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COMPOSITIONS AND METHODS FOR IDENTIFYING AND DETECTING SITES OF TRANSLOCATION AND DNA FUSION JUNCTIONS

  • US 20120178635A1
  • Filed: 08/06/2010
  • Published: 07/12/2012
  • Est. Priority Date: 08/06/2009
  • Status: Abandoned Application
First Claim
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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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