Compilations of nucleic acids and arrays and methods of using them
First Claim
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1. An array comprising:
- a plurality of nucleic acid segments, wherein each nucleic acid segment is immobilized to a discrete and known spot on a substrate surface to form an array of nucleic acids, and each spot comprises a segment of genomic nucleic acid selected to detect a genetic syndrome, wherein the array-immobilized genomic nucleic acid segments are covalently bound to the substrate surface through a compound having the general formula;
R1—
X—
R2, and wherein R1 is a cyclic ether, an aldehyde, or a chloromethylphenyl moiety;
X is a moiety chemically suitable for linking the R1 moiety to the R2 moiety, and the R2 moiety has the general formula
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Abstract
In one aspect the invention provides compilations of nucleic acids, articles of manufacture, e.g., arrays, and methods for the detection of chromosomal abnormalities, such as a chromosomal aneuploidies, deletions, amplifications, and the like, and the diagnosis or prognosis of syndromes associated with a contiguous gene abnormality. Kits are also provided.
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Citations
98 Claims
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1. An array comprising:
- a plurality of nucleic acid segments, wherein each nucleic acid segment is immobilized to a discrete and known spot on a substrate surface to form an array of nucleic acids, and each spot comprises a segment of genomic nucleic acid selected to detect a genetic syndrome, wherein the array-immobilized genomic nucleic acid segments are covalently bound to the substrate surface through a compound having the general formula;
R1—
X—
R2, and wherein R1 is a cyclic ether, an aldehyde, or a chloromethylphenyl moiety;
X is a moiety chemically suitable for linking the R1 moiety to the R2 moiety, and the R2 moiety has the general formula - View Dependent Claims (2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18)
- a plurality of nucleic acid segments, wherein each nucleic acid segment is immobilized to a discrete and known spot on a substrate surface to form an array of nucleic acids, and each spot comprises a segment of genomic nucleic acid selected to detect a genetic syndrome, wherein the array-immobilized genomic nucleic acid segments are covalently bound to the substrate surface through a compound having the general formula;
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19. A compilation of nucleic acids for diagnosis of a genetic syndrome, the compilation comprising a plurality of nucleic acid segments, wherein each nucleic acid segment comprises a segment of genomic nucleic acid selected to detect a genetic syndrome, wherein the nucleic acid segments further comprise a compound having the general formula
R1—- X—
Si(OR2)m(Cl)n(R)k,wherein m+k is the integer 3, and n can be 0 if m is greater than 0, or n+k is the integer 3 and m can be 0 if n is greater than 0;
X is an inert linker;
R1 comprises a group reactive toward the biological molecule;
R is an alkyl group; and
R2 is an alkyl group.- View Dependent Claims (20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50)
- X—
-
33. An array comprising:
- a plurality of nucleic acid segments, wherein each nucleic acid segment is immobilized to a discrete and known spot on a substrate surface to form an array of nucleic acids, and each spot comprises a segment of genomic nucleic acid selected to detect a genetic syndrome, wherein the array-immobilized genomic nucleic acid segments are covalently bound to the substrate surface through a compound having the general formula;
R1—
X—
R2, wherein R1 is an amino group, R2 is an alkoxysilane group or a chlorohalide group; and
X is a moiety chemically suitable for linking the R1 group and the R2 group.
- a plurality of nucleic acid segments, wherein each nucleic acid segment is immobilized to a discrete and known spot on a substrate surface to form an array of nucleic acids, and each spot comprises a segment of genomic nucleic acid selected to detect a genetic syndrome, wherein the array-immobilized genomic nucleic acid segments are covalently bound to the substrate surface through a compound having the general formula;
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51. A method for selecting a genomic nucleic acid segment for use as a hybridization target in a comparative genomic hybridization (CGH) reaction for the detection of a chromosomal aneuploidy comprising (a) selecting a chromosomal segment that hybridizes to a single locus comprising a segment of the chromosome comprising the aneuploidy to be detected;
- (b) selecting a chromosomal segment having at least 15% to 25% unique sequence such that at least 75% to 85% of the sequence within the chromosomal segment is repetitive, except for chromosomal segments from the X chromosome or Y chromosome, which can have up to 90% to 95% repetitive sequences; and
(c) selecting a segment selected in both step (a) and step (b), thereby selecting a genomic nucleic acid segment for use as a hybridization target in a comparative genomic hybridization (CGH) reaction for the detection of a chromosomal aneuploidy. - View Dependent Claims (52)
- (b) selecting a chromosomal segment having at least 15% to 25% unique sequence such that at least 75% to 85% of the sequence within the chromosomal segment is repetitive, except for chromosomal segments from the X chromosome or Y chromosome, which can have up to 90% to 95% repetitive sequences; and
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53. A compilation of nucleic acids for diagnosis of a genetic syndrome, the compilation comprising a plurality of nucleic acid segments, wherein each nucleic acid segment comprises a segment of genomic nucleic acid selected to detect a genetic syndrome, wherein the nucleic acid segments further comprise a compound having the general formula:
- R1—
X—
R2, wherein R1 is a cyclic ether, an aldehyde, or a chloromethylphenyl moiety;
X is a moiety chemically suitable for linking the R1 moiety to the R2 moiety, and the R2 moiety has the general formula - View Dependent Claims (54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66)
- R1—
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67. A compilation of nucleic acids for diagnosis of a genetic syndrome, the compilation comprising a plurality of nucleic acid segments, wherein each nucleic acid segment comprises a segment of genomic nucleic acid selected to detect a genetic syndrome, wherein the nucleic acid segments further comprise a compound having the general formula:
- R1—
X—
R2, wherein R1 is an amino group, R2 is an alkoxysilane group or a chlorohalide group; and
X is a moiety chemically suitable for linking the R1 group and the R2 group. - View Dependent Claims (68, 69, 70, 71, 72, 73, 74, 75, 76, 77, 78, 79, 80)
- R1—
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81. An array comprising:
- a plurality of nucleic acid segments, wherein each nucleic acid segment is immobilized to a discrete and known spot on a substrate surface to form an array of nucleic acids, and each spot comprises a segment of genomic nucleic acid selected to detect a genetic syndrome, wherein the array-immobilized genomic nucleic acid segments are covalently bound to the substrate surface through a compound having the general formula
R1—
X—
Si(OR2)m(Cl)n(R)k,wherein m+k is the integer 3, and n can be 0 if m is greater than 0, or n+k is the integer 3 and m can be 0 if n is greater than 0;
X is an inert linker;
R1 comprises a group reactive toward a biological molecule;
R is an alkyl group; and
, R2 is an alkyl group.- View Dependent Claims (82, 83, 84, 85, 86, 87, 88, 89, 90, 91, 92, 93, 94, 95, 96, 97, 98)
- a plurality of nucleic acid segments, wherein each nucleic acid segment is immobilized to a discrete and known spot on a substrate surface to form an array of nucleic acids, and each spot comprises a segment of genomic nucleic acid selected to detect a genetic syndrome, wherein the array-immobilized genomic nucleic acid segments are covalently bound to the substrate surface through a compound having the general formula
Specification