Quantification of HTLV-1 clonality and TCR diversity.

ABSTRACT: Estimation of immunological and microbiological diversity is vital to our understanding of infection and the immune response. For instance, what is the diversity of the T cell repertoire? These questions are partially addressed by high-throughput sequencing techniques that enable identification of immunological and microbiological "species" in a sample. Estimators of the number of unseen species are needed to estimate population diversity from sample diversity. Here we test five widely used non-parametric estimators, and develop and validate a novel method, DivE, to estimate species richness and distribution. We used three independent datasets: (i) viral populations from subjects infected with human T-lymphotropic virus type 1; (ii) T cell antigen receptor clonotype repertoires; and (iii)

SUBMITTER: Laydon DJ 

PROVIDER: S-EPMC4063693 | biostudies-literature | 2014 Jun

REPOSITORIES: biostudies-literature