Data clustering describes a set of frequently employed techniques in exploratory data analysis to extract “natural” group structure in data. Such groupings need to be validated to separate the signal in the data from spurious structure. In this context, finding an appropriate number of clusters is a particularly important model selection question. We introduce a measure of cluster stability to assess the validity of a cluster model. This stability measure quantifies the reproducibility of clustering solutions on a second sample, and it can be interpreted as a classification risk with regard to class labels produced by a clustering algorithm. The preferred number of clusters is determined by minimizing this classification risk as a function of the number of clusters. Convincing results are achieved on simulated as well as gene expression data sets. Comparisons to other methods demonstrate the competitive performance of our method and its suitability as a general validation tool for clustering solutions in real-world problems.

In the last few years, the support vector machine (SVM) method has motivated new interest in kernel regression techniques. Although the SVM has been shown to exhibit excellent generalization properties in many experiments, it suffers from several drawbacks, both of a theoretical and a technical nature: the absence of probabilistic outputs, the restriction to Mercer kernels, and the steep growth of the number of support vectors with increasing size of the training set. In this paper, we present a different class of kernel regressors that effectively overcome the above problems. We call this approach generalized LASSO regression. It has a clear probabilistic interpretation, can handle learning sets that are corrupted by outliers, produces extremely sparse solutions, and is capable of dealing with large-scale problems. For regression functionals which can be modeled as iteratively reweighted least-squares (IRLS) problems, we present a highly efficient algorithm with guaranteed global convergence. This defies a unique framework for sparse regression models in the very rich class of IRLS models, including various types of robust regression models and logistic regression. Performance studies for many standard benchmark datasets effectively demonstrate the advantages of this model over related approaches.

Many viruses, including the clinically relevant RNA viruses HIV (human immunodeficiency virus) and HCV (hepatitis C virus), exist in large populations and display high genetic heterogeneity within and between infected hosts. Assessing intra-patient viral genetic diversity is essential for understanding the evolutionary dynamics of viruses, for designing effective vaccines, and for the success of antiviral therapy. Next-generation sequencing (NGS) technologies allow the rapid and cost-effective acquisition of thousands to millions of short DNA sequences from a single sample. However, this approach entails several challenges in experimental design and computational data analysis. Here, we review the entire process of inferring viral diversity from sample collection to computing measures of genetic diversity. We discuss sample preparation, including reverse transcription and amplification, and the effect of experimental conditions on diversity estimates due to in vitro base substitutions, insertions, deletions, and recombination. The use of different NGS platforms and their sequencing error profiles are compared in the context of various applications of diversity estimation, ranging from the detection of single nucleotide variants (SNVs) to the reconstruction of whole-genome haplotypes. We describe the statistical and computational challenges arising from these technical artifacts, and we review existing approaches, including available software, for their solution. Finally, we discuss open problems, and highlight successful biomedical applications and potential future clinical use of NGS to estimate viral diversity.

Chronic infection with hepatitis C virus (HCV) is a major cause of liver disease worldwide.¹ x 1 Ghany, M.G., Strader, D.B., Thomas, D.L. et al. Diagnosis, management, and treatment of hepatitis C: an update. Hepatology. 2009; 49: 1335–1374 Crossref | PubMed | Scopus (2365) | Google Scholar See all References The current standard therapy of chronic hepatitis C (CHC) achieves an overall sustained virologic response (SVR) in ∼55% of patients.¹ x 1 Ghany, M.G., Strader, D.B., Thomas, D.L. et al. Diagnosis, management, and treatment of hepatitis C: an update. Hepatology. 2009; 49: 1335–1374 Crossref | PubMed | Scopus (2365) | Google Scholar See all References The treatment requires up to 72 weeks of weekly subcutaneous injection of pegylated interferon (pegIFN)-α combined with twice-daily intake of ribavirin tablets. Pretreatment predictors of response are useful for advising patients. SVR rates are higher in patients infected with HCV genotype non-1 (mostly genotypes 2 and 3) and in those with a viral load of less than 600,000 IU/mL.¹ x 1 Ghany, M.G., Strader, D.B., Thomas, D.L. et al. Diagnosis, management, and treatment of hepatitis C: an update. Hepatology. 2009; 49: 1335–1374 Crossref | PubMed | Scopus (2365) | Google Scholar See all References Other less consistently reported baseline characteristics associated with a favorable response include female gender, age younger than 40 years, nonblack race, lower body weight (<75 kg), the absence of insulin resistance, and the absence of bridging fibrosis or cirrhosis on liver biopsy.¹ x 1 Ghany, M.G., Strader, D.B., Thomas, D.L. et al. Diagnosis, management, and treatment of hepatitis C: an update. Hepatology. 2009; 49: 1335–1374 Crossref | PubMed | Scopus (2365) | Google Scholar See all References Infection with HCV can activate the endogenous IFN system in the liver. However, despite a strong induction of hundreds of IFN-stimulated genes (ISGs) in the liver, the activation of the endogenous IFN system in CHC is ineffective in clearing the infection and even impedes the response to therapy, most likely by inducing a refractory state of the IFN signaling pathway.² x 2 Sarasin-Filipowicz, M., Oakeley, E.J., Duong, F.H. et al. Interferon signaling and treatment outcome in chronic hepatitis C. Proc Natl Acad Sci U S A. 2008; 105: 7034–7039 Crossref | PubMed | Scopus (521) | Google Scholar See all References ^{, 3} x 3 Chen, L., Borozan, I., Feld, J. et al. Hepatic gene expression discriminates responders and nonresponders in treatment of chronic hepatitis C viral infection. Gastroenterology. 2005; 128: 1437–1444 Abstract | Full Text | Full Text PDF | PubMed | Scopus (390) | Google Scholar See all References ^{, 4} x 4 Asselah, T., Bieche, I., Narguet, S. et al. Liver gene expression signature to predict response to pegylated interferon plus ribavirin combination therapy in patients with chronic hepatitis C. Gut. 2008; 57: 516–524 Crossref | PubMed | Scopus (185) | Google Scholar See all References ^{, 5} x 5 Sarasin-Filipowicz, M., Wang, X., Yan, M. et al. Alpha interferon induces long-lasting refractoriness of JAK-STAT signaling in the mouse liver through induction of USP18/UBP43. Mol Cell Biol. 2009; 29: 4841–4851 Crossref | PubMed | Scopus (103) | Google Scholar See all References The causal factors and the mechanism underlying this preactivation of the IFN system in some patients with CHC are not well understood. We have shown that the cleavage of mitochondrial antiviral signaling protein by HCV NS3-4A protease correlates with a reduced activation of the endogenous IFN system.⁶ x 6 Bellecave, P., Sarasin-Filipowicz, M., Donze, O. et al. Cleavage of mitochondrial antiviral signaling protein in the liver of patients with chronic hepatitis C correlates with a reduced activation of the endogenous interferon system. Hepatology. 2010; 51: 1127–1136 Crossref | PubMed | Scopus (72) | Google Scholar See all References Recently, several groups reported a strong association between allelic variants of the IL28B gene encoding IFNλ3 and response to treatment. Failure to respond to treatment was associated with the minor alleles of rs12979860 (T),⁷ x 7 Ge, D., Fellay, J., Thompson, A.J. et al. Genetic variation in IL28B predicts hepatitis C treatment-induced viral clearance. Nature. 2009; 461: 399–401 Crossref | PubMed | Scopus (2750) | Google Scholar See all References rs8099917 (G),⁸ x 8 Rauch, A., Kutalik, Z., Descombes, P. et al. Genetic variation in IL28B is associated with chronic hepatitis C and treatment failure: a genome-wide association study. Gastroenterology. 2010; 138: 1338–1345 (1345 e1–7) Abstract | Full Text | Full Text PDF | PubMed | Scopus (922) | Google Scholar See all References ^{, 9} x 9 Suppiah, V., Moldovan, M., Ahlenstiel, G. et al. IL28B is associated with response to chronic hepatitis C interferon-alpha and ribavirin therapy. Nat Genet. 2009; 41: 1100–1104 Crossref | PubMed | Scopus (1531) | Google Scholar See all References ^{, 10} x 10 Tanaka, Y., Nishida, N., Sugiyama, M. et al. Genome-wide association of IL28B with response to pegylated interferon-alpha and ribavirin therapy for chronic hepatitis C. Nat Genet. 2009; 41: 1105–1109 Crossref | PubMed | Scopus (1785) | Google Scholar See all References and rs12980275 (G).¹⁰ x 10 Tanaka, Y., Nishida, N., Sugiyama, M. et al. Genome-wide association of IL28B with response to pegylated interferon-alpha and ribavirin therapy for chronic hepatitis C. Nat Genet. 2009; 41: 1105–1109 Crossref | PubMed | Scopus (1785) | Google Scholar See all References The association was significant in HCV genotypes 1 and 4 but not in HCV genotypes 2 and 3.⁸ x 8 Rauch, A., Kutalik, Z., Descombes, P. et al. Genetic variation in IL28B is associated with chronic hepatitis C and treatment failure: a genome-wide association study. Gastroenterology. 2010; 138: 1338–1345 (1345 e1–7) Abstract | Full Text | Full Text PDF | PubMed | Scopus (922) | Google Scholar See all References Moreover, the IL28B genotype was also associated with the rate of spontaneous clearance of HCV infection.⁸ x 8 Rauch, A., Kutalik, Z., Descombes, P. et al. Genetic variation in IL28B is associated with chronic hepatitis C and treatment failure: a genome-wide association study. Gastroenterology. 2010; 138: 1338–1345 (1345 e1–7) Abstract | Full Text | Full Text PDF | PubMed | Scopus (922) | Google Scholar See all References ^{, 11} x 11 Thomas, D.L., Thio, C.L., Martin, M.P. et al. Genetic variation in IL28B and spontaneous clearance of hepatitis C virus. Nature. 2009; 461: 798–801 Crossref | PubMed | Scopus (1576) | Google Scholar See all References The functional mechanism underlying the association of IL28B polymorphisms with response to treatment is unknown, but 2 groups observed a lower expression of IFNλ3 in peripheral blood mononuclear cells (PBMCs) in individuals carrying the minor rs8099917 IL28B allele that is associated with nonresponse to treatment.⁹ x 9 Suppiah, V., Moldovan, M., Ahlenstiel, G. et al. IL28B is associated with response to chronic hepatitis C interferon-alpha and ribavirin therapy. Nat Genet. 2009; 41: 1100–1104 Crossref | PubMed | Scopus (1531) | Google Scholar See all References ^{, 10} x 10 Tanaka, Y., Nishida, N., Sugiyama, M. et al. Genome-wide association of IL28B with response to pegylated interferon-alpha and ribavirin therapy for chronic hepatitis C. Nat Genet. 2009; 41: 1105–1109 Crossref | PubMed | Scopus (1785) | Google Scholar See all References We hypothesized that allelic variants in IL28B might be responsible for the difference of endogenous IFN activation and studied the association between IL28B polymorphisms and hepatic ISG expression as well as the predictive power of the different factors. Here we show that IL28B genotype and hepatic ISG expression are independent predictors of treatment response in CHC. There is no direct link between altered IFNλ3 expression and preactivation of the endogenous IFN system in the liver. Importantly, hepatic ISG expression is by far the better predictor of treatment response than IL28B genotype.

The HIV-1 reservoir is the major hurdle to a cure. We here evaluate viral and host characteristics associated with reservoir size and long-term dynamics in 1,057 individuals on suppressive antiretroviral therapy for a median of 5.4 years. At the population level, the reservoir decreases with diminishing differences over time, but increases in 26.6% of individuals. Viral blips and low-level viremia are significantly associated with slower reservoir decay. Initiation of ART within the first year of infection, pretreatment viral load, and ethnicity affect reservoir size, but less so long-term dynamics. Viral blips and low-level viremia are thus relevant for reservoir and cure studies.