US 6,785,614 B1Granted

End sequence profiling

AssigneeThe Regents of the University of California

InventorsColin Collins, Stanislav Volik, Joe W. Gray

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Abstract

The present invention provides a novel method to identify rearrangements in a test genome, e.g., a tumor genome, when compared to a reference genome. This method provides major improvements over previous methods in terms of efficiency, rapidity, and cost-effectiveness. Briefly, this method involves generating or obtaining a large insert vector library from a test genome, sequencing the ends of the inserts in the library, and comparing the co-linearity of the sequenced ends in the library with corresponding sequences within a substantially-sequenced reference genome. This invention is useful for any of a number of applications, including for identifying rearrangements in tumor genomes and for determining genetic differences between closely related species as well as between different strains of the same species.

Claims24

Dependent claims

A method for comparing a test genome to a reference genome, said method comprising:

(i) providing a plurality of clones of known size that substantially cover at least a portion of said test genome;
(ii) obtaining sequence information from the termini of each of said plurality of clones, thereby obtaining a pair of terminal sequences;
(iii) identifying a pair of sequences within said reference genome that corresponds to each of said pairs of terminal sequences;
and
(iv) determining the relationship between the members of each pair of corresponding sequences within said reference genome;
wherein a difference in the observed relationship between the members of any of said pairs of corresponding sequences within said reference genome and the expected relationship based upon said known size of said plurality of clones indicates the presence of a rearrangement in said test genome compared to said reference genome and wherein said test genome is obtained from an individual with a disease associated with chromosomal rearrangements.

3 more elements

Dependencies are inferred from the claim text.