Method of constructing sequencing library

• US 10,456,769 B2
• Filed: 08/03/2017
• Issued: 10/29/2019
• Est. Priority Date: 02/04/2015
• Status: Active Grant

• Current Assignee: BGI Shenzhen, MGI Holdings LP (Mr. Gatti's, L.P.)
• Original Assignee: BGI Shenzhen & BGI Shenzhen Company Limited
• Inventors: Wang, Ou, Cheng, Xiaofang, Zou, Liangying, Chang, Cankun, Jiang, Hui, Zhang, Wenwei
• Primary Examiner(s): Vivlemore, Tracy
• Assistant Examiner(s): Kaup, Sahana S
• Application Number:
  US15/667,841
• Publication Number:
  US 20170341051A1
• Time in Patent Office: 817 Days
• Field of Search: None
• CPC Class Codes: B01J 19/0046 Sequential or parallel reactions, e.g. for the synthesis of polypeptides or polynucleotides; Apparatus and devices for combinatorial chemistry or for making molecular arrays synthesis methods per se C40B50/00
• CPC Class Codes: B01J 2219/00317 Microwell devices, i.e. having large numbers of wells
• CPC Class Codes: B01J 2219/00587 High throughput processes
• CPC Class Codes: B01J 2219/00599 Solution-phase processes
• CPC Class Codes: B01J 2219/00716 Heat activated synthesis
• CPC Class Codes: B01J 2219/00722 Nucleotides
• CPC Class Codes: C12N 15/1068 Template (nucleic acid) mediated chemical library synthesis, e.g. chemical and enzymatical DNA-templated organic molecule synthesis, libraries prepared by non ribosomal polypeptide synthesis [NRPS], DNA/RNA-polymerase mediated polypeptide synthesis
• CPC Class Codes: C12Q 1/6806 Preparing nucleic acids for analysis, e.g. for polymerase chain reaction [PCR] assay C12Q1/6804 takes precedence
• CPC Class Codes: C12Q 2521/507 Recombinase
• CPC Class Codes: C12Q 2525/155 incorporating/generating a new priming site
• CPC Class Codes: C12Q 2525/161 incorporating target specific and non-target specific sites
• CPC Class Codes: C12Q 2525/191 incorporating an adaptor
• CPC Class Codes: C12Q 2531/119 Strand displacement amplification [SDA]
• CPC Class Codes: C12Q 2535/122 Massive parallel sequencing
• CPC Class Codes: C12Q 2563/159 Microreactors, e.g. emulsion PCR or sequencing, droplet PCR, microcapsules, i.e. non-liquid containers with a range of different permeability's for different reaction components
• CPC Class Codes: C12Q 2563/179 the label being a nucleic acid
• 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: C40B 50/06 Biochemical methods, e.g. using enzymes or whole viable microorganisms
• CPC Class Codes: C40B 50/08 Liquid phase synthesis, i.e. wherein all library building blocks are in liquid phase or in solution during library creation; Particular methods of cleavage from the liquid support
• CPC Class Codes: C40B 60/14 for creating libraries

Abstract

Provided is a method of constructing a sequencing library. The method includes 1) providing a single-stranded DNA fragment from a biological sample; 2) subjecting the single-stranded DNA fragment to whole genomic amplification to obtain a whole genome amplification product; 3) fragmenting the whole genome amplification product using a transposase embedded with two adaptors to obtain a fragmented product with two adaptors respectively at two ends; and 4) amplifying the fragmented product with two adaptors respectively at two ends using a tag sequence and a pair of primers to obtain said sequencing library.

Claims

1. A customized 5184-well plate-based method of constructing a sequencing library in a length ranging from 550 bp to 1000 bp, comprising steps of:

1) providing a single-stranded DNA fragment from a biological sample and distributing the single-stranded DNA fragments extracted from 10 to 500 cells into said 5184-well plate such that a probability of homologous chromosome fragments deriving from both mother and father at the same site in their respective genomes presenting in each well is less than 1%;

2) subjecting the single-stranded DNA fragment to whole genomic amplification to obtain a whole genome amplification product;

3) fragmenting the whole genome amplification product using a transposase embedded with two adaptors to obtain a fragmented product with two adaptors respectively at two ends; and

4) amplifying the fragmented product with two adaptors respectively at two ends using a tag sequence and a pair of primers to obtain said sequencing library,

wherein each well of said 5184-well plate has a volume of 350 nL and an effective volume of 200 nL.

2. The method according to claim 1, wherein the biological sample is derived from a plant, an animal or a microorganism.

3. The method according to claim 1, wherein the step of providing the single-stranded DNA fragment from the biological sample further comprises:

extracting a genomic DNA fragment from the biological sample, wherein the genomic DNA fragment has a length not less than 100 kb; and

subjecting the genomic DNA fragment to denaturation in an alkaline solution at 20°

C. to 30°

C. for 1 minute to 3 minutes to obtain the single-stranded DNA fragment.

4. The method according to claim 3, wherein the genomic DNA fragment is in an amount of 100 pg to 1000 pg.

5. The method according to claim 1, wherein the step of extracting the single-stranded DNA fragment from the biological sample further comprises:

incubating the biological sample in an alkaline solution at 80°

C. to 90°

C. for 1 to 3 minutes to obtain the single-stranded DNA fragment.

6. The method according to claim 1, wherein the whole genome amplification is multiple displacement amplification (MDA).

7. The method according to claim 6, wherein the multiple displacement amplification is carried out by incubation of the single-stranded DNA fragment first at 30°

C. to 37°

C. for 45 minute to 60 minutes and then at 65°

C. for 5 minutes in the presence of random primers.

8. The method according to claim 7, wherein the random primers each have a length of 5 bp to 20 bp.

9. The method according to claim 1, wherein the transposase is embedded with a first adaptor and a second adaptor, and the first adaptor is of a sequence different from that of the second sequence.

10. The method according to claim 9, wherein the first adaptor comprises a first long-chain sequence and a first short-chain sequence, and the first long-chain sequence is composed of a region unpaired with the first short-chain sequence and a region paired with the first short-chain sequence in order from the 5′

end to the 3′

end; and

the second adaptor comprises a second long-chain sequence and a second short-chain sequence, and the second long-chain sequence is composed of a region unpaired with the second short-chain sequence and a region paired with the second short-chain sequence in order from the 5′

end to the 3′

end.

11. The method according to claim 1, wherein the whole genome amplification product is fragmented by incubation of the whole genome amplification product at 50°

C. to 60°

C. for 5 minute to 20 minutes in the presence of the transposase embedded with two adaptors.

12. The method according to claim 1, wherein the fragmented product with two adaptors respectively at two ends has a length in a range of 300 bp to 1000 bp.

13. The method according to claim 10, wherein the tag sequence comprises a first tag sequence and a second tag sequence,

wherein the first tag sequence is composed of a third adaptor, a first random fragment and a first single-stranded DNA sequence in order from the 5′

end to the 3′

end; and

the second tag sequence is composed of a fourth adaptor, a second random fragment and a second single-stranded DNA sequence in order from the 5′

end to the 3′

end,

wherein the first single-stranded DNA sequence is identical to the region unpaired with the first short-chain sequence of the first long-chain sequence of the first adaptor; and

the second single-stranded DNA sequence is identical to the region unpaired with the second short-chain sequence of the second long-chain sequence of the second adaptor.

14. The method according to claim 13, wherein the first random fragment and the second random fragment each have a length of 5 bp to 20 bp.

15. The method according to claim 13, wherein the pair of primers comprise a first primer and a second primer, wherein the first primer is of a sequence is identical or complementary to part of the sequence of the third adaptor;

and the second primer is of a sequence identical or complementary to part of the sequence of the fourth adaptor.

16. The method according to claim 1, further comprising:

sorting the sequencing library by magnetic beads or agarose electrophoresis to obtain the desired sequencing library in the length ranging from 550 bp to 1000 bp.

18. The method according to claim 1, wherein the probability of homologous chromosome fragments derived from both mother and father at the same site in their respective genomes presenting in one same well satisfies the formula below:

17. A method of constructing a sequencing library in a length ranging from 550 bp to 1000 bp using a customized 5184-well plate, comprising:

1) providing a single-stranded DNA fragment from a biological sample;

2) distributing the single-stranded DNA fragments extracted from 10 to 500 cells into said 5184-well plate such that a probability of homologous chromosome fragments deriving from both mother and father at the same site in their respective genomes presenting in each well is less than 1%;

3) subjecting the single-stranded DNA fragment in each well of said 5184-well plate to whole genomic amplification to obtain a whole genome amplification product, wherein a reaction system in each well is in a volume less than 100 nL;

4) fragmenting the whole genome amplification product in each well of said 5184-well plate using a transposase embedded with two adaptors to obtain a fragmented product with two adaptors respectively at two ends; and

5) amplifying the fragmented product with two adaptors respectively at two ends in each well of said 5184-well plate using a tag sequence and a pair of primers to obtain said sequencing library,

wherein the tag sequence comprises a first tag sequence and a second tag sequence,

wherein the first tag sequence is composed of a third adaptor, a first random fragment and a first single-stranded DNA sequence in order from the 5′

end to the 3′

end; and

the second tag sequence is composed of a fourth adaptor, a second random fragment and a second single-stranded DNA sequence in order from the 5′

end to the 3′

end,

wherein the first tag sequence comprises 72 tag sequences containing different said first random fragments respectively, and

the second tag sequence comprises 72 tag sequences containing different said second random fragments respectively,

wherein each well of said 5184-well plate has a volume of 350 nL and an effective volume of 200 nL.