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Nucleic acid analysis by random mixtures of non-overlapping fragments

  • US 7,709,197 B2
  • Filed: 06/13/2006
  • Issued: 05/04/2010
  • Est. Priority Date: 06/15/2005
  • Status: Active Grant
First Claim
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1. A method of characterizing nucleotide sequences of one or more target polynucleotides, said method comprising the steps of:

  • (a) fragmenting said one or more target polynucleotides present in a predetermined coverage amount to form a population containing overlapping first-sized fragments having an average length less than those of said target polynucleotides;

    (b) forming a number of separate mixtures from said population of first-sized fragments, such number being selected such that a majority of first-sized fragments in each separate mixture is non-overlapping with every other first-sized fragment of the same mixture and such that the mixture of origin of each such first-sized fragment is determinable;

    (c) generating for each of said separate mixtures a plurality of target concatemers from said first-sized fragments, each target concatemer comprising multiple copies of at least a portion of a first-sized fragment;

    (d) disposing said target concatemers on a surface; and

    (e) generating a number of sequence reads from target concatemers of each of said separate mixtures, such sequence reads each having a length less than those of said first-sized fragments, and such numbers of sequence reads being selected such that said sequence reads of each separate mixture covers a majority of first-sized fragments therein, andproviding complete or partial nucleotide sequences of said one or more target polynucleotides by ordering said sequence reads from said target concatemers.

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