Error correction and statistical analyses for intra-host comparisons of feline immunodeficiency virus diversity from high-throughput sequencing data.
Error correction and statistical analyses for intra-host comparisons of feline immunodeficiency virus diversity from high-throughput sequencing data.
复制标题
DOI：
10.1186/s12859-015-0607-z
复制
发表时间：
2015-06-30
影响因子：
3
通讯作者：
Poss M
中科院分区：
文献类型：
--
作者：
Liu Y;Chiaromonte F;Ross H;Malhotra R;Elleder D;Poss M
猫免疫缺陷病毒（FIV）感染会导致免疫抑制疾病，如果猫同时感染减毒FIV毒株（PLV），其后果就不那么严重。我们使用病毒多样性的测量，这反映了复制能力和病毒对各种条件的反应，以测试是否多样性的毒FIV在淋巴组织中的PLV的存在下改变。我们的数据包括来自FIV单独感染或FIV和PLV感染的动物的三种组织的FIV基因组的3′半，通过454技术测序。由于罕见的变异占病毒群体的主导地位，我们必须仔细区分序列变异与实验方案和测序引起的错误。我们考虑了一个指数正态卷积模型用于背景校正的微阵列数据，并修改它制定了一个错误校正方法，来自高通量测序的次要等位基因频率。类似于计数中的过度分散，这解释了频率中的误差膨胀变化-并且非常有效地再现了经验观察到的分布。在获得错误校正的次要等位基因频率后，我们应用基于线性混合模型的方差分析（ANOVA），发现FIV基因中的保守位点和转换频率在双感染猫和单感染猫的组织中不同。此外，对单个FIV基因组位点的次要等位基因频率的分析显示，242个位点受到感染状态（双重与单一）或感染状态与组织相互作用的显著影响。总之，我们的结果表明，在PLV的存在下，骨髓中FIV多样性降低。重要的是，当用其他方法进行纠错时，这些影响被削弱或不可检测（次要等位基因频率的阈值化;读段的概率聚类）。我们还查询了病毒基因组上胞苷脱氨酶活性的数据，这会导致G到A置换的不对称增加，但没有发现这种宿主防御策略的证据。我们针对次要等位基因频率的纠错方法（比其他算法更敏感和计算效率更高）和我们的变异统计处理（ANOVA）对于有效使用高通量测序数据来理解病毒多样性至关重要。我们发现，与PLV的共感染将FIV多样性从骨髓转移到淋巴结和脾脏。本文的在线版本（doi：10.1186/s12859-015-0607-z）包含补充材料，可供授权用户使用。
Infection 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. Since 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. Our 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. The online version of this article (doi:10.1186/s12859-015-0607-z) contains supplementary material, which is available to authorized users.
登录
查看更多内容
影响因子：
4.4
作者：
Morelli MJ;Wright CF;Knowles NJ;Juleff N;Paton DJ;King DP;Haydon DT
通讯作者：
Haydon DT
影响因子：
4.3
作者：
Hashimoto TB;Edwards MD;Gifford DK
通讯作者：
Gifford DK
影响因子：
14.9
作者：
Hoffmann C;Minkah N;Leipzig J;Wang G;Arens MQ;Tebas P;Bushman FD
通讯作者：
Bushman FD
影响因子：
2.1
作者：
Irizarry, RA;Hobbs, B;Speed, TP
通讯作者：
Speed, TP
影响因子：
1.8
作者：
Hayward JJ;Rodrigo AG
通讯作者：
Rodrigo AG