METHODS FOR TAGGING AND AMPLIFYING RNA TEMPLATE MOLECULES FOR PREPARING SEQUENCING LIBRARIES

• US 20180163201A1
• Filed: 12/12/2017
• Published: 06/14/2018
• Est. Priority Date: 12/12/2016
• Status: Abandoned Application

• Current Assignee: GRAIL, Inc.
• Original Assignee: GRAIL, Inc.
• Inventors: Larson, Matthew
• Application Number:
  US15/839,386
• Publication Number:
  US 20180163201A1
• Time in Patent Office: Days
• CPC Class Codes: C12N 15/1096 cDNA Synthesis; Subtracted cDNA library construction, e.g. RT, RT-PCR
• CPC Class Codes: C12Q 1/6844 Nucleic acid amplification reactions
• CPC Class Codes: C12Q 1/6853 using modified primers or templates
• CPC Class Codes: C12Q 1/6855 Ligating adaptors
• CPC Class Codes: C12Q 2521/107 RNA dependent DNA polymerase,(i.e. reverse transcriptase)
• CPC Class Codes: C12Q 2521/131 Terminal transferase
• CPC Class Codes: C12Q 2521/501 Ligase
• CPC Class Codes: C12Q 2525/155 incorporating/generating a new priming site
• CPC Class Codes: C12Q 2531/119 Strand displacement amplification [SDA]
• CPC Class Codes: C12Q 2533/107 Probe or oligonucleotide ligation
• CPC Class Codes: C12Y 207/07049 RNA-directed DNA polymerase (2.7.7.49), i.e. telomerase or reverse-transcriptase
• CPC Class Codes: C12Y 605/01003 RNA ligase (ATP) (6.5.1.3)
• CPC Class Codes: C40B 40/06 Libraries containing nucleotides or polynucleotides, or derivatives thereof

Abstract

Aspects of the invention include methods for preparing sequencing libraries comprising a plurality of RNA molecules. In some embodiments, the subject methods comprise sequencing at least a portion of a sequencing library to obtain sequencing data or sequence reads from a test sample (e.g., a biological sample from a subject).

Claims

1. A method for preparing a sequencing library from a test sample comprising RNA, the method comprising the steps:

(a) obtaining a test sample comprising RNA sequences, and purifying the RNA sequences from the test sample;

(b) synthesizing first complementary DNA (cDNA) strands based on the RNA sequences and C-tailing 3′

-end of cDNA strand;

(c) annealing a complementary template switching oligonucleotide to the C-tail of the cDNA and ligating the complementary template switching oligonucleotide to the 5′

-ends of the RNA sequences to produce RNA templates; and

(d) synthesizing a plurality of cDNA strands from the RNA templates using a strand-displacement reverse transcriptase.

3. The method of any one of the preceding claims, wherein the test sample comprises cell-free RNA (cfRNA).

4. The method of claim 3, wherein the cfRNA-comprising test sample is from a whole blood, a blood fraction, plasma, serum, urine, fecal, saliva, a tissue biopsy, pleural fluid, pericardial fluid, cerebral spinal fluid, or peritoneal fluid test sample.

5. The method of any one of the preceding claims, wherein the one or more RNA sequences are fragmented after purification of the one or more RNA sequences from the test sample.

6. The method of claim 1, wherein the first cDNA strand synthesis (step (b)) utilizes a first primer, and wherein the second cDNA strand synthesis (step (d)) utilizes a second primer.

7. The method of any one of the preceding claims, wherein the first and/or second RNA primers are random hexamer primers.

8. The method of any one of the preceding claims, wherein the first and/or second RNA primers are poly T primers.

9. The method of any one of the preceding claims, wherein the reverse transcriptase is MMLV reverse transcriptase.

12. The method of any one of the preceding claims, wherein the ligation step utilizes T4 RNA ligase.

16. The method of claim 1, wherein reverse complement DNA strands are synthesized from the plurality of cDNA strands obtained in step (d) to generate a dsDNA sequencing library.

18. The method of claims 16-17, wherein the DNA library is sequenced.

19. The method of claim 18, wherein the UMI or unique sequence tag are used for error correction.

26. The method of any one of the preceding claims, wherein the reverse transcriptase is MMLV reverse transcriptase.

2. A method for preparing a sequencing library from a test sample comprising RNA, the method comprising the steps:

(a) obtaining a test sample comprising one or more RNA sequences, and purifying the one or more RNA sequences from the test sample;

(b) annealing a first RNA primer to the one or more RNA sequences;

(c) extending the first RNA primer in a first nucleic acid extension reaction using reverse transcriptase, wherein the reverse transcriptase comprises reverse transcription and terminal transferase activities, to generate a plurality of DNA sequences complementary to the one or more RNA templates, and wherein the complementary DNA (cDNA) sequences further comprise a plurality of non-templated bases at the 3′

-end of the cDNA sequences;

(d) annealing a complementary nucleic acid sequence to the non-templated bases at the 3′

-end of the cDNA sequence, wherein the complementary nucleic acid sequence further comprises a unique molecular identifier (UMI) or a unique sequence tag;

(e) ligating the complementary nucleic acid sequence to the 5′

-end of the one or more RNA sequences to generate one or more RNA templates, wherein the one or more RNA templates comprise the original one or more RNA sequences covalently linked to the complementary nucleic acid sequence comprising the UMI or unique sequence tag;

(f) annealing one or more second RNA primers to the one or more RNA template; and

(g) extending the one or more second RNA primers in a second nucleic acid extension reaction using a strand-displacement reverse transcriptase to generate a plurality of DNA sequence complementary to the one or more RNA templates, wherein the plurality of complementary DNA (cDNA) sequences each comprise the complementary DNA sequence and a UMI or unique sequence tag.

10. The method of claim 2, wherein the terminal transferase activity adds a poly-C tail to the 3′

-end of the cDNA sequences in step (c).

11. The method of claim 2, complementary nucleic acid sequence to the non-templated bases at the 3′

-end of the cDNA sequence in step (d) further comprises a universal primer sequence for initiating second strand cDNA synthesis.

13. The method of claim 2, wherein steps (b) through (g) are carried out in a single reaction step utilizing a reaction mixture.

14. The method of claim 13, wherein the reaction mixture comprises a strand-displacement reverse transcriptase and T4 RNA ligase.

15. The method of claim 14, wherein the reaction mixture further comprises T4 polynucleotide kinase.

17. The method of claim 2, wherein reverse complement DNA strands are synthesized from the plurality of cDNA strands obtained in step (g) to generate a dsDNA sequencing library.

20. A method for preparing a sequencing library from a test sample comprising RNA, the method comprising the steps:

(a) obtaining a test sample comprising one or more RNA sequences, and purifying the one or more RNA sequences from the test sample;

(b) annealing a first RNA primer to the one or more RNA sequences;

(c) extending the first RNA primer in a first nucleic acid extension reaction using a reverse transcriptase, wherein the reverse transcriptase comprises reverse transcription and terminal transferase activities, to generate a plurality of DNA sequences complementary to the one or more RNA templates, wherein the terminal transferase activity adds a cytosine (C) tail to the 3′

-end of the complementary DNA (cDNA) sequences;

(d) annealing a template switching oligonucleotide to the 3′

-cytosine tail of the cDNA sequence, wherein the template switching oligonucleotide sequence further comprises a unique molecular identifier (UMI) or a unique sequence tag;

(e) ligating the template switching oligonucleotide to the 5′

-end of the one or more RNA sequences with T4 RNA ligase to generate one or more RNA templates, wherein the RNA templates comprise the original one or more RNA sequences covalently linked to the template switching oligonucleotide and the UMI or unique sequence tag;

(f) annealing a plurality of second RNA primers to the one or more RNA templates; and

(g) extending the plurality of second RNA primers in a second nucleic acid extension reaction using a strand-displacement reverse transcriptase to generate a plurality of DNA sequence complementary to the one or more RNA templates, wherein the plurality of complementary DNA (cDNA) each comprise the complementary DNA sequence and a UMI or unique sequence tag.

21. The method of claim 20, wherein the test sample comprises cell-free RNA (cfRNA).

22. The method of claim 21, wherein the cfRNA-comprising test sample is from a whole blood, a blood fraction, plasma, serum, urine, fecal, saliva, a tissue biopsy, pleural fluid, pericardial fluid, cerebral spinal fluid, or peritoneal fluid test sample.

23. The method of claim 20, wherein the one or more RNA sequences are fragmented after purification of the one or more RNA sequences from the test sample.

24. The method of claim 20, wherein the first and/or second RNA primers are random hexamer primers.

25. The method of claim 20, wherein the first and/or second RNA primers are poly T primers.

27. The method of claim 20, wherein steps (b) through (g) are carried out in a single reaction step.

28. The method of claim 20, wherein complementary DNA strands are synthesized from the plurality of cDNA strands obtained in step (g) to generate a dsDNA sequencing library.

29. The method of claim 28, wherein the DNA library is sequenced.

30. The method of claim 29, wherein the UMI or unique sequence tag are used for error correction.