Monitoring health and disease status using clonotype profiles

• US 9,416,420 B2
• Filed: 11/08/2013
• Issued: 08/16/2016
• Est. Priority Date: 11/07/2008
• Status: Active Grant

• Current Assignee: Adaptive Biotechnologies Corp.
• Original Assignee: Adaptive Biotechnologies Corp.
• Inventors: Faham, Malek, Willis, Thomas
• Primary Examiner(s): Wilder, Cynthia B
• Application Number:
  US14/075,075
• Publication Number:
  US 20140235454A1
• Time in Patent Office: 1,012 Days
• Field of Search: 435/6.1, 435/91.2
• US Class Current: 1/1
• CPC Class Codes: C12Q 1/6881 for tissue or cell typing, e.g. human leukocyte antigen [HLA] probes
• 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 2600/118 Prognosis of disease development
• CPC Class Codes: C12Q 2600/156 Polymorphic or mutational markers
• CPC Class Codes: C12Q 2600/158 Expression markers
• CPC Class Codes: C12Q 2600/16 Primer sets for multiplex assays

Abstract

There is a need or improved methods for determining the diagnosis and prognosis of patients with conditions, including autoimmune disease and cancer, especially lymphoid neoplasms, such as lymphomas and leukemias. Provided herein are methods for using DNA sequencing to identify personalized, or patient-specific biomarkers in patients with lymphoid neoplasms, autoimmune disease and other conditions. Identified biomarkers can be used to determine and/or monitor the disease state for a subject with an associated lymphoid disorder or autoimmune disease or other condition. In particular, the invention provides a sensitive method for monitoring lymphoid neoplasms that undergo clonal evolutions without the need to development alternative assays for the evolved or mutated clones serving as patient-specific biomarkers.

Claims

1. A method of simultaneously measuring lymphocyte numbers and cellular clonotype expression levels in a sample, the method comprising the steps of:

extracting RNA from a sample comprising T cells and/or B cells;

reverse transcribing the extracted RNA to form recombined cDNA molecules capable of encoding immune receptor molecules;

extracting genomic DNA comprising recombined DNA molecules capable of encoding immune receptor molecules from the sample and adding a known quantity of an exogenous internal standard to the extracted genomic DNA,

spatially isolating individual molecules of the exogenous internal standard and recombined DNA molecules from the extracted genomic DNA on a solid support;

sequencing spatially isolated individual molecules of the exogenous internal standard and recombined DNA molecules from the extracted genomic DNA to determine a number of lymphocytes in the sample by comparing the number of sequence reads of the exogenous internal standard and the number of sequence reads of recombined DNA molecules from the genomic DNA;

spatially isolating individual recombined cDNA molecules on a solid support;

sequencing spatially isolated individual recombined cDNA molecules to obtain sequence reads corresponding to cellular expression levels of clonotypes for lymphocytes of the sample; and

determining cellular clonotype expression levels in lymphocytes of the sample by comparing the number of sequence reads determined from the spatially isolated individual recombined DNA molecules from the genomic DNA and the number of sequence reads determined from the spatially isolated individual recombined cDNA molecules from RNA for each clonotype.

2. The method of claim 1 wherein said sample is a peripheral blood sample having a defined volume and said step of determining includes determining said numbers of said lymphocytes in said sample by counting said clonotypes determined from sequence reads of said isolated individual recombined DNA molecules obtained from said genomic DNA.

3. The method of claim 1 wherein said step of determining said cellular clonotype expression levels includes dividing said number of sequence reads determined from said isolated individual recombined cDNA molecules from said RNA by said number of sequence reads determined from said isolated individual recombined DNA molecules obtained from said genomic DNA for each clonotype.

4. The method of claim 1 wherein said step of sequencing said spatially isolated individual recombined cDNA molecules includes labeling each of said spatially isolated individual recombined cDNA molecules with a first label indicating its RNA origin and wherein said step of sequencing said spatially isolated individual recombined DNA molecules from said genomic DNA includes labeling each of said spatially isolated individual recombined DNA molecules with a second label indicating its genomic DNA origin such that he first label is distinguishable from the second label.

5. The method of claim 1 wherein said sample comprises with ninety-nine percent probability every lymphocyte expressing a distinct clonotype having a frequency of 0.01 percent or greater.

6. The method of claim 5 wherein said sample comprises B cells.

7. The method of claim 5 wherein said sample comprises T cells.

8. The method of claim 1 wherein said sample comprises at least 10,000 T cells and wherein each of said individual recombined DNA molecules and said individual recombined cDNA molecules comprises a VDJ region.

9. The method of claim 1 wherein said sample comprises at least 10,000 B cells and wherein each of said individual recombined DNA molecules and said individual recombined cDNA molecules comprises a VDJ region.

10. The method of claim 4 wherein said first label and said second label are oligonucleotide tags.

11. A method of measuring lymphocyte numbers in a sample, the method comprising the steps of:

extracting DNA comprising recombined DNA molecules capable of encoding immune receptor molecules from a sample comprising T cells and/or B cells,

attaching an oligonucleotide tag to each recombined DNA molecule of the extracted DNA to form tagged polynucleotides;

spatially isolating individual molecules of the tagged polynucleotides;

sequencing by synthesis spatially isolated individual molecules of the tagged polynucleotides to obtain sequence reads thereof;

determining tagged polynucleotide sequences from the sequence reads; and

measuring the number of lymphocytes in the sample from the number of unique oligonucleotide tags among the tagged polynucleotide sequences.

12. The method of claim 11 wherein said recombined DNA molecules comprise T cell receptor genes or immunoglobulin genes.

13. The method of claim 12 wherein said recombined DNA molecules comprise VDJ regions.

14. The method of claim 11 wherein said sample comprises with ninety-nine percent probability every lymphocyte expressing a distinct clonotype having a frequency of 0.01 percent or greater.

15. A method of measuring lymphocyte numbers in a sample, the method comprising the steps of:

extracting genomic DNA comprising recombined DNA molecules capable of encoding immune receptor molecules from a sample of a defined volume comprising T cells and/or B cells and adding known amounts of one or more exogenous internal standards to the extracted genomic DNA;

spatially isolating individual molecules of the one or more exogenous internal standards and the recombined DNA molecules;

sequencing by synthesis spatially isolated individual molecules of the one or more exogenous internal standards and the recombined DNA molecules of said cells to provide sequence reads of the one or more exogenous internal standards and sequence reads of the recombined DNA molecules;

estimating lymphocyte numbers in the sample by counting relative numbers of sequence reads of each recombined DNA molecule to sequence reads of the one or more exogenous internal standard.

16. The method of claim 15 wherein said sample is a peripheral blood sample having a defined volume.

17. The method of claim 15 wherein said sample comprises with ninety-nine percent probability every lymphocyte expressing a distinct clonotype having a frequency of 0.01 percent or greater.

18. The method of claim 15 wherein said recombined DNA molecules comprise VDJ regions and said sample comprises at least 10,000 T cells.

19. The method of claim 15 wherein said recombined DNA molecules comprise VDJ regions and said sample comprise at least 10,000 B cells.