Tagged fragment library configured for genome or cDNA sequence analysis
원문보기
IPC분류정보
국가/구분
United States(US) Patent
등록
국제특허분류(IPC7판)
C12P-019/34
C12Q-001/68
C07H-021/04
C07K-001/04
출원번호
US-0971806
(2013-08-20)
등록번호
US-9637785
(2017-05-02)
발명자
/ 주소
Drmanac, Radoje
출원인 / 주소
Complete Genomics, Inc.
대리인 / 주소
Kilpatrick Townsend & Stockton LLP
인용정보
피인용 횟수 :
1인용 특허 :
112
초록▼
The invention provides methods and kits for ordering sequence information derived from one or more target polynucleotides. In one aspect, one or more tiers or levels of fragmentation and aliquoting are generated, after which sequence information is obtained from fragments in a final level or tier. E
The invention provides methods and kits for ordering sequence information derived from one or more target polynucleotides. In one aspect, one or more tiers or levels of fragmentation and aliquoting are generated, after which sequence information is obtained from fragments in a final level or tier. Each fragment in such final tier is from a particular aliquot, which, in turn, is from a particular aliquot of a prior tier, and so on. For every fragment of an aliquot in the final tier, the aliquots from which it was derived at every prior tier is known, or can be discerned. Thus, identical sequences from overlapping fragments from different aliquots can be distinguished and grouped as being derived from the same or different fragments from prior tiers. When the fragments in the final tier are sequenced, overlapping sequence regions of fragments in different aliquots are used to register the fragments so that non-overlapping regions are ordered. In one aspect, this process is carried out in a hierarchical fashion until the one or more target polynucleotides are characterized, e.g. by their nucleic acid sequences, or by an ordering of sequence segments, or by an ordering of single nucleotide polymorphisms (SNPs), or the like.
대표청구항▼
1. A DNA library configured for nucleotide sequencing of a genome, the library comprising a plurality of constructs wherein: each construct contains a fragment of the genome tagged with an oligonucleotide;at least 96 of the constructs contain different genome fragments joined to oligonucleotide tags
1. A DNA library configured for nucleotide sequencing of a genome, the library comprising a plurality of constructs wherein: each construct contains a fragment of the genome tagged with an oligonucleotide;at least 96 of the constructs contain different genome fragments joined to oligonucleotide tags having different sequences;some of the constructs contain different genome fragments joined to oligonucleotide tags having the same sequence; andconstructs that contain oligonucleotide tags having the same sequence more often contain fragment sequences that occur within 100 kb of each other in the genome, compared with constructs in the library that contain oligonucleotide tags having different sequences. 2. The DNA library of claim 1, wherein some of the fragments containing oligonucleotide tags having different sequences are aliquoted into separate aliquots, and fragments containing oligonucleotide tags having the same sequences are contained in the same aliquot. 3. The DNA library of claim 1, wherein the constructs are combined in a single mixture. 4. The DNA library of claim 1, wherein the constructs further contain one or more adaptor sequences that are common to most of the constructs. 5. The DNA library of claim 1, wherein the constructs are configured so that sequence reads of no more than 1,000 nucleotides can be obtained that include the sequence of the respective oligonucleotide tag and at least part of the sequence of the respective fragment. 6. The DNA library of claim 1, wherein the median length of the fragments is 30 to 3,000 bases. 7. The DNA library of claim 1, wherein the probability of constructs in the library containing fragments of the genome having overlapping sequences joined to oligonucleotide tags having the same sequence is less than 1%. 8. The DNA library of claim 1, wherein the constructs contain two fragments that have sequences that are nearby but not immediately beside each other in the genome separated by a common adaptor sequence. 9. The DNA library of claim 1, wherein all the constructs together contain at least a majority of the nucleotide sequence of the genome. 10. The DNA library of claim 1, containing genomes of multiple organisms. 11. A library configured for nucleotide sequencing of a target polynucleotide, the library comprising a plurality of nucleic acid constructs wherein: each construct contains a fragment of the target polynucleotide tagged with an oligonucleotide;at least 96 of the constructs contain different fragments of the target polynucleotide joined to oligonucleotide tags having different sequences;some of the constructs contain different fragments of the target polynucleotide joined to oligonucleotide tags having the same sequence; andconstructs that contain oligonucleotide tags having the same sequence more often contain fragments that occur within 100 kb of each other in the target polynucleotide, compared with constructs in the library that contain oligonucleotide tags having different sequences. 12. The library of claim 11, wherein the target polynucleotide comprises a mammalian genome. 13. The library of claim 11, wherein the target polynucleotide comprises cDNA prepared from a biological sample. 14. A cDNA library configured for characterizing gene expression in a biological sample, the library comprising a plurality of constructs wherein: each construct contains at least a fragment of a cDNA sequence obtained by reverse transcribing an mRNA transcript in the biological sample joined to an oligonucleotide tag;at least 96 of the constructs contain different cDNA sequences tagged with oligonucleotides having different sequences;some of the constructs contain different cDNA sequences tagged with oligonucleotides having the same sequence; andconstructs that contain oligonucleotide tags having the same sequence more often contain sequences from an mRNA transcript of the same gene, compared with constructs in the library that contain oligonucleotide tags having different sequences. 15. The cDNA library of claim 14, wherein the constructs are configured so that sequence reads of no more than 1,000 nucleotides can be obtained that include the sequence of the respective oligonucleotide tag and at least part of the sequence of the respective fragment. 16. The cDNA library of claim 14, wherein the median length of the fragments is 30 to 3,000 bases. 17. The cDNA library of claim 14, wherein the probability of constructs in the library containing fragments of the cDNA having overlapping sequences joined to oligonucleotide tags having the same sequence is less than 1%. 18. The cDNA library of claim 14, wherein the constructs are mate pairs containing two fragments that have sequences that are nearby but not immediately beside each other in the cDNA separated by a common adaptor sequence. 19. The cDNA library of claim 14, wherein some of the fragments containing oligonucleotide tags having different sequences are aliquoted into separate aliquots and fragments containing oligonucleotide tags having the same sequences are contained in a common aliquot. 20. The cDNA library of claim 14, wherein the constructs are combined in a single mixture.
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이 특허에 인용된 특허 (112)
Barany, Francis; Liu, Jianzhao; Kirk, Brian W.; Zirvi, Monib; Gerry, Norman P.; Paty, Philip B., Accelerating identification of single nucleotide polymorphisms and alignment of clones in genomic sequencing.
Birkenmeyer Larry G. (Chicago IL) Carrino John J. (Gurnee IL) Dille Bruce J. (Antioch IL) Hu Hsiang-Yun (Libertyville IL) Kratochvil Jon D. (Kenosha WI) Laffler Thomas G. (Libertyville IL) Marshall R, Amplification of target nucleic acids using gap filling ligase chain reaction.
Whiteley Norman M. (San Carlos CA) Hunkapiller Michael W. (San Carlos CA) Glazer Alexander N. (Orinda CA), Detection of specific sequences in nucleic acids.
Pirrung Michael C. (Durham NC) Read J. Leighton (Palo Alto CA) Fodor Stephen P. A. (Palo Alto CA) Stryer Lubert (Stanford CA), Large scale photolithographic solid phase synthesis of polypeptides and receptor binding screening thereof.
Albrecht Glenn ; Brenner Sydney,GBX ; DuBridge Robert B. ; Lloyd David H. ; Pallas Michael C., Massively parallel signature sequencing by ligation of encoded adaptors.
Adams Christopher P. (Winter Hill MA) Kron Stephen Joseph (Boston MA), Method for performing amplification of nucleic acid with two primers bound to a single solid support.
Drmanac Radoje T. (Beograd YUX) Crkvenjakov Radomir B. (Beograd YUX), Method of determining an ordered sequence of subfragments of a nucleic acid fragment by hybridization of oligonucleotide.
Rothberg,Jonathan M.; Bader,Joel S.; Dewell,Scott B.; McDade,Keith; Simpson,John W.; Berka,Jan; Colangelo,Christopher M., Method of sequencing a nucleic acid.
Rothberg,Jonathan M.; Bader,Joel S.; Dewell,Scott B.; McDade,Keith; Simpson,John W.; Berka,Jan; Colangelo,Christopher M., Method of sequencing a nucleic acid.
Drmanac Radoje T. (Zvecanska 46 Beograd 11000) Crkvenjakov Radomir B. (Bulevar JNA 118 Beograd YUX 11000), Method of sequencing of genomes by hybridization of oligonucleotide probes.
Brennan Thomas M. (2000 Broadway ; No. 705 San Francisco CA 94115) Heyneker Herbert L. (360 Forest Ave. ; No. 506 Palo Alto CA 94301), Methods and compositions for determining the sequence of nucleic acids.
Drmanac Radoje T. ; Drmanac Snezana ; Hou Aaron ; Hauser Brian, Methods for sequencing repetitive sequences and for determining the order of sequence subfragments.
Heller Michael J. (Encinitas CA) Tu Eugene (San Diego CA) Butler William F. (Carlsbad CA), Molecular biological diagnostic systems including electrodes.
Mirkin, Chad A.; Letsinger, Robert L.; Mucic, Robert C.; Storhoff, James J.; Elghanian, Robert; Taton, Thomas A., Nanoparticles having oligonucleotides attached thereto and uses therefor.
Urdea Michael S. (Alamo CA) Warner Brian (Martinez CA) Horn Thomas (Berkeley CA), Nucleic acid multimers and amplified nucleic acid hybridization assays using same.
Newman Peter J. (Shorewood WI) Aster Richard H. (Milwaukee WI), Polymorphism of human platelet membrane glycoprotein IIIa and diagnostic and therapeutic applications thereof.
Rabbani,Elazar; Stavrianopoulos,Jannis G.; Kirtikar,Dollie; Johnston,Kenneth H.; Thalenfeld,Barbara E., System, array and non-porous solid support comprising fixed or immobilized nucleic acids.
Cantor, Charles R.; Siddiqi, Fouad A., Use of nucleotide analogs in the analysis of oligonucleotide mixtures and in highly multiplexed nucleic acid sequencing.
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