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ObjectiveWe present the final analysis results of the phase 2 JADE study (ClinicalTrials.gov Identifier:NCT03361956).Design232 patients with chronic hepatitis B (CHB) not currently treated at study start (NCT) at study start or virologically suppressed were randomised to receive 75 mg (part 1) or 250 mg (part 2) JNJ-56136379, a hepatitis B virus (HBV)–capsid assembly modulator, one time per day or placebo with nucleos(t)ide analogue (NA) (tenofovir disoproxil fumarate/entecavir) or JNJ-56136379 alone (NCT-only) for ≥24 and ≤48 weeks.ResultsIn patients who are NCT hepatitis B e-antigen (HBeAg) positive, JNJ-56136379 75 mg+NA and 250 mg+NA showed limited mean (SE) hepatitis B surface antigen (HBsAg) declines (0.14 (0.10) and 0.41 (0.15), respectively) from baseline at Week 24 (primary endpoint; placebo+NA: 0.25 (0.11) log10international unit (IU)/mL).In patients who are NCT HBeAg positive, mean (SE) HBV DNA declines at Week 24 were 5.53 (0.23) and 5.88 (0.34) for JNJ-56136379 75 mg+NA and 250 mg+NA, respectively, versus 5.21 (0.42) log10IU/mL for placebo+NA. In NCT patients, mean (SE) HBV RNA declines were 2.96 (0.23) and 3.15 (0.33) versus 1.33 (0.32) log10copies/mL, respectively.Patients with HBsAg declines had HBeAg and hepatitis B core-related antigen (HBcrAg) declines and some early on-treatment isolated alanine aminotransferase flares. Viral breakthrough occurred with JNJ-56136379 monotherapy with the emerging resistant-variant T33N, but not with JNJ-56136379+NA. JNJ-56136379 treatment beyond Week 24 had a generally small additional effect on viral markers.No study treatment-related serious adverse events or clinically significant changes in laboratory parameters occurred.ConclusionsIn patients with non-cirrhotic CHB, JNJ-56136379+NA showed pronounced reductions in HBV DNA and HBV RNA, limited HBsAg or HBeAg declines in patients who are NCT HBeAg positive, and was well tolerated, but no clear benefit with regards to efficacy of JNJ-56136379 over NA was observed.

Despite the availability of effective vaccines against COVID-19, booster vaccinations are needed to maintain vaccine-induced protection against variant strains and breakthrough infections. This study aimed to investigate the efficacy, safety, and immunogenicity of the Ad26.COV2.S vaccine (Janssen) as primary vaccination plus a booster dose.ENSEMBLE2 is a randomised, double-blind, placebo-controlled, phase 3 trial including crossover vaccination after emergency authorisation of COVID-19 vaccines. Adults aged at least 18 years without previous COVID-19 vaccination at public and private medical practices and hospitals in Belgium, Brazil, Colombia, France, Germany, the Philippines, South Africa, Spain, the UK, and the USA were randomly assigned 1:1 via a computer algorithm to receive intramuscularly administered Ad26.COV2.S as a primary dose plus a booster dose at 2 months or two placebo injections 2 months apart. The primary endpoint was vaccine efficacy against the first occurrence of molecularly confirmed moderate to severe-critical COVID-19 with onset at least 14 days after booster vaccination, which was assessed in participants who received two doses of vaccine or placebo, were negative for SARS-CoV-2 by PCR at baseline and on serology at baseline and day 71, had no major protocol deviations, and were at risk of COVID-19 (ie, had no PCR-positive result or discontinued the study before day 71). Safety was assessed in all participants; reactogenicity, in terms of solicited local and systemic adverse events, was assessed as a secondary endpoint in a safety subset (approximately 6000 randomly selected participants). The trial is registered with ClinicalTrials.gov, NCT04614948, and is ongoing.Enrolment began on Nov 16, 2020, and the primary analysis data cutoff was June 25, 2021. From 34 571 participants screened, the double-blind phase enrolled 31 300 participants, 14 492 of whom received two doses (7484 in the Ad26.COV2.S group and 7008 in the placebo group) and 11 639 of whom were eligible for inclusion in the assessment of the primary endpoint (6024 in the Ad26.COV2.S group and 5615 in the placebo group). The median (IQR) follow-up post-booster vaccination was 36·0 (15·0-62·0) days. Vaccine efficacy was 75·2% (adjusted 95% CI 54·6-87·3) against moderate to severe-critical COVID-19 (14 cases in the Ad26.COV2.S group and 52 cases in the placebo group). Most cases were due to the variants alpha (B.1.1.7) and mu (B.1.621); endpoints for the primary analysis accrued from Nov 16, 2020, to June 25, 2021, before the global dominance of delta (B.1.617.2) or omicron (B.1.1.529). The booster vaccine exhibited an acceptable safety profile. The overall frequencies of solicited local and systemic adverse events (evaluated in the safety subset, n=6067) were higher among vaccine recipients than placebo recipients after the primary and booster doses. The frequency of solicited adverse events in the Ad26.COV2.S group were similar following the primary and booster vaccinations (local adverse events, 1676 [55·6%] of 3015 vs 896 [57·5%] of 1559, respectively; systemic adverse events, 1764 [58·5%] of 3015 vs 821 [52·7%] of 1559, respectively). Solicited adverse events were transient and mostly grade 1-2 in severity.A homologous Ad26.COV2.S booster administered 2 months after primary single-dose vaccination in adults had an acceptable safety profile and was efficacious against moderate to severe-critical COVID-19. Studies assessing efficacy against newer variants and with longer follow-up are needed.Janssen ResearchDevelopment.

The capsid assembly modulator JNJ-56136379 (bersacapavir) disrupts hepatitis B virus replication. It is metabolized via cytochrome P450 (CYP) 3A, but little is known about the drug-drug interactions of JNJ-56136379 when combined with drugs that inhibit or are metabolized by CYP3A. In a phase 1, open-label trial (NCT03945539), healthy adults received 1 dose of JNJ-56136379 with and without 21 days of prior exposure to itraconazole 200 mg (CYP3A inhibitor). In a second phase 1, open-label trial (NCT03111511), healthy women received 1 dose of drospirenone/ethinyl estradiol and midazolam before and after 15 days of JNJ-56136379. Itraconazole increased the area under the plasma concentration-time curve (AUC) of JNJ-56136379 by 38%. JNJ-56136379 reduced the maximum observed concentration and AUC of midazolam (CYP3A substrate) by 42%-54%, increased AUC of ethinyl estradiol by 1.6-fold, but had no effect on drospirenone pharmacokinetics. Overall, these results demonstrated that a strong CYP3A inhibitor (itraconazole) modestly increased JNJ-56136379 exposure. Furthermore, JNJ-56136379 was a weak inducer of CYP3A (midazolam) and increased ethinyl estradiol exposure; coadministration of high-dose estrogen-based contraceptives and JNJ-56136379 is not recommended.

Multitargeted kinase inhibitors have shown clinical efficacy in a range of cancer types. However, two major problems associated with these drugs are the low fraction of patients for which these treatments provide initial clinical benefit and the occurrence of resistance during prolonged therapy. Several types of predictive biomarkers have been suggested, such as expression level and phosphorylation status of the major targeted kinase(s), mutational status of the kinases involved and of key components of the downstream signaling cascades, and gene expression signatures. In this work, we describe the development of a response prediction platform that does not require prior knowledge of the relevant kinases targeted by the inhibitor; instead, a phosphotyrosine peptide profile using peptide arrays with a kinetic readout is derived in lysates in the presence and absence of a kinase inhibitor. We show in a range of cell lines and in xenograft tumors that this approach allows for the stratification of responders and nonresponders to a multitargeted kinase inhibitor. [Mol Cancer Ther 2009;8(7):1846–55]

Purpose: Histone deacetylase (HDAC) inhibitors have shown promising clinical activity in the treatment of hematologic malignancies, but their activity in solid tumor indications has been limited. Most HDAC inhibitors in clinical development only transiently induce histone acetylation in tumor tissue. Here, we sought to identify a second-generation class I HDAC inhibitor with prolonged pharmacodynamic response in vivo, to assess whether this results in superior antitumoral efficacy.Experimental Design: To identify novel HDAC inhibitors with superior pharmacodynamic properties, we developed a preclinical in vivo tumor model, in which tumor cells have been engineered to express fluorescent protein dependent on HDAC1 inhibition, thereby allowing noninvasive real-time evaluation of the tumor response to HDAC inhibitors.Results:In vivo pharmacodynamic analysis of 140 potent pyrimidyl-hydroxamic acid analogues resulted in the identification of JNJ-26481585. Once daily oral administration of JNJ-26481585 induced continuous histone H3 acetylation. The prolonged pharmacodynamic response translated into complete tumor growth inhibition in Ras mutant HCT116 colon carcinoma xenografts, whereas 5-fluorouracil was less active. JNJ-26481585 also fully inhibited the growth of C170HM2 colorectal liver metastases, whereas again 5-fluorouracil/Leucovorin showed modest activity. Further characterization revealed that JNJ-26481585 is a pan-HDAC inhibitor with marked potency toward HDAC1 (IC50, 0.16 nmol/L).Conclusions: The potent antitumor activity as a single agent in preclinical models combined with its favorable pharmacodynamic profile makes JNJ-26481585 a promising second-generation HDAC inhibitor. The compound is currently in clinical studies, to evaluate its potential applicability in a broad spectrum of both solid and hematologic malignancies. (Clin Cancer Res 2009;15(22):684151)

Supplementary Figure 1 from Response prediction to a multitargeted kinase inhibitor in cancer cell lines and xenograft tumors using high-content tyrosine peptide arrays with a kinetic readout

Supplementary Figure 2 from Response prediction to a multitargeted kinase inhibitor in cancer cell lines and xenograft tumors using high-content tyrosine peptide arrays with a kinetic readout

Supplementary Data from JNJ-26481585, a Novel Second-Generation Oral Histone Deacetylase Inhibitor, Shows Broad-Spectrum Preclinical Antitumoral Activity

Background Pharmacokinetics and safety of JNJ-64530440, a hepatitis B virus capsid assembly modulator producing normal empty capsids (CAM-N), in healthy volunteers were evaluated. Methods This Phase I study (NCT03439488) was a double-blind, randomised, placebo-controlled study. Adults ( n = 10/cohort, five Asian/five non-Asian), randomised 4:1, received single-ascending doses of oral JNJ-64530440 (first- and second-generation formulations) or placebo under fasted (50, 150, 300 and 900 mg) or fed (300, 750, 1,000, 2000 and 4000 mg) conditions. Multiple-ascending doses of 750 or 2000 mg once daily and 750 mg twice daily JNJ-64530440 (second-generation formulation) for 7 days were evaluated. Pharmacokinetic parameters were estimated from plasma concentrations. Safety was assessed throughout. Results Less than dose-proportional increases in maximum plasma concentrations (Cmax) and area under the plasma concentration–time curves (AUCs) were observed across the doses. Mean plasma half-lives ranged from 9.3 to 14.5 h. Cmax and AUC were ∼two fold higher under fed versus fasting conditions and slightly higher in Asians versus Caucasians. JNJ-64530440 doses ≥750 mg achieved plasma levels higher than protein-binding adjusted concentrations demonstrating in vitro antiviral activity. No serious adverse events (AEs), treatment discontinuations or dose-limiting toxicities were seen. AE frequency/severity did not increase with dose. Conclusions Single (up to 4000 mg) and multiple doses (up to 2000 mg for 7 days) of JNJ-64530440 were well tolerated in healthy volunteers. Multiple doses ≥750 mg/day achieved plasma concentrations expected to have antiviral activity that may lower hepatitis B surface antigen. No clinically relevant differences in tolerability or pharmacokinetic parameters were seen between Asians versus Caucasians.

Hepatitis B viral capsid assembly is an attractive target for new antiviral treatments. JNJ-56136379 (JNJ-6379) is a potent capsid assembly modulator in vitro with a dual mode of action. In Part 1 of this first-in-human study in healthy adults, the pharmacokinetics (PK), safety and tolerability of JNJ-6379 were evaluated following single ascending and multiple oral doses.This was a double-blind, randomized, placebo-controlled study in 30 healthy adults. Eighteen subjects were randomized to receive single doses of JNJ-6379 (25 to 600 mg) or placebo. Twelve subjects were randomized to receive 150 mg JNJ-6379 or placebo twice daily for 2 days, followed by 100 mg JNJ-6379 or placebo daily for 10 days.The maximum observed plasma concentration and the area under the curve increased dose proportionally from 25 to 300 mg JNJ-6379. Following multiple dosing, steady-state conditions were achieved on day 8. Steady-state clearance was similar following single and multiple dosing, suggesting time-linear PK. All adverse events (AEs) reported were mild to moderate in severity. There were no serious AEs or dose-limiting toxicities and no apparent relationship to dose for any AE.JNJ-6379 was well tolerated in this study. Based on the safety profile and plasma exposures of JNJ-6379 in healthy subjects, a dosing regimen was selected for Part 2 of this study in patients with chronic hepatitis B. This is anticipated to achieve trough plasma exposures of JNJ-6379 at steady state of more than three times the 90% effective concentration of viral replication determined in vitro.Clinicaltrials.gov identifier, NCT02662712.Janssen Pharmaceutica.

Background JNJ-73763989 comprises two hepatitis B virus (HBV)-specific, liver-targeted N-galactosamine-conjugated short interfering RNA triggers, JNJ-73763976 and JNJ-73763924. JNJ-73763989 pharmacokinetics, safety and tolerability were assessed in two phase 1 studies: Japanese (NCT04002752), and non-Japanese healthy participants and chronic hepatitis B (CHB) patients also receiving the HBV capsid assembly modulator JNJ-56136379 and a nucleos(t)ide analogue (NA) (NCT03365947). Methods Healthy participant cohorts were double-blind and randomized to receive a single subcutaneous JNJ-73763989 dose (non-Japanese participants, 35, 100, 200, 300 or 400 mg; Japanese participants, 25, 100 or 200 mg) or placebo. JNJ-73763976 and JNJ-73763924 plasma concentrations were assessed over 48 h. CHB patients received JNJ-73763989 200 mg every 4 weeks plus daily oral JNJ-56136379 250 mg and NA in an open-label fashion. Safety and tolerability were assessed through Day 28 (healthy participants) or Day 112 (patients). Results Thirty non-Japanese ( n = 4/dose; placebo, n = 10) and 24 Japanese healthy participants ( n = 6/dose; placebo, n = 6) were randomized. JNJ-73763976 and JNJ-73763924 exposure generally increased in a dose-proportional manner. Mean plasma half-life was 4–9 h. No differences between pharmacokinetic parameters were apparent between non-Japanese and Japanese healthy participants. In the 12 CHB patients, mean JNJ-73763976, JNJ-73763924 and JNJ-56136379 plasma concentrations 2 h post-dose on Day 29 were 663, 269 and 14,718 ng/mL, respectively. In both studies, all adverse events were mild/moderate. Conclusion JNJ-73763976 and JNJ-73763924 had short plasma half-lives and exposure generally increased in a dose-proportional manner; there were no pharmacokinetic differences between Japanese and non-Japanese healthy adults. JNJ-73763989 with or without JNJ-56136379 and NA was generally safe and well tolerated.

Objectives We investigated JNJ-64530440 (a hepatitis B virus capsid assembly modulator) safety, antiviral activity and pharmacokinetics in patients with chronic hepatitis B (CHB) (Phase 1b, NCT03439488). Methods Twenty treatment-naive, HBeAg-positive or -negative CHB patients were randomized 4‍:‍1 to JNJ-64530440 750 mg once or twice daily, or placebo for 28 days. Results All patients (mean age 43.8 years; 85% male; 70% White; 20% HBeAg positive) completed dosing/28 day follow-up. Mild-to-moderate treatment-emergent adverse events occurred in 3/4 (placebo), 6/8 (once-daily) and 4/8 (twice-daily) patients; mostly fatigue, increased alanine aminotransferase, decreased neutrophil count, and headache. Hepatitis B virus (HBV) DNA was substantially reduced; mean (range) changes from baseline at day 29 were: −3.2 (−2.4 to −3.9) (once-daily) and −3.3 (−2.6 to −4.1) (twice-daily) log10 IU/mL; placebo 0.1 (0.7 to −0.6) log10 IU/mL. HBV DNA levels were below the lower limit of quantification (LLOQ) in 5/8 (once-daily) and 3/8 (twice-daily) patients. For patients with detectable baseline HBV RNA, mean (SE) changes versus baseline in HBV RNA at day 29 were: −2.65 (0.81) (once-daily) and −2.94 (0.33) (twice-daily) log10 copies/mL. HBV RNA levels were ‘target not detected’ in 4/6 (once-daily) and 3/7 (twice-daily) patients. JNJ-64530440 pharmacokinetics in CHB patients were comparable with those in healthy volunteers. Conclusions JNJ-64530440 750 mg once-daily or twice-daily for 28 days was well tolerated and achieved potent antiviral activity in CHB patients.

Background & Aims JNJ-56136379 (JNJ-6379), a capsid assembly modulator that blocks hepatitis B virus (HBV) replication, was well tolerated and demonstrated dose-proportional pharmacokinetics in healthy participants in part 1 of its first clinical trial. In part 2, we have evaluated the safety, pharmacokinetics, and antiviral activity of multiple doses of JNJ-6379 in patients with chronic HBV infection. Methods We performed a double-blind study of 57 treatment-naive patients with HB e antigen-positive or -negative (74%) chronic HBV infection without cirrhosis. Patients were randomly assigned to groups given JNJ-6379 at 25 mg (100 mg loading dose), 75 mg, 150 mg, or 250 mg or placebo daily for 4 weeks with an 8-week follow-up period. Results Twenty-three (56%) of 41 patients given JNJ-6379 had at least 1 adverse event (AE) during treatment, compared with 10 (63%) of 16 patients given placebo. No serious AEs were reported during the treatment period. Three patients (7%) given JNJ-6379 vs none given placebo had grade 3 AEs; of these, 1 patient (150 mg) also had an isolated grade 4 increase in the level of alanine aminotransferase that led to treatment discontinuation. JNJ-6379 exposure increased with dose, with time-linear pharmacokinetics. HBV-DNA and HBV-RNA decreased from baseline in patients receiving all doses of JNJ-6379, independently of viral genotype and HB e antigen status. On day 29, 13 (32%) of 41 patients had levels of HBV DNA below the lower limit of quantification. No clinically significant changes in levels of HB surface antigen were observed. Conclusions In a phase 1 study of treatment-naive patients with chronic HBV infection, all doses tested of JNJ-6379 were well tolerated, showed dose-dependent pharmacokinetics, and had potent antiviral activity in patients with CHB. The findings support a phase 2a study to evaluate JNJ-6379 ± nucleos(t)ide analogs in patients with chronic HBV infection, which is under way. ClinicalTrials.gov identifier: NCT02662712

Four weeks of once-daily oral JNJ-56136379 (JNJ-6379; 25, 75, 150 or 250 mg), a class-N capsid assembly modulator (CAM-N), was well tolerated with potent antiviral activity in treatment-naive, chronic hepatitis B e antigen-positive and hepatitis B e antigen-negative patients (NCT02662712). Hepatitis B virus (HBV) genome sequence analysis, using HBV DNA next-generation sequence technology, was performed, and impact of substitutions on efficacy was assessed. Analyses focused on HBV core protein amino acid positions associated with JNJ-6379 and/or other CAMs in vitro resistance, and those within the CAM-binding pocket. 31/57 patients had ≥ 1 polymorphism at any of the core amino acid positions of interest, most frequently at positions 38 (32%), 105 (23%) and 109 (14%). None of these polymorphisms are known to reduce JNJ-6379 in vitro activity (fold change [FC] in 50% effective concentration

The identification of the minimum effective dose is of high importance in the drug development process. In early stage screening experiments, establishing the minimum effective dose can be translated into a model selection based on information criteria. The presented alternative, Bayesian variable selection approach, allows for selection of the minimum effective dose, while taking into account model uncertainty. The performance of Bayesian variable selection is compared with the generalized order restricted information criterion on two dose-response experiments and through the simulations study. Which method has performed better depends on the complexity of the underlying model and the effect size relative to noise. Martin Otava and Ziv Shkedy gratefully acknowledge the support from the IAP Research Network P7/06 of the Belgian State (Belgian Science Policy). Martin Otava gratefully acknowledge the financial support of the Research Project BOF11DOC09 of Hasselt University.

Although much is known about the terrestrial locomotion of great apes, their arboreal locomotion has been studied less extensively. This study investigates arboreal locomotion in bonobos (Pan paniscus), focusing on the gait characteristics and spatio-temporal variables associated with locomotion on a pole. These features are compared across different substrate inclinations (0°, 30°, 45°, 60°, and 90°), and horizontal quadrupedal walking is compared between an arboreal and a terrestrial substrate. Our results show greater variation in footfall patterns with increasing incline, resulting in more lateral gait sequences. During climbing on arboreal inclines, smaller steps and strides but higher stride frequencies and duty factors are found compared to horizontal arboreal walking. This may facilitate better balance control and dynamic stability on the arboreal substrate. We found no gradual change in spatio-temporal variables with increasing incline; instead, the results for all inclines were clustered together. Bonobos take larger strides at lower stride frequencies and lower duty factors on a horizontal arboreal substrate than on a flat terrestrial substrate. We suggest that these changes are the result of the better grip of the grasping feet on an arboreal substrate. Speed modulation of the spatio-temporal variables is similar across substrate inclinations and between substrate types, suggesting a comparable underlying motor control. Finally, we contrast these variables of arboreal inclined climbing with those of terrestrial bipedal locomotion, and briefly discuss the results with respect to the origin of habitual bipedalism. Am. J. Primatol. 78:1165-1177, 2016. © 2016 Wiley Periodicals, Inc.

During drug discovery and development, the early identification of adverse effects is expected to reduce costly late-stage failures of candidate drugs. As risk/safety assessment takes place rather late during the development process and due to the limited ability of animal models to predict the human situation, modern unbiased high-dimensional biology readouts are sought, such as molecular signatures predictive for in vivo response using high-throughput cell-based assays. In this theoretical proof of concept, we provide findings of an in-depth exploration of a single chemical core structure. Via transcriptional profiling, we identified a subset of close analogues that commonly downregulate multiple tubulin genes across cellular contexts, suggesting possible spindle poison effects. Confirmation via a qualified toxicity assay (in vitro micronucleus test) and the identification of a characteristic aggregate-formation phenotype via exploratory high-content imaging validated the initial findings. SAR analysis triggered the synthesis of a new set of compounds and allowed us to extend the series showing the genotoxic effect. We demonstrate the potential to flag toxicity issues by utilizing data from exploratory experiments that are typically generated for target evaluation purposes during early drug discovery. We share our thoughts on how this approach may be incorporated into drug development strategies.

Background Alternative gene splicing is a common phenomenon in which a single gene gives rise to multiple transcript isoforms. The process is strictly guided and involves a multitude of proteins and regulatory complexes. Unfortunately, aberrant splicing events do occur which have been linked to genetic disorders, such as several types of cancer and neurodegenerative diseases (Fan et al., Theor Biol Med Model 3:19, 2006). Therefore, understanding the mechanism of alternative splicing and identifying the difference in splicing events between diseased and healthy tissue is crucial in biomedical research with the potential of applications in personalized medicine as well as in drug development. Results We propose a linear mixed model, Random Effects for the Identification of Differential Splicing (REIDS), for the identification of alternative splicing events. Based on a set of scores, an exon score and an array score, a decision regarding alternative splicing can be made. The model enables the ability to distinguish a differential expressed gene from a differential spliced exon. The proposed model was applied to three case studies concerning both exon and HTA arrays. Conclusion The REIDS model provides a work flow for the identification of alternative splicing events relying on the established linear mixed model. The model can be applied to different types of arrays. Electronic supplementary material The online version of this article (doi:10.1186/s12859-017-1687-8) contains supplementary material, which is available to authorized users.

Motivation : In virology, massively parallel sequencing (MPS) opens many opportunities for studying viral quasi-species, e.g. in HIV-1- and HCV-infected patients. This is essential for understanding pathways to resistance, which can substantially improve treatment. Although MPS platforms allow in-depth characterization of sequence variation, their measurements still involve substantial technical noise. For Illumina sequencing, single base substitutions are the main error source and impede powerful assessment of low-frequency mutations. Fortunately, base calls are complemented with quality scores (Qs) that are useful for differentiating errors from the real low-frequency mutations. Results : A variant calling tool, Q-cpileup, is proposed, which exploits the Qs of nucleotides in a filtering strategy to increase specificity. The tool is imbedded in an open-source pipeline, VirVarSeq, which allows variant calling starting from fastq files. Using both plasmid mixtures and clinical samples, we show that Q-cpileup is able to reduce the number of false-positive findings. The filtering strategy is adaptive and provides an optimized threshold for individual samples in each sequencing run. Additionally, linkage information is kept between single-nucleotide polymorphisms as variants are called at the codon level. This enables virologists to have an immediate biological interpretation of the reported variants with respect to their antiviral drug responses. A comparison with existing SNP caller tools reveals that calling variants at the codon level with Q-cpileup results in an outstanding sensitivity while maintaining a good specificity for variants with frequencies down to 0.5%. Availability : The VirVarSeq is available, together with a user’s guide and test data, at sourceforge: http://sourceforge.net/projects/virtools/?source=directory Contact : bie.verbist@ugent.be Supplementary information: Supplementary data are available at Bioinformatics online.

This study could not confirm the association between the Catechol-O-Methyltransferase Val158Met polymorphism (COMT) and electroencephalographic (EEG) alpha peak frequency (APF) in two independent cohorts of 187 (96 depressed and 91 healthy participants) and 413 healthy participants. If COMT and APF play a role in depression or antidepressant treatment response, they do not have a shared pathway. We emphasize the importance of publishing null-findings for obtaining more accurate overall estimates of genetic effects. (C) 2014 Elsevier Ireland Ltd. All rights reserved.

Background & Aims NVR 3-778 is a first-in-class hepatitis B virus (HBV) capsid assembly modulator that can inhibit HBV replication. We performed a proof-of-concept study to examine the safety, pharmacokinetics, and antiviral activity of NVR 3-778 in patients with chronic HBV infection. Methods We performed a phase 1 study in 73 hepatitis B envelope antigen (HBeAg)-positive patients with chronic HBV infection without cirrhosis. In a 2-part study (part 1 in New Zealand and part 2 in Hong Kong, Singapore, Taiwan, Korea, and the United States), patients were randomly assigned to groups that were given oral NVR 3-778 (100 mg, 200 mg, or 400 mg daily or 600 mg or 1000 mg twice daily) or placebo for 4 weeks. Additional groups received combination treatment with pegylated interferon (pegIFN) and NVR 3-778 (600 mg twice daily) or pegIFN with placebo. Results Reductions in serum levels of HBV DNA and HBV RNA were observed in patients receiving ≥1200 mg/d NVR 3-778. The largest mean reduction in HBV DNA was observed in the group given NVR 3-778 plus pegIFN (1.97 log10 IU/mL), compared with the groups given NVR 3-778 or pegIFN alone (1.43 log10 IU/mL and 1.06 log10 IU/mL, respectively). The mean reduction in HBV RNA was also greatest in the group given NVR 3-778 plus pegIFN (2.09 log10 copies/mL), compared with the groups given NVR 3-778 or pegIFN alone (1.42 log10 copies/mL and 0.89 log10 copies/mL, respectively). There was no significant mean reduction in HBsAg during the 4-week treatment period. There were no discontinuations and no pattern of dose-related adverse effects with NVR 3-778. Conclusions In a phase 1 study of HBeAg-positive patients with chronic HBV infection without cirrhosis, NVR 3-778 was well tolerated and demonstrated antiviral activity. The agent reduced serum levels of HBV DNA and HBV RNA, to the greatest extent in combination with pegIFN. The observed reductions in HBV RNA confirmed the novel mechanism of NVR 3-778. Clinicaltrials.gov no. NCT02112799 (single-center) and NCT02401737 (multicenter).

Motivation: Current clinical and biological studies apply different biotechnologies and subsequently combine the resulting -omics data to test biological hypotheses. The plethora of -omics data and their combination generates a large number of hypotheses and apparently increases the study power. Contrary to these expectations, the wealth of -omics data may even reduce the statistical power of a study because of a large correction factor for multiple testing. Typically, this loss of power in analyzing -omics data are caused by an increased false detection rate (FDR) in measurements, like falsely detected DNA copy number changes, or falsely identified differentially expressed genes. The false detections are random and, therefore, not related to the tested conditions. Thus, a high FDR considerably decreases the discovery power of studies, especially if different -omics data are involved. Results: On a HapMap data set, where known CNVs have to be re-detected, I/NI call filtering was much more efficient than v...

Proven Methods for Big Data Analysis As big data has become standard in many application areas, challenges have arisen related to methodology and software development, including how to discover meaningful patterns in the vast amounts of data. Addressing these problems, Applied Biclustering Methods for Big and High-Dimensional Data Using R shows how to apply biclustering methods to find local patterns in a big data matrix. The book presents an overview of data analysis using biclustering methods from a practical point of view. Real case studies in drug discovery, genetics, marketing research, biology, toxicity, and sports illustrate the use of several biclustering methods. References to technical details of the methods are provided for readers who wish to investigate the full theoretical background. All the methods are accompanied with R examples that show how to conduct the analyses. The examples, software, and other materials are available on a supplementary website.

The modern drug discovery process involves multiple sources of high-dimensional data. This imposes the challenge of data integration. A typical example is the integration of chemical structure (fingerprint features), phenotypic bioactivity (bioassay read-outs) data for targets of interest, and transcriptomic (gene expression) data in early drug discovery to better understand the chemical and biological mechanisms of candidate drugs, and to facilitate early detection of safety issues prior to later and expensive phases of drug development cycles. In this paper, we discuss a joint model for the transcriptomic and the phenotypic variables conditioned on the chemical structure. This modeling approach can be used to uncover, for a given set of compounds, the association between gene expression and biological activity taking into account the influence of the chemical structure of the compound on both variables. The model allows to detect genes that are associated with the bioactivity data facilitating the identification of potential genomic biomarkers for compounds efficacy. In addition, the effect of every structural feature on both genes and pIC50 and their associations can be simultaneously investigated. Two oncology projects are used to illustrate the applicability and usefulness of the joint model to integrate multi-source high-dimensional information to aid drug discovery.

Background & Aims Sustained virological response (SVR) following peginterferon (pegIFN) and ribavirin (RBV) treatment in hepatitis C virus (HCV)-infected patients has been linked with the IL28B genotype and lower peripheral levels of the CXCR3-binding chemokine IP-10 (CXCL10). To further improve the understanding of these biomarkers we investigated plasma levels of the other CXCR3-binding chemokines and activity of the dipeptidyl peptidase IV (DPP4, CD26) protease, which cleaves IP-10, in relation to treatment response. Methods African-American and Caucasian HCV genotype 1-infected patients (n = 401) were treated with pegIFN/RBV for 48 weeks (ViraHep-C cohort). Pretreatment plasma levels of MIG (CXCL9), I-TAC (CXCL11) and the type III interferon IL29 were investigated by Luminex and DPP4 activity by using a luciferase assay. Results Patients achieving SVR had higher baseline MIG plasma levels and lower DPP4 activity than non-SVR patients. MIG was higher in Caucasians, IL28B CC (rs1297860) genotype carriers and patients with higher ALT levels. MIG correlated with IP-10 in SVR patients, but not in non-SVRs. A high DPP4 activity correlated with higher IP-10 levels, while DPP4 activity was not associated with MIG or I-TAC levels. Conclusions The associations of MIG with SVR status and IL28B genotype imply that higher MIG plasma levels could reflect a beneficial immunological state for response to pegIFN/RBV treatment. The correlation between MIG and IP-10 observed only in SVR patients may contribute to a better treatment response, whereas this MIG/IP-10 balance might be disrupted in non-SVR patients because of the increased DPP4 cleavage of IP-10 into a dysfunctional form.

Motivation: Phosphorylation by protein kinases is a central theme in biological systems. Aberrant protein kinase activity has been implicated in a variety of human diseases (e.g. cancer). Therefore, modulation of kinase activity represents an attractive therapeutic approach for the treatment of human illnesses. Thus, identification of signature peptides is crucial for protein kinase targeting and can be achieved by using PamChip® microarray technology. We propose a flexible semiparametric mixed model for analyzing PamChip® data. This approach enables the estimation of the phosphorylation rate (Velocity) as a function of time together with pointwise confidence intervals. Results: Using a publicly available dataset, we show that our model is capable of adequately fitting the kinase activity profiles and provides velocity estimates over time. Moreover, it allows to test for differences in the velocity of kinase inhibition between responding and non-responding cell lines. This can be done at individual time point as well as for the entire velocity profile. Contact: pushpike@med.kuleuven.be Supplementary information: Supplementary data are available at Bioinformatics online.

Recently, preclinical microarray experiments have become increasingly common laboratory tools to investigate the activity of thousands of genes simultaneously and their response to a certain treatment (Amaratunga and Cabrera 2004). In some experiments, in addition to the gene expressions, other responses are also available. In such situations, the primary question of interest is to identify whether or not the gene expressions can serve as biomarkers for the responses. In addition to gene expressions, metabolites are potential biomarkers for some responses as well. In the present study, we focus on the identification of genomic biomarkers, based on gene and metabolite expression for depression. One measure of the level of depression is the Hamilton Depression Scale (HDS or HAMD) which is a test measuring the severity of depressive symptoms in individuals. The data for this study are a result of a clinical trial in which both HAMD and gene/metabolites expression were measured. We use three modeling approaches commonly used in the surrogate marker validation theory to select and evaluate a set of genes and metabolites as possible biomarkers for depression, as measured by the HAMD score. In addition to gene and metabolite specific biomarkers, we use supervised principal components analysis and supervised partial least squares regression technique to construct a joint biomarker that uses information from all genes/metabolites in the array. The authors gratefully acknowledge support from IAP research Network P6/03 of the Belgian Government (Belgian Science Policy).

Conditions experienced during early development may affect both adult phenotype and performance later during life. Phenotypic traits may hence be used to indicate past growing conditions and predict future survival probabilities. Relationships between phenotypic markers and future survival are, however, highly heterogeneous, possibly because poor- and high-quality individuals cannot be morphologically discriminated when developing under good environmental conditions. Sub-optimal breeding conditions, in contrast, may unmask poor-quality individuals in a measurable way at the morphological level. We thus predict stronger associations between phenotype and performance under stress. In this field study, we test this hypothesis, experimentally challenging the homeostasis of great tit (Parus major) nestlings by short-term deprivation of parental care, which had no immediate effect on nestling fitness. The experiment was replicated during two subsequent breeding seasons with contrasting ambient weather conditions. Experimental (short-term) stress affected tarsus growth but not residual mass at fledging, whereas ambient (continuous) stress affected residual mass but not tarsus growth. Short-term stress effects on tarsus length and tarsus fluctuating asymmetry were only apparent when ambient conditions were unfavourable. Residual mass and hatching date, but none of the other phenotypic traits, predicted local survival, whereby the strength of the relationship did not vary between both years. Because effects of stress on develop- mental homeostasis are likely to be trait-specific and condition-dependent, studies on the use of phenotypic markers for individual fitness should integrate multiple traits comprising different levels of developmental complexity. © 2010 The Linnean Society of London, Biological Journal of the Linnean Society, 2010, 100, 103-110.

Purpose: Histone deacetylase (HDAC) inhibitors have shown promising clinical activity in the treatment of hematologic malignancies, but their activity in solid tumor indications has been limited. Most HDAC inhibitors in clinical development only transiently induce histone acetylation in tumor tissue. Here, we sought to identify a second-generation class I HDAC inhibitor with prolonged pharmacodynamic response in vivo, to assess whether this results in superior antitumoral efficacy. Experimental Design: To identify novel HDAC inhibitors with superior pharmacodynamic properties, we developed a preclinical in vivo tumor model, in which tumor cells have been engineered to express fluorescent protein dependent on HDAC1 inhibition, thereby allowing noninvasive real-time evaluation of the tumor response to HDAC inhibitors. Results: In vivo pharmacodynamic analysis of 140 potent pyrimidyl-hydroxamic acid analogues resulted in the identification of JNJ-26481585. Once daily oral administration of JNJ-26481585 induced continuous histone H3 acetylation. The prolonged pharmacodynamic response translated into complete tumor growth inhibition in Ras mutant HCT116 colon carcinoma xenografts, whereas 5-fluorouracil was less active. JNJ-26481585 also fully inhibited the growth of C170HM2 colorectal liver metastases, whereas again 5-fluorouracil/Leucovorin showed modest activity. Further characterization revealed that JNJ-26481585 is a pan-HDAC inhibitor with marked potency toward HDAC1 (IC50, 0.16 nmol/L). Conclusions: The potent antitumor activity as a single agent in preclinical models combined with its favorable pharmacodynamic profile makes JNJ-26481585 a promising second-generation HDAC inhibitor. The compound is currently in clinical studies, to evaluate its potential applicability in a broad spectrum of both solid and hematologic malignancies. (Clin Cancer Res 2009;15(22):684151)

SNP arrays offer the opportunity to get a genome-wide view on copy number alterations and are increasingly used in oncology. DNA from formalin-fixed paraffin-embedded material (FFPE) is partially degraded which limits the application of those technologies for retrospective studies. We present the use of Affymetrix GeneChip SNP6.0 for identification of copy number alterations in fresh frozen (FF) and matched FFPE samples. Fifteen pairs of adenocarcinomas with both frozen and FFPE embedded material were analyzed. We present an optimization of the sample preparation and show the importance of correcting the measured intensities for fragment length and GC-content when using FFPE samples. The absence of GC content correction results in a chromosome specific "wave pattern" which may lead to the misclassification of genomic regions as being altered. The highest concordance between FFPE and matched FF were found in samples with the highest call rates. Nineteen of the 23 high level amplifications (83%) seen using FF samples were also detected in the corresponding FFPE material. For limiting the rate of "false positive" alterations, we have chosen a conservative False Discovery Rate (FDR). We observed better results using SNP probes than CNV probes for copy number analysis of FFPE material. This is the first report on the detection of copy number alterations in FFPE samples using Affymetrix GeneChip SNP6.0.

Capsule Regrowth rate of tail feathers is more strongly affected compared to feather length and symmetry. Aims To assess the value of avian feathers as bioindicators. Methods The origin and persistence of fluctuating asymmetry (FA) in homologous pairs of regrowing feathers was studied in captive birds under different levels of environmental stress, respresented by exposure to lead (Pb). Homologous feathers of individually housed birds were plucked synchronously or with a delay of seven days. We measured growth rate, regeneration time, final size and FA of regrown feathers and related them to Pb stress. Results Asymmetry decreased as feathers reached their final length. This was not due to compensatory growth but rather a consequence of the programmed growth trajectory of single feathers. Tail feathers grown under higher Pb pollution showed increased regeneration times, decreased growth rates and shorter lengths, but no changes in development times nor in FA. For differences between both (i) original and i...

Probe-level data from Affymetrix GeneChips can be summarized in many ways to produce probe-set level gene expression measures (GEMs). Disturbingly, the different approaches not only generate quite different measures but they could also yield very different analysis results. Here, we explore the question of how much the analysis results really do differ, first at the gene level, then at the biological process level. We demonstrate that, even though the gene level results may not necessarily match each other particularly well, as long as there is reasonably strong differentiation between the groups in the data, the various GEMs do in fact produce results that are similar to one another at the biological process level. Not only that the results are biologically relevant. As the extent of differentiation drops, the degree of concurrence weakens, although the biological relevance of findings at the biological process level may yet remain.Contact: damaratu@prdus.jnj.comSupplementary information: Supplementary data are available at Bioinformatics online.

Although much is known about the terrestrial locomotion of great apes, their arboreal locomotion has been studied less extensively. This study investigates arboreal locomotion in bonobos (Pan paniscus), focusing on the gait characteristics and spatio-temporal variables associated with locomotion on a pole. These features are compared across different substrate inclinations (0°, 30°, 45°, 60°, and 90°), and horizontal quadrupedal walking is compared between an arboreal and a terrestrial substrate. Our results show greater variation in footfall patterns with increasing incline, resulting in more lateral gait sequences. During climbing on arboreal inclines, smaller steps and strides but higher stride frequencies and duty factors are found compared to horizontal arboreal walking. This may facilitate better balance control and dynamic stability on the arboreal substrate. We found no gradual change in spatio-temporal variables with increasing incline; instead, the results for all inclines were clustered together. Bonobos take larger strides at lower stride frequencies and lower duty factors on a horizontal arboreal substrate than on a flat terrestrial substrate. We suggest that these changes are the result of the better grip of the grasping feet on an arboreal substrate. Speed modulation of the spatio-temporal variables is similar across substrate inclinations and between substrate types, suggesting a comparable underlying motor control. Finally, we contrast these variables of arboreal inclined climbing with those of terrestrial bipedal locomotion, and briefly discuss the results with respect to the origin of habitual bipedalism. Am. J. Primatol. 78:1165-1177, 2016. © 2016 Wiley Periodicals, Inc.

Summary Background Fibrosis progression in hepatitis C virus (HCV)-infected patients varies greatly between individuals. Chemokines recruit immune cells to the infected liver and may thus play a role in the fibrosis process. Aim To investigate plasma levels of a diverse chemokine panel in relation to liver fibrosis. Methods African-American and Caucasian HCV genotype 1 infected patients were treated with peginterferon (pegIFN) and ribavirin (RBV) for 48 weeks (VIRAHEP-C cohort). Plasma levels of 13 cytokines were studied at baseline (n = 386). Subsequently, GROα levels were assessed in a sub cohort (n = 99) at baseline, and at 4 and 12 weeks after start of pegIFN/RBV treatment. Results Increased severity of fibrosis (Ishak fibrosis score 0–2 vs. 3–6) was associated with increased plasma IP-10 (CXCL10) and IL-8 (CXCL8) levels, and decreased plasma levels of the chemokine growth-related oncogene (GRO, CXCL1-3). Plasma GRO levels were also positively correlated with platelet counts, and were higher in African-American as compared to Caucasian patients. In response to pegIFN/RBV treatment, GROα levels increased in Caucasian but not African-American patients from week 4 onwards. Conclusions The association with severity of fibrosis and platelet count positions plasma GRO as a potential biomarker for liver fibrosis in HCV-infected patients. The secretion of GRO by platelets may explain the correlation between GRO plasma level and platelet count. The ethnic difference in GRO levels both pre-treatment and in response to pegIFN/RBV might be driven by a genetic polymorphism in GROα associated with higher plasma levels and more common in the African-American population.

Integrating gene expression profiles with certain proteins can improve our understanding of the fundamental mechanisms in protein-ligand binding. This paper spotlights the integration of gene expression data and target prediction scores, providing insight into mechanism of action (MoA). Compounds are clustered based upon the similarity of their predicted protein targets and each cluster is linked to gene sets using Linear Models for Microarray Data. MLP analysis is used to generate gene sets based upon their biological processes and a qualitative search is performed on the homogeneous target-based compound clusters to identify pathways. Genes and proteins were linked through pathways for 6 of the 8 MCF7 and 6 of the 11 PC3 clusters. Three compound clusters are studied; (i) the target-driven cluster involving HSP90 inhibitors, geldanamycin and tanespimycin induces differential expression for HSP90-related genes and overlap with pathway response to unfolded protein. Gene expression results are in agreement with target prediction and pathway annotations add information to enable understanding of MoA. (ii) The antipsychotic cluster shows differential expression for genes LDLR and INSIG-1 and is predicted to target CYP2D6. Pathway steroid metabolic process links the protein and respective genes, hypothesizing the MoA for antipsychotics. A sub-cluster (verepamil and dexverepamil), although sharing similar protein targets with the antipsychotic drug cluster, has a lower intensity of expression profile on related genes, indicating that this method distinguishes close sub-clusters and suggests differences in their MoA. Lastly, (iii) the thiazolidinediones drug cluster predicted peroxisome proliferator activated receptor (PPAR) PPAR-alpha, PPAR-gamma, acyl CoA desaturase and significant differential expression of genes ANGPTL4, FABP4 and PRKCD. The targets and genes are linked via PPAR signalling pathway and induction of apoptosis, generating a hypothesis for the MoA of thiazolidinediones. Our analysis show one or more underlying MoA for compounds and were well-substantiated with literature.

Bayesian modeling of dose–response data offers the possibility to establish the relationship between a clinical or a genomic response and increasing doses of a therapeutic compound and to determine the nature of the relationship wherever it exists. In this article, we focus on an order-restricted one-way ANOVA model which can be used to test the null hypothesis of no dose effect against an ordered alternative. Within the framework of the dose–response modeling, a model uncertainty can be addressed using model averaging techniques. In this setting, the uncertainty is related to the number of all possible models that can be fitted to the data and should be taken into account for both inference and estimation. In this article, we propose an order-restricted Bayesian variable selection model that addresses the model uncertainty and can be used for both inference and estimation. The proposed method is applied to two case studies and is compared to the likelihood ratio test and the multiple contrast tests in both the analyses of the case studies and a simulation study. This article has online supplementary material. Martin Otava and Ziv Shkedy gratefully acknowledge the support from the IAP Research Network P7/06 of the Belgian State (Belgian Science Policy).

Inhibition of conditioned avoidance behavior in rats is generally considered predictive for antipsychotic activity in man. The present study investigated the mGlu2-mediated modulation of conditioned avoidance and compared mGlu2 agonists with available antipsychotics for their relative effects on conditioned avoidance behavior and locomotion. The mGlu2/3 orthosteric agonist 4-amino-2-thiabicyclo[3.1.0]hexane-4,6-dicarboxylic acid 2,2-dioxide (LY-404039) and mGlu2 positive allosteric modulator (PAM) 3-(cyclopropylmethyl)-7-(4-phenylpiperidin-1-yl)-8-(trifluoromethyl)[1,2,4]triazolo[4,3-a]pyridine (JNJ-42153605) inhibited avoidance and blocked escape behavior. The mGlu2/3 negative allosteric modulators (NAMs) 7-(dimethylamino)-4-(3-pyridin-3-ylphenyl)-8-(trifluoromethyl)-1,3-dihydro-2 H-1,5-benzodiazepin-2-one (JNJ-42112265) and 4-[3-(2,6-dimethylpyridin-4-yl)phenyl]-7-methyl-8-(trifluoromethyl)-1,3-dihydro-2H-1,5-benzodiazepin-2-one (RO-4491533) reversed the LY-404039-induced impairment of avoidance and escape. JNJ-42112265 also reversed the impairment of avoidance and escape induced by the mGlu2-specific PAM JNJ-42153605, suggesting that the effects on conditioned avoidance are specifically mGlu2-mediated. The mGlu2/3 antagonist (2-(2-carboxycyclopropyl)-3-(9H-xanthen-9-yl)-d-alanine (LY-341495; s.c.) reversed the LY-404039-induced escape impairment but failed to restore avoidance, suggesting interfering side effects. Like the tested antipsychotics, mGlu2/3 orthosteric and allosteric agonists inhibited avoidance behavior and locomotion at similar doses. Hence no clear-cut differences between mGlu2 modulators and currently available antipsychotics in the way they interfere with avoidance behavior in relation to inhibition of locomotion could be established.

Major depressive disorder has a large impact on patients and society and is projected to be the second greatest global burden of disease by 2020. The brain-derived neurotrophic factor (BDNF) gene is considered to be one of the important factors in the etiology of major depressive disorder. In a recent study, alpha power was found to mediate between BDNF Met and subclinical depressed mood. The current study looked at a population of patients with major depressive disorder (N = 107) to examine the association between the BDNF Val66Met polymorphism, resting state EEG alpha power, and depression severity. For this purpose, repeated-measures analysis of variance, partial correlation, and multiple linear models were used. Results indicated a negative association between parietal-occipital alpha power in the eyes open resting state and depression severity. In addition, Met/Met patients showed lower global absolute alpha power in the eyes closed condition compared with Val-carriers. These findings are in accordance with the previously uncovered pathway between BDNF Val66Met, resting state EEG alpha power, and depression severity. Additional research is needed for the clarification of this tentative pathway and its implication in personalized treatment of major depressive disorder.

Benchmark datasets are important for the validation and optimization of the analysis routes. Lately, a new benchmark dataset, ‘Platinum Spike’, for the Affymetrix GeneChip experiments has been introduced. We performed a quality check of the Platinum Spike dataset by using probe-level linear mixed models. The results have shown that there are ‘empty’ probe sets detecting transcripts, spiked in at different concentrations, and, reversely, there are probe sets that do not detect transcripts, spiked in at different concentrations, even though they were designed to do so. We proposed a formal inference procedure for testing the assumption of independence of all technical replicates in the data and concluded that for almost 10% of probe sets arrays cannot be treated independently, which has strong implications for the normalization procedures and testing for the differential expression. The proposed diagnostics procedure is used to facilitate a thorough exploration of gene expression Affymetrix data beyond the preprocessing and differential expression analysis.

The modern process of discovering candidate molecules in early drug discovery phase includes a wide range of approaches to extract vital information from the intersection of biology and chemistry. A typical strategy in compound selection involves compound clustering based on chemical similarity to obtain representative chemically diverse compounds (not incorporating potency information). In this paper, we propose an integrative clustering approach that makes use of both biological (compound efficacy) and chemical (structural features) data sources for the purpose of discovering a subset of compounds with aligned structural and biological properties. The datasets are integrated at the similarity level by assigning complementary weights to produce a weighted similarity matrix, serving as a generic input in any clustering algorithm. This new analysis work flow is semi-supervised method since, after the determination of clusters, a secondary analysis is performed wherein it finds differentially expressed genes associated to the derived integrated cluster(s) to further explain the compound-induced biological effects inside the cell. In this paper, datasets from two drug development oncology projects are used to illustrate the usefulness of the weighted similarity-based clustering approach to integrate multi-source high-dimensional information to aid drug discovery. Compounds that are structurally and biologically similar to the reference compounds are discovered using this proposed integrative approach.

Illumina bead arrays are microarrays that contain a random number of technical replicates (beads) for every probe (bead type) within the same array. Typically around 30 beads are placed at random positions on the array surface, which opens unique opportunities for quality control. Most preprocessing methods for Illumina bead arrays are ported from the Affymetrix microarray platform and ignore the availability of the technical replicates. The large number of beads for a particular bead type on the same array, however, should be highly correlated, otherwise they just measure noise and can be removed from the downstream analysis. Hence, filtering bead types can be considered as an important step of the preprocessing procedure for Illumina platform. This paper proposes a filtering method for Illumina bead arrays, which builds upon the mixed model framework. Bead types are called informative/non-informative (I/NI) based on a trade-off between within and between array variabilities. The method is illustrated on a publicly available Illumina Spike-in data set (Dunning et al., 2008) and we also show that filtering results in a more powerful analysis of differentially expressed genes.

The significance analysis of microarrays (SAM) Tusher et al. (Proc Natl Acad Sci 98:5116–5121, 2001) is a widely used testing procedure that estimates the FDR by using permutations under the assumption that all null hypotheses are true. The procedure consists of three components: (1) the adjusted test statistics, (2) an approximation of the distribution of the test statistics based on permutations, and (3) the control of the FDR. In Chap. 8, we discuss the implementation SAM for the setting of dose-response microarray experiments and illustrate how to use the IsoGene package for SAM.