Methods for determining nature of repeat units in DNA

• US 6,207,373 B1
• Filed: 02/25/1998
• Issued: 03/27/2001
• Est. Priority Date: 02/25/1998
• Status: Expired due to Term

• Current Assignee: Gamida for Life B.V.
• Original Assignee: Nanogen, Inc.
• Inventors: Tu, Eugene, Sosnowski, Ronald G.
• Primary Examiner(s): Horlick, Kenneth R.
• Assistant Examiner(s): Siew, Jeffrey
• Application Number:
  US09/030,156
• Time in Patent Office: 1,126 Days
• Field of Search: 435/6, 435/91.1, 435/91.2, 435/9.21, 536/24.3, 536/24.31, 536/24.32, 536/24.33
• US Class Current: 435/6.12
• CPC Class Codes: B01J 2219/00653 the compounds being bound to electrodes embedded in or on the solid supports
• CPC Class Codes: B01J 2219/00659 Two-dimensional arrays
• CPC Class Codes: C12Q 1/6825 Nucleic acid detection involving sensors
• CPC Class Codes: C12Q 1/6827 for detection of mutation or polymorphism
• CPC Class Codes: C12Q 1/6837 using probe arrays or probe chips C12Q1/6874 takes precedence
• CPC Class Codes: C12Q 1/6876 Nucleic acid products used in the analysis of nucleic acids, e.g. primers or probes
• CPC Class Codes: C12Q 2525/151 repeat or repeated sequences, e.g. VNTR, microsatellite, concatemer
• CPC Class Codes: C12Q 2537/125 Sandwich assay format
• CPC Class Codes: C12Q 2565/518 characterised by the immobilisation of the nucleic acid sample or target
• CPC Class Codes: C12Q 2565/607 being a sensor, e.g. electrode
• CPC Class Codes: C12Q 2600/156 Polymorphic or mutational markers
• CPC Class Codes: H01L 29/6656 using multiple spacer layers, e.g. multiple sidewall spacers

Abstract

Methods and apparatus are provided for the analysis and determination of the nature of repeat units in a genetic target. In one method of this invention, the nature of the repeat units in the genetic target is determined by the steps of providing a plurality of hybridization complex assays arrayed on a plurality of test sites, where the hybridization complex assay includes at least a nucleic acid target containing a simple repetitive DNA sequence, a capture probe having a first unique flanking sequence and n repeat units, where n=0,1,2 . . . , or fractions thereof, being complementary to the target sequence, and a reporter probe having a selected sequence complementary to the same target sequence strand wherein the selected sequence of the reporter includes a second unique flanking sequence and m repeat units, where m=0,1,2 . . . , or fractions thereof, but where the sum of repeat units in the capture probe plus reporter probe is greater than 0 (n+m>0). Concordance and discordance among the hybridization complex assays at the test sites is determined at least in part by hybridization stability. Electronic stringency control may be utilized. Applications include paternity testing, forensic use, and disease diagnostics, such as for the identification of the existence of a clonal tumor.

Claims

1. A method for determining the nature of repeat units in a genetic target, comprising the steps of:

providing a plurality of hybridization complex assays arrayed on a plurality of test sites by;

providing a nucleic acid target containing repetitive DNA sequences,

providing a capture probe having a first unique flanking sequence and n repeat units, where n≧

0 complementary to the target sequence, and

providing a reporter probe having a selected sequence complementary to the same target sequence strand, the reporter including attributes selected from the group consisting of;

a) a second unique flanking sequence,

b) a sequence complementary to a variant region of the target sequence, and

c) a second unique flanking sequence and a sequence complementary to a variant region of the target sequence,

wherein the sum of the number of repeat units in the capture plus the reporter is greater than zero,

the sequence of the capture probe differing at at least two test sites of the array,

determining concordance and discordance among the hybridization complex assays at the test sites as determined at least in part by hybridization stability without the use of an enzymatic reaction and

determining the nature of the repeat units in the target sequences based upon determination of the concordant site and further based upon the knowledge of the pre-determined sequences of the probes located in the hybridization complex at that site.

2. The method of claim 1 wherein the location of the concordant test site indicates the nature of the target sequence repeat units by the number of repeat units present in the target, based upon the knowledge of the pre-determined sequences of the probes located at that test site.

3. The method of claim 2 wherein at the concordant test site, the number of repeat units in the target equals the sum of the number of repeat units in the capture probe and the number of repeat units in the reporter probe.

4. The method of claim 1 wherein the location of the concordant test site indicates the nature of the target sequence repeat units by the detection of microvariants in the target sequence.

5. The method of claim 4 wherein the microvariants include one or more selected from the group consisting of:

deletions, insertions, transitions and transversions.

6. The method of claim 5 wherein the microvariant affects a single base.

7. The method of claim 5 wherein the microvariant affects more than a single base.

8. The method of claim 1 wherein the location of the concordant test site indicates the nature of the target sequence repeat units by the number of repeat units and by the detection of microvariants in the target sequence.

9. The method of claim 8 wherein the microvariants include one or more selected from the group consisting of:

deletions, insertions, transitions, and transversions.

10. The method of claim 9 wherein the microvariant affects a single base.

11. The method of claim 9 wherein the microvariant affects more than a single base.

12. The method of claim 1 wherein a test site is determined to be concordant when the hybridization complex present there is stable relative to other test sites for the same locus.

13. The method of claim 12 wherein stability is enhanced by complementary match of bases in the hybridization complex including the capture, reporter and target.

14. The method of claim 12 wherein stability is enhanced by juxtaposed terminal nucleotides of reporter and capture being contiguous to permit base stacking.

15. The method of claim 14 further including selection of juxtaposed terminal nucleotides to increase energy difference between concordance and discordance.

16. The method of claim 15 wherein the selection is determine, at least in part, with reference to base stacking interactions.

17. The method of claim 16 wherein the base stacked pair is 5′

GpC3′

.

18. The method of claim 16 wherein the base stacked pair is 5′

TpA3′

.

19. The method of claim 12 further including modifications of terminal nucleotides which increase base stacking.

20. The method of claim 19 wherein the terminal nucleotide is modified with propynyl groups.

21. The method of claim 19 wherein the terminal nucleotide is modified with methyl groups.

22. The method of claim 19 wherein the terminal nucleotide is modified with cholesterol groups.

23. The method of claim 12 wherein stability is enhanced with ligation techniques.

24. The method of claim 23 wherein the ligation is enzymatic ligation.

25. The method of claim 23 wherein the ligation is chemical ligation.

26. The method of claim 1 wherein discordance includes a gap between the capture and the reporter.

27. The method of claim 1 wherein the discordance includes an overlap between the capture and the reporter.

28. The method of claim 1 wherein discordance includes a base variation in the repeat region.

29. The method of claim 28 wherein the base variation includes a deletion.

30. The method of claim 28 wherein the base variation includes a insertion.

31. The method of claim 28 wherein the base variation includes a transition.

32. The method of claim 28 wherein the base variation includes a transversion.

33. The method of claim 1 wherein discordance includes a single nucleotide variant between the capture and the reporter or in the repeat region.

34. The method of claim 1 wherein discordance includes base variations which are greater than a single nucleotide between the capture and the reporter or in the repeat region.

35. The method of claim 1 wherein discordance includes base variation plus overlap between the capture and the reporter or in the repeat region.

36. The method of claim 1 wherein discordance includes base variation plus gap between the capture and the reporter or in the repeat region.

37. The method of claim 1 wherein the number of bases in the repeat unit is 2-50.

38. The method of claim 37 wherein the number of bases in the repeat unit is 3-6.

39. The method of claim 1 wherein the number of repeat units including microvariants is 5-50.

40. The method of claim 1 wherein the number of repeat units including microvariants is 2-2500.

41. The method of claim 1 wherein the number of loci analyzed at one time is one.

42. The method of claim 1 wherein the number of loci analyzed at one time is three.

43. The method of claim 1 wherein the number of loci analyzed at one time is less than five.

44. The method of claim 1 wherein the number of loci analyzed at one time is less than ten.

45. The method of claim 1 wherein the number of loci analyzed at one time is thirteen.

46. The method of claim 1 wherein the number of loci analyzed at one time is less than twenty.

47. The method of claim 1 wherein the number of loci analyzed at one time is less than one hundred.

48. The method of claim 1 wherein the hybridization stability is determined, at least in part, by electronic stringency (ESC) control.

49. The method of claim 1 wherein the hybridization stability is determined, at least in part, by thermal regulation of stringency.

50. The method of claim 1 wherein the hybridization stability is determined, at least in part, by chemical regulation of stringency .

51. The method of claim 1 wherein the hybridization stability is determined, at least in part, by electronic stringency (ESC) and thermal control.

52. The method of claim 1 wherein the hybridization stability is determined, at least in part, by electronic stringency (ESC) and chemical control.

53. The method of claim 1 wherein the hybridization stability is determined, at least in part, by electronic stringency (ESC), thermal and chemical control.

54. The method of claim 1 further including electronic stringency conditions during the hybridizations of capture probe with the nucleic acid target.

55. The method of claim 54 whereby the unique flanking sequence is hybridized in proper index with the target.

56. The method of claim 54 whereby the electronic stringency conditions ensures proper indexing of the repeat units.

57. The method of claim 54 whereby the electronic stringency conditions restrict slippage between the repeat units of reporter, capture, and target probes.

58. The method of claim 54 wherein initial hybridization step occurs in 10 minutes or less.

59. The method of claim 58 wherein initial hybridization step occurs in 5 minutes or less.

60. The method of claim 54 wherein initial hybridization step occurs in 1 minute or less.

61. The method of claim 54 wherein electronic stringency control includes electrical currents and buffers.

62. The method of claim 1 further including stringent conditions during the hybridizations of capture probe with the nucleic acid target.

63. The method of claim 62 wherein the stringent conditions include thermal regulation of stringency.

64. The method of claim 62 stringency conditioning include thermal and electronic regulation of stringency.

65. The method of claim 62 stringency conditioning include chemical regulation of stringency.

66. The method of claim 62 wherein the stringent conditions chemical and electronic regulation of stringency.

67. The method of claim 62 wherein the stringent conditions chemical, thermal and electronic regulation of stringency.

68. The method of claim 1 further including electronic stringency conditions during the hybridization of the reporter probe with the capture probe nucleic acid target hybridization complex.

69. The method of claim 68 whereby the unique flanking sequence is hybridized in proper index with the target.

70. The method of claim 1 whereby the electronic stringency conditions ensures proper indexing of the repeat units.

71. The method of claim 1 whereby the electronic stringency conditions restrict slippage between repeat units of reporter, capture, and target probes.

72. The method of claim 68 wherein initial hybridization step occurs in 10 minutes or less.

73. The method of claim 68 wherein initial hybridization step occurs in 5 minutes or less.

74. The method of claim 68 wherein initial hybridization step occurs in 1 minute or less.

75. The method of claim 68 wherein electronic stringency conditions includes electrical currents and buffers.

76. The method of claim 1 further including stringent conditions during the hybridizations of the reporter probe with the capture probe nucleic acid target hybridization complex.

77. The method of claim 76 wherein the stringency includes thermal regulation of stringency.

78. The method of claim 76 wherein the stringency includes thermal and electronic regulation of stringency.

79. The method of claim 76 wherein the stringency includes chemical regulation of stringency.

80. The method of claim 76 wherein the stringency includes chemical and electronic regulation of stringency.

81. The method of claim 76 wherein the stringency includes chemical, thermal and electronic regulation of stringency.

82. The method of claim 1 wherein the hybridization complex is labeled.

83. The method of claim 82 wherein the step of determining concordance and discordance includes detecting of the amounts of labeled hybridization complex at the test sites.

84. The method of claim 83 wherein the detecting is imaging.

85. The method of claim 84 wherein the imaging is optical imaging.

86. The method of claim 84 wherein the imaging is electronic imaging.

87. The method of claim 84 wherein the imaging is CCD imaging.

88. The method of claim 84 wherein the imaging is integrated optical imaging.

89. The method of claim 83 wherein the imaging detection is quantified.

90. The method of claim 1 further including a statistical analysis step.

91. The method of claim 82 wherein the labeled portion of complex is the target.

92. The method of claim 82 wherein the labeled portion of complex is the capture.

93. The method of claim 82 wherein the labeled portion of complex is the reporter.

94. The method of claim 82 wherein the labeling is by fluorescent labeling.

95. The method of claim 94 wherein the fluorescent labeling is with Bodipy Texas Red.

96. The method of claim 94 wherein the fluorescent labeling is with Bodipy 630/650.

97. The method of claim 94 wherein the fluorescent labeling is with Lucifer Yellow.

98. The method of claim 82 wherein the labeling is by colormetric labeling.

99. The method of claim 82 wherein the labeling is by chemiluminescent labeling.

100. The method of claim 1 further including energy transfer between molecules in the hybridization complex.

101. The method of claim 1 further including fluorescent perturbation analysis.

102. The method of claim 100 wherein the energy transfer includes quenching.

103. The method of claim 100 wherein the energy transfer includes electron transport between donor and acceptor molecules, which is facilitated by double-stranded match hybridization complexes.

104. The method of claim 103 wherein the transfer is mediated by electron conductance through double-stranded DNA.

105. The method of claim 100 wherein the energy transfer includes electron transport which is facilitated by double-stranded match hybridization complexes.

106. The method of claim 82 wherein the label is amplified.

107. The method of claim 106 wherein the label further includes branched DNA.

108. The method of claim 1 wherein the hybridization complex is unlabeled.

109. The method of claim 108 wherein the detection of concordance is based at least in part on conduction of electrons along hybridized DNA.

110. The method of claim 108 wherein the detection of concordance is based at least in part on mass detection.

111. The method of claim 1 further including a redundant assay.

112. The method of claim 111 wherein the redundant assay is a serial redundant assay.

113. The method of claim 112 wherein the serial redundant assay includes the following steps, after at least the step of determining concordance and discordance,

increasing denaturation stringency to remove said reporter probe at all sites, whether concordant or discordant,

hybridizing a second reporter probe where the number of repeat units in said second reporter probe differs from the number of repeat units in said reporter probe,

wherein the location of the concordant test site indicates the number of repeat units present in the target, based upon the knowledge of the pre-determined sequences of the probes located at that test site,

wherein at the concordant test site, the number of repeat units in the target equals the sum of the number of repeat number in the capture probe and the number of repeat units in the reporter probe,

determining concordant and discordant test sites among the hybridization complex assays at the test sites as determined at least in part by hybridization stability, and

comparing these results with the initial complex hybridization assay for confirmation of target repeat unit number.

114. The method of claim 111 further including the step of repeating the redundant assay until a statistically significant result is obtained.

115. The method of claim 111 wherein the redundant assay includes multiple arrays.

116. The method of claim 115 further including the step of hybridizing target to at least two independent sets of assays,

hybridizing said reporter to a first set and a second reporter to a second set, where the number of repeat units in said reporter probe differs from the number of repeat units in the second reporter,

determining concordant and discordant test sites among the hybridization complex assays at the test sites as determined at least in part by hybridization stability, wherein the location of the concordant test site indicates the number of repeat units present in the target, based upon the knowledge of the pre-determined sequences of the probes located at that test site, and p1 comparing these results with the two complexes'"'"' hybridization assay for confirmation of target repeat unit number.

117. The method of claim 116 including the step of simultaneous hybridization of differently labeled reporters.

118. The method of claim 117 wherein two reporters differing in the number of repeat units in their nucleic acid sequence, and which are differentially labeled, includes the reporters then being simultaneously provided to the device.

119. The method of claim 117 wherein the differently labeled reporters are distinguishable chromophores.

120. The method of claim 119 wherein the chromophores are fluorescent.

121. The method of claim 119 wherein the chromophores are luminescent.

122. The method of claim 119 wherein the chromophores are electrochemiluminescent.

123. The method of claim 119 wherein the chromophores include combinations of fluorescent, luminescent and electrochemiluminescent materials.

124. The method of claim 117 wherein the location of the concordant test site indicates the number of repeat units present in the target, based upon the knowledge of the pre-determined sequences of the probes located at that test site.

125. The method of claim 117 wherein the detected presence of a first label at a first test site indicates the pre-determined number of repeat units associated with that reporter and capture sequence at the test site, which is confirmed by the detected presence of a second label at the second test site which indicates the pre-determined number of repeat units associated with that reporter and capture sequence at the test site.

126. The method of claim 115 wherein the two sets of arrays are on the same device.

127. The method of claim 115 wherein the two sets of arrays are on different devices.

128. The method of claim 1 wherein the target DNA is purified.

129. The method of claim 1 wherein the target is unamplified.

130. The method of claim 1 wherein the target is amplified.

131. The method of claim 130 wherein the amplification is an exponential methods of target DNA amplification.

132. The method of claim 131 wherein the amplification includes PCR amplified DNA.

133. The method of claim 131 wherein the amplification includes strand displacement amplification (SDA) amplified DNA.

134. The method of claim 131 wherein the amplification includes linear methods of DNA amplification.

135. The method of claim 134 wherein the amplification includes rolling circle amplification.

136. The method of claim 134 wherein the amplification includes transcriptional run-off amplification.

137. The method of claim 1 wherein the target DNA is unpurified.

138. The method of claim 137 wherein the target is unamplified.

139. The method of claim 137 wherein the target is amplified.

140. The method of claim 139 wherein the amplification is an exponential method of target DNA amplification.

141. The method of claim 140 wherein the amplification includes PCR amplified DNA.

142. The method of claim 140 wherein the amplification includes SDA amplified DNA.

143. The method of claim 139 wherein the amplification is a linear method of DNA amplification.

144. The method of claim 143 wherein the amplification includes rolling circle amplification.

145. The method of claim 143 wherein the amplification includes run-off amplification.

146. The method of claim 1 wherein the plurality of hybridization complex assays arrayed at the test sites include at least one site for each allele of a locus.

147. The method of claim 146 wherein the allele includes an integral number of repeat units.

148. The method of claim 146 wherein the allele includes an integral number of repeat units plus at least one microvariant.

149. The method of claim 1 wherein each concordant test site identifies the repeat unit number of the target.

150. The method of claim 1 wherein the group of discordant test sites indicates the repeat unit number of the target.

151. The method of claim 1 wherein the number of concordant test sites per locus array is one or two for a homogeneous sample in a nonredundant, multiple array redundant or serial redundant assay.

152. The method of claim 1 wherein the number of concordant test sites is more than one for a mixed sample.

153. The method of claim 117 wherein the number of concordant test sites is more than one for a simultaneous hybridization of differently labeled reporters redundant assay.

154. The method of claim 1 wherein the nature of the hybridization complex may be resolved into match, mismatch/gap, and mismatch/overlap.

155. The method of claim 154 wherein the resolution is determined from the signal intensity of the hybridization complex assay.

156. The method of claim 155 wherein the resolution is determined from gradient application of a selection of electronic, chemical and thermal stringency conditions and resulting change in the signal intensity of the hybridization complex assay.

157. The method of claim 154 wherein the resolution is determined from the knowledge of the pre-determined sequences of the probes present in the hybridization complex assay.

158. The method of claim 1 wherein the number of test sites is fewer than required to provide a test site for each allele.

159. The method of claim 1 wherein the target is applied to a reduction of test sites necessary to identify the number of repeat units in the target DNA.

160. The method of claim 159 wherein the reduction increases the statistical significance of results.

161. The method of claim 1 wherein the target material constitutes homozygous allele for a locus.

162. The method of claim 1 wherein the target material constitutes heterozygous allele for a locus.

163. The method of claim 1 wherein the target material constitutes more than one allele per locus for a mixed sample.

164. The method of claim 163 wherein the mixed sample further includes sample from more than one individual.

165. The method of claim 164 wherein the mixed sample further includes tumor tissue mixed with normal tissue.

166. The method of claim 165 wherein the tumor tissue is normal tissue.

167. The method of claim 165 wherein the tumor tissue is diseased tissue.

168. The method of claim 1 wherein the target material includes tumor tissue.

169. The method of claim 1 wherein the target material includes plant material.

170. The method of claim 1 wherein the target material includes animal material.

171. The method of claim 170 wherein the animal material is mammal material.

172. The method of claim 170 wherein the animal material is human material.

173. The method of claim 170 wherein the target material includes bird material.

174. The method of claim 170 wherein the target material includes fish material.

175. The method of claim 1 wherein the target material constitutes microbial material.

176. The method of claim 175 wherein the microbial materials is viral.

177. The method of claim 175 wherein the microbial material s is bacterial.

178. The method of claim 175 wherein the microbial materials is protozoa.

179. The method of claim 1 wherein the method is used for identification.

180. The method of claim 1 wherein the method is used for paternity testing.

181. The method of claim 1 wherein the method is used for forensics.

182. The method of claim 1 wherein the method is used for disease diagnostics.

183. The method of claim 1 wherein the method is used for breeding.

184. The method of claim 164 wherein the mixed sample further including sample from one individual which includes monoclonal and polyclonal cell sources.

185. The method of claim 106 wherein the label is amplified by enzymatic label amplification.

186. A method for utilizing electronic techniques in determining the nature of repeat units in a genetic target, comprising the steps of:

providing a plurality of hybridization complex assays arrayed on a plurality of test sites, where the hybridization complex assay includes at least;

a nucleic acid target containing repetitive DNA sequence,

a capture probe having a first unique flanking sequence and n repeat units, where n≧

0. complementary to the target sequence, and

a reporter probe having a selected sequence complementary to the same target sequence strand, the reporter including attributes selected from the group consisting of;

a) a second unique flanking sequence and n repeat units, where n≧

0,

b) a sequence complementary to a microvariant region of the target sequence,

c) a second unique flanking sequence and n repeat units, where n≧

0 and a sequence complementary to a microvariant region of the target sequence,

wherein the sum of repeat units in the capture plus the reporter is greater than zero,

the sequence of the capture probe differing at at least two test sites on the array, determining concordance and discordance among the hybridization complex assays at

the test sites as determined at least in part by hybridization stability, and determining the nature of the repeat units in the target sequences based upon

determination of the concordant site and further based upon the knowledge of the pre-determined sequences of the probes located in the hybridization complex at that site.

187. A method for determining the nature of repeat units in a genetic target, comprising the steps of:

provide a platform for the identification of the genetic target, including a set of probes having a first unique flanking sequence, a variable number of intervening repeat units and a second unique flanking sequence,

hybridizing the genetic target with the probes, including electronic hybridization stringency conditions during the hybridization, whereby the unique flanking sequence is properly indexed with the target, and

determining concordance and discordance at the test sites as determined at least in part by electronic hybridization stability,

whereby a loop out is formed in discordant hybridizations, thereby providing energetically less favorable condition than in the concordant hybridization.

188. A method for determining the nature of repeat units in a genetic target, comprising the steps of:

provide a platform for the identification of the genetic target, including a set of probes having a first unique flanking sequence, a variable number of intervening repeat units and a second unique flanking sequence,

hybridizing the genetic target with the probes, including electronic hybridization stringency conditions during the hybridization, whereby the unique flanking sequence is properly indexed with the target, and

determining concordance and discordance at the test sites,

whereby a loop out is formed in discordant hybridizations, thereby providing energetically less favorable condition than in the concordant hybridization.

189. A method for determining the nature of repeat units in a genetic target, comprising the steps of:

provide a platform for the identification of the genetic target, including a set of probes having a first unique flanking sequence, a variable number of intervening repeat units and a second unique flanking sequence,

hybridizing the genetic target with the probes, and

determining concordance and discordance at the test sites as determined at least in part by electronic hybridization stability,

whereby a loop out is formed in discordant hybridizations, thereby providing energetically less favorable condition than in the concordant hybridization.

190. A method for determining the nature of repeat units in a genetic target, comprising the steps of:

providing a platform for the identification of the genetic target, including probes selected from the group consisting of;

1) a probe having a first unique flanking sequence, an intervening repeat region and a second unique flanking sequence, and

2) a sandwich assay comprising a capture probe having a first unique flanking sequence and n≧

0 repeat units and a reporter probe having n≧

0 repeat units in sequence with a second unique flanking sequence, wherein the sum of the repeat units is >

0,

hybridizing the target with the probes under electronic stringent conditions so as to provide proper indexing, and

determining concordance and discordance at the test sites as determined at least in part by hybridization stability,

wherein hybridization stability includes electronic hybridization stability.

191. A method for determining the nature of repeat units in a genetic target, comprising the steps of:

providing a plurality of hybridization complex assays on a plurality of test sites, where the hybridization complex assays includes at least;

a nucleic acid target containing repetitive DNA sequence,

a capture probe having a first unique flanking sequence and n repeat units,

where n≧

0, complementary to the target sequence, and

a reporter probe having a selected sequence complementary to the same target sequence strand, the reporter including a second unique flanking sequence, and n≧

0 repeat units,

wherein the sum of repeat units in the capture plus the reporter is greater then zero,

the sequence of the capture probe differing at at least two test sites on the array,

determining concordance and discordance among the hybridization complex assays at the test sites as determined at least in part by hybridization stability and

determining the nature of the repeat units in the target sequences based upon determination of the concordant site and further based upon the knowledge of the pre-determined sequences of the probes located in the hybridization complex at that site.

192. A method for determining the nature of repeat units in a genetic target, comprising the steps of:

providing a plurality of hybridization complex assays arrayed on a plurality of test sites by;

providing a nucleic acid target containing repetitive DNA sequences,

providing a capture probe having a first unique flanking sequence and n repeat units, where n≧

0 complementary to the target sequence, the capture probe having a terminal nucleotide, and

providing a reporter probe having a selected sequence complementary to the same target sequence strand, the reporter probe having a terminal nucleotide, the juxtaposed terminal nucleotides of the capture probe and reporter probe selected to provide increased base stacking properties, the reporter including attributes selected from the group consisting of;

a) a second unique flanking sequence,

b) a sequence complementary to a variant region of the target sequence, and

c) a second unique flanking sequence and a sequence complementary to a variant region of the target sequence,

wherein the sum of the number of repeat units in the capture plus the reporter is greater than zero,

the sequence of the capture probe differing at at least two test sites of the array,

determining concordance and discordance among the hybridization complex assays at the test sites as determined at least in part by hybridization stability and

determining the nature of the repeat units in the target sequences based upon determination of the concordant site and further based upon the knowledge of the pre-determined sequences of the probes located in the hybridization complex at that site.

193. The method of claim 192 wherein the location of the concordant test site indicates the nature of the target sequence repeat units by the number of repeat units present in the target, based upon the knowledge of the pre-determined sequences of the probes located at that test site.

194. The method of claim 193 wherein at the concordant test site, the number of repeat units in the target equals the sum of the number of repeat units in the capture probe and the number of repeat units in the reporter probe.

195. The method of claim 192 wherein the location of the concordant test site indicates the nature of the target sequence repeat units by the detection of microvariants in the target sequences.

196. The method of claim 192 wherein the location of the concordant test site indicates the nature of the target sequence repeat units by the number of repeat units and by the detection of microvariants in the target sequence.

197. The method of claim 192 wherein a test site is determined to be concordant when the hybridization complex present there is stable relative to other test sites for the same locus.

198. The method of claim 192 wherein the hybridization stability is determined, at least in part, by electronic stringency (ESC) control.

199. The method of claim 192 further including stringent conditions during the hybridizations of capture probe with the nucleic acid target.

200. The method of claim 192 further including electronic stringency conditions during the hybridization of the reporter probe with the capture probe nucleic acid target hybridization complex.

201. The method of claim 192 wherein the hybridization complex is labeled.

202. The method of claim 192 further including a statistical analysis step.

203. The method of claim 192 further including fluorescent perturbation analysis.

204. The method of claim 201 wherein the label is amplified.

205. The method of claim 201 wherein the hybridization complex is unlabeled.

206. The method of claim 192 further including a serial redundant assay includes the following steps, after at least the step of determining concordance and discordance,

increasing denaturation stringency to remove said reporter probe at all sites, whether concordant or discordant,

hybridizing a second reporter probe where the number of repeat units in said second reporter probe differs from the number of repeat units in said reporter probe,

wherein the location of the concordant test site indicates the number of repeat units present in the target, based upon the knowledge of the pre-determined sequences of the probes located at that test site,

wherein at the concordant test site, the number of repeat units in the target equals the sum of the number of repeat number in the capture probe and the number of repeat units in the reporter probe,

determining concordant and discordant test sites among the hybridization complex assays at the test sites as determined at least in part by hybridization stability, and

comparing these results with the initial complex hybridization assay for confirmation of target repeat unit number.

207. The method of claim 192 wherein the plurality of hybridization complex assays arrayed at the test sites include at least one site for each allele of a locus.

208. The method of claim 192 wherein each concordant test site identifies the repeat unit number of the target.

209. The method of claim 192 wherein the group of discordant test sites indicates the repeat unit number of the target.

210. The method of claim 192 wherein the resolution is determined from gradient application of a selection of electronic, chemical and thermal stringency conditions and resulting change in the signal intensity of the hybridization complex assay.

211. The method of claim 192 wherein the number of test sites is fewer than required to provide a test site for each allele.

212. The method of claim 192 wherein the target material constitutes more than one allele per locus for a mixed sample.

213. The method of claim 192 further including a mixed sample which includes tumor tissue mixed with normal tissue.

214. The method of claim 192 wherein the method is used for identification.

215. The method of claim 192 wherein the method is used for disease diagnostics.

216. The method of claim 192 wherein the method is used for breeding.

217. The method of claim 192 further including a mixed sample having monoclonal and polyclonal cell sources.

218. The method of claim 201 wherein the label is amplified by enzymatic label amplification.

219. A method for determining the nature of repeat units in a genetic target, comprising the steps of:

providing in the presence of an electric field a plurality of hybridization complex assays arrayed on a plurality of test sites by;

providing a nucleic acid target containing repetitive DNA sequences,

providing a capture probe having a first unique flanking sequence and n repeat units, where n≧

0, complementary to the target sequence, the capture probe having a terminal nucleotide, and

providing a reporter probe having a selected sequence complementary to the same target sequence strand, the reporter probe having a terminal nucleotide, the juxtaposed terminal nucleotides of the capture probe and reporter probe selected to provide increased base stacking properties, the reporter including attributes selected from the group consisting of;

a) a second unique flanking sequence,

b) a sequence complementary to a variant region of the target sequence, and

c) a second unique flanking sequence and a sequence complementary to a variant region of the target sequence,

wherein the sum of the number of repeat units in the capture plus the reporter is greater than zero,

the sequence of the capture probe differing at at least two test sites of the array,

determining concordance and discordance among the hybridization complex assays, at the test sites as determined at least in part by hybridization stability including thermal stringency and

determining the nature of the repeat units in the target sequences based upon determination of the concordant site and further based upon the knowledge of the pre-determined sequences of the probes located in the hybridization complex at that site.

220. The method of claim 219 wherein the location of the concordant test site indicates the nature of the target sequence repeat units by the number of repeat units present in the target, based upon the knowledge of the pre-determined sequences of the probes located at that test site.

221. The method of claim 220 wherein at the concordant test site, the number of repeat units in the target equals the sum of the number of repeat units in the capture probe and the number of repeat units in the reporter probe.

222. The method of claim 219 wherein the location of the concordant test site indicates the nature of the target sequence repeat units by the detection of microvariants in the target sequence.

223. The method of claim 219 wherein the location of the concordant test site indicates the nature of the target sequence repeat units by the number of repeat units and by the detection of microvariants in the target sequence.

224. The method of claim 219 wherein a test site is determined to be concordant when the hybridization complex present there is stable relative to other test sites for the same locus.

225. The method of claim 219 further including stringent conditions during the hybridizations of capture probe with the nucleic acid target.

226. The method of claim 219 further including electronic stringency conditions during the hybridization of the reporter probe with the capture probe nucleic acid target hybridization complex.

227. The method of claim 219 wherein the hybridization complex is labeled.

228. The method of claim 219 further including a statistical analysis step.

229. The method of claim 219 further including fluorescent perturbation analysis.

230. The method of claim 227 wherein the label is amplified.

231. The method of claim 219 wherein the hybridization complex is unlabeled.

232. The method of claim 219 further including a serial redundant assay includes the following steps, after at least the step of determining concordance and discordance,

increasing denaturation stringency to remove said reporter probe at all sites, whether concordant or discordant,

hybridizing a second reporter probe where the number of repeat units in said second reporter probe differs from the number of repeat units in said reporter probe,

wherein the location of the concordant test site indicates the number of repeat units present in the target, based upon the knowledge of the pre-determined sequences of the probes located at that test site,

wherein at the concordant test site, the number of repeat units in the target equals the sum of the number of repeat number in the capture probe and the number of repeat units in the reporter probe,

determining concordant and discordant test sites among the hybridization complex assays at the test sites as determined at least in part by hybridization stability, and

comparing these results with the initial complex hybridization assay for confirmation of target repeat unit number.

233. The method of claim 219 wherein the plurality of hybridization complex assays arrayed at the test sites include at least one site for each allele of a locus.

234. The method of claim 219 wherein each concordant test site identifies the repeat unit number of the target.

235. The method of claim 219 wherein the group of discordant test sites indicates the repeat unit number of the target.

236. The method of claim 219 wherein the resolution is determined from gradient application of a selection of electronic, chemical and thermal stringency conditions and resulting change in the signal intensity of the hybridization complex assay.

237. The method of claim 219 wherein the number of test sites is fewer than required to provide a test site for each allele.

238. The method of claim 219 wherein the target material constitutes more than one allele per locus for a mixed sample.

239. The method of claim 219 further including a mixed sample which includes tumor tissue mixed with normal tissue.

240. The method of claim 219 wherein the method is used for identification.

241. The method of claim 219 wherein the method is used for disease diagnostics.

242. The method of claim 219 wherein the method is used for breeding.

243. The method of claim 219 further including a mixed sample having monoclonal and polyclonal cell sources.

244. The method of claim 227 wherein the label is amplified by enzymatic label amplification.