Compositions and method for measuring and calibrating amplification bias in multiplexed PCR reactions

• US 9,371,558 B2
• Filed: 01/09/2015
• Issued: 06/21/2016
• Est. Priority Date: 05/08/2012
• Status: Active Grant

• Current Assignee: Adaptive Biotechnologies Corp.
• Original Assignee: Adaptive Biotechnologies Corp.
• Inventors: Carlson, Christopher Scott, Robins, Harlan Saul, Livingston, Robert J., Emerson, Ryan O., Sherwood, Anna M.
• Primary Examiner(s): Strzelecka, Teresa E
• Application Number:
  US14/594,007
• Publication Number:
  US 20150203897A1
• Time in Patent Office: 529 Days
• US Class Current: 1/1
• 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 1/6851 Quantitative amplification
• CPC Class Codes: C12Q 1/6881 for tissue or cell typing, e.g. human leukocyte antigen [HLA] probes
• CPC Class Codes: C12Q 2527/143 Concentration of primer or probe
• CPC Class Codes: C12Q 2537/143 Multiplexing, i.e. use of multiple primers or probes in a single reaction, usually for simultaneously analyse of multiple analysis
• CPC Class Codes: C12Q 2545/101 with an internal standard/control
• CPC Class Codes: C12Q 2545/113 with an external standard/control, i.e. control reaction is separated from the test/target reaction
• CPC Class Codes: C12Q 2600/156 Polymorphic or mutational markers
• CPC Class Codes: C12Q 2600/16 Primer sets for multiplex assays
• CPC Class Codes: C12Q 2600/166 Oligonucleotides used as internal standards, controls or normalisation probes

Abstract

Compositions and methods are described for standardizing the DNA amplification efficiencies of a highly heterogeneous set of oligonucleotide primers as may typically be used to amplify a heterogeneous set of DNA templates that contains rearranged lymphoid cell DNA encoding T cell receptors (TCR) or immunoglobulins (IG). The presently disclosed embodiments are useful to overcome undesirable bias in the utilization of a subset of amplification primers, which leads to imprecision in multiplexed high throughput sequencing of amplification products to quantify unique TCR or Ig encoding genomes in a sample. Provided is a composition comprising a diverse plurality of template oligonucleotides in substantially equimolar amounts, for use as a calibration standard for amplification primer sets. Also provided are methods for identifying and correcting biased primer efficiency during amplification.

Claims

1. A method for determining non-uniform nucleic acid amplification potential among members of a set of oligonucleotide primers that is capable of amplifying rearranged nucleic acid molecules encoding one or more adaptive immune receptors in a biological sample from a mammalian subject, the method comprising:

(a) amplifying a composition comprising a plurality of synthetic template oligonucleotides comprising sequences of rearranged nucleic acid molecules encoding one or more adaptive immune receptors and one or more additional unique random polynucleotide sequences using a set of oligonucleotide primers in a single multiplex PCR reaction to obtain a plurality of amplified synthetic template oligonucleotides;

(b) sequencing said plurality of amplified synthetic template oligonucleotides to determine, for each unique synthetic template oligonucleotide comprising said plurality,

(i) a synthetic template oligonucleotide sequence and

(ii) a frequency of occurrence of said synthetic template oligonucleotide sequence; and

(c) comparing a frequency of occurrence of each of said synthetic template oligonucleotide sequences to an expected distribution, wherein a deviation between said frequency of occurrence of said synthetic template oligonucleotide sequences and said expected distribution indicates a non-uniform nucleic acid amplification potential among members of the set of oligonucleotide amplification primers.

2. The method in claim 1, wherein said expected distribution is based on determining predetermined molar ratios of said plurality of synthetic template oligonucleotides comprising said composition.

3. The method of claim 2, wherein said predetermined molar ratios are equimolar.

4. The method in claim 1, wherein said expected distribution is determined based on quantifying frequencies of each unique synthetic template oligonucleotide.

5. The method of claim 1, wherein said expected distribution comprises a uniform amplification level for said plurality of synthetic template oligonucleotides amplified by said set of oligonucleotide primers.

6. The method of claim 1, further comprising adjusting the relative representation of the oligonucleotide primer member in the set of oligonucleotide amplification primers for each member of the set of oligonucleotide primers that exhibits non-uniform amplification potential relative to the expected distribution.

7. The method of claim 6, wherein adjusting comprises:

increasing the relative representation of the member in the set of oligonucleotide primers, thereby correcting non-uniform nucleic acid amplification potential among members of the set of oligonucleotide primers, or decreasing the relative representation of the member in the set of oligonucleotide primers, thereby correcting non-uniform nucleic acid amplification potential among members of the set of oligonucleotide primers.

8. The method of claim 2, further comprising calculating a proportionately increased or decreased frequency of occurrence of the amplified template nucleic acid molecules for each member of the set of oligonucleotide amplification primers that exhibits non-uniform amplification potential relative to the expected distribution, thereby correcting for non-uniform nucleic acid amplification potential among members of the set of oligonucleotide primers.

9. The method of claim 1 wherein each amplified synthetic template nucleic acid molecule is less than 1000, 900, 800, 700, 600, 500, 400, 300, 200, 100, 90, 80 or 70 nucleotides in length.

10. The method of claim 1 wherein said set of oligonucleotide primers does not include oligonucleotide primers that specifically hybridize to a V-region pseudogene or orphon or to a J-region pseudogene or orphon.

11. The method of claim 1 wherein said plurality of synthetic template oligonucleotides each comprise an oligonucleotide sequence of a general formula:

5′

-U1-B1-V-B2-R-B3-J-B4-U2-3′

 

 

[I]

wherein;

(a) V is an oligonucleotide sequence comprising at least 20 and not more than 1000 contiguous nucleotides of an adaptive immune receptor variable (V) region encoding gene sequence, or the complement thereof, and each V comprising a unique V-region oligonucleotide sequence;

(b) J is an oligonucleotide sequence comprising at least 15 and not more than 600 contiguous nucleotides of an adaptive immune receptor joining (J) region encoding gene sequence, or the complement thereof, and each J comprising a unique J-region oligonucleotide sequence;

(c) U1 is either nothing or comprises an oligonucleotide sequence that is selected from (i) a first universal adaptor oligonucleotide sequence and (ii) a first sequencing platform-specific oligonucleotide sequence that is linked to and positioned 5′

to a first universal adaptor oligonucleotide sequence;

(d) U2 is either nothing or comprises an oligonucleotide sequence that is selected from (i) a second universal adaptor oligonucleotide sequence, and (ii) a second sequencing platform-specific oligonucleotide sequence that is linked to and positioned 5′

to a second universal adaptor oligonucleotide sequence;

(e) at least one of B1, B2, B3, and B4 is present and each of B1, B2, B3, and B4 comprises an oligonucleotide comprising a barcode sequence of 3-25 contiguous nucleotides, that uniquely identifies, as a paired combination, (i) the unique V-region oligonucleotide sequence of (a) and (ii) the unique J-region oligonucleotide sequence of (b);

(f) R is either nothing or comprises a restriction enzyme recognition site that comprises an oligonucleotide sequence that is absent from (a)-(e); and

(g) one or more unique random polynucleotide sequences positioned between or within components of formula I.

12. The method of claim 11 wherein the one or more unique random polynucleotide sequences each comprises at least 2, 3, 4, 5, 6, 7, 8, 9, 1,0 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 45, 50, 55, 60, 70, 80, 90, 100, 200, 300, 400, 500 or more contiguous nucleotides.

13. The method of claim 11 wherein the plurality of synthetic template oligonucleotides comprises a number of at least a or at least b unique oligonucleotide sequences, whichever is larger, wherein a is the number of unique adaptive immune receptor V region-encoding gene segments in the subject and b is the number of unique adaptive immune receptor J region-encoding gene segments in the subject, and the composition comprises at least one synthetic template oligonucleotide for each unique V-region oligonucleotide sequence and at least one synthetic template oligonucleotide for each unique J-region oligonucleotide sequence.

14. The method of claim 13, wherein a ranges from 1 to a number of maximum V gene segments in the mammalian genome of the subject.

15. The method of claim 13, wherein b ranges from 1 to a number of maximum J gene segments in the mammalian genome of the subject.

16. The method of claim 13, wherein the plurality of template oligonucleotides comprises at least (a ×

b) unique oligonucleotide sequences, where a is the number of unique adaptive immune receptor V region-encoding gene segments in the mammalian subject and b is the number of unique adaptive immune receptor J region-encoding gene segments in the mammalian subject, and the composition comprises at least one template oligonucleotide for every possible combination of a V region-encoding gene segment and a J region-encoding gene segment.

17. The method of claim 11, wherein J comprises an oligonucleotide sequence comprising a constant region of the adaptive immune receptor J region encoding gene sequence.

18. The method of claim 1, wherein the one or more adaptive immune receptors is selected from the group consisting of TCRB, TCRG, TCRA, TCRD, IGH, IGK, and IGL.

19. The method of claim 11, wherein the V oligonucleotide sequence of (a) encodes a TCRB, TCRG, TCRA, TCRD, IGH, IGK, or IGL receptor V-region polypeptide.

20. The method of claim 11, wherein the J oligonucleotide sequence of (b) encodes a TCRB, TCRG, TCRA, TCRD, IGH, IGK, or IGL receptor J-region polypeptide.

21. The method of claim 11, further comprising a stop codon sequence between V and B2.

22. The method of claim 11, wherein V is an oligonucleotide sequence comprising at least 30 contiguous nucleotides of the adaptive immune receptor V region encoding gene sequence, or the complement thereof.

23. The method of claim 11, wherein V is an oligonucleotide sequence comprising not more than 900, 800, 700, 600 or 500 contiguous nucleotides of an adaptive immune receptor V region encoding gene sequence, or the complement thereof.

24. The method of claim 11, wherein J is an oligonucleotide sequence comprising at least 16 contiguous nucleotides of an adaptive immune receptor J region encoding gene sequence, or the complement thereof.

25. The method of claim 11, wherein J is an oligonucleotide sequence comprising not more than 500 contiguous nucleotides of an adaptive immune receptor J region encoding gene sequence, or the complement thereof.

26. The method of claim 11, wherein each synthetic template oligonucleotide is less than 1000, 900, 800, 700, 600, 500, 400, 300 or 200 nucleotides in length.

27. The method of claim 1 wherein said one or more additional unique random polynucleotide sequences each comprises at least 2 contiguous nucleotides.