Monitoring health and disease status using clonotype profiles
First Claim
1. A method of determining the likelihood that a lymphoid neoplasm in a patient with defined cancer clonotypes has acquired new genetic changes comprising the steps of:
- (a) determining a clonotype profile from recombined DNA sequences in T-cells and/or B-cells comprising the steps of;
(i) amplifying molecules of recombined nucleic acids from a patient sample comprising T-cells and/or B-cells in a multiplex polymerase chain reaction (PCR);
(ii) spatially isolating individual molecules of the amplified recombined nucleic acid on a solid support;
(iii) sequencing by synthesis the spatially isolated individual molecules of recombined nucleic acid to provide sequence reads and identifying clonotypes therefrom to form a clonotype profile; and
(b) detecting from said clonotype profile the presence of one or more evolved clonotypes from the patient, wherein said evolved clonotypes comprise previously unrecorded clones that are at least 90% homologous to said defined cancer clonotypes.
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Abstract
There is a need for 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.
395 Citations
28 Claims
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1. A method of determining the likelihood that a lymphoid neoplasm in a patient with defined cancer clonotypes has acquired new genetic changes comprising the steps of:
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(a) determining a clonotype profile from recombined DNA sequences in T-cells and/or B-cells comprising the steps of; (i) amplifying molecules of recombined nucleic acids from a patient sample comprising T-cells and/or B-cells in a multiplex polymerase chain reaction (PCR); (ii) spatially isolating individual molecules of the amplified recombined nucleic acid on a solid support; (iii) sequencing by synthesis the spatially isolated individual molecules of recombined nucleic acid to provide sequence reads and identifying clonotypes therefrom to form a clonotype profile; and (b) detecting from said clonotype profile the presence of one or more evolved clonotypes from the patient, wherein said evolved clonotypes comprise previously unrecorded clones that are at least 90% homologous to said defined cancer clonotypes. - View Dependent Claims (2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14)
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15. A method of determining the likelihood that a lymphoid neoplasm in a patient with defined cancer clonotypes has acquired new genetic changes comprising the steps of:
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(a) determining a clonotype profile from nucleic acid sequences in T-cells and/or B-cells comprising the steps of; (i) reverse transcribing RNA obtained from a patient sample comprising T cells and/or B-cells to obtain cDNA encoding rearranged immune receptors; (ii) amplifying cDNA encoding rearranged immune receptors in a multiplex polymerase chain reaction (PCR); (iii) spatially isolating individual molecules of the amplified cDNA encoding rearranged immune receptors on a solid surface; (iv) sequencing by synthesis the individual molecules the amplified cDNA encoding rearranged immune receptors to provide sequence reads and identifying clonotypes therefrom to form a clonotype profile; and (b) detecting from said clonotype profile the presence of one or more evolved clonotypes from the patient wherein a evolved clonotype comprises a previously unrecorded clone that is at least 90% homologous to said defined cancer clonotypes of the patient. - View Dependent Claims (16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28)
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Specification