Methods for detection of nucleic acid sequences in urine

Abstract

Described are non-invasive methods of detecting the presence of specific nucleic acid sequences as well as nucleic acid modifications and alterations by analyzing urine samples for the presence of transrenal nucleic acids. More specifically, the present invention encompasses methods of detecting specific fetal nucleic acid sequences and fetal sequences that contained modified nucleotides by analyzing maternal urine for the presence of fetal nucleic acids. The invention further encompasses methods of detecting specific nucleic acid modifications for the diagnosis of disease, such as cancer and pathogen infections, and detection of genetic predisposition to various disease. The invention specifically encompasses methods of analyzing specific nucleic acid modifications for the monitoring of cancer treatment. The invention further encompasses methods of analyzing specific nucleic acids in urine to track the success of transplanted cells, tissues and organs. The invention also encompasses methods for evaluating the effects of environmental factors and aging on the genome.

1. A method of monitoring transplanted material  rejection or acceptance of cells, tissue or organs that are transplanted in areas other than the urinary tract in a patient, comprising:
 a) providing a  urine samples from a patient suspected of containing cell- free, transrenal  nucleic acids of the transplanted material, which transplanted material is located outside of the urinary tract  from the cells, tissue or organs that are transplanted in areas other than the urinary tract in the patient; and  
 b) quantitatively analyzing said urine sample for nucleic acids from the cell genome of the transplanted material that are different from nucleic acids of the recipient and that have crossed the kidney barrier  for one or more specific sequences of the cell- free, transrenal nucleic acids from dying cells in the transplanted cells, tissues or organs that are different from sequences of nucleic acids of the patient wherein said analyzing comprises the step of detecting said one or more specific sequences of nucleic acids from the transplanted cells, tissues or organs in the nucleic acids that are no more than  1000  nucleotides in length from urine samples and have crossed the kidney barrier to monitor rejection or acceptance of the transplanted cells, tissues or organs .  
 
     
     
       2. The method of  claim 1 , wherein said nucleic acid sequence is not present in cells of the urinary tract of said patient. 
     
     
       3. The method of  claim 1 , wherein said analyzing comprises amplifying said nucleic acid sequence with a primer substantially complementary to a part of said nucleic acid sequence that does not occur in cells of the urinary tract of the patient, to make amplified target DNA, and detecting the presence of said amplified target DNA  the one or more specific sequences of said the cell- free, transrenal nucleic acids from step  ( b )  and detecting the presence of said amplified target nucleic acid sequences . 
     
     
       4. The method of  claim 3 , wherein amplifying comprises performing a polymerase chain reaction. 
     
     
       5. The method of  claim 1 , further comprising step (a)(i)  reducing DNA  nucleic acid degradation in said urine samples. 
     
     
       6. The method of  claim 5 , wherein reducing DNA degradation is by treatment  nucleic acid degradation comprises inhibiting nuclease activity by increased pH, increased salt concentration, heat inactivation, or by treating said urine samples with a compound selected from the group consisting of:
 ethylenediaminetetraacetic acid, guanidine-HCI, guanidine isothiocyanate, N-lauroylsarcosine, and Na-  sodium dodecylsulphate.  
 
     
     
       7. The method of  claim 1 , wherein said urine samples has  have been held in the bladder less than 12 hours. 
     
     
       8. The method of  claim 1 , further comprising step (a)(i)  substantially isolating said nucleic acid sequence  cell- free, transrenal nucleic acids . 
     
     
       9. The method of  claim 8 , wherein said nucleic acid sequence is  cell- free, transrenal nucleic acids from step  ( b )  are  substantially isolated by precipitation. 
     
     
       10. The method of  claim 8 , wherein said nucleic acid sequence is  cell- free, transrenal nucleic acids from step  ( b )  are  substantially isolated by adsorption of said nucleic acids on a resin. 
     
     
       11. The method of  claim 1 , further comprising step (a)(1)  filtering said urine samples to remove contaminants. 
     
     
       12. The method of  claim 11 , wherein said filtering removes DNA  nucleic acids comprising more than about 1000 nucleotides. 
     
     
       13. The method of  claim 1 , wherein said cell- free, transrenal nucleic acids from step  ( b )  are DNA.   
     
     
       14. The method of  claim 1 , wherein said cell- free, transrenal nucleic acids from step  ( b )  are RNA.   
     
     
       15. The method of  claim 11 , wherein said filtering removes nucleic acids comprising more than about  1000  base pairs. 
     
     
       16. The method of  claim 11 , wherein said filtering removes nucleic acids comprising more than about  300  nucleotides. 
     
     
       17. The method of  claim 13 , wherein said filtering removes nucleic acids comprising more than about  300  base pairs. 
     
     
       18. A method of monitoring cells, tissues or organs transplanted in areas other than the urinary tract in a patient, comprising:
   a )  obtaining an urine sample from said patient;        b )  reducing nucleic acid degradation in said urine sample, wherein said reducing comprises inhibiting nuclease activity by increased pH, increased salt concentration, heat inactivation, or by treating said urine sample with a compound selected from the group consisting of: ethylenediaminetetraacetic acid, guanidine - HCl, guanidine isothiocyanate, N - lauroylsarcosine, and sodium dodecylsulphate;        c )  obtaining a fraction of nucleic acids that are made up of fewer than about  300  base pairs from said urine sample and have crossed the kidney barrier; and        d )  analyzing said fraction for one or more specific sequences of non - patient nucleic acids from the transplanted cells, tissues or organs that are different from sequences of nucleic acids of the patient and have crossed the kidney barrier to monitor the cells, tissues or organs transplanted in areas other than the urinary tract in the patient.     
     
     
       19. The method of  claim 18 , wherein said urine sample has been held in the bladder less than  12  hours. 
     
     
       20. The method of  claim 18 , further comprising substantially isolating said nucleic acids in step ( c ). 
     
     
       21. The method of  claim 20 , wherein said isolating is by adsorption of said nucleic acids on a resin. 
     
     
       22. A method of monitoring cells, tissues or organs transplanted in areas other than the urinary tract in a patient, comprising:
   a )  obtaining an urine sample from said patient;        b )  filtering said urine sample to remove contaminants;        c )  obtaining a fraction of nucleic acids that are made up of fewer than about  300  base pairs from said urine sample and have crossed the kidney barrier; and        d )  analyzing said fraction for one or more specific sequences of non - patient nucleic acids from the transplanted cells, tissues or organs that are different from sequences of nucleic acids of the patient and have crossed the kidney barrier to monitor the cells, tissues or organs transplanted in areas other than the urinary tract in the patient.     
     
     
       23. A method of detecting non- host nucleic acids originating in areas other than the urinary tract in a patient, comprising:      a )  obtaining an urine sample from said patient, wherein said urine sample has been held in the bladder less than  12  hours;        b )  removing nucleic acids greater than  1000  nucleotides from said urine sample; and        c )  analyzing said urine sample for one or more specific sequences of non - patient nucleic acids that are different from sequences of nucleic acids of the patient and have crossed the kidney barrier wherein said analyzing comprises the step of detecting said one or more specific sequences in the nucleic acids less than  1000  nucleotides in length from said urine sample.     
     
     
       24. A method of detecting non- host nucleic acids originating in areas other than the urinary tract in a patient, comprising:      a )  obtaining an urine sample from said patient;        b )  substantially isolating said non - host nucleic acids by using a solid adsorbent material or by adsorption of said non - host nucleic acids on a resin and recovering nucleic acids that are no more than  1000  nucleotides in length from said non - host nucleic acids; and        c )  analyzing said urine sample for one or more specific sequences of said non - host nucleic acids that are different from sequences of nucleic acids of the patient and have crossed the kidney barrier wherein said analyzing comprises the step of detecting said one or more specific sequences from the non - host in the nucleic acids no more than  1000  nucleotides in length.     
     
     
       25. A method of detecting non- host nucleic acids originating in areas other than the urinary tract in a patient, comprising:      a )  obtaining an urine sample from said patient;        b )  filtering said urine sample to remove contaminants and obtaining non - host nucleic acids that are no more than  1000  nucleotides in length; and        c )  analyzing said urine sample for one or more specific sequences of non - host nucleic acids that are different from sequences of nucleic acids of the patient and have crossed the kidney barrier wherein said analyzing comprises the step of detecting said one or more specific sequences from the non - host in the nucleic acids less than  1000  nucleotides in length.     
     
     
       26. The method of  claim 25 , wherein said filtering removes nucleic acids comprising more than about  300  nucleotides. 
     
     
       27. The method of  claim 25 , wherein said filtering removes nucleic acids comprising more than about  300  base pairs. 
     
     
       28. The method of  claim 25 , wherein said analyzing comprises quantifying said non- host nucleic acids.   
     
     
       29. A method of detecting nucleic acids of a pathogen, wherein said nucleic acids originate in areas other than the urinary tract in a patient, comprising:
 ( a )  obtaining an urine sample from said patient; and      ( b )  analyzing said urine sample for one or more specific sequences of pathogen nucleic acids that are different from sequences of nucleic acids of the patient and are from pathogen nucleic acids that are no more than  1000  nucleotides in length and that have crossed the kidney barrier wherein said analyzing comprises the step of detecting said one or more specific sequences from the pathogen.     
     
     
       30. The method of  claim 29  wherein said pathogen nucleic acids are DNA. 
     
     
       31. The method of  claim 29  wherein said pathogen nucleic acids are RNA. 
     
     
       32. The method of  claim 29  wherein the pathogen is selected from the group consisting of a virus, a bacterium, a fungus, a mycoplasma, and a protozoan. 
     
     
       33. The method of  claim 32 , wherein the pathogen is a virus. 
     
     
       34. The method of  claim 32 , wherein the pathogen is a fungus. 
     
     
       35. The method of  claim 32 , wherein the pathogen is a mycoplasma. 
     
     
       36. The method of  claim 32 , wherein the pathogen is a protozoan. 
     
     
       37. The method of  claim 32 , wherein the pathogen is a bacterium. 
     
     
       38. The method of  claim 29 , wherein said step of analyzing said urine sample includes a technique selected from the group consisting of hybridization, cycling probe reaction, polymerase chain reaction, nested polymerase chain reaction, PCR to analyze single strand conformation polymorphisms, ligase chain reaction, strand displacement amplification and PCR to analyze restriction fragments length polymorphisms. 
     
     
       39. The method of  claim 29 , wherein said step of analyzing said urine sample includes a polymerase chain reaction that uses primers sufficiently complementary to hybridize with a target sequence of said pathogen nucleic acids of said pathogen. 
     
     
       40. The method of  claim 29 , wherein nucleic acid degradation in said urine sample is reduced. 
     
     
       41. The method of  claim 40 , wherein reducing nucleic acid degradation comprises inhibiting nuclease activity by increased pH, increased salt concentration, heat inactivation, or by treating said urine sample with a compound selected from the group consisting of: ethylenediaminetetraacetic acid, guanidine- HCI guanidine isothiocyanate, N - lauroylsarcosine, and sodium dodecylsulphate.   
     
     
       42. The method of  claim 29 , wherein said urine sample has been held in the bladder less than  12  hours. 
     
     
       43. The method of  claim 29 , wherein step ( b )  comprises substantially isolating said pathogen nucleic acids in said urine sample.   
     
     
       44. The method of  claim 43 , wherein said isolation is by precipitation. 
     
     
       45. The method of  claim 43 , wherein said isolation is by using a solid adsorbent material. 
     
     
       46. The method of  claim 43 , wherein said isolation is by adsorption of said pathogen nucleic acids on a resin. 
     
     
       47. The method of  claim 29 , further comprising filtering said urine sample to remove contaminants. 
     
     
       48. The method of  claim 47 , wherein said filtering removes nucleic acids comprising more than about  1000  nucleotides. 
     
     
       49. The method of  claim 47 , wherein said filtering removes nucleic acids comprising more than about  1000  base pairs. 
     
     
       50. The method of  claim 47 , wherein said filtering removes nucleic acids comprising more than about  300  nucleotides. 
     
     
       51. The method of  claim 47 , wherein said filtering removes nucleic acids comprising more than about  300  base pairs. 
     
     
       52. The method of  claim 29 , wherein said analyzing comprises quantifying said pathogen nucleic acids. 
     
     
       53. A method of detecting nucleic acids of a virus, wherein said nucleic acids originate in areas other than the urinary tract in a patient, comprising:
 ( a )  obtaining an urine sample from said patient,      ( b )  analyzing said urine sample for one or more specific sequences of viral nucleic acids that are different from sequences of nucleic acids of the patient and are from viral nucleic acids that are no more than  1000  nucleotides in length and that have crossed the kidney barrier wherein said analyzing comprises the step of detecting said one or more specific sequences from the virus.     
     
     
       54. The method of  claim 53 , wherein said viral nucleic acids are DNA. 
     
     
       55. The method of  claim 53 , wherein said viral nucleic acids are RNA. 
     
     
       56. The method of  claim 53 , wherein said step of analyzing said urine sample includes a technique selected from the group consisting of hybridization, cycling probe reaction, polymerase chain reaction, nested polymerase chain reaction, PCR to analyze single strand conformation polymorphisms, ligase chain reaction, strand displacement amplification and PCR to analyze restriction fragments length polymorphisms. 
     
     
       57. The method of  claim 53 , wherein said step of analyzing said urine sample includes a polymerase chain reaction that uses primers sufficiently complementary to hybridize with a target sequence of said viral nucleic acids. 
     
     
       58. The method of  claim 53 , wherein nucleic acid degradation in said urine sample is reduced. 
     
     
       59. The method of  claim 58 , wherein reducing nucleic acid degradation comprises inhibiting nuclease activity by increased pH, increased salt concentration, heat inactivation, or by treating said urine sample with a compound selected from the group consisting of: ethylenediaminetetraacetic acid, guanidine- HCI, guanidine isothiocyanate, N - lauroylsarcosine, and sodium dodecylsulphate.   
     
     
       60. The method of  claim 53 , wherein said urine sample has been held in the bladder less than  12  hours. 
     
     
       61. The method of  claim 53 , wherein step ( b )  comprises substantially isolating said viral nucleic acids in said urine sample.   
     
     
       62. The method of  claim 61 , wherein said isolation is by precipitation. 
     
     
       63. The method of  claim 61 , wherein said isolation is by using a solid adsorbent material. 
     
     
       64. The method of  claim 61 , wherein said isolation is by adsorption of said nucleic acids on a resin. 
     
     
       65. The method of  claim 53 , further comprising filtering said urine sample to remove contaminants. 
     
     
       66. The method of  claim 65 , wherein said filtering removes nucleic acids comprising more than about  1000  nucleotides. 
     
     
       67. The method of  claim 65 , wherein said filtering removes nucleic acids comprising more than about  1000  base pairs. 
     
     
       68. The method of  claim 65 , wherein said filtering removes nucleic acids comprising more than about  300  nucleotides. 
     
     
       69. The method of  claim 65 , wherein said filtering removes nucleic acids comprising more than about  300  base pairs. 
     
     
       70. The method of  claim 53 , wherein said analyzing comprises quantifying said viral nucleic acids. 
     
     
       71. A method of detecting nucleic acids of a bacterium, wherein said nucleic acids originate in areas outside the urinary tract in a patient, comprising:
 ( a )  obtaining an urine sample from said patient; and      ( b )  analyzing said urine sample for one or more specific sequences of bacterial nucleic acids that are different from sequences of nucleic acids of the patient and are from bacterial nucleic acids that are no more than  1000  nucleotides in length and that have crossed the kidney barrier wherein said analyzing comprises the step of detecting said one or more specific sequences from the bacteria.     
     
     
       72. The method of  claim 71 , wherein said bacterial nucleic acids are DNA. 
     
     
       73. The method of  claim 71 , wherein said bacterial nucleic acids are RNA. 
     
     
       74. The method of  claim 71 , wherein said step of analyzing said urine sample includes a technique selected from the group consisting of hybridization, cycling probe reaction, polymerase chain reaction, nested polymerase chain reaction, PCR to analyze single strand conformation polymorphisms, ligase chain reaction, strand displacement amplification and PCR to analyze restriction fragments length polymorphisms. 
     
     
       75. The method of  claim 71 , wherein said step of analyzing said urine sample includes a polymerase chain reaction that uses primers sufficiently complementary to hybridize with a target sequence of said nucleic acids of a bacterium. 
     
     
       76. The method of  claim 71 , wherein nucleic acid degradation in said urine sample is reduced. 
     
     
       77. The method of  claim 76 , wherein reducing nucleic acid degradation comprises inhibiting nuclease activity by increased pH, increased salt concentration, heat inactivation, or by treating said urine sample with a compound selected from the group consisting of: ethylenediaminetetraacetic acid, guanidine- HCI, guanidine isothiocyanate, N - lauroylsarcosine, and sodium dodecylsulphate.   
     
     
       78. The method of  claim 71 , wherein said urine sample has been held in the bladder less than  12  hours. 
     
     
       79. The method of  claim 71 , wherein step ( b )  comprises substantially isolating said bacterial nucleic acids in said urine sample.   
     
     
       80. The method of  claim 79 , wherein said isolation is by precipitation. 
     
     
       81. The method of  claim 79 , wherein said isolation is by using a solid adsorbent material. 
     
     
       82. The method of  claim 79 , wherein said isolation is by adsorption of said nucleic acids on a resin. 
     
     
       83. The method of  claim 71 , further comprising filtering said urine sample to remove contaminants. 
     
     
       84. The method of  claim 83 , wherein said filtering removes nucleic acids comprising more than about  1000  nucleotides. 
     
     
       85. The method of  claim 83 , wherein said filtering removes nucleic acids comprising more than about  1000  base pairs. 
     
     
       86. The method of  claim 83 , wherein said filtering removes nucleic acids comprising more than about  300  nucleotides. 
     
     
       87. The method of  claim 83 , wherein said filtering removes nucleic acids comprising more than about  300  base pairs. 
     
     
       88. The method of  claim 71 , wherein said analyzing comprises quantifying said bacterial nucleic acids. 
     
     
       89. A method of testing an urine sample from a patient for target non- host nucleic acids in urine, comprising:    ( a )  obtaining an urine consisting of said target non - host nucleic acids that are no more than  1000  nucleotides in length from a patient; and      ( b )  analyzing said urine sample for one or more specific sequences of said target non - host nucleic acids that are different from sequences of nucleic acids of the patient and have crossed the kidney barrier wherein said analyzing comprises the step of detecting said one or more specific sequences in said urine sample.     
     
     
       90. The method of  claim 89 , wherein said target nucleic acids are DNA. 
     
     
       91. The method of  claim 89 , wherein said target nucleic acids are RNA. 
     
     
       92. The method of  claim 89 , wherein said step of analyzing said urine sample includes a technique selected from the group consisting of hybridization, cycling probe reaction, polymerase chain reaction, nested polymerase chain reaction, PCR to analyze single strand conformation polymorphisms, ligase chain reaction, strand displacement amplification and PCR to analyze restriction fragments length polymorphisms. 
     
     
       93. The method of  claim 89 , wherein said step of analyzing said urine sample includes a polymerase chain reaction that uses primers sufficiently complementary to hybridize with the target nucleic acids. 
     
     
       94. The method of  claim 89 , wherein nucleic acid degradation in said urine sample is reduced. 
     
     
       95. The method of  claim 94 , wherein reducing nucleic acid degradation comprises inhibiting nuclease activity by increased pH, increased salt concentration, heat inactivation, or by treating said urine sample with a compound selected from the group consisting of: ethylenediaminetetraacetic acid, guanidine- HCI, guanidine isothiocyanate, N - lauroylsarcosine, and sodium dodecylsulphate.   
     
     
       96. The method of  claim 89 , wherein said urine sample has been held in the bladder less than  12  hours. 
     
     
       97. The method of  claim 89 , wherein step ( b )  comprises substantially isolating said target nucleic acids in said urine sample.   
     
     
       98. The method of  claim 97 , wherein said isolation is by precipitation. 
     
     
       99. The method of  claim 97 , wherein said isolation is by using a solid adsorbent material. 
     
     
       100. The method of  claim 97 , wherein said isolation is by adsorption of the target nucleic acids on a resin. 
     
     
       101. The method of  claim 89 , further comprising filtering said urine sample to remove contaminants. 
     
     
       102. The method of  claim 101 , wherein said filtering removes nucleic acids comprising more than about  300  nucleotides. 
     
     
       103. The method of  claim 101 , wherein said filtering removes nucleic acids comprising more than about  300  base pairs. 
     
     
       104. The method of  claim 89 , wherein said analyzing comprises quantifying said target non- host nucleic acids.   
     
     
       105. A method of detecting non- host nucleic acids originating in areas other than the urinary tract in a patient, comprising:      a )  obtaining an urine sample from said patient;        b )  reducing nucleic acid degradation in said urine sample, wherein said reducing nucleic acid degradation comprises inhibiting nuclease activity by increased pH, increased salt concentration, heat inactivation, or by treating said urine sample with a compound selected from the group consisting of ethylenediaminetetraacetic acid, guanidine - HCl, guanidine isothiocyanate, N - lauroylsarcosine, and sodium dodecylsulphate;        c )  obtaining a fraction of nucleic acids that are made up of fewer than about  300  base pairs from said urine sample and have crossed the kidney barrier; and        d )  analyzing said fraction for one or more specific sequences of non - host nucleic acids that are different from sequences of nucleic acids of the patient and have crossed the kidney barrier wherein said analyzing comprises the step of detecting said one or more specific sequences from the non - host in said fraction.     
     
     
       106. The method of  claim 105 , wherein said urine sample has been held in bladder less than  12  hours. 
     
     
       107. The method of  claim 105 , wherein said non- host nucleic acids in said urine sample are substantially isolated by precipitation.   
     
     
       108. The method of  claim 105 , wherein said non- host nucleic acids in said urine sample are substantially isolated using a solid adsorbent material.   
     
     
       109. The method of  claim 105 , wherein said non- host nucleic acids in said urine sample are substantially isolated by adsorption of said non - host nucleic acids on a resin.   
     
     
       110. The method of  claim 105 , further comprising filtering said urine sample to remove contaminants. 
     
     
       111. The method of  claim 105 , wherein said analyzing comprises quantifying said non- host nucleic acids.   
     
     
       112. A method of detecting nucleic acids of a pathogen, wherein said nucleic acids originate in areas other than the urinary tract in a patient, comprising:
   a )  obtaining an urine sample suspected of containing said nucleic acids of a pathogen from said patient;        b )  obtaining a fraction of nucleic acids that are made up of fewer than about  300  base pairs from said urine sample; and        c )  analyzing said fraction for one or more specific sequences of pathogen nucleic acids that are different from sequences of nucleic acids of the patient and are from pathogen nucleic acids that have crossed the kidney barrier wherein said analyzing comprises the step of detecting said one or more specific sequences from the pathogen in said fraction.     
     
     
       113. The method of  claim 112 , wherein the pathogen is a virus. 
     
     
       114. The method of  claim 112 , wherein the pathogen is a fungus. 
     
     
       115. The method of  claim 112 , wherein the pathogen is a protozoan. 
     
     
       116. The method of  claim 112 , wherein the pathogen is a bacterium. 
     
     
       117. The method of  claim 112 , further comprising reducing said nucleic acid degradation in said urine sample, wherein reducing said nucleic acid degradation comprises inhibiting nuclease activity by increased pH, increased salt concentration, heat inactivation, or by treating said urine sample with a compound selected from the group consisting of: ethylenediaminetetraacetic acid, guanidine- HCl, guanidine isothiocyanate, N - lauroylsarcosine, and sodium dodecylsulphate.   
     
     
       118. The method of  claim 112 , wherein said urine sample has been held in the bladder less than  12  hours. 
     
     
       119. The method of  claim 112 , wherein said nucleic acids of said pathogen in said urine sample are substantially isolated by precipitation. 
     
     
       120. The method of  claim 112 , wherein said nucleic acids of said pathogen in said urine sample are substantially isolated using a solid adsorbent material. 
     
     
       121. The method of  claim 112 , wherein said nucleic acids of said pathogen in said urine sample are substantially isolated by adsorption of said nucleic acids on a resin. 
     
     
       122. The method of  claim 112 , further comprising filtering said urine sample to remove contaminants. 
     
     
       123. The method of  claim 112 , wherein said analyzing comprises quantifying said nucleic acids. 
     
     
       124. A method of detecting nucleic acids of a virus, wherein said nucleic acids originate in areas other than the urinary tract in a patient, comprising:
   a )  obtaining an urine sample from said patient;        b )  reducing nucleic acid degradation in said urine sample, wherein said reducing nucleic acid degradation comprises inhibiting nuclease activity by increased pH, increased salt concentration, heat inactivation, or by treating said urine sample with a compound selected from the group consisting of ethylenediaminetetraacetic acid, guanidine - HCl, guanidine isothiocyanate, N - lauroylsarcosine, and sodium dodecylsulphate;        c )  obtaining a fraction of nucleic acids that are made up of fewer than about  300  base pairs from said urine sample; and        d )  analyzing said fraction for one or more specific sequences of viral nucleic acids that are different from sequences of nucleic acids of the patient and are from viral nucleic acids that have crossed the kidney barrier wherein said analyzing comprises the step of detecting said one or more specific sequences from the virus in said fraction.     
     
     
       125. The method of  claim 124 , wherein said urine sample has been held in the bladder less than  12  hours. 
     
     
       126. The method of  claim 124 , wherein said nucleic acids of said virus in said urine sample are substantially isolated by precipitation. 
     
     
       127. The method of  claim 124 , wherein said nucleic acids of said virus in said urine sample are substantially isolated using a solid adsorbent material. 
     
     
       128. The method of  claim 124 , wherein said nucleic acids of said virus in said urine sample are substantially isolated by adsorption of said nucleic acids on said virus on a resin. 
     
     
       129. The method of  claim 124  further comprising filtering said urine sample to remove contaminants. 
     
     
       130. The method of  claim 124  wherein said analyzing comprises quantifying said viral nucleic acids. 
     
     
       131. A method of detecting nucleic acids of a bacterium, wherein said nucleic acids originate in areas outside the urinary tract in a patient, comprising:
   a )  obtaining an urine sample from said patient;        b )  reducing nucleic acid degradation in said urine sample, wherein said reducing nucleic acid degradation comprises inhibiting nuclease activity by increased pH, increased salt concentration, heat inactivation, or by treating said urine sample with a compound selected from the group consisting of ethylenediaminetetraacetic acid, guanidine - HCl, guanidine isothiocyanate, N - lauroylsarcosine, and sodium dodecylsulphate;        c )  obtaining a fraction of nucleic acids that are made up of fewer than about  300  base pairs from said urine sample; and        d )  analyzing said fraction for one or more specific sequences of bacterium nucleic acids that are different from sequences of nucleic acids of the patient and are from bacterium nucleic acids that have crossed the kidney barrier wherein said analyzing comprises the step of detecting said one or more specific sequences from the bacterium in said fraction.     
     
     
       132. The method of  claim 131 , wherein said urine sample has been held in the bladder less than  12  hours. 
     
     
       133. The method of  claim 131 , wherein said nucleic acids of said bacterium in said urine sample are substantially isolated by precipitation. 
     
     
       134. The method of  claim 131 , wherein said nucleic acids of said bacterium in said urine sample are substantially isolated using a solid adsorbent material. 
     
     
       135. The method of  claim 131 , wherein said nucleic acids of said bacterium in said urine sample are substantially isolated by adsorption of said nucleic acids on a resin. 
     
     
       136. The method of  claim 131 , further comprising filtering said urine sample to remove contaminants. 
     
     
       137. The method of  claim 131 , wherein said analyzing comprises quantifying said bacterium nucleic acids.