biostudies-literatureUnknownYu PNCATS NIH HHSInference from immunological data on cells in the adaptive immune system may benefit from modeling specifications that describe variation in the sizes of various clonal sub-populations. We develop one such specification in order to quantify the effects of surrogate selection assays, which we confirm may lead to an enrichment for amplified, potentially disease-relevant T cell clones. Our specification couples within-clonotype birth-death processes with an exchangeable model across clonotypes. Beyond enrichment questions about the surrogate selection design, our framework enables a study of sampling properties of elementary sample diversity statistics; it also points to new statistics that may usefully measure the burden of somatic genomic alterations associated with clonal expansion. We exabioRxiv : the preprint server for biology2023.07.13.548950https://www.ebi.ac.uk/biostudies/studies/S-EPMC10369934biostudies-literatureSURROGATE SELECTION OVERSAMPLES EXPANDED T CELL CLONOTYPES.PMC10369934UL1 TR002373Albertini RJYu PLian YAlbertini MRNewton MAZuleger CLfalseSURROGATE SELECTION OVERSAMPLES EXPANDED T CELL CLONOTYPES.Inference from immunological data on cells in the adaptive immune system may benefit from modeling specifications that describe variation in the sizes of various clonal sub-populations. We develop one such specification in order to quantify the effects of surrogate selection assays, which we confirm may lead to an enrichment for amplified, potentially disease-relevant T cell clones. Our specification couples within-clonotype birth-death processes with an exchangeable model across clonotypes. Beyond enrichment questions about the surrogate selection design, our framework enables a study of sampling properties of elementary sample diversity statistics; it also points to new statistics that may usefully measure the burden of somatic genomic alterations associated with clonal expansion. We exa2023-01-01T00:00:00Z2023 Jul2025-08-23T03:09:10.393Z2025-08-23T03:09:10.393ZS-EPMC103699343750311810.1101/2023.07.13.548950