives a stop instruction; and a data analysis system that receives test results of the process line and automatically processes the test results to make a determination regarding the biological sample in the reaction vessel is provided. [0010]
  • The APL can run unattended continuously with a continuous sample throughput and is capable of analyzing on the order of 10,000-50,000 genotypes per day. The results are highly accurate and reproducible. [0011]
  • Also provided herein are methods for automated analysis of biopolymers using the integrated APL system. In preferred embodiments, provided are automated methods for preparing a biological sample for analysis; introducing the sample into an analytical instrument; recording sample data; automatically processing and interpreting the data; and storing the data in a bioinformatics database. In a particular embodiment, patient DNA samples are automatically analyzed to determine genotype.[0012]
  • BRIEF DESCRIPTION OF THE DRAWINGS
  • FIG. 1 is a diagram of the components of the automated process line. [0013]
  • FIG. 2 shows a magnetic strip construction of the magnetic lift illustrated in FIG. 1. [0014]
  • FIG. 3 shows a point-magnet construction of the magnetic lift illustrated in FIG. 1. [0015]
  • FIG. 4 shows the robotic interface between the chip processor and the mass spectrometer of the automated process line illustrated in FIG. 1. [0016]
  • FIG. 5 shows a comparison of a mass spectrum of a test sample with stored spectra from samples with known genotypes. [0017]
  • FIG. 6 is a flow diagram that illustrates the data analysis processing steps performed by the automated process line of FIG. 1. [0018]
  • FIG. 7 shows an example of the user interface to the APL system. [0019]
  • FIG. 8 shows an example of the interface to a database of experimental mass spectral data. [0020]
  • DETAILED DESCRIPTION AND PREFERRED EMBODIMENTS
  • Definitions [0021]
  • Unless defined otherwise, all technical and scientific terms used herein have the same meaning as is commonly understood by one of skill in the art to which this invention belongs. All patents, patent applications and publications referred to herein are, unless noted otherwise, incorporated by reference in their entirety. In the event a definition in this section is not consistent with definitions elsewhere, the definition set forth in this section will control. [0022]
  • As used herein, a molecule refers to any molecule or compound that is linked to the bead. Typically such molecules are macromolecules or components or precursors thereof, such as peptides, proteins, small organics, oligonucleotides or monomeric units of the peptides, organics, nucleic acids and other macromolecules. A monomeric unit refers to one of the constituents from which the resulting compound is built. Thus, monomeric units include, nucleotides, amino acids, and pharmacophores from which small organic molecules are synthesized. [0023]
  • As used herein, macromolecule refers to any molecule having a molecular weight from the hundreds up to the millions. Macromolecules include peptides, proteins, nucleotides, nucleic acids, and other such molecules that are generally synthesized by biological organisms, but can be prepared synthetically or using recombinant molecular biology methods. [0024]
  • As used herein, a biological particle refers to a virus, such as a viral vector or viral capsid with or without packaged nucleic acid, phage, including a phage vector or phage capsid, with or without encapsulated nucleotide acid, a single cell, including eukaryotic and prokaryotic cells or fragments thereof, a liposome or micellar agent or other packaging particle, and other such biological materials. For purposes herein, biological particles include molecules that are not typically considered macromolecules because they are not generally synthesized, but are derived from cells and viruses. [0025]
  • As used herein, the term “nucleic acid” refers to single-stranded and/or double-stranded polynucleotides such as deoxyribonucleic acid (DNA), and ribonucleic acid (RNA) as well as analogs or derivatives of either RNA or DNA. Also included in the term “nucleic acid” are analogs of nucleic acids such as peptide nucleic acid (PNA), phosphorothioate DNA, and other such analogs and derivatives. [0026]
  • As used herein, the term “biological sample” refers to any material obtained from any living source (e.g., human, animal, plant, bacteria, fungi, protist, virus). For purposes herein, the biological sample will typically contain a nucleic acid molecule. Examples of appropriate biological samples include, but are not limited to: solid materials (e.g., tissue, cell pellets, biopsies) and biological fluids (e.g., urine, blood, saliva, amniotic fluid, mouth wash, cerebral spinal fluid and other body fluids). [0027]
  • As used herein, the phrases “chain-elongating nucleotides” and “chain-terminating nucleotides” are used in accordance with their art recognized meaning. For example, for DNA, chain-elongating nucleotides include 2′deoxyribonucleotides (e.g., dATP, dCTP, dGTP and dTTP) and chain-terminating nucleotides include 2′, 3′-dideoxyribonucleotides (e.g., ddATP, ddCTP, ddGTP, ddTTP). For RNA, chain-elongating nucleotides include ribonucleotides (e.g., ATJP, CTP, GTP and UTP) and chain-terminating nucleotides include 3′-deoxyribonucleotides (e.g., 3′dA, 3′dC, 3′dG and 3′dU). A complete set of chain elongating nucleotides refers to dATP, dCTP, dGTP and dTTP. The term “nucleotide” is also well known in the art. [0028]
  • As used herein, nucleotides include nucleoside mono-, di-, and triphosphates. Nucleotides also include modified nucleotides such as phosphorothioate nucleotides and deazapurine nucleotides. A complete set of chain-elongating nucleotides refers to four different nucleotides that can hybridize to each of the four different bases comprising the DNA template. [0029]
  • As used herein, “multiplexing” refers to the simultaneously detection of more than one analyte, such as more than one (mutated) loci on a particular captured nucleic acid fragment (on one spot of an array). [0030]
  • As used herein, the term “biopolymer” is used to mean a biological molecule composed of two or more monomeric subunits, or derivatives thereof, which are linked by a bond or a macromolecule. A biopolymer can be, for example, a polynucleotide, a polypeptide, a carbohydrate, or a lipid, or derivatives or combinations thereof, for example, a nucleic acid molecule containing a peptide nucleic acid portion or a glycoprotein, respectively. The methods and systems herein, though described with reference to biopolymers, can be adapted for use with other synthetic schemes and assays, such as organic syntheses of pharmacuticals, or inorganics and any other reaction or assay performed on a solid support or in a well in nanoliter volumes. [0031]
  • As used herein, the term “nucleic acid” refers to single-stranded and/or double-stranded polynucleotides such as deoxyribonucleic acid (DNA), and ribonucleic acid (RNA) as well as analogs or derivatives of either RNA or DNA. Also included in the term “nucleic acid” are analogs of nucleic acids such as peptide nucleic acid (PNA), phosphorothioate DNA, and other such analogs and derivatives. [0032]
  • As used herein, the term “polynucleotide” refers to an oligomer or polymer containing at least two linked nucleotides or nucleotide derivatives, including a deoxyribonucleic acid (DNA), a ribonucleic acid (RNA), and a DNA or RNA derivative containing, for example, a nucleotide analog or a “backbone” bond other than a phosphodiester bond, for example, a phosphotriester bond, a phosphoramidate bond, a phophorothioate bond, a thioester bond, or a peptide bond (peptide nucleic acid). The term “oligonucleotide” also is used herein essentially synonymously with “polynucleotide,” although those in the art will recognize that oligonucleotides, for example, PCR primers, generally are less than about fifty to one hundred nucleotides in length. [0033]
  • Nucleotide analogs contained in a polynucleotide can be, for example, mass modified nucleotides, which allows for mass differentiation of polynucleotides; nucleotides containing a detectable label such as a fluorescent, radioactive, luminescent or chemiluminescent label, which allows for detection of a polynucleotide; or nucleotides containing a reactive group such as biotin or a thiol group, which facilitates immobilization of a polynucleotide to a solid support. A polynucleotide also can contain one or more backbone bonds that are selectively cleavable, for example, chemically, enzymatically or photolytically. For example, a polynucleotide can include one or more deoxyribonucleotides, followed by one or more ribonucleotides, which can be followed by one or more deoxyribonucleotides, such a sequence being cleavable at the ribonucleotide sequence by base hydrolysis. A polynucleotide also can contain one or more bonds that are relatively resistant to cleavage, for example, a chimeric oligonucleotide primer, which can include nucleotides linked by peptide nucleic acid bonds and at least one nucleotide at the 3′ end, which is linked by a phosphodiester bond, or the like, and is capable of being extended by a polymerase. Peptide nucleic acid sequences can be prepared using well known methods (see, for example, Weiler et al., [0034] Nucleic acids Res. 25:2792-2799 (1997)).
  • A polynucleotide can be a portion of a larger nucleic acid molecule, for example, a portion of a gene, which can contain a polymorphic region, or a portion of an extragenic region of a chromosome, for example, a portion of a region of nucleotide repeats such as a short tandem repeat (STR) locus, a variable number of tandem repeats (VNTR) locus, a microsatellite locus or a minisatellite locus. A polynucleotide also can be single stranded or double stranded, including, for example, a DNA-RNA hybrid, or can be triple stranded or four stranded. Where the polynucleotide is double stranded DNA, it can be in an A, B, L or Z configuration, and a single polynucleotide can contain combinations of such configurations. [0035]
  • As used herein, the term “polypeptide,” means at least two amino acids, or amino acid derivatives, including mass modified amino acids and amino acid analogs, that are linked by a peptide bond, which can be a modified peptide bond. A polypeptide can be translated from a polynucleotide, which can include at least a portion of a coding sequence, or a portion of a nucleotide sequence that is not naturally translated due, for example, to it being located in a reading frame other than a coding frame, or it being an intron sequence, a 3′ or 5′ untranslated sequence, a regulatory sequence such