TCR/BCR profiling using enrichment with pools of capture probes
Inventors
Perera, Jason • Harding, Taylor • Mineo, Brittany • Khan, Aly A. • Blidner, Richard • Malinauskas, Jenna L.
Assignees
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Publication Number
US-12129519-B2
Publication Date
2024-10-29
Expiration Date
Abstract
This present disclosure relates to systems, methods, and compositions useful for profiling T cell receptor (TCR) and B cell receptor (BCR) repertoire using next-generation sequencing (NGS) methods. The present disclosure also relates to systems and methods for diagnosing, treating, or predicting infection, disease, medical conditions, therapeutic outcome, or therapeutic efficacy based on the TCR/BCR profile data from a subject in need thereof.
Core Innovation
The invention provides a method of determining the TCR/BCR profile of a patient who has cancer by isolating RNA from a cancerous sample. The method enriches the isolated RNA for TCR/BCR genes using TCR/BCR hybrid-capture probes and enriches for a targeted whole transcriptome panel using transcriptome hybrid-capture probes. The enriched RNA is sequenced to generate sequencing data, which is analyzed to determine the patient’s TCR/BCR profile.
A central aspect is the composition of the hybrid-capture probe sets, where the TCR/BCR hybrid-capture probes comprise a pool of TCR constant region probes, a pool of TCR non-constant region probes, a pool of BCR constant region probes, and a pool of BCR non-constant region probes. In addition, a transcriptome hybrid-capture probe pool is included. The claims further specify relative ratios between the transcriptome hybrid-capture probes and the probe pools, and impose a constraint that 2% or less of the reads in the sequencing data map to TCR/BCR genes.
The invention also provides a method for identifying TCR/BCR non-constant region sequences that are enriched in a cohort of patients with a cancer. RNA is isolated from each patient in the cohort and enriched for TCR/BCR genes using TCR/BCR hybrid-capture probes and enriched for a targeted whole transcriptome panel using transcriptome hybrid-capture probes. Sequencing and analysis determine the TCR/BCR profiles of the patients, and the method identifies TCR/BCR non-constant region sequences enriched in the cohort compared to a control group without the cancer.
Claims Coverage
The document includes three independent claims: determining a patient’s TCR/BCR profile, identifying enriched TCR/BCR non-constant region sequences across a cancer cohort, and determining a cancer patient’s TCR/BCR profile with specified probe-pool ratios and a low TCR/BCR mapping constraint. Across the independent claims, the core inventive elements are RNA isolation, hybrid-capture enrichment with defined probe pools for TCR/BCR genes and a targeted whole transcriptome panel, sequencing to generate sequencing data, and analysis to produce TCR/BCR profiles and enrichment findings.
Hybrid-capture based determination of a patient TCR/BCR profile in cancer
Isolating RNA from a cancerous sample, enriching the RNA for TCR/BCR genes using TCR/BCR hybrid-capture probes and enriching for a targeted whole transcriptome panel using transcriptome hybrid-capture probes, sequencing the enriched RNA to generate sequencing data, and analyzing the sequencing data to determine the TCR/BCR profile of the patient, where the set comprises first to fourth pools for TCR and BCR constant and non-constant region probes and a fifth pool comprising the transcriptome hybrid-capture probes.
Enriched non-constant TCR/BCR sequence identification across a cancer cohort
Isolating RNA from each patient in a cohort, enriching for TCR/BCR genes using TCR/BCR hybrid-capture probes and enriching for a targeted whole transcriptome panel using transcriptome hybrid-capture probes, determining the sequence of the enriched RNA to generate sequencing data, analyzing the sequencing data to determine the TCR/BCR profile of the patients in the cohort, and identifying TCR/BCR non-constant region sequences that are enriched in the cohort as compared to a control group without the cancer, where the hybrid-capture probe set comprises four pools for TCR/BCR constant/non-constant regions and a fifth transcriptome hybrid-capture pool.
Specified probe-pool ratios and low TCR/BCR read mapping in patient TCR/BCR profiling
Isolating RNA from a sample comprising cancer cells, enriching for TCR/BCR genes using TCR/BCR hybrid-capture probes and enriching for a targeted whole transcriptome panel using transcriptome hybrid-capture probes, sequencing the enriched RNA to generate sequencing data, and analyzing the sequencing data to determine the TCR/BCR profile of the patient, where the probe set includes BCR constant, BCR non-constant, TCR constant, and TCR non-constant pools, where the ratio of the transcriptome hybrid-capture probes and the four pools is 10:1:2.5:100:100, and where 2% or less of the reads map to TCR/BCR genes.
Across the independent claims, the patent centers on targeted hybrid-capture probe pools for TCR/BCR gene regions plus transcriptome panel enrichment, followed by sequencing and analysis to determine patient TCR/BCR profiles or to identify enriched non-constant region sequences in a cancer cohort, with explicit probe-pool composition, specified relative ratios, and a low fraction of reads mapping to TCR/BCR genes in the specified profiling method.
Stated Advantages
Not explicitly described in patent.
Documented Applications
Not explicitly described in patent.
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