Pair Matcher (PaM): fast model-based optimization of treatment/case-control matches.

MOTIVATION: In clinical trials, individuals are matched using demographic criteria, paired and then randomly assigned to treatment and control groups to determine a drug's efficacy. A chief cause for the irreproducibility of results across pilot to Phase-III trials is population stratification bias caused by the uneven distribution of ancestries in the treatment and control groups. RESULTS: Pair Matcher (PaM) addresses stratification bias by optimizing pairing assignments a priori and/or a posteriori to the trial using both genetic and demographic criteria. Using simulated and real datasets, we show that PaM identifies ideal and near-ideal pairs that are more genetically homogeneous than those identified based on competing methods, including the commonly used principal component analysis (PCA). Homogenizing the treatment (or case) and control groups can be expected to improve the accuracy and reproducibility of the trial or genetic study. PaM's ancestral inferences also allow characterizing responders and developing a precision medicine approach to treatment. AVAILABILITY AND IMPLEMENTATION: PaM is freely available via Rhttps://github.com/eelhaik/PAM and a web-interface at http://elhaik-matcher.sheffield.ac.uk/ElhaikLab/. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.

A Computational Approach for the Prediction of Fatigue Behaviour in Peripheral Stents: Application to a Clinical Case.

Nickel-Titanium (NiTi) peripheral stents are commonly used for the treatment of diseased femoropopliteal arteries (FPA). However, cyclic deformations of the vessel, induced by limb movements affect device performance and fatigue failure may occur. Stent strut fracture has been described in the literature, and is implicated as a potential causative factor in vessel re-occlusion. In this paper, a numerical approach is proposed to predict the fatigue behaviour of peripheral NiTi stents within patient-specific arterial geometries, as additional information to aid clinician intervention planning. The procedure needs some patient-specific vessel features derived from routine clinical images but, when this information is not available, reference data from the literature may be used, obviously increasing the uncertainties of the results. In addition, specific stent material data are required and can be obtained from experimental tests. Several 3D finite element models resembling stented vessel segments are built and used for fatigue analyses. For each model, axial cyclic boundary conditions are obtained from a patient-specific lumped parameter model representing the entire artery as a series of suitable springs. This allows the simplification of stiffness changes along the vessel due to plaque and stent that affect local axial deformations. Imposed local cyclic bending values depend on the stent location along the FPA. The procedure is exemplified by its application to an actual clinical case that showed two strut fractures at 18 months follow-up. Interestingly, despite the lack of some of patient-specific information and the use of data from the literature to inform the model, the numerical approach was able to interpret the in vivo fractures.

Efficacy and safety of caspofungin in obese patients.

Safety and efficacy outcomes were retrospectively compared for obese versus non-obese patients who received standard caspofungin doses for different clinical conditions in nine clinical trials within the Merck caspofungin database. Favorable outcomes were as defined in specific protocols. Safety was assessed based on drug-related adverse experiences (AEs). The proportion of obese patients in the esophageal candidiasis and invasive aspergillosis studies was lower than seen in the invasive candidiasis and empirical therapy studies. The proportions of patients with a favorable response were generally similar in non-obese and obese patients with invasive candidiasis (73% versus 77%) or patients receiving empirical therapy (33% versus 40%). The efficacy analysis in patients with invasive aspergillosis or esophageal candidiasis was limited due to the small number of obese patients. The proportion of favorable responses in these two infections was similar among normal/underweight patients as compared to obese/overweight patients, i.e., esophageal candidiasis 81% versus 88% and invasive aspergillosis 48% versus 44%, respectively. AEs related to caspofungin occurred in similar proportions with non-obese and obese patients across all and within the four clinical conditions. The proportion of obese patients with serious drug-related AEs (1%) or caspofungin discontinuations due to toxicity (5%) was low. In the post-hoc analysis, caspofungin appeared to be as efficacious and well-tolerated in obese patients as in non-obese patients.

Raltegravir with optimized background therapy for resistant HIV-1 infection.

BACKGROUND: Raltegravir (MK-0518) is an inhibitor of human immunodeficiency virus type 1 (HIV-1) integrase active against HIV-1 susceptible or resistant to older antiretroviral drugs. METHODS: We conducted two identical trials in different geographic regions to evaluate the safety and efficacy of raltegravir, as compared with placebo, in combination with optimized background therapy, in patients infected with HIV-1 that has triple-class drug resistance in whom antiretroviral therapy had failed. Patients were randomly assigned to raltegravir or placebo in a 2:1 ratio. RESULTS: In the combined studies, 699 of 703 randomized patients (462 and 237 in the raltegravir and placebo groups, respectively) received the study drug. Seventeen of the 699 patients (2.4%) discontinued the study before week 16. Discontinuation was related to the study treatment in 13 of these 17 patients: 7 of the 462 raltegravir recipients (1.5%) and 6 of the 237 placebo recipients (2.5%). The results of the two studies were consistent. At week 16, counting noncompletion as treatment failure, 355 of 458 raltegravir recipients (77.5%) had HIV-1 RNA levels below 400 copies per milliliter, as compared with 99 of 236 placebo recipients (41.9%, P<0.001). Suppression of HIV-1 RNA to a level below 50 copies per milliliter was achieved at week 16 in 61.8% of the raltegravir recipients, as compared with 34.7% of placebo recipients, and at week 48 in 62.1% as compared with 32.9% (P<0.001 for both comparisons). Without adjustment for the length of follow-up, cancers were detected in 3.5% of raltegravir recipients and in 1.7% of placebo recipients. The overall frequencies of drug-related adverse events were similar in the raltegravir and placebo groups. CONCLUSIONS: In HIV-infected patients with limited treatment options, raltegravir plus optimized background therapy provided better viral suppression than optimized background therapy alone for at least 48 weeks. (ClinicalTrials.gov numbers, NCT00293267 and NCT00293254.)

Subgroup and resistance analyses of raltegravir for resistant HIV-1 infection.

BACKGROUND: We evaluated the efficacy of raltegravir and the development of viral resistance in two identical trials involving patients who were infected with human immunodeficiency virus type 1 (HIV-1) with triple-class drug resistance and in whom antiretroviral therapy had failed. METHODS: We conducted subgroup analyses of the data from week 48 in both studies according to baseline prognostic factors. Genotyping of the integrase gene was performed in raltegravir recipients who had virologic failure. RESULTS: Virologic responses to raltegravir were consistently superior to responses to placebo, regardless of the baseline values of HIV-1 RNA level; CD4 cell count; genotypic or phenotypic sensitivity score; use or nonuse of darunavir, enfuvirtide, or both in optimized background therapy; or demographic characteristics. Among patients in the two studies combined who were using both enfuvirtide and darunavir for the first time, HIV-1 RNA levels of less than 50 copies per milliliter were achieved in 89% of raltegravir recipients and 68% of placebo recipients. HIV-1 RNA levels of less than 50 copies per milliliter were achieved in 69% and 80% of the raltegravir recipients and in 47% and 57% of the placebo recipients using either darunavir or enfuvirtide for the first time, respectively. At 48 weeks, 105 of the 462 raltegravir recipients (23%) had virologic failure. Genotyping was performed in 94 raltegravir recipients with virologic failure. Integrase mutations known to be associated with phenotypic resistance to raltegravir arose during treatment in 64 patients (68%). Forty-eight of these 64 patients (75%) had two or more resistance-associated mutations. CONCLUSIONS: When combined with an optimized background regimen in both studies, a consistently favorable treatment effect of raltegravir over placebo was shown in clinically relevant subgroups of patients, including those with baseline characteristics that typically predict a poor response to antiretroviral therapy: a high HIV-1 RNA level, low CD4 cell count, and low genotypic or phenotypic sensitivity score. (ClinicalTrials.gov numbers, NCT00293267 and NCT00293254.)