Compositions and methods for accurately identifying mutations

• US 10,450,606 B2
• Filed: 06/30/2016
• Issued: 10/22/2019
• Est. Priority Date: 02/17/2012
• Status: Active Grant

• Current Assignee: Fred Hutchinson Cancer Center
• Original Assignee: Fred Hutchinson Cancer Research Center (Fred Hutchinson Cancer Research Center|Argus Genetics|Mars)
• Inventors: Bielas, Jason H.
• Primary Examiner(s): Zhang, Kaijiang
• Application Number:
  US15/199,784
• Publication Number:
  US 20160326578A1
• Time in Patent Office: 1,209 Days
• Field of Search: None
• CPC Class Codes: C12N 15/10 Processes for the isolation, preparation or purification of DNA or RNA chemical preparation of DNA or RNA C07H21/00; preparation of non-structural polynucleotides from microorganisms or with enzymes C12P19/34
• CPC Class Codes: C12N 15/1065 Preparation or screening of tagged libraries, e.g. tagged microorganisms by STM-mutagenesis, tagged polynucleotides, gene tags
• CPC Class Codes: C12N 15/1093 General methods of preparing gene libraries, not provided for in other subgroups
• CPC Class Codes: C12N 15/70 Vectors or expression systems specially adapted for E. coli
• CPC Class Codes: C12N 15/81 for yeasts
• CPC Class Codes: C12N 15/85 for animal cells
• CPC Class Codes: C12Q 1/6827 for detection of mutation or polymorphism
• CPC Class Codes: C12Q 1/6869 Methods for sequencing
• CPC Class Codes: C12Q 1/6874 involving nucleic acid arrays, e.g. sequencing by hybridisation
• CPC Class Codes: C12Q 2535/119 Double strand sequencing
• CPC Class Codes: C12Q 2535/122 Massive parallel sequencing
• CPC Class Codes: C40B 40/08 Libraries containing RNA or DNA which encodes proteins, e.g. gene libraries
• CPC Class Codes: C40B 50/06 Biochemical methods, e.g. using enzymes or whole viable microorganisms
• CPC Class Codes: Y02E 50/10 Biofuels, e.g. bio-diesel

Abstract

The present disclosure provides compositions and methods for accurately detecting mutations by uniquely tagging double stranded nucleic acid molecules with dual cyphers such that sequence data obtained from a sense strand can be linked to sequence data obtained from an anti-sense strand when sequenced, for example, by massively parallel sequencing methods.

Claims

1. A method for accurately detecting a true mutation in a nucleic acid molecule, comprising:

amplifying a collection of double-stranded nucleic acids comprising a plurality of target nucleic acid molecules and a plurality of double-stranded cyphers, wherein the double-stranded nucleic acids have a formula of X^a—

Y—

X^b (in 5′

to 3′

order), wherein;

(a) X^a comprises a first cypher;

(b) Y comprises a target nucleic acid molecule, and

(c) X^b comprises a second cypher,

wherein each of the plurality of cyphers comprises an exogenous polynucleotide ranging from about 5 nucleotides to about 50 nucleotides in length, wherein each strand of the plurality of target nucleic acid molecules and plurality of double-stranded cyphers are amplified;

sequencing each amplified strand of the plurality of target nucleic acid molecules and plurality of cyphers to obtain sequencing reads for each strand of the plurality of target nucleic acid molecules and the plurality of cyphers;

grouping sequencing reads from both strands of a target nucleic acid molecule comprising an identical first and second cypher pair; and

detecting the true mutation over a background rate of artifact mutations, wherein the true mutation is a mutation detected in both strands of a target nucleic acid molecule.

2. The method of claim 1 wherein the plurality of cyphers each have the same number of nucleotides and comprise a length of about 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, or 20 nucleotides.

3. The method of claim 1, wherein the target nucleic acid molecule of Y comprises from about 10 nucleotides to about 10,000 nucleotides or from about 100 nucleotides to about 1,000 nucleotides.

4. The method of claim 1, wherein the amplifying is by bridge amplification, emulsion amplification, nano-ball amplification, or PCR amplification.

5. The method of claim 1, wherein the sequencing is sequencing by synthesis, pyrosequencing, reversible dye-terminator sequencing or polony sequencing.

6. The method of claim 1, wherein the sequence of one strand of a target nucleic acid molecule associated with the first cypher aligned with the sequence of the complementary strand associated with the second cypher results in a measureable sequencing error rate ranging from about 10⁻

6 to about 10<sup>−

8</sup>.

7. The method of claim 1, comprising generating a consensus sequence for the grouped sequencing reads.

8. The method of claim 7, wherein generating the consensus sequence comprises computationally eliminating mutations arising during amplifying or during sequencing.

9. The method of claim 1, wherein each target nucleic acid molecule in the collection of double-stranded nucleic acids library is associated with a unique pair of double-stranded first and second cyphers.

10. The method of claim 1, comprising aligning sequencing reads of complementary strands of the same target nucleic acid molecule to detect mutations arising during amplifying or during sequencing.

11. The method of claim 1, wherein the double-stranded sequence of the X^a cypher for each target nucleic acid molecule is different from the double-stranded sequence of the X^b cypher.

12. The method of claim 11, wherein none of the double-stranded sequences of the X^a cypher is the same as the double-stranded sequence of any other X^a cypher, wherein none of the double-stranded sequences of the X^b cypher is the same as the double-stranded sequence of any other X^b cypher, and wherein none of the double-stranded sequences of the X^a cypher and the X^b cypher are the same.

13. The method of claim 1, wherein the double-stranded X^a cypher is identical to the double-stranded X^b cypher for one or more target nucleic acid molecules, provided that the combination of double-stranded cyphers for each target nucleic acid molecule is different.

14. The method of claim 1, wherein detecting the true mutation comprises sequencing the plurality of target nucleic acid molecules with an error rate ranging from about 10⁻

6 to about 10<sup>−

8</sup>.

15. The method of claim 1, wherein detecting the true mutation comprises simultaneously sequencing a plurality of different target nucleic acid molecules with an error rate of 5×

10<sup>−

6</sup> or less, 10<sup>−

6</sup> or less, 5×

10<sup>−

7</sup> or less, 10<sup>−

8</sup> or less, 5×

10<sup>−

8</sup> or less, or 10<sup>−

8</sup> or less.

16. The method of claim 1, wherein detecting the true mutation comprises sequencing a single target nucleic acid molecule in depth with an error rate of 5×

10<sup>−

7</sup> or less, 10<sup>−

7</sup> or less, 5×

10<sup>−

8</sup> or less, or 10<sup>−

8</sup> or less.

17. The method of claim 1, wherein the first and/or second cyphers are random cyphers.

18. The method of claim 1, wherein the first and/or second cyphers are cataloged cyphers.

19. The method of claim 1, wherein the first and/or second cyphers are cataloged random cyphers.

20. The method of claim 1, wherein the sequencing reads do not cover the entire sequence of a double-stranded target nucleic acid molecule.

21. The method of claim 20, wherein none of the double-stranded sequences of the X^a cypher is the same as the double-stranded sequence of any other X^a cypher, wherein none of the double-stranded sequences of the X^b cypher is the same as the double-stranded sequence of any other X^b cypher, and wherein none of the double-stranded sequences of the X^a cypher and the X^b cypher are the same.

22. The method of claim 20, comprising linking sequencing reads obtained from one end of the double-stranded target molecule to sequencing reads obtained from the opposite end of the same double-stranded target molecule.

23. The method of claim 1, wherein the plurality of target nucleic acid molecules comprise a target nucleic acid molecule derived from a circulating tumor cell (CTC), a circulating tumor mitochondrial DNA (ctmtDNA), or a viral DNA.

24. The method of claim 1, wherein a true mutation is a mutation detected in all or substantially all sequencing reads from both strands of the target nucleic acid molecule.

25. The method of claim 1, wherein the target nucleic acid molecules are original double-stranded nucleic acid molecules from a sample of a subject.