Genetic test apparatus and method

• US 20040014097A1
• Filed: 04/07/2003
• Published: 01/22/2004
• Est. Priority Date: 05/06/2002
• Status: Abandoned Application

• Current Assignee: Access Genetics LLC
• Original Assignee: Access Genetics LLC
• Inventors: Franks, Aaron, Holmes, Sabine, Schuldt, Robert P., Williamson, Naomi M., McGlennen, Ronald C.
• Application Number:
  US10/409,337
• Publication Number:
  US 20040014097A1
• Time in Patent Office: Days
• US Class Current: 435/6
• CPC Class Codes: B01L 1/52 Transportable laboratories; Field kits
• CPC Class Codes: B01L 9/06 Test-tube stands; Test-tube holders
• CPC Class Codes: G16H 10/40 for data related to laboratory analysis, e.g. patient specimen analysis
• CPC Class Codes: G16H 15/00 ICT specially adapted for medical reports, e.g. generation or transmission thereof
• CPC Class Codes: G16H 40/67 for remote operation

Abstract

The invention involves creation of an integrated genetic testing kit. The kit combines materials and components to aid in performance of each of the steps in a genetic assay. Additionally, the invention describes a variety of electronic tools and adjunct materials to make easier the collection and organization of patient related information that is used in interpretation of the analytic genetic data. One aspect of this invention is as a stand-alone integrated test kit, the test results of which may be in the form of fluoroscopic output. Another aspect of this invention is a telemedicine model. In this model, the invention is a larger genetic testing system in which procurement of genetic material, its testing, and its interpretation may occur at different locations. The telemedicine model comprises the integrated kit, instrumentation, and an electronic transmission system for delivery of the genetic test data to a remote data system where it is interpreted and a report is generated.

Claims

1. A method of performing genetic testing in a telemedicine model, in which test results are transmitted to a central location at which expertise in interpretation of genetic testing resides.

6. The method of performing genetic testing in a telemedicine model of claim 1, wherein the genetic test data is generated according to a protocol of an integrated test kit in conjunction with other components of the kit.

7. The method of performing genetic testing in a telemedicine model of claim 6, also comprising a method of (a) entry of patient demographic data, (b) ordering a genetic test, (c) ordering kit components, (c) calculating reagent volumes as a function of the number of test specimens, (d) calculating reagent reaction times, (e) presentation of protocol steps, (f) reading the genetic test data presented by denatured and marked nucleic acid, (g) analyzing the nucleic acid test data, (h) analyzing sorting and selecting, according to an expert system algorithm, information from a genetic database to interpret the nucleic acid test data and generate an initial interpretive report, and (i) generating a final interpretive report of a licensed physician.

8. The method of claim 6, wherein bar code labeled components of the integrated test kit can be ordered from a remote site electronically.

82. The ordering form of claim 1, wherein the contents of the ordering form are inputed into an expert system having a database of genetic information for initial evaluation of whether a genetic test is indicated and if so the appropriate test and kit components and subsequent licensed physician review and approval, disapproval, or revision of the initial evaluation.

2. A method of genetic testing in which genetic source material is tested at a location different from a location at which analysis of results of the testing and preparation of interpretive genetic testing reports occurs.

3. A genetic test data gathering process that, automatically or as initiated by a remote site or central location, gathers from a remote site database genetic data relevant to a desired genetic test to be performed at the remote site and subsequently interpreted at the central location.

4. An interpretive report generator:

(a) a database 823, accessible by an expert system 650, the database containing genetic reference information 818;

(b) a clinical data collection system 300 containing patient data 407, the clinical data collection system accessible to the database for storage of the patient data in the database;

(c) the expert system comprising a control mechanism for (i) inspecting the patient data in the database, (ii) searching the genetic reference information stored in the database, said search parameters based on the patient data, and (iii) generating a data report 700, which contains an interpretation of the patient data, the data report accessible to the clinical data collection system.

5. The interpretive report generator of claim 4, wherein the generated data report is analyzed by a health care professional and revised as may be deemed necessary by the health care professional.

9. A test kit for performing a molecular genetic assay of a specimen, comprising components for (i) purification of specimen nucleic acid and (ii) denaturing and marking the purified nucleic acid, so that characteristics of target genes can be identified.

10. The components of the test kit of claim 9, comprising an extraction rack, a mixing rack, a microtitor, and an assay protocol.

11. The test kit of claim 10, also comprising components from the group including a specimen sample, liquid collection media, treated paper for cell capture, template guide, graduated transfer pipette, microcentrifuge tube, a kit box, filter basket, mineral oil, wax;

label, genetic test order form, component order form, pipette tip, tube snap top, assay protocol, pipette tip, skirted microtitor base, extractor rack face plate, mixing rack face plate, a record and store device, training material, calculator tool, disposable materials, reagents such as protein buffer, probe, oligonucleotide, first fluorescent marker, second fluorescent marker, and thermostable endonucleolytic enzyme, and containers for certain of the foregoing components in the group.

12. The test kit of claim 10, wherein at least one of the components is bar coded with information relating to the component.

13. The test kit of claim 9, also comprising a device to record and store information about the kit selected from the group consisting of material safety, quality control, expiration, environmental condition as a function of time and duration, and location as a function of time and duration.

14. An extractor rack for purification of nucleic acid, comprising a rack body constructed of a material and a face of the rack body comprised of a matrix of adjacent rows and adjacent columns with sized and spaced apertures at each intersection of a row and column.

15. The extractor rack of claim 14, wherein the number of rows corresponds to the number of specimens from which nucleic acid is to be extracted.

16. The extractor rack of claim 15, wherein each specimen is confined to one row.

17. The extractor rack of claim 15, wherein there is a column for the blood specimen.

18. The extractor rack of claim 17, wherein there is a column for each successive steps in the process of extraction of nucleic acid from a specimen.

19. The extractor rack of claim 18, wherein a first column contains blood specimens, a second column adjacent to the first column contains a buffy coat fraction, a third column adjacent to the second column contains a wash solution and a blood fraction, a fourth column adjacent to the third column contains a wash and an elution solution and a blood fraction;

and a fifth column adjacent to the fourth column contains an elution solution and the purified nucleic acid.

20. The extractor rack of claim 14, wherein each column is labeled to indicate its contents or its function.

21. The extractor rack of claim 14, including at least one aperture, in addition to those at the intersections of the rows and columns, for containment of at least one reagent as may be required for a specific genetic test, such as red blood cell lysis, nucleated cell lysis buffers, washing buffer, nucleic acid elution solution, or hydration buffers.

22. The extractor rack of claim 14, wherein the first step in the purification of the nucleic acid of a specimen in a row is performed in a column adjacent to the column in which the specimen is located and each successive step in the purification process is performed in a column adjacent to the column where the previous step was performed.

23. The extractor rack of claim 14, wherein a plurality of specimens, each in a separate row, is purified by (i) moving a first specimen in a first row of a first column to an adjacent second column in the first row where the first specimen is processed according to a first protocol step, moving a second specimen in a second row of the first column to the adjacent second column in the first row where the specimen is processed according to the first protocol step, and moving each remaining specimen in successive rows to the adjacent second column in each respective row where each specimen is processed according to the first protocol step and (ii) moving each specimen in the manner described in subsection (i) of this claim to each of the columns in the extractor rack where each specimen is processed in each column according to a protocol step specified for each column.

24. The extractor rack of claim 14, wherein the number of rows is eight.

25. The extractor rack of claim 14, wherein the spacing between the columns, rows, and apertures within each column and row is the same as the spacing between the columns, rows, and apertures within each column and row of a microtiter into which specimen fractions are to be transferred.

26. The extractor rack of claim 16, wherein the apertures for containing the specimen are sized to accommodate the specimen container.

27. The extractor rack of claim 18, wherein the apertures in the columns for the successive steps in the process of extraction of nucleic acid from a specimen are sized to accommodate a microcentrifuge tube.

28. The extractor rack of claim 17, wherein there is a column for each successive steps in the process of extraction of nucleic acid from a specimen.

29. The extractor rack of claim 14, wherein the rack body is dimensioned to be of a depth to accommodate the length of the tubes in the apertures.

30. The extractor rack of claim 14, wherein the apertures are spaced to accommodate a multichannel pipette without realignment of the multichannel pipette tips for transfer of aliquoted amounts of specimen fractions from column to column and from the elution and DNA column to a microtitor.

31. A mixing rack for creation of a master mix and for organizing control samples, comprising a rack body constructed of a material and a matrix of sized and spaced apertures in a face of the rack body.

32. The mixing rack of claim 31, also comprising a face plate.

33. The mixing rack of claim 32, wherein the face plate is releasably adhered to the face of the rack body in which the matrix of sized and spaced apertures is located.

34. The mixing rack of claim 32, wherein the number of apertures in the face plate is equal to or less than the number of apertures in the matrix of sized and spaced apertures in the rack body face.

35. The mixing rack of claim 34, wherein a plurality of apertures in the face plate are in registry with the apertures in the rack body face.

36. The mixing rack of claim 31, wherein the apertures are sized for containing microcentrifuge tubes.

37. The mixing rack of claim 31, wherein the rack is insulated.

38. The mixing rack of claim 31, configured for processing one specimen at a time.

39. The mixing rack of claim 33, wherein the face plate is labeled to guide sequencing of protocol steps for the creation of a master mix and for organizing control specimens, whereby the master mix and the control specimens may be used to mark and denature nucleic acid for Factor V Leiden and Factor II genetic tests.

40. The mixing rack of claim 38, wherein the face plate is comprised of (i) a first column labeled, Factor V Leiden controls, of four apertures, the first aperture labeled, wild type, the second aperture labeled, HET (heterozygot), the third aperture labeled, mutant type, and the fourth aperture labeled, no target;

(ii) a second column labeled, Factor II controls, of four apertures adjacent the first column, each aperture labeled the same as the corresponding aperture in the first column;

(iii) a third column of seven apertures, the first aperture labeled, buffer, the second labeled, probe, the third labeled, oligo, the fourth labeled, Fret 1, the fifth labeled, Fret 2, the sixth labeled, cleavage enzyme, and the seventh labeled, Factor V Leiden master mix; and

(iii) a fourth column of seven apertures adjacent the third column, each of the first six apertures labeled the same as the corresponding apertures in the third column and the last aperture labeled, Factor II master mix.

41. The mixing rack of claim 40, wherein the first column labeled, Factor V Leiden controls, is the same color as the area around the aperture labeled, Factor V Leiden master mix, in the third column and the second column labeled, Factor II controls, is the same color as the area around the aperture labeled, Factor II master mix, in the fourth column.

42. The mixing rack of claim 41, wherein the area around each successive aperture in the first and third columns is a successively darker shade of the color of the first and third columns and the area around each successive aperture in the second and fourth columns is a successively darker shade of the color of the second and fourth columns.

44. The mixing rack of claim 31, wherein the spacing between apertures within each column of the mixing rack is the same as the spacing between apertures in a microtiter, whereby control samples contained in the mixing rack may be efficiently transferred to the microtiter.

45. The mixing rack of claim 31, wherein the rack body is dimensioned to be of a depth to accommodate the length of the tubes in the apertures.

43. The process of creating a master mix comprising sequentially transferring, according to steps of a protocol, to a master mix container in a mixing rack column an aliquoted amount of a (i) protein buffer, (ii) probe, (iii) oligonucleotide, (iv) first fluorescent marker, (v) second fluorescent marker, and (vi) thermostable endonucleolytic enzyme from each container of the foregoing reagents i through vi, which containers are located in the same column as the master mix container.

46. A microtitor for containment of specimen purified nucleic acid, master mix, and specimen controls.

47. The microtitor claim 46, also comprising a skirted base

48. A template guide comprising a material;

a matrix of rows and columns of apertures, the apertures spaced to correspond to the center-to-center distance between the microtiter wells; and

labeling.

49. The template guide of claim 48, wherein the guide has a template on each side.

50. The template guide of claim 48, also comprising reference marks to guide alignment of the template with the microtiter.

51. The template guide of claim 48, labeled to guide a reaction in the presence of mutant nucleotides.

52. The template guide of claim 48, labeled to guide a reaction in the presence of wild type nucleotides.

53. The template guide of claim 48, labeled to guide a genetic reaction without the presence of an enzyme.

54. The template guide of claim 48, labeled to guide a genetic reaction in the presence of an enzyme.

55. The template guide of claim 48, wherein the apertures are numbered.

56. The template guide of claim 48, labeled to guide a reaction for a plurality of purified specimens.

57. A kit box means for packaging, shipping, and storage of components;

organizing the components; and

using the components to perform genetic tests.

58. A kit box comprising compartments enclosed within the box and a cover, so that the kit components are contained in the compartments in an organized manner.

59. The kit box of claim 58 also comprising a means for removably supporting a protocol manual.

60. The kit box of claim 58 wherein the support means is affixed on the inside of the cover.

61. The kit box of claim 58 wherein the support means is a bench stand with a triangular base to stabilize the stand on the bench, hold open the pages of the protocol manual, allow the pages to be turned, and to maintain the desired pages open.

62. The kit box of claim 58, wherein one or more of the compartments are insulated.

63. The kit box of claim 58, configured for testing batches of specimens of various batch sizes.

64. An assay protocol, comprising steps for operating a genetic test kit to perform genetic tests.

65. The protocol of claim 64, wherein the protocol is recorded in electronic media.

66. The protocol of claim 65, wherein the protocol is implemented in a software application.

67. The protocol of claim 64, wherein the protocol is recorded in hard copy media.

68. The protocol of claim 64, wherein at least one-step is described in detail in text and illustration.

69. The protocol of claim 68, wherein the text and the illustration are side-by-side.

70. The protocol of claim 64, also comprising a guide bar.

71. The protocol of claim 70, wherein a guide bar is visually proximate the detailed description of each step.

72. The guide bar of claim 70, comprising a short text statement of at least one step of the protocol.

73. The guide bar of claim 72, comprising a short text statement for each of the steps of the protocol.

74. The guide bar of claim 70, also comprising a slide bar.

75. The guide bar of claim 70, comprising a short text statement for each of the steps of the protocol with the step described in detail marked on the slide bar.

76. The guide bar of claim 75, wherein the short text statement of the step described in detail is marked on the slide bar by an illustration of a magnifying glass.

77. The protocol of claim 64, also comprising forms for (i) entry of patient demographic data, (ii) presentation of genetic test data, and (iii) interpretation of genetic test data.

78. The protocol of claim 64, also comprising a tool for calculation of (i) the volumes of reagents used for purification, marking, and denaturing nucleic acids upon entering the number of specimens in a test batch and (ii) reaction times.

79. The protocol of claim 64, also comprising a form for ordering genetic tests and genetic test kit components comprising questions to be answered by the ordering person, said questions designed to elicit patient demographic data and other information necessary for a licensed physician to determine whether a genetic test is indicated and if so the appropriate test and kit components.

80. A form for ordering genetic tests and genetic test kit components comprising questions to be answered by the ordering person, said questions designed to elicit patient demographic data and other information necessary for a licensed physician to determine whether a genetic test is indicated and if so the appropriate test and kit components.

81. The ordering form of claim 80, wherein the form is in an electronic media and its contents are sent electronically to a remote site.

83. A tool for calculation of (i) the volumes of reagents used for purification, marking, and denaturing nucleic acids upon entering the number of specimens in a test batch and (ii) reaction times.

84. The tool of claim 83, wherein the tool is a software application

85. The tool of claim 84, wherein the tool is a software application accessible at an Internet site.

86. A method of purifying nucleic acid, comprising performing a series of steps according to a laboratory assay protocol in conjunction with using an extractor rack.

87. A method of purifying the nucleic acid of a whole blood specimen, comprising the steps of (a) placing a container of at least one specimen in a first row in a specimen column of an extractor rack, (b) transferring an aliquot amount of the specimen to a first row container in a buffy coat column of the extractor rack, centrifuging the buffy coat container to fractionate the specimen into plasma, buffy coat, and red blood cells, returning the centrifuged container to the first row in the buffy coat column, and transferring an aliquot amount of the buffy coat into a filter basket in a container in the first row in a wash column of the extractor rack, (b) adding wash solution to the center of the filter basket, centrifuging the wash container until a red tinged fluid collects at the bottom of the container, and transferring the filter basket to a container in its respective row in a wash and elution column of the extractor rack, (c) adding a wash solution to the wash and elution container, centrifuging the container, adding elution solution, centrifuging the wash and elution container again, and transferring the filter basket from the wash and elution container to a container in its respective row in an elution and DNA/RNA column of the extractor rack, and (d) adding elution solution, heating the elution and DNA/RNA container, centrifuging the container, returning the container to its respective row in the elution and DNA/RNA column, and discarding the filter basket.

88. A method of denaturing and marking purified nucleic acid, comprising performing a series of steps according to a laboratory assay protocol in conjunction with using a mixing rack and a microtitor.

89. A method of denaturing and marking purified nucleic acid for the Factor V Leiden genetic assay, comprising the steps of (a) transferring a mixed, aliquoted amount of each of the unfrozen protein buffer, probe, olgionucleotide, first FRET, second FRET, and cleavage enzyme reagents and each of the wildtype, HET, mutant, and targetless control samples into containers in the respectively labeled aperture in a mixing rack, centrifuging each of the containers, and returning the containers to their respective aperture, (b) transferring an aliquoted amount of each of the reagents, one at a time, to the container in the master mix aperture in the mixing rack, mixing the master mix contents, centrifuging the master mix, and returning the centrifuged master mix container to its respective aperture. (d) transferring an aliquoted amount of wild type control sample to a microtitor well in a first column, HET control sample to a second well in the same column, mutant control sample to a third well in the same column, and targetless control sample to a fourth well in the same column, (e) transferring an aliquoted amount of purified nucleic acid from the elution and DNA column of the extractor rack to four wells in a second column adjacent to the first column in the microtitor, each of the four wells in a row adjacent the wells of the first column, (f) dispensing an aliquoted amount of mineral oil on top of each of the control sample wells and each of the purified nucleic acid wells, (g) heating the microtitor for a first period of time at a first temperature, (h) while heating the microtitor at a second lower temperature, transferring an aliquoted amount of master mix to each of the control samples and each of the purified nucleic acid wells by extending the tip of a pipette containing the master mix below the mineral oil, (i) continuing to heat the microtitor at the second temperature for a second period of time to incubate.

90. A method of reading the incubated microtitor wells of claim, comprising placing the microtitor in a fluorometer and initiating reading.