DNA Diagnostics Based on Mass Spectrometry

• US 20090023150A1
• Filed: 06/27/2008
• Published: 01/22/2009
• Est. Priority Date: 11/06/1996
• Status: Abandoned Application

• Current Assignee: Sequenom Incorporated (Laboratory Corporation Of America Holdings)
• Original Assignee: Sequenom Incorporated (Laboratory Corporation Of America Holdings)
• Inventors: Little, Daniel P., Lough, David M., Ruppert, Andreas, Xiang, Guobing, Braun, Andreas, van den Boom, Dirk, Koster, Hubert, Jurinke, Christian
• Application Number:
  US12/163,923
• Publication Number:
  US 20090023150A1
• Time in Patent Office: Days
• US Class Current: 435/6
• CPC Class Codes: B01J 19/0046 Sequential or parallel reactions, e.g. for the synthesis of polypeptides or polynucleotides; Apparatus and devices for combinatorial chemistry or for making molecular arrays synthesis methods per se C40B50/00
• CPC Class Codes: B01J 2219/00315 Microtiter plates
• CPC Class Codes: B01J 2219/00317 Microwell devices, i.e. having large numbers of wells
• CPC Class Codes: B01J 2219/00387 Applications using probes
• CPC Class Codes: B01J 2219/00468 by manipulation of individual beads
• CPC Class Codes: B01J 2219/00497 Features relating to the solid phase supports
• CPC Class Codes: B01J 2219/005 Beads
• CPC Class Codes: B01J 2219/00504 Pins
• CPC Class Codes: B01J 2219/00511 Walls of reactor vessels
• CPC Class Codes: B01J 2219/0052 in the shape of elongated tubes
• CPC Class Codes: B01J 2219/00527 Sheets
• CPC Class Codes: B01J 2219/00585 Parallel processes
• CPC Class Codes: B01J 2219/00596 Solid-phase processes
• CPC Class Codes: B01J 2219/00605 the compounds being directly bound or immobilised to solid supports
• CPC Class Codes: B01J 2219/0061 The surface being organic
• CPC Class Codes: B01J 2219/00612 the surface being inorganic
• CPC Class Codes: B01J 2219/00626 Covalent
• CPC Class Codes: B01J 2219/0063 Other, e.g. van der Waals forces, hydrogen bonding
• CPC Class Codes: B01J 2219/00637 by coating it with another layer
• CPC Class Codes: B01J 2219/00641 the porous medium being continuous, e.g. porous oxide substrates
• CPC Class Codes: B01J 2219/00648 : by the use of solid beads
• CPC Class Codes: B01J 2219/00659 : Two-dimensional arrays
• CPC Class Codes: B01J 2219/00707 : separated from the reactor apparatus
• CPC Class Codes: B01J 2219/0072 : Organic compounds
• CPC Class Codes: B01J 2219/00722 : Nucleotides
• CPC Class Codes: B01J 2219/00725 : Peptides
• CPC Class Codes: B01L 3/0268 : using pulse dispensing or spraying, eg. inkjet type, piezo actuated ejection of droplets from capillaries
• CPC Class Codes: C07B 2200/11 : Compounds covalently bound to a solid support
• CPC Class Codes: C07F 9/2408 : of hydroxyalkyl compounds
• CPC Class Codes: C07F 9/2429 : of arylalkanols
• CPC Class Codes: C07H 21/00 : Compounds containing two or more mononucleotide units having separate phosphate or polyphosphate groups linked by saccharide radicals of nucleoside groups, e.g. nucleic acids
• CPC Class Codes: C12Q 1/6837 : using probe arrays or probe chips C12Q1/6874 takes precedence
• CPC Class Codes: C12Q 1/6858 : Allele-specific amplification
• CPC Class Codes: C12Q 1/6865 : Promoter-based amplification, e.g. nucleic acid sequence amplification [NASBA], self-sustained sequence replication [3SR] or transcription-based amplification system [TAS]
• CPC Class Codes: C12Q 1/6872 : involving mass spectrometry
• CPC Class Codes: C12Q 2523/10 : Characterised by chemical treatment
• CPC Class Codes: C12Q 2525/197 : incorporating a spacer/coupling moiety
• CPC Class Codes: C12Q 2531/113 : PCR
• CPC Class Codes: C12Q 2535/101 : Sanger sequencing method, i.e. oligonucleotide sequencing using primer elongation and dideoxynucleotides as chain terminators
• CPC Class Codes: C12Q 2565/507 : characterised by the density of the capture oligonucleotide
• CPC Class Codes: C12Q 2565/518 : characterised by the immobilisation of the nucleic acid sample or target
• CPC Class Codes: C12Q 2565/537 : characterised by the capture oligonucleotide acting as a primer
• CPC Class Codes: C12Q 2565/627 : being a mass spectrometer
• CPC Class Codes: C40B 40/06 : Libraries containing nucleotides or polynucleotides, or derivatives thereof
• CPC Class Codes: C40B 40/10 : Libraries containing peptides or polypeptides, or derivatives thereof
• CPC Class Codes: C40B 60/14 : for creating libraries
• CPC Class Codes: G01N 2035/00237 : Handling microquantities of analyte, e.g. microvalves, capillary networks
• CPC Class Codes: G01N 2035/1037 : Using surface tension, e.g. pins or wires
• CPC Class Codes: G01N 2035/1069 : by adjusting the spacing between multiple probes of a single transferring head
• CPC Class Codes: G01N 35/1067 : for transfer to or from containers having different spacing
• CPC Class Codes: G01N 35/1074 : arranged in a two-dimensional array
• CPC Class Codes: H01J 49/00 : Particle spectrometers or separator tubes

Abstract

Fast and highly accurate mass spectrometry-based processes for detecting a particular nucleic acid sequence in a biological sample are provided. Depending on the sequence to be detected, the processes can be used, for example, to diagnose a genetic disease or chromosomal abnormality; a predisposition to a disease or condition, infection by a pathogenic organism, or for determining identity or heredity.

Claims

1-103. -103. (canceled)

104. A process for characterizing the structure of one or more target nucleic acids from a biological sample, comprising:

a) determining the base composition of at least one nucleic acid molecule having a known sequence;

b) amplifying one or more target nucleic acid molecules from a biological sample;

c) ionizing and volatilizing the product of step b);

d) analyzing a product of step c) by mass spectrometry to determine an observed molecular mass of said product of step c);

e) obtaining a number of possible base compositions of said product of step c) from the observed molecular mass determined in step d);

f) constraining the number of possible base compositions obtained in step e); and

g) comparing at least one base composition obtained in step e) or at least one base composition constrained in step f) with the base composition determined in step a);

whereby the structure of the one or more target nucleic acids is characterized based on the comparison of (g).

105. The process of claim 104 wherein step d) further comprises analyzing a second product of step c) by mass spectrometry to determine an observed molecular mass of the second product of step c), wherein said second product of step c) is the amplification product complementary to the product of step c), and wherein step e) further comprises obtaining a number of possible base compositions of the second product of step c) from the observed molecular mass of the second product of step c), and wherein step f) further comprises constraining the number of possible base compositions of the second product of step c).

106. The process of claim 105 wherein step f) comprises constraining the number of possible base compositions of said product of step c) using a composition constraint, said composition constraint comprising the base composition obtained in step e) for the second product of step c), or the base composition constrained in step f) for the second product of step c).

107. The process of claim 104 wherein step f) comprises making a mass measurement with an accuracy allowing detection of a mass shift of 0.03% to 0.005%.

108. The process of claim 104 wherein electrospray mass spectrometry is used in step d).

109. The process of claim 104 wherein step f) comprises the use of a composition constraint.

110. The process of claim 109 wherein said composition constraint comprises the length of the product of step c).

111. The process of claim 109 wherein said composition constraint comprises at least one known nucleotide in the sequence of the product of step c).

112. The process of claim 111 wherein said known nucleotide is a nucleotide in the sequence of an amplification primer used to generate the product of step c).

113. The process of claim 109 wherein said composition constraint comprises sequence information of a nucleic acid complementary to the product of step c).

114. The process of claim 113 wherein said sequence information comprises at least one known nucleotide in the sequence of the nucleic acid complementary to the product of step c).

115. The process of claim 113 wherein said composition constraint comprises the base composition of a second product of step c), wherein said second product of step c) is the amplification product complementary to the product of step c).

116. The process of claim 104, wherein amplification step b) is performed by PCR using primers complementary to sequences of the target nucleic acid molecule.

117. The process of claim 116, wherein step f) comprises the use of a composition constraint, said composition constraint comprising sequence information from a nucleic acid molecule known to be amplifiable using the primers complementary to sequences of the target nucleic acid molecule.

118. The process of claim 104, wherein said determining in step a) comprises calculating the base composition of the at least one nucleic acid molecule having a known sequence.

119. The process of claim 104, wherein said characterizing the structure of one or more target nucleic acids in a biological sample comprises determining the molecular mass of one or more target nucleic acids in a biological sample.

120. The process of claim 104, wherein said characterizing the structure of one or more target nucleic acids in a biological sample comprises determining the base composition of one or more target nucleic acids in a biological sample.

121. The process of claim 104, wherein said characterizing the structure of one or more target nucleic acids in a biological sample comprises determining the length of one or more target nucleic acids in a biological sample.

122. A process for characterizing the structure of one or more target nucleic acids from a biological sample, comprising:

a) determining the base composition and molecular mass of at least one nucleic acid molecule having a known sequence;

b) amplifying one or more target nucleic acid molecules from a biological sample;

c) ionizing and volatilizing the product of step b);

d) analyzing a product of step c) by mass spectrometry to determine an observed molecular mass for said product of step c);

e) obtaining a number of possible base compositions of said product of step c) from the observed molecular mass determined in step d);

f) constraining the number of possible base compositions obtained in step e); and

g) comparing at least one base composition obtained in step e) with the base composition determined in step a), or comparing at least one base composition obtained in step f) with the base composition determined in step a), or comparing the observed molecular mass determined in step d) with the molecular mass determined in step a);

whereby the structure of the one or more target nucleic acids is characterized based on the comparison of (g).

123. The process of claim 122 wherein step d) further comprises analyzing a second product of step c) by mass spectrometry to determine an observed molecular mass of the second product of step c), wherein said second product of step c) is the amplification product complementary to the product of step c), and wherein step e) further comprises obtaining a number of possible base compositions of the second product of step c) from the observed molecular mass of the second product of step c), and wherein step f) further comprises constraining the number of possible base compositions of the second product of step c).

124. The process of claim 123 wherein step f) comprises constraining the number of possible base compositions of said product of step c) using a composition constraint, said composition constraint comprising the base composition obtained in step e) for the second product of step c), or the base composition constrained in step f) for the second product of step c).

125. The process of claim 122 wherein step f) comprises making a mass measurement with an accuracy allowing detection of a mass shift of 0.03% to 0.005%.

126. The process of claim 122 wherein electrospray mass spectrometry is used in step d).

127. The process of claim 122 wherein step f) comprises the use of a composition constraint.

128. The process of claim 127 wherein said composition constraint comprises the length of the product of step c).

129. The process of claim 127 wherein said composition constraint comprises at least one known nucleotide in the sequence of the product of step c).

130. The process of claim 129 wherein said known nucleotide is a nucleotide in the sequence of an amplification primer used to generate the product of step c).

131. The process of claim 127 wherein said composition constraint comprises sequence information of a nucleic acid complementary to the product of step c).

132. The process of claim 131 wherein said sequence information comprises at least one known nucleotide in the sequence of the nucleic acid complementary to the product of step c).

133. The process of claim 131 wherein said composition constraint comprises the base composition of a second product of step c), wherein said second product of step c) is the amplification product complementary to the product of step c).

134. The process of claim 122, wherein said amplification step b) is performed using PCR with primers complementary to sequences of the target nucleic acid molecule.

135. The process of claim 134, wherein step f) comprises the use of a composition constraint, said composition constraint comprising sequence information from a nucleic acid molecule known to be amplifiable using the primers complementary to sequences of the target nucleic acid molecule.

136. The process of claim 122, wherein said determining in step a) comprises calculating the base composition and molecular mass of the at least one nucleic acid molecule having a known sequence.

137. The process of claim 122, wherein said characterizing the structure of one or more target nucleic acids in a biological sample comprises determining the molecular mass of one or more target nucleic acids in a biological sample.

138. The process of claim 122, wherein said characterizing the structure of one or more target nucleic acids in a biological sample comprises determining the base composition of one or more target nucleic acids in a biological sample.

139. The process of claim 122, wherein said characterizing the structure of one or more target nucleic acids in a biological sample comprises determining the length of one or more target nucleic acids in a biological sample.