Arrays, computer program products and methods for in silico array-based comparative binding arrays

• US 20050014184A1
• Filed: 08/10/2004
• Published: 01/20/2005
• Est. Priority Date: 03/27/2002
• Status: Active Grant

• Current Assignee: Perkinelmer Health Sciences Incorporated (Perkinelmer Incorporated)
• Original Assignee: Perkinelmer Health Sciences Incorporated (Perkinelmer Incorporated)
• Inventors: Shah, Shishir
• Granted Patent: US 7,994,296 B2
• Time in Patent Office: Days
• US Class Current: 506/4
• CPC Class Codes: C12Q 1/6809 Methods for determination or identification of nucleic acids involving differential detection
• CPC Class Codes: C12Q 1/6837 using probe arrays or probe chips C12Q1/6874 takes precedence
• CPC Class Codes: C12Q 2545/101 with an internal standard/control
• CPC Class Codes: C12Q 2545/114 involving a quantitation step
• CPC Class Codes: C12Q 2565/513 characterised by the pattern of the arrayed oligonucleotides
• CPC Class Codes: C40B 30/04 by measuring the ability to specifically bind a target molecule, e.g. antibody-antigen binding, receptor-ligand binding
• CPC Class Codes: G01N 33/6845 Methods of identifying protein-protein interactions in protein mixtures
• CPC Class Codes: G16B 25/00 ICT specially adapted for hybridisation; ICT specially adapted for gene or protein expression

Abstract

The invention provides computer systems, computer program products and methods for in silico array-based methods for determining the relative amount of biological molecules (e.g., nucleic acid sequences) in two or more samples. The invention also provides novel arrays comprising immobilized calibration molecules (e.g., nucleic acids) for normalizing the results of array-based binding assays (e.g., hybridization reactions).

Claims

1-89. -89. (canceled)

90. An array for determining the relative amount of a biological molecule in a sample, the array comprising a plurality of biological molecules immobilized to a plurality of discrete and known spots on a substrate surface to form the array of biological molecules, wherein the array of spots comprises a plurality of test spots and at least one calibration spot, and the calibration spot comprises at least one copy of a sequence from each test spot on the array.

91. The array of claim 90, wherein the calibration spot comprises an equimolar mixture of all the biological molecules spotted on the array.

92. The array of claim 90, comprising at least a second calibration spot comprising an equimolar dilution of the mixture of biological molecules spotted on a first calibration spot.

93. The array of claim 92, comprising a plurality of calibration spots, wherein each calibration spot represents a different equimolar dilution of the mixture of biological molecules spotted on the array.

94. The array of claim 92, wherein the array comprises a first substrate surface comprising a first array and a second substrate surface comprising a second array, wherein the first and second arrays are separated by a hydrophobic barrier such that a first sample can be applied to the first array at the same time a second sample is applied to the second array without the two samples mixing together, and the first and the second arrays comprise the same calibration spots.

95. The array of claim 92, wherein the biological molecule comprises a nucleic acid.

96. The array of claim 95, wherein the nucleic acid comprises a DNA or an RNA.

97. The array of claim 92, wherein the biological molecule comprises a polypeptide or a peptide.

98. The array of claim 92, wherein the biological molecule comprises a lipid or a polysaccharide.

101. The array of claim 90, wherein the calibration spot comprises a mixture of all the biological molecules spotted on the array that is not equimolar.

102. The array of claim 92, wherein the array comprises a first substrate surface comprising a first array and a second substrate surface comprising a second array, wherein the first and second arrays are not separated by a hydrophobic barrier, and the first and the second arrays comprise the same calibration spots.

103. The array of claim 96, wherein the DNA is genomic DNA.

104. The array of claim 103, wherein the genomic DNA is cloned in a construct comprising a vector.

105. The array of claim 104, wherein the vector comprises an artificial chromosome.

106. The array of claim 105, wherein the artificial chromosome comprises a bacterial artificial chromosome (BAC).

107. The array of claim 105, wherein the artificial chromosome is selected from the group consisting of a human artificial chromosome (HAC) a yeast artificial chromosome (YAC), a transformation-competent artificial chromosome (TAC) and a bacteriophage P1-derived artificial chromosome (PAC).

108. The array of claim 105, wherein the array-immobilized nucleic acid segment is cloned in a construct comprising a vector selected from the group consisting of a cosmid vector, a plasmid vector and a viral vector.

109. The array of claim 103, wherein the genomic nucleic acid comprises a substantially complete chromosome or a known subset of a chromosome.

110. The array of claim 103, wherein the genomic nucleic acid comprises a substantially complete genome or a known subset of a genome.

111. The array of claim 103, wherein the genomic nucleic acid is derived from a genome of a normal cell.

112. The array of claim 103, wherein the genomic nucleic acid is derived from a genome of a mammalian cell.

113. The array of claim 112, wherein the mammalian cell is a human cell.

114. The array of claim 104, wherein the calibration spot nucleic acid comprises vector nucleic acid.

99. A multiplexed system for performing comparative binding assays using an array comprising:

(a) an array comprising a plurality of biological molecules immobilized to a plurality of discrete and known spots on a substrate surface to form an array of biological molecules, wherein the array of spots comprises a plurality of test spots and at least one calibration spot, and the calibration spot comprises at least one copy of a biological molecule from each test spot on the array, or (ii) a first substrate surface comprising a first array and a second substrate surface comprising a second array, wherein the first and second arrays are separated by a hydrophobic barrier such that a first sample can be applied to the first array at the same time a second sample is applied to the second array without the two samples mixing together, and the first and the second arrays comprise the same calibration spots;

(b) a device for detecting a detectable label, wherein the device can measure which detectable labels are on which spots on the substrate surface.

100. A multiplexed system for performing comparative genomic hybridization (CGH) using an array comprising:

(a) an array comprising (i) a plurality of nucleic acids immobilized to a plurality of discrete and known spots on a substrate surface to form an array of nucleic acids, wherein the array of spot comprises a plurality of test spots and at least one calibration spot, and the calibration spot comprises at least one copy of a sequence from each test spot on the array, or (ii) a first substrate surface comprising a first array and a second substrate surface comprising a second array, wherein the first and second arrays are separated by a hydrophobic barrier such that a first sample can be applied to the first array at the same time a second sample is applied to the second array without the two samples mixing together, and the first and the second arrays comprise the same calibration spots;

(b) a device for detecting a detectable label, wherein the device can measure which detectable labels are on which spots on the substrate surface.

115. An array for determining the relative amount of a nucleic acid in a sample, the array comprising a plurality of nucleic acid molecules immobilized to a plurality of discrete and known spots on a substrate surface to form the array of nucleic acid molecules, wherein the array of spots comprises a plurality of test spots and at least one calibration spot, and the calibration spot comprises nucleic acid sequences from a genome other than that spotted on the array or in the sample.

116. The array of claim 115, wherein the genome other than that in the sample or on the array is genomic DNA of Mus, Drosophila or equivalent.

117. The array of claim 115, wherein detectable label is incorporated into the array-immobilized nucleic acid.

118. The array of claim 117, wherein the detectable label is incorporated into the test spots and the at least one calibration spot.

119. The array of claim 117, wherein the detectable label is incorporated into the test spot and not into the calibration spot.

120. The array of claim 117, wherein the detectable label is incorporated into the calibration spot and not into the test spot.

121. The array of claim 117, wherein the detectable label is a fluorescent dye.

122. The array of claim 121, wherein the fluorescent dye is Cy3™

or Cy5™

.

123. The array of claim 117, wherein the detectable label is radioactive.

124. The array of claim 117, wherein the detectable label is selected from the group consisting of ³²P, ³⁵H, ¹⁴C, ¹²⁵I and ¹³¹I.