Compositions and methods for intramolecular nucleic acid rearrangement

Patent metadata

Field	Value
Publication number	US-9410150-B2
Application number	US-201514939728-A
Country	US
Kind code	B2
Filing date	Nov 12, 2015
Priority date	Aug 20, 2009
Publication date	Aug 9, 2016
Grant date	Aug 9, 2016

Abstract

Aspects of the present invention are drawn to processes for moving a region of interest in a polynucleotide from a first position to a second position with regard to a domain within the polynucleotide, also referred to as a “reflex method”. In certain embodiments, the reflex method results in moving a region of interest into functional proximity to specific domain elements present in the polynucleotide (e.g., primer sites and/or multiplex identifier). Compositions, kits and systems that find use in carrying out the reflex processes described herein are also provided.

First claim

That which is claimed is:

1. A composition comprising:
a) a first plurality of different segments of DNA from a first sample, wherein the first plurality of different segments of DNA are derived from a first nucleic acid molecule of a locus in genomic DNA and wherein each of said first plurality of different segments is appended to a first sequence tag; and
b) a second plurality of different segments of DNA from the first sample, wherein the second plurality of different segments of DNA are derived from a second nucleic acid molecule of the locus and wherein each of said second plurality of different segments is appended to a second sequence tag and said first sequence tag and said second sequence tag are different.

2. The composition of claim 1 , wherein the first and second pluralities of different segments are in a mixture.

3. The composition of claim 1 , wherein said genomic DNA is mammalian genomic DNA.

4. The composition of claim 3 , wherein said mammalian genomic DNA is human genomic DNA.

5. The composition of claim 1 , wherein the segments of a) and b) are in the range of 100 to 5,000 bp in length.

6. The composition of claim 1 , wherein the segments of a) and b) are 400 bp or less in length.

7. The composition of claim 1 , wherein:
the first plurality of different segments are distributed along the first nucleic acid molecule; and
the second plurality of different segments are distributed along the second nucleic acid molecule.

8. The composition of claim 1 , wherein:
substantially all of the first nucleic acid molecule is represented in the first plurality of segments; and
substantially all of the second nucleic acid molecule is represented in the second plurality of segments.

9. The composition of claim 1 , further comprising:
c) a third plurality of different segments of DNA, wherein:
the third plurality of different segments of DNA are derived from a third nucleic acid molecule of the locus,
each of said first plurality of segments is appended to a third sequence tag; and
the third sequence tag is different to the first and second sequence tags.

10. The composition of claim 1 , wherein the first plurality of different segments and the second plurality of different segments comprise one or more of an amplification primer sequence and a sequencing primer sequence appended thereto.

11. The composition of claim 1 , wherein the first and second sequence tags are in the range of 2 to 100 nucleotide in length.

12. The composition of claim 1 , wherein the first plurality of different segments the second plurality of different segments further comprise a multiplex identifier (MID) sequence that identifies the source of the segments of DNA.

13. The composition of claim 12 , wherein the MID sequence identifies an individual person, a tissue, a cell, or a time point.

14. The composition of claim 1 , wherein the first and/or second nucleic acid molecules contain at least two polymorphisms that are linked.

15. The composition of claim 1 , the first and second nucleic acid molecules are from two homologous chromosomes.

16. The composition of claim 1 , wherein the first and second nucleic acid molecules are from a viral genome.

17. The composition of claim 1 , wherein the first and second nucleic acid molecules are obtained from a patient.

18. The composition of claim 1 , wherein the first and second nucleic acid molecules are obtained from a culture of cells.

19. The composition of claim 1 , wherein the first and second nucleic acid molecules are obtained from a single cell.

Assignees

• 10X Genomics Inc

Inventors

• Brenner Sydney
• Mikawa Gi
• Osborne Robert
• Slatter Andrew

Classifications

• C12N15/1065 Primary

  Preparation or screening of tagged libraries, e.g. tagged microorganisms by STM-mutagenesis, tagged polynucleotides, gene tags · CPC title

• C12Q1/6806

  Preparing nucleic acids for analysis, e.g. for polymerase chain reaction [PCR] assay (C12Q1/6804 takes precedence) · CPC title

• C12Q1/6874 Primary

  involving nucleic acid arrays, e.g. sequencing by hybridisation · CPC title

• C12Q1/686

  Polymerase chain reaction [PCR] · CPC title

• C12Q1/6855 Primary

  Ligating adaptors · CPC title