Monitoring health and disease status using clonotype profiles

摘要

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.

主权项

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.