Accelerating identification of single nucleotide polymorphisms and alignment of clones in genomic sequencing

• US 8,367,322 B2
• Filed: 07/17/2002
• Issued: 02/05/2013
• Est. Priority Date: 01/06/1999
• Status: Expired due to Fees

• Current Assignee: Cornell Research Foundation Incorporated (Cornell University), Sloan-Kettering Institute For Cancer Research (Memorial Sloan-Kettering Cancer Center)
• Original Assignee: Cornell Research Foundation Incorporated (Cornell University), Sloan-Kettering Institute For Cancer Research (Memorial Sloan-Kettering Cancer Center)
• Inventors: Barany, Francis, Kirk, Brian W., Zirvi, Monib, Gerry, Norman P., Paty, Philip B., Kiu, Jianzhao
• Primary Examiner(s): Lu, Frank W
• Application Number:
  US10/198,235
• Publication Number:
  US 20030190634A1
• Time in Patent Office: 3,856 Days
• Field of Search: 435/6, 435/91.1, 435/91.2, 435/183, 435/6.1, 435/6.11, 435/6.12, 436/94, 536/23.1, 536/24.3, 536/24.33, 536/25.3
• US Class Current: 435/6.1
• CPC Class Codes: C12Q 1/6827 for detection of mutation or polymorphism
• CPC Class Codes: C12Q 1/6855 Ligating adaptors
• CPC Class Codes: C12Q 1/6874 involving nucleic acid arrays, e.g. sequencing by hybridisation
• CPC Class Codes: C12Q 2525/191 incorporating an adaptor
• CPC Class Codes: C12Q 2539/107 Representational Difference Analysis [RDA]
• CPC Class Codes: C12Q 2561/125 Ligase Detection Reaction [LDR]
• CPC Class Codes: C12Q 2565/501 being an array of oligonucleotides
• CPC Class Codes: C12Q 2565/514 characterised by the use of the arrayed oligonucleotides as identifier tags, e.g. universal addressable array, anti-tag or tag complement array
• CPC Class Codes: G16B 30/00 ICT specially adapted for sequence analysis involving nucleotides or amino acids

Abstract

The present invention is directed to a method of assembling genomic maps of an organism'"'"'s DNA or portions thereof. A library of an organism'"'"'s DNA is provided where the individual genomic segments or sequences are found on more than one clone in the library. Representations of the genome are created, and nucleic acid sequence information is generated from the representations. The sequence information is analyzed to determine clone overlap from a representation. The clone overlap and sequence information from different representations is combined to assemble a genomic map of the organism. Once the genomic map is obtained, genomic sequence information from multiple individuals can be applied to the map and compared with one another to identify single nucleotide polymorphisms. These single nucleotide polymorphisms can be detected, and alleles quantified, by conducting (1) a global PCR amplification which creates a genome representation, and (2) a ligation detection reaction process whose ligation products are captured by hybridization to a support.

Claims

1. A method of assembling a map of an organism'"'"'s genome or portions thereof comprising:

providing a library of an organism'"'"'s DNA, wherein individual genomic segments are found in more than one clone in the library with at least some of the said individual genomic segments have overlapping DNA sequences;

creating representations of the genomic segments in individual clones by selecting a subpopulation of genomic segments out of a larger set of the genomic segments in each of the individual clones, wherein said selecting a subpopulation of genomic segments comprises;

subjecting more than one individual clone to a restriction endonuclease, wherein the restriction endonuclease is effective in recognizing a restriction site recognition sequence and cleaving the DNA in said more than one individual clone at a restriction site of the restriction site recognition sequence thereby creating a plurality of clone fragments having 2 base overhangs and adding 1 to 12 linker-adapters, each of which is non-palindromic, to the overhangs in the presence of ligase and the restriction endonuclease and producing a plurality of clone fragments comprising said 1 to 12 linker-adapters, wherein said plurality of clones fragments comprising said 1 to 12 linker-adapters are selected as the representations, wherein the linker-adapters contain single stranded overhangs of a formula NN/N′

N′

where said NN/N′

N′

is selected from the group consisting of AA/TT, AC/GT, AG/CT, CA/TG, GA/TC, and GG/CC;

generating DNA sequence information from the representations;

analyzing the DNA sequence information thereby determining clone overlap from the representations; and

combining said clone overlap and DNA sequence information from the representations thereby assembling a map of the organism'"'"'s genome or portions thereof.

2. The method according to claim 1, wherein said adding 1 to 12 linker-adapters is carried out by adding 4 to 6 of said linker-adapters.

3. The method according to claim 1, wherein the restriction endonuclease is selected from the group consisting of DrdI, BglI, DraIII, AlwNI, PflMI, AccI, BsiHKAI, SanDI, SexAI, PpuI, AvaII, EcoO109, Bsu36I, BsrDI, BsgI, BpmI, SapI, and isoschizomers thereof.

4. The method according to claim 1, wherein said generating DNA sequence information is carried out by DNA sequencing reactions using one or more sequencing primers.

5. The method according to claim 4, wherein the sequencing primers have a 5′

sequence that is complementary to the linker-adapters and have a 3′

sequence that is complementary to the 2 base overhangs and/or adjacent to the restriction site recognition sequence in the DNA sequencing reactions to obtain sequence information adjacent to the restriction site.

6. The method according to claim 5, wherein said one or more sequencing primers are 1 to 12 sequencing primers, wherein the sequencing primers have 3′

ends of NN or N′

N′

, with said N being any nucleotide and said N′

being the complement of said N.

7. The method according to claim 4, wherein said one or more sequencing primers are 1 to 16 sequencing primers wherein the sequencing primers have 3′

ends of NAA, NAC, NAG, NAT, NCA, NCC, NCG, NCT, NGA, NGC, NGG, NGT, NTA, NTC, NTG, or NTT, with said N being any nucleotide.

8. The method according to claim 4, wherein the quantity of the sequencing primers is 1 to 16 sequencing primers to obtain DNA sequence information adjacent to the restriction site wherein the sequencing primers having 3′

ends of NAA, NAC, NAG, NAT, NCA, NCC, NCG, NCT, NGA, NGC, NGG, NGT, NTA, NTC, NTG, or NTT, with said N being any nucleotide.

9. The method according to claim 4, wherein the DNA sequence information generated from the representations comprises unique sequencing data.

10. The method according to claim 4, wherein the DNA sequence information generated from the representations comprises two overlapping sequences.

11. The method according to claim 4, wherein the DNA sequence information generated from the representations comprises three overlapping sequences.

12. The method according to claim 4, wherein the sequencing primers have one or two additional bases on their 3′

end used for obtaining unique singlet sequence information.

13. A method of assembling a map of an organism'"'"'s genome or portions thereof comprising:

providing a library of an organism'"'"'s DNA, wherein individual genomic segments are found in more than one clone in the library;

creating representations of the genomic segments in individual clones by selecting a subpopulation of genomic segments out of a larger set of the genomic segments in each of the individual clones, wherein said selecting a subpopulation of genomic segments comprises;

subjecting more than one individual clone to a restriction endonuclease, wherein the restriction endonuclease is effective in recognizing a restriction site recognition sequence and cleaving the DNA in said more than one individual clone at a restriction site of the restriction site recognition sequence thereby creating a plurality of clone fragments having 2 base overhangs and adding linker-adapters, each of which is non-palindromic, to the overhangs in the presence of ligase and the first restriction endonuclease and producing a plurality of clone fragments comprising said linker-adapters, wherein said plurality of clone fragments comprising said linker-adapters are selected as the representations, wherein the linker-adapters contain single stranded overhangs of a formula NN/N′

N′

where said NN/N′

N′

is selected from the group consisting of AA/TT, AC/GT, AG/CT, CA/TG, GA/TC, and GG/CC;

generating DNA sequence information from the representations;

analyzing the DNA sequence information thereby determining clone overlap from the representations, wherein said analyzing the DNA sequence information comprises;

analyzing sequencing data generated by deconvoluting one or more singlet, doublet and/or triplet sequences contained in the representations; and

combining said clone overlap and DNA sequence information from the representations thereby assembling a map of the organism'"'"'s genome or portions thereof.

14. The method according to claim 13, wherein said analyzing sequencing data comprises:

comparing data from two singlet sequences in the same representation of said representations and

evaluating data for the two singlet sequences of separate clone fragments in the same representation of said representations for overlap by aligning the sequencing data and scoring identity in at least 8 bases which are beyond the restriction recognition sequence with less than 3 discordant positions.

15. The method according to claim 13, wherein said analyzing sequencing data comprises:

comparing data from a singlet sequence and a doublet sequence in the same representation of said representations and

evaluating data for the singlet and doublet sequences contained in the representations for said clone overlap by aligning the sequencing data and either scoring for at least 8 bases which are identical in a doublet sequencing run and a singlet sequencing run and said bases are beyond the restriction recognition sequence or, alternatively, by scoring at least 16 bases which are beyond the restriction recognition sequence where the bases of the singlet sequence corresponds to the bases in the doublet sequence with less than 3 discordant positions.

16. The method according to claim 13, wherein said analyzing sequencing data comprises:

comparing data from a singlet and a triplet sequence in the same representation of said representations and

evaluating data for said clone overlap by aligning the sequencing data, and either scoring identity in at least 8 bases which are identical in a triplet sequencing run and a singlet sequencing run and said bases are beyond the restriction recognition sequence or, alternatively, by scoring at least 16 bases which are beyond the restriction recognition sequence where the bases of the singlet corresponds to the bases in the triplet sequence, with less than 3 discordant positions.

17. The method according to claim 13, wherein said analyzing sequencing data comprises:

comparing two doublet sequences in the same representation of the representations and

evaluating data for said clone overlap by aligning the sequencing data and scoring identity in at least 16 bases which are beyond the restriction recognition sequence where the two doublet sequences has an identical base, or where both said doublet sequences have two identical bases, with less than 3 discordant positions.

18. The method according to claim 13, wherein said analyzing sequencing data comprises:

comparing a doublet sequence and a triplet sequence in the same representation of the representations and

evaluating data for said clone overlap by aligning the sequencing data, and scoring identity in at least 16 bases which are beyond the restriction recognition sequence where either the doublet sequence and the triplet sequence has an identical base, or where the doublet sequence and triplet sequence have two identical bases, with less than 3 discordant positions.

19. The method according to claim 13, wherein said analyzing sequencing data comprises:

comparing two sequences from the same representation of the representations with a singlet, doublet, or triplet sequence; and

evaluating data to determine whether the clones are likely not to overlap.

20. A method of assembling a map of an organism'"'"'s genome or portions thereof comprising:

providing a library of an organism'"'"'s DNA, wherein individual genomic segments are found in more than one clone in the library with at least some of the said individual genomic segments have overlapping DNA sequences;

creating representations of the genomic segments in individual clones by selecting a subpopulation of genomic segments out of a larger set of the genomic segments in each of the individual clones, wherein said selecting a subpopulation of genomic segments comprises;

subjecting more than one individual clone to a restriction endonuclease, wherein the restriction endonuclease is effective in recognizing a restriction site recognition sequence and cleaving the DNA in said more than one individual clone at a restriction site of the restriction site recognition sequence thereby creating a plurality of clone fragments having an overhang; and

adding a linker-adapter which is non-palindromic to the overhang in the presence of ligase and the restriction endonuclease and producing a plurality clone fragments comprising said linker-adapters, wherein said plurality of clone fragments comprising said linker-adapters are selected as the representations, wherein the linker-adapters contain single stranded overhangs of a formula NN/N′

N′

where NN/N′

N′

is selected from the group consisting of AA/TT, AC/GT, AG/CT, CA/TG, GA/TC, and GG/CC;

generating DNA sequence information from the representations;

analyzing the DNA sequence information thereby determining clone overlap from the representations; and

combining said clone overlap and DNA sequence information from the representations thereby assembling a map of the organism'"'"'s genome or portions thereof, wherein said combining said clone overlap and DNA sequence information comprises;

comparing the DNA sequence information in a pair of said plurality of clone fragments comprising said linker-adaptors in the representations which have identical contiguous portions.