COMPOSITIONS AND METHODS FOR IDENTIFYING AND DETECTING SITES OF TRANSLOCATION AND DNA FUSION JUNCTIONS
First Claim
1. A method for identifying a structural variation in a chromosome, said method comprising:
- a. constructing a ChromPET library from a DNA sample, fragmenting said DNA, and adding a Y-shaped adapter with a bar code to both ends of said fragments wherein paired-end tags are formed;
b. preparing RNA bait;
c. heat denaturing said ChromPET library DNA and hybridizing said ChromPET library DNA to said RNA bait;
d. capturing said RNA-DNA hybrid;
e. washing away said RNA, converting annealed DNA to double-stranded DNA, and sequencing said DNA, forming an Anchored ChromPET library;
f. identifying said ChromPETs from said Anchored ChromPET library using the bar code of the paired-end tags;
g. mapping said ChromPETs from said Anchored ChromPET library to a targeted sequence region, extracting a sequence of interest, and indexing said sequence of interest;
h. classifying said ChromPETs from said Anchored ChromPET library as normal or aberrant ChromPETs, wherein said aberrant ChromPET is optionally a junctional ChromPET;
i. mapping said junctional ChromPETs to the genome; and
j. predicting chromosomal breakpoints, thereby identifying a structural variation in a chromosome.
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Abstract
The present invention provides a powerful technique based on ultra high-throughput sequencing that finds structural aberrations of chromosomes and defines breakpoints. It is disclosed herein that, Anchored ChromPET, a technique to capture and interrogate targeted sequences in the genome, is a cost-effective means to identify chromosomal aberrations and define breakpoints. Using this method, we defined the BCR-ABL1 translocation DNA breakpoint to a base-pair resolution in Philadelphia chromosome positive cell lines and patient cells. This DNA-based method is highly sensitive and can detect signal using samples from which it is hard to obtain RNA or cells where the RNA expression has been silenced. These data demonstrate that ChromPET is a cost-effective and powerful technology that can identify and follow the appearance of chromosomal aberrations in various organisms, including, but not limited to, humans.
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Citations
32 Claims
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1. A method for identifying a structural variation in a chromosome, said method comprising:
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a. constructing a ChromPET library from a DNA sample, fragmenting said DNA, and adding a Y-shaped adapter with a bar code to both ends of said fragments wherein paired-end tags are formed; b. preparing RNA bait; c. heat denaturing said ChromPET library DNA and hybridizing said ChromPET library DNA to said RNA bait; d. capturing said RNA-DNA hybrid; e. washing away said RNA, converting annealed DNA to double-stranded DNA, and sequencing said DNA, forming an Anchored ChromPET library; f. identifying said ChromPETs from said Anchored ChromPET library using the bar code of the paired-end tags; g. mapping said ChromPETs from said Anchored ChromPET library to a targeted sequence region, extracting a sequence of interest, and indexing said sequence of interest; h. classifying said ChromPETs from said Anchored ChromPET library as normal or aberrant ChromPETs, wherein said aberrant ChromPET is optionally a junctional ChromPET; i. mapping said junctional ChromPETs to the genome; and j. predicting chromosomal breakpoints, thereby identifying a structural variation in a chromosome. - View Dependent Claims (2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 18, 19, 20, 21, 25, 30, 31)
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14-16. -16. (canceled)
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22-24. -24. (canceled)
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26-29. -29. (canceled)
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32. A kit for identifying and measuring a structural variation in a chromosome, said kit comprising:
- a list of reagents for pre-treatment of selected DNA sites for anchoring;
polymerase chain reaction reagents;
primer sequences;
a list of reagents for sequencing;
instructions and reagents for making the DNA library for paired end tag sequencing;
DNA sequence based bar codes to distinguish libraries from different patients;
list of materials for computational platform;
algorithm for searching the ChromPET sequences to identify translocation junctions;
primers to PCR amplify the translocation junction and sequence the junctional fragments for confirmation; and
an instructional material for the use thereof.
- a list of reagents for pre-treatment of selected DNA sites for anchoring;
Specification