RARE CLONOTYPES AND USES THEREOF

• US 20130196328A1
• Filed: 03/15/2013
• Published: 08/01/2013
• Est. Priority Date: 11/07/2008
• Status: Active Grant

• Current Assignee: Adaptive Biotechnologies Corp.
• Original Assignee: Sequenta LLC
• Inventors: Faham, Malek, Moorhead, Martin, Pepin, Francois
• Granted Patent: US 9,528,160 B2
• Time in Patent Office: Days
• US Class Current: 435/6.11
• CPC Class Codes: C12Q 1/6883 for diseases caused by alterations of genetic material
• CPC Class Codes: C12Q 1/6886 for cancer immunoassay for cancer G01N33/574
• CPC Class Codes: C12Q 2600/158 Expression markers

Abstract

The invention is directed to a method of selecting disease-correlated clonotypes that have a reduced likelihood of producing a false positive signal of relapse when, used to monitor minimal residual disease. In accordance with the invention, candidate correlating clonotype are obtained from a patient, the rarity of each is determined either by comparison with a clonotype database or a clonotype model, and one or more of the rarest of such clonotypes are used to monitor the minimal residual disease.

Claims

1. A method of selecting one or more patient-specific clonotypes correlated with a lymphoid neoplasm for monitoring a minimal residual disease thereof the method comprising the steps of:

(a) obtaining a sample from the patient, comprising T-cells and/or B-cells;

(b) amplifying molecules of nucleic acid from the T-cells and/or B-cells of the sample, the molecules of nucleic acid comprising recombined DMA sequences from. T-cell receptor genes or immunoglobulin genes;

(c) sequencing the amplified molecules of nucleic acid to form a clonotype profile;

(d) comparing clonotypes from the clonotype profile to clonotypes of a clonotype database containing clonotypes from at least one individual other than the patient to determine a presence, absence and/or level in the clonotype database of each clonotype from the clonotype profile; and

(e) selecting the one or more patient-specific clonotypes for monitoring the minimal residual disease which axe each correlated with the lymphoid neoplasm and which are each absent from the clonotype database or at a level in the clonotype database below a predetermined frequency.

2. The method of claim 1 wherein said clonotype database contains clonotype profile data from each individual from a population of individuals.

3. The method of claim 2 wherein said said population comprises at least 10 individuals.

4. The method of claim 2 wherein, said clonotype profile data from each, individual comprises nucleotide sequences of at least 10⁴ clonotypes.

5. The method of claim 1 wherein said first and. second clonotype profiles each comprise at least 10⁴ clonotypes.

6. The method of claim 1 wherein said clonotypes are each 25 to 400 nucleotide sequences encoding a segment of an immune receptor or immune receptor component selected from the group consisting of a VDJ rearrangement of IgH, a DJ rearrangement of IgH, a VJ rearrangement, of IgK, a VJ rearrangement of IgL, a VDJ rearrangement of TCRβ

, a DJ rearrangement of TCRβ

, a VJ rearrangement of TCRα

, a VJ rearrangement of TCRγ

, a VDJ rearrangement of TCRδ

, and a VD rearrangement of TCRδ

.

7. The method of claim 1 wherein said predetermined frequency of said clonotype in said clonotype database is less than 10⁻

6.

8. The method of claim 1 wherein said step of comparing includes counting said clonotype in said clonotype profile as present in said clonotype database if a clonotype to said clonotype database is a member of the same clan as said clonotype in said clonotype profile.

9. The method of claim 8 wherein said clonotype of said clonotype database is in the same clan as said clonotype of said clonotype profile if (a) such clonotype is at least ninety percent identical to said clonotype of said clonotype profile;

(b) such clonotype and said clonotype from said clonotype profiles each comprise recombined sequences from immunoglobulin heavy chain and are related by a VH replacement;

(c) such clonotype and said clonotype from said clonotype profile have identically mutated V region and J region but have a different NDN region, or (d) such clonotype and said clonotype from said clonotype profiles each comprise recombined sequences from immunoglobulin heavy chain and are related by hypermutation.

10. A method for determining whether a tissue sample comprising T cells and/or B cells from a first individual contaminates a tissue sample comprising T cells and/or B cells from a second individual, the method comprising the steps of:

generating a first clonotype profile from nucleic acid of the tissue sample from the first individual;

generating a second clonotype profile from nucleic acid of the tissue sample from the second individual;

comparing clonotypes from the first and second clonotype profiles to clonotypes of a clonotype database containing clonotypes from at least one individual other than the first and second individual to determine a presence, absence and/or level in the clonotype database of each clonotype from the first and second clonotype profiles which are each absent from the clonotype database or at a level in the clonotype database below a predetermined threshold; and

classifying the tissue sample from the first individual as contaminated by nucleic acids from the second individual whenever any of such determined clonotypes are present in both the first and second clonotype profiles.

11. A method of selecting one or more pattern-specific clonotypes correlated with a lymphoid neoplasm for monitoring a minimal residual disease thereof, the method comprising the steps of:

(a) obtaining a sample from the patient comprising T-cells and/or B-cells;

(b) amplifying molecules of nucleic acid front the T-cells and/or B-cells of the sample, the molecules of nucleic acid comprising recombined DNA sequences from T-cell receptor genes or immunoglobulin genes;

(c) sequencing the amplified molecules of nucleic acid to form a clonotype profile;

(d) comparing constituent regions of each clonotypes from, the clonotype profile to corresponding regions of a clonotype model to determine expected frequencies of occurrence for each constituent region; and

(e) selecting the one or more patient-specific clonotypes for monitoring the minimal residual disease which are each correlated with the lymphoid neoplasm and whose product of frequencies of occurrence are below a predetermined frequency.