Detection of genomic rearrangements by sequence capture
First Claim
1. A method of sample analysis, comprising:
- (a) hybridizing fragmented genomic DNA from a test genome with a population of first oligonucleotides of the formula V1-B-V2 in the presence of one or more second oligonucleotides;
wherein;
(i) the nucleic acid sequence B is the same for each of said first oligonucleotides and is at least 15 nucleotides in length;
(ii) the nucleic acid sequence V1 is variable;
(iii) the nucleic acid sequence V2 is variable;
(iv) within each first oligonucleotide, the V1 and V2 sequences hybridize to sites that are at least 10 kb apart in a reference genome; and
(v) said one or more second oligonucleotides hybridize to nucleic acid sequence B;
(b) contacting the product of (a) with ligase to join the ends of said fragmented genomic DNA that are hybridized to V1 and V2 to the one or more second oligonucleotides; and
(c) subjecting the product of (b) to polymerase chain reaction conditions using amplification primers that hybridize to sites that are provided by said one or more second oligonucleotides,wherein production of a product by step (c) indicates that said test genome contains a chromosomal rearrangement relative to said reference genome.
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Abstract
Provided herein is a method of sample analysis. In some embodiments, the method comprises hybridizing fragmented genomic DNA from a test genome with a population of first oligonucleotides of the formula V1-B-V2 in the presence of one or more second oligonucleotides; contacting the product with ligase to join the ends of the fragmented genomic DNA that are hybridized to V1 and V2 to the one or more second oligonucleotides; and subjecting the product to polymerase chain reaction conditions using amplification primers that hybridize to sites that are provided by the one or more second oligonucleotides, wherein production of a product indicates that the test genome contains a chromosomal rearrangement relative to the reference genome.
4 Citations
16 Claims
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1. A method of sample analysis, comprising:
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(a) hybridizing fragmented genomic DNA from a test genome with a population of first oligonucleotides of the formula V1-B-V2 in the presence of one or more second oligonucleotides;
wherein;(i) the nucleic acid sequence B is the same for each of said first oligonucleotides and is at least 15 nucleotides in length; (ii) the nucleic acid sequence V1 is variable; (iii) the nucleic acid sequence V2 is variable; (iv) within each first oligonucleotide, the V1 and V2 sequences hybridize to sites that are at least 10 kb apart in a reference genome; and (v) said one or more second oligonucleotides hybridize to nucleic acid sequence B; (b) contacting the product of (a) with ligase to join the ends of said fragmented genomic DNA that are hybridized to V1 and V2 to the one or more second oligonucleotides; and (c) subjecting the product of (b) to polymerase chain reaction conditions using amplification primers that hybridize to sites that are provided by said one or more second oligonucleotides, wherein production of a product by step (c) indicates that said test genome contains a chromosomal rearrangement relative to said reference genome. - View Dependent Claims (2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16)
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Specification