# US 6,785,614 B1 · End sequence profiling > Agents: this data is available as JSON from the patentgrep API and MCP server — see https://patentgrep.com/llms.txt - Number: US 6,785,614 B1 - Document ID: US6785614B1 - Status: Granted - Kind: B1 - Application number: 09/586,529 - Filed: 2000-05-31 - Granted: 2004-08-31 - Earliest claimed: 2000-05-31 - Assignees: The Regents of the University of California - Inventors: Colin Collins; Stanislav Volik; Joe W. Gray - Web page: https://patentgrep.com/patent/US6785614B1 ## CPC - C12Q 1/6869: Methods for sequencing - C12Q 1/6827: for detection of mutation or polymorphism - C12Q: MEASURING OR TESTING PROCESSES INVOLVING ENZYMES, NUCLEIC ACIDS OR MICROORGANISMS (immunoassay G01N33/53); COMPOSITIONS OR TEST PAPERS THEREFOR; PROCESSES OF PREPARING SUCH COMPOSITIONS; CONDITION-RESPONSIVE CONTROL IN MICROBIOLOGICAL OR ENZYMOLOGICAL PROCESSES ## 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. ## Claims ### Claim 1 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. ### Claim 2 (depends on 1) The method of claim 1, further comprising determining the sequence of said test genome over a region spanning at least one breakpoint of said rearrangement. ### Claim 3 (depends on 1) The method of claim 1, wherein said reference genome is a human genome. ### Claim 4 (depends on 1) The method of claim 1, wherein said test genome is from a tumor cell. ### Claim 5 (depends on 1) The method of claim 1, wherein said reference genome and said test genome are from different species. ### Claim 6 (depends on 1) The method of claim 1, wherein said plurality of clones covers substantially all of said test genome. ### Claim 7 (depends on 1) The method of claim 1, further comprising determining the frequency of each of said terminal sequences within said plurality of clones, wherein an increased or decreased relative frequency of any of said terminal sequences indicates the presence of an amplification or a deletion in said test genome that includes said terminal sequence. ### Claim 8 (depends on 1) The method of claim 1, wherein said plurality of clones are BAC clones. ### Claim 9 (depends on 1) The method of claim 1, wherein said plurality of clones are PAC clones. ### Claim 10 (depends on 1) The method of claim 1, wherein said plurality of clones represents a redundancy of at least about 10 fold of said test genome or said portion of said test genome. ### Claim 11 (depends on 10) The method of claim 10, wherein said plurality of clones represents a redundancy of at least about 20 fold of said test genome or said portion of said test genome. ### Claim 12 (depends on 1) The method of claim 1, wherein said terminal sequences are present on average between about every 5 kb to about every 500 kb throughout said test genome or said portion of said test genome. ### Claim 13 (depends on 12) The method of claim 12, wherein said terminal sequences are present on average every 50 kb or less throughout said test genome or said portion of said test genome. ### Claim 14 (depends on 13) The method of claim 13, wherein said terminal sequences are present on average every 10 kb or less throughout said test genome or said portion of said test genome. ### Claim 15 (depends on 14) The method of claim 14, wherein said terminal sequences are present on average every 5 kb or less throughout said test genome or said portion of said test genome. ### Claim 16 (depends on 1) The method of claim 1, wherein said reference genome is a human genome, and wherein said plurality of clones comprises at least about 100,000 clones. ### Claim 17 (depends on 16) The method of claim 16, wherein said plurality of clones comprises at least about 200,000 clones. ### Claim 18 (depends on 17) The method of claim 17, wherein said plurality of clones comprises at least about 250,000 clones. ### Claim 19 (depends on 1) The method of claim 1, wherein said terminal sequences are determined by automated sequencing. ### Claim 20 (depends on 1) The method of claim 1, wherein said pairs of terminal sequences from said test genome are compared to said pairs of corresponding sequences within said reference genome using a computer. ### Claim 21 (depends on 1) The method of claim 1, wherein the determining step (iv) comprises determining the genetic or physical distance the pair of sequences. ### Claim 22 (depends on 1) The method of claim 1, wherein the determining step (iv) comprises determining whether the pair of sequences are present in the same vector or chromosome. ### Claim 23 (depends on 1) The method of claim 1, wherein the reference genome is substantially sequenced and is present in a searchable database and the pair of sequences within said reference genome that corresponds to each of said pairs of terminal sequences are identified by comparing the terminal sequences to the reference genome using a computer. ### Claim 24 (depends on 1) The method of claim 1, wherein the clones are cDNA clones.