Show simple item record Doria-Rose, Nicole A. Altae-Tran, Han R. Roark, Ryan S. Schmidt, Stephen D. Sutton, Matthew S. Louder, Mark K. Chuang, Gwo-Yu Bailer, Robert T. Cortez, Valerie Kong, Rui McKee, Krisha O'Dell, Sijy Wang, Felicia Abdool Karim, Salim S. Binley, James M. Connors, Mark Haynes, Barton F. Martin, Malcolm A. Montefiori, David C. Morris, Lynn Overbaugh, Julie Kwong, Peter D. Mascola, John R. Georgiev, Ivelin S. 2017-01-10T14:05:33Z 2017-01-10T14:05:33Z 2017-01-04
dc.identifier doi:10.5061/dryad.c73q1
dc.identifier.citation Doria-Rose NA, Altae-Tran HR, Roark RS, Schmidt SD, Sutton MS, Louder MK, Chuang G, Bailer RT, Cortez V, Kong R, McKee K, O'Dell S, Wang F, Abdool Karim SS, Binley JM, Connors M, Haynes BF, Martin MA, Montefiori DC, Morris L, Overbaugh J, Kwong PD, Mascola JR, Georgiev IS (2017) Mapping polyclonal HIV-1 antibody responses via next-generation neutralization fingerprinting. PLOS Pathogens 13(1): e1006148.
dc.identifier.issn 1553-7366
dc.description Computational neutralization fingerprinting, NFP, is an efficient and accurate method for predicting the epitope specificities of polyclonal antibody responses to HIV-1 infection. Here, we present next-generation NFP algorithms that substantially improve prediction accuracy for individual donors and enable serologic analysis for entire cohorts. Specifically, we developed algorithms for: (a) selection of optimized virus neutralization panels for NFP analysis, (b) estimation of NFP prediction confidence for each serum sample, and (c) identification of sera with potentially novel epitope specificities. At the individual donor level, the next-generation NFP algorithms particularly improved the ability to detect multiple epitope specificities in a sample, as confirmed both for computationally simulated polyclonal sera and for samples from HIV-infected donors. Specifically, the next-generation NFP algorithms detected multiple specificities in twice as many samples of simulated sera. Further, unlike the first-generation NFP, the new algorithms were able to detect both of the previously confirmed antibody specificities, VRC01-like and PG9-like, in donor CHAVI 0219. At the cohort level, analysis of ~150 broadly neutralizing HIV-infected donor samples suggested a potential connection between clade of infection and types of elicited epitope specificities. Most notably, while 10E8-like antibodies were observed in infections from different clades, an enrichment of such antibodies was predicted for clade B samples. Ultimately, such large-scale analyses of antibody responses to HIV-1 infection can help guide the design of epitope-specific vaccines that are tailored to take into account the prevalence of infecting clades within a specific geographic region. Overall, the next-generation NFP technology will be an important tool for the analysis of broadly neutralizing polyclonal antibody responses against HIV-1.
dc.relation.haspart doi:10.5061/dryad.c73q1/2
dc.relation.haspart doi:10.5061/dryad.c73q1/3
dc.relation.isreferencedby doi:10.1371/journal.ppat.1006148
dc.title Data from: Mapping polyclonal HIV-1 antibody responses via next-generation neutralization fingerprinting
dc.type Article
prism.publicationName PLOS Pathogens

Files in this package

Content in the Dryad Digital Repository is offered "as is." By downloading files, you agree to the Dryad Terms of Service. To the extent possible under law, the authors have waived all copyright and related or neighboring rights to this data. CC0 (opens a new window) Open Data (opens a new window)

Downloaded 26 times
Description Instructions for supplementary data/source code
Download README.docx (22.22 Kb)
Details View File Details
Title Archive of data
Downloaded 32 times
Download (3.496 Gb)
Details View File Details

Search for data

Be part of Dryad

We encourage organizations to: