Error correction and statistical analyses for intra-host comparisons of feline immunodeficiency virus diversity from high-throughput sequencing data

BMC Bioinformatics

Research Article

Howard Ross¹  Mary Poss²  Daniel Elleder³  Raunaq Malhotra⁴  Yang Liu⁵  Francesca Chiaromonte⁵ 

[1] Bioinformatics Institute, School of Biological Sciences, University of Auckland, 1142, Auckland, New Zealand;Department of Biology, The Pennsylvania State University, 16802, University Park, PA, USA;Department of Veterinary and Biomedical Sciences, The Pennsylvania State University, 16802, University Park, PA, USA;The Huck Institutes of the Life Sciences, The Pennsylvania State University, 16802, University Park, PA, USA;Department of Biology, The Pennsylvania State University, 16802, University Park, PA, USA;The Huck Institutes of the Life Sciences, The Pennsylvania State University, 16802, University Park, PA, USA;Current address: Institute of Molecular Genetics, Academy of Sciences of the Czech Republic, Videnska 1083, 14000, Prague, Czech Republic;Department of Computer Science and Engineering, The Pennsylvania State University, 16802, University Park, PA, USA;Department of Statistics, The Pennsylvania State University, 16802, University Park, PA, USA;The Huck Institutes of the Life Sciences, The Pennsylvania State University, 16802, University Park, PA, USA;

关键词: Virus Population Dynamics;    Next Generation Sequencing;    FIV;    Error Correction;    Linear Mixed Model;    Viral Coinfection;   

DOI  :  10.1186/s12859-015-0607-z

 received in 2014-03-06, accepted in 2015-04-29,  发布年份 2015

来源: Springer

【 摘 要 】

BackgroundInfection with feline immunodeficiency virus (FIV) causes an immunosuppressive disease whose consequences are less severe if cats are co-infected with an attenuated FIV strain (PLV). We use virus diversity measurements, which reflect replication ability and the virus response to various conditions, to test whether diversity of virulent FIV in lymphoid tissues is altered in the presence of PLV. Our data consisted of the 3′ half of the FIV genome from three tissues of animals infected with FIV alone, or with FIV and PLV, sequenced by 454 technology.ResultsSince rare variants dominate virus populations, we had to carefully distinguish sequence variation from errors due to experimental protocols and sequencing. We considered an exponential-normal convolution model used for background correction of microarray data, and modified it to formulate an error correction approach for minor allele frequencies derived from high-throughput sequencing. Similar to accounting for over-dispersion in counts, this accounts for error-inflated variability in frequencies – and quite effectively reproduces empirically observed distributions. After obtaining error-corrected minor allele frequencies, we applied ANalysis Of VAriance (ANOVA) based on a linear mixed model and found that conserved sites and transition frequencies in FIV genes differ among tissues of dual and single infected cats. Furthermore, analysis of minor allele frequencies at individual FIV genome sites revealed 242 sites significantly affected by infection status (dual vs. single) or infection status by tissue interaction. All together, our results demonstrated a decrease in FIV diversity in bone marrow in the presence of PLV. Importantly, these effects were weakened or undetectable when error correction was performed with other approaches (thresholding of minor allele frequencies; probabilistic clustering of reads). We also queried the data for cytidine deaminase activity on the viral genome, which causes an asymmetric increase in G to A substitutions, but found no evidence for this host defense strategy.ConclusionsOur error correction approach for minor allele frequencies (more sensitive and computationally efficient than other algorithms) and our statistical treatment of variation (ANOVA) were critical for effective use of high-throughput sequencing data in understanding viral diversity. We found that co-infection with PLV shifts FIV diversity from bone marrow to lymph node and spleen.

【 授权许可】

Unknown   
© Liu et al. 2015. This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/4.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly credited. The Creative Commons Public Domain Dedication waiver (http://creativecommons.org/publicdomain/zero/1.0/) applies to the data made available in this article, unless otherwise stated.