Multiplex nucleic acid analysis using archived or fixed samples
First Claim
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1. A method for determining the expression level of target sequences in an archived tissue sample, said method comprising:
- (a) contacting a nucleic acid molecule derived from an archived tissue sample with a plurality of probe sets under conditions where complementary probes form hybridization complexes with said target sequences, each of said probe sets comprising at least two universal priming sites and a target-specific sequence;
(b) amplifying said probes forming said hybridization complexes to produce amplicons, each amplicon corresponding to one of said probe sets;
(c) detecting said amplicons, wherein the detection of each of said amplicons indicates the presence of one of said plurality of target sequence in said archived tissue sample; and
(d) determining the expression level of said target sequences.
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Abstract
The present invention is directed to compositions and methods for multiplex analyses of nucleic acids from archival tissues.
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Citations
124 Claims
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1. A method for determining the expression level of target sequences in an archived tissue sample, said method comprising:
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(a) contacting a nucleic acid molecule derived from an archived tissue sample with a plurality of probe sets under conditions where complementary probes form hybridization complexes with said target sequences, each of said probe sets comprising at least two universal priming sites and a target-specific sequence;
(b) amplifying said probes forming said hybridization complexes to produce amplicons, each amplicon corresponding to one of said probe sets;
(c) detecting said amplicons, wherein the detection of each of said amplicons indicates the presence of one of said plurality of target sequence in said archived tissue sample; and
(d) determining the expression level of said target sequences. - View Dependent Claims (2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23)
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24. A method for determining the expression level of target sequences in an archived tissue sample, said method comprising:
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(a) contacting a nucleic acid molecule derived from an archived tissue sample with a plurality of probe sets under conditions where complementary probes form hybridization complexes with said target sequences, each of said probe sets comprising at least two universal priming sites and a target-specific sequence;
(b) amplifying said probes forming said hybridization complexes to produce amplicons, each amplicon corresponding to one of said probe sets; and
(c) detecting said amplicons, wherein the detection of each of said amplicons indicates the presence of one of said plurality of target sequence in said archived tissue sample. - View Dependent Claims (25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47)
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48. A method for determining the expression level of target sequences in an archived tissue sample, said method comprising:
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(a) contacting a nucleic acid molecule derived from an archived tissue sample with a plurality of probe sets under conditions where complementary probes form hybridization complexes with said target sequences, each of said probe sets comprising at least two universal priming sites and a target-specific sequence having less than fifty nucleotides;
(b) amplifying said probes forming said hybridization complexes to produce amplicons, each amplicon corresponding to one of said probe sets;
(c) detecting said amplicons, wherein the detection of each of said amplicons indicates the presence of one of said plurality of target sequence in said archived tissue sample; and
(d) determining the expression level of said target sequences. - View Dependent Claims (49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67, 68, 69, 70)
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71. A method for detecting a target sequence in an archived tissue sample, said method comprising:
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(a) contacting a nucleic acid molecule derived from an archived tissue sample with a set of ligation probe pairs, each of said pairs capable of forming a ligation complex with said target sequence, each of said ligation probes of said pair comprising a universal priming site and a target-specific sequence;
(b) ligating said ligation complexes to form ligated probes;
(c) amplifying said ligated probes to produce amplicons, each amplicon corresponding to one of said sets of probe pairs;
(d) detecting said amplicons, wherein the detection of said amplicons indicates the presence of said target sequence in said archived tissue sample; and
(e) determining the expression level of said target sequences. - View Dependent Claims (72, 73, 74, 75, 76, 77, 78, 79, 80, 81, 82, 83, 84, 85, 86, 87, 88, 89, 90, 91, 92, 93, 94, 95, 96, 97)
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98. A method for detecting a plurality of target sequences in an archived tissue sample, said method comprising:
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(a) contacting a nucleic acid molecule derived from an archived tissue sample with a plurality of sets of ligation probe pairs, each set comprising ligation probe pairs capable of forming a ligation complex with one of said plurality of target sequences, each of said ligation probes of said pair comprising a universal priming site and a target-specific sequence;
(b) ligating said ligation probe pairs of said ligation complexes to form ligated probes;
(c) amplifying said ligated probes to produce amplicons, each amplicon corresponding to one of said sets of ligation probe pairs; and
(d) detecting said amplicons, wherein the detection of each of said amplicons indicates the presence of one of said plurality of target sequences in said archived tissue sample. - View Dependent Claims (99, 100, 101, 102, 103, 104, 105, 106, 107, 108, 109, 110, 111, 112, 113, 114, 115, 116, 117, 118, 119, 120, 121, 122, 123, 124)
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Specification