ArticleNature methods2006
Direct measurement of T-cell receptor repertoire diversity with AmpliCot.
Article in Nature methods, 2006. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 13 papers.
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Who cites it
13 citing papers in PubMed.
- Next generation sequencing based assessment of the alloreactive T cell receptor repertoire in kidney transplant patients during rejection: a prospective cohort study.BMC nephrology · 2019Trial
- Supranormal thymic output up to 2 decades after HIV-1 infection.AIDS (London, England) · 2016Article
- Longitudinal analysis of peripheral blood T cell receptor diversity in patients with systemic lupus erythematosus by next-generation sequencing.Arthritis research & therapy · 2015Observational
- Methods for diversity and overlap analysis in T-cell receptor populations.Journal of mathematical biology · 2013Article
- A generalized mathematical model to estimate T- and B-cell receptor diversities using AmpliCot.Biophysical journal · 2012Article
- Article
- Design, construction, and validation of a modular library of sequence diversity standards for polymerase chain reaction.Analytical biochemistry · 2011Article
- Analysis of HIV diversity using a high-resolution melting assay.AIDS research and human retroviruses · 2010Article
- Automation in the high-throughput selection of random combinatorial libraries--different approaches for select applications.Molecules (Basel, Switzerland) · 2010Review
- A calibrated diversity assay for nucleic acid libraries using DiStRO--a Diversity Standard of Random Oligonucleotides.Nucleic acids research · 2010Article
- High throughput sequencing reveals a complex pattern of dynamic interrelationships among human T cell subsets.Proceedings of the National Academy of Sciences of the United States of America · 2010Article
- High frequencies of virus-specific CD8+ T-cell precursors.Journal of virology · 2009Article
- The application of real-time PCR to the analysis of T cell repertoires.Nucleic acids research · 2008Article
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2 authors.
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Abstract
Many studies require the measurement of nucleic acid sequence diversity. Here we describe a method, called AmpliCot, that measures the sequence diversity of PCR products on the basis of DNA hybridization kinetics, thereby avoiding the time, expense and biases associated with cloning and sequencing. SYBR Green dye is used to measure DNA hybridization kinetics in a homogeneous, automated fashion. PCR products are prepared in wholly double-stranded homoduplex form for a baseline measurement of DNA concentration. The DNA is melted and then reannealed under stringent conditions that allow only homoduplexes to form. The sequence diversity of a sample is proportional to the product of its concentration and the time required for it to anneal. After validating AmpliCot with a library of diverse sequences, we use it to measure the diversity of expressed rearrangements of the gene encoding the T-cell antigen receptor (TCR) beta chain. AmpliCot measurements are in good agreement with previous estimates of murine TCR repertoire diversity that required extensive cloning and sequencing.
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