In situ cloning from pathological tissue specimens
First Claim
1. A method of cloning a nucleic acid from a biological sample, wherein said biological sample is fixed, said method comprising:
- (a) providing a population of oligonucleotide sequence probes to said fixed biological sample, wherein each of said oligonucleotide sequence probes comprises a sequence tag flanked by a 5′
-end extension sequence and a 3′
-end extension sequence, wherein said 5′
-end and 3′
-end extension sequences are not found in the mammalian genome, further wherein said sequence tag is a degenerate sequence and wherein at least one of said 5′
-end extension sequence and said 3′
-end extension sequence comprises a detection sequence;
(b) hybridizing said population of oligonucleotide sequence probes with said nucleic acid in said biological sample, thereby forming a population of hybridized oligonucleotide sequences probes and a population of unhybridized oligonucleotide sequence probes;
(c) washing away said population of unhybridized oligonucleotide sequence probes; and
(d) isolating said population of hybridized oligonucleotide sequence probes thereby forming an isolated population of hybridized oligonucleotide sequence probes, thereby cloning said nucleic acid from said biological sample,wherein said fixed biological sample comprises fixed cells.
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Abstract
The present invention pertains to methods related to cloning nucleic acids from biological samples, particularly pathological tissue samples. This method includes hybridizing a population of oligonucleotide sequence probes comprising degenerate sequence tags to a fixed tissue, isolating the hybridized oligonucleotide sequence probes and amplifying the sequence tags in the hybridized oligonucleotide sequence probes. This method can be utilized to identify genes associated with disease and to quantitate the expression of disease-related transcripts. The method can also be used to identify truncated mRNAs.
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Citations
17 Claims
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1. A method of cloning a nucleic acid from a biological sample, wherein said biological sample is fixed, said method comprising:
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(a) providing a population of oligonucleotide sequence probes to said fixed biological sample, wherein each of said oligonucleotide sequence probes comprises a sequence tag flanked by a 5′
-end extension sequence and a 3′
-end extension sequence, wherein said 5′
-end and 3′
-end extension sequences are not found in the mammalian genome, further wherein said sequence tag is a degenerate sequence and wherein at least one of said 5′
-end extension sequence and said 3′
-end extension sequence comprises a detection sequence;(b) hybridizing said population of oligonucleotide sequence probes with said nucleic acid in said biological sample, thereby forming a population of hybridized oligonucleotide sequences probes and a population of unhybridized oligonucleotide sequence probes; (c) washing away said population of unhybridized oligonucleotide sequence probes; and (d) isolating said population of hybridized oligonucleotide sequence probes thereby forming an isolated population of hybridized oligonucleotide sequence probes, thereby cloning said nucleic acid from said biological sample, wherein said fixed biological sample comprises fixed cells. - View Dependent Claims (2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16)
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17. A method of identifying a truncated mRNA sequence from a biological sample, wherein said biological sample is fixed, said method comprising:
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(a) providing a population of oligonucleotide sequence probes, wherein each of said oligonucleotide sequence probes comprises a sequence tag flanked by a 5′
-end extension sequence and a 3′
-end extension sequence, wherein said 5′
-end and 3′
-end extension sequences are not found in the mammalian genome, further wherein said sequence tag is a degenerate sequence and wherein at least one of said 5′
-end extension sequence and said 3′
-end extension sequence comprises a detection sequence;(b) hybridizing said population of oligonucleotide sequence probes with said nucleic acid in said biological sample, thereby forming a population of hybridized oligonucleotide sequences probes and a population of unhybridized oligonucleotide sequence probes; (c) washing away said population of unhybridized oligonucleotide sequence probes; (d) isolating said population of hybridized oligonucleotide sequence probes thereby forming an isolated population of hybridized oligonucleotide sequence probes, (e) amplifying said isolated population of hybridized oligonucleotide sequence probes to produce a population of amplified fragments comprising sequence tags; (f) annealing a detection oligonucleotide comprising a detectable label to at least one of said 5′
-end extension sequence and said 3′
-end extension sequence of each of said oligonucleotide sequence probe to form a population of detectably labeled amplified fragments, wherein said detection oligonucleotide is complementary to a detection sequence;(g) hybridizing said population of detectably labeled amplified fragments to a microarray, wherein said microarray is capable of detecting sequences for at least two different regions of at least one mRNA; (h) detecting the detectable label to obtain a signal for each of said at least two different regions of said at least one mRNA; (i) comparing said signals from said at least two different regions of said at least one mRNA, whereby a difference in signal strength or an absence of a signal from one region and not another is indicative of a truncation in said mRNA, wherein the fixed biological sample comprises fixed cells.
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Specification