Detection of elusive DNA copy-number variations in hereditary disease and cancer through the use of noncoding and off-target sequencing reads.

Copy-number variants (CNVs) play a substantial role in the molecular pathogenesis of hereditary disease and cancer, as well as in normal human interindividual variation. However, they are still rather difficult to identify in mainstream sequencing projects, especially involving exome sequencing, because they often occur in DNA regions that are not targeted for analysis. To overcome this problem, we developed OFF-PEAK, a user-friendly CNV detection tool that builds on a denoising approach and the use of "off-target" DNA reads, which are usually discarded by sequencing pipelines. We benchmarked OFF-PEAK on data from targeted sequencing of 96 cancer samples, as well as 130 exomes of individuals with inherited retinal disease from three different populations. For both sets of data, OFF-PEAK demonstrated excellent performance (>95% sensitivity and >80% specificity vs. experimental validation) in detecting CNVs from in silico data alone, indicating its immediate applicability to molecular diagnosis and genetic research.

Effects of the Glaucoma Drugs Latanoprost and Brimonidine on Corneal Temperature.

PURPOSE: The aim of this study was to investigate the effects of the glaucoma drugs latanoprost, brimonidine, and the combination of both on the central corneal temperature (CT) of healthy subjects by means of infrared thermography. Changes of the central CT may reflect changes of ocular blood flow. METHODS: Before application and during 2 hours after the application of latanoprost, brimonidine, or the combination of both in one eye, the CT in both eyes of 40 healthy subjects was measured repeatedly. RESULTS: Brimonidine reduced CT by approximately 0.5°C. This effect was statistically significant (P < 0.0001). Latanoprost, however, had a very small and insignificant influence (P = 0.47). Accordingly, the combination of brimonidine and latanoprost also reduced CT up to 0.5°C, and this effect was statistically significant (P < 0.0001). CONCLUSIONS: Brimonidine, but not latanoprost, had a significant effect on central CT. This cooling effect of brimonidine is most probably due to a drug-induced reduction of blood circulation in the ciliary body and iris and to a certain extent also to a reduction of blood flow in the fundus of the eye. TRANSLATIONAL RELEVANCE: This study shows evidence that thermography of the cornea provides indirect information on the influence of drugs on the blood flow to the anterior segment of the patient's eye.

Cornea Thermography: Optimal Evaluation of the Outcome and the Resulting Reproducibility.

PURPOSE: The aim of the study was to establish a standardized quantitative evaluation of corneal temperature (CT) that includes anchoring reference points in the topography and minimization of artifacts. We further investigated the distribution and the short- and long-term reproducibility of the CT values, as well as the influence of the core temperatures. METHODS: The CT values in both eyes of 40 healthy subjects were measured through thermography. These examinations took place over the course of four visits within 2 consecutive weeks. At each visit, the CTs were measured twice in both eyes with intervals of 15 minutes between measurements. RESULTS: CT values were not significantly different between the right and left eyes and their distribution was nearly normal. The CTs increased slightly when measured twice over the 15-minute intervals (short-term reproducibility) but remained stable over a period of 2 weeks (long-term reproducibility). In addition, the CT values depended on the core temperatures. CONCLUSIONS: Ocular surface thermography is a fast and noninvasive examination. The methods of optimized and standardized evaluation of the CT values facilitate comparisons and follow-ups. TRANSLATIONAL RELEVANCE: Thermography can be used clinically and scientifically only if both the measurement and its evaluation are efficient and standardized and if the outcomes are highly reproducible.

Diurnal and menstrual cycles in body temperature are regulated differently: a 28-day ambulatory study in healthy women with thermal discomfort of cold extremities and controls.

Diurnal cycle variations in body-heat loss and heat production, and their resulting core body temperature (CBT), are relatively well investigated; however, little is known about their variations across the menstrual cycle under ambulatory conditions. The main purpose of this study was to determine whether menstrual cycle variations in distal and proximal skin temperatures exhibit similar patterns to those of diurnal variations, with lower internal heat conductance when CBT is high, i.e. during the luteal phase. Furthermore, we tested these relationships in two groups of women, with and without thermal discomfort of cold extremities (TDCE). In total, 19 healthy eumenorrheic women with regular menstrual cycles (28-32 days), 9 with habitual TDCE (ages 29 ± 1.5 year; BMI 20.1 ± 0.4) and 10 controls without these symptoms (CON: aged 27 ± 0.8 year; BMI 22.7 ± 0.6; p < 0.004 different to TDCE) took part in the study. Twenty-eight days continuous ambulatory skin temperature measurements of distal (mean of hands and feet) and proximal (mean of sternum and infraclavicular regions) skin regions, thighs, and calves were carried out under real-life, ambulatory conditions (i-Buttons® skin probes, sampling rate: 2.5 min). The distal minus proximal skin temperature gradient (DPG) provided a valuable measure for heat redistribution from the core to the shell, and, hence, for internal heat conduction. Additionally, basal body temperature was measured sublingually directly after waking up in bed. Mean diurnal amplitudes in skin temperatures increased from proximal to distal skin regions and the 24-h mean values were inversely related. TDCE compared to CON showed significantly lower hand skin temperatures and DPG during daytime. However, menstrual cycle phase did not modify these diurnal patterns, indicating that menstrual and diurnal cycle variations in skin temperatures reveal additive effects. Most striking was the finding that all measured skin temperatures, together with basal body temperature, revealed a similar menstrual cycle variation (independent of BMI), with highest and lowest values during the luteal and follicular phases, respectively. These findings lead to the conclusion that in contrast to diurnal cycle, variations in CBT variation across the menstrual cycle cannot be explained by changes in internal heat conduction under ambulatory conditions. Although no measurements of metabolic heat production were carried out increased metabolic heat generation during the luteal phase seems to be the most plausible explanation for similar body temperature increases.

Diurnal blood pressure variations are associated with changes in distal-proximal skin temperature gradient.

It is generally assumed that skin vascular resistance contributes only to a small extent to total peripheral resistance and hence to blood pressure (BP). However, little is known about the impact of skin blood flow (SBF) changes on the diurnal variations of BP under ambulatory conditions. The main aim of the study was to determine whether diurnal patterns of distal SBF are related to mean arterial BP (MAP). Twenty-four-hour ambulatory measurements of BP, heart rate (HR) and distal (mean of hands and feet) as well as proximal (mean of sternum and infraclavicular region) skin temperatures were carried out in 51 patients (men/women = 18/33) during a 2-d eye hospital investigation. The standardized ambulatory protocol allowed measurements with minimal interference from uncontrolled parameters and, hence, some conclusive interpretations. The distal minus proximal skin temperature gradient (DPG) provided a measure for distal SBF. Individual cross-correlation analyses revealed that the diurnal pattern of MAP was nearly a mirror image of DPG and hence of distal SBF. Scheduled lunch and dinner induced an increase in DPG and a decline in MAP, while HR increased. Low daytime DPG (i.e. low distal SBF) levels significantly predicted sleep-induced BP dipping (r = -.436, p = .0014). Preliminary path analysis suggested that outdoor air temperature and atmospheric pressure may act on MAP via changed distal SBF. Changes in distal SBF may contribute to diurnal variation in MAP, including sleep-induced BP dipping and changes related to food intake. This finding might have an impact on individual cardiovascular risk prediction with respect to diurnal, seasonal and weather variations; however, the underlying mechanisms remain to be discovered.

Half a pack of cigarettes a day more than doubles DNA breaks in circulating leukocytes.

BACKGROUND: The mechanisms by which smoking induces damage is not known for all diseases. One mechanism believed to play a role is oxidative stress. Oxidative stress leads to cellular damage including DNA damage, particularly DNA breaks. We conducted this study to test the hypothesis that smokers have increased DNA breaks in their circulating leukocytes. METHODS: A comparative quantification of single-stranded DNA breaks was performed by comet assay analysis in the circulating leukocytes of ten healthy smokers (average smoking rate: half a pack a day, range: 9-12 cigarettes a day) and ten age and sex matched healthy non-smokers. DNA breaks lead to smaller pieces of DNA, which migrate out of the nucleus forming a tail during gel-electrophoresis. Damage of an individual cell was quantified by the parameters tail moment and olive moment. RESULTS: Smoking had a clear effect on both study parameters (tail and olive moment). Smokers had more than double the amount of ss-DNA breaks in their circulating leukocytes than non-smokers [tail moment: 0·75 AU [smokers] compared to 0·2 AU [non-smokers]; olive moment: 0·85 AU [smokers] compared to 0·3 AU [non-smokers]; both p < 0·001]. CONCLUSION: Smoking half a pack a day interferes with DNA integrity. One potential explanation for the enhanced DNA breaks in smokers is oxidative stress.

Smell perception in normal tension glaucoma patients.

PURPOSE: The aim of this study was to quantify the ability to identify odors in normal tension glaucoma (NTG) patients and healthy subjects with and without a primary vascular dysregulation (PVD). METHODS: Both self-assessment of smell perception and evaluation of odor identification by means of the 12-item odor identification test ("Sniffin' Sticks") were performed in the following groups of subjects: 1) 18 NTG patients with PVD (G+), 2) 18 NTG patients without PVD (G-), 3) 18 healthy subjects with PVD (H(+)) and 4) 18 healthy subjects without PVD (H-). The subjects self-assessment of smell perception was evaluated before the Sniffin' Sticks test by asking them to judge their ability to identify odors as either "average," "better than average," or "worse than average." RESULTS: Subjects with a PVD (G+ and H(+)) can identify odors significantly better than those without a PVD (G- and H-; in a score scale of 1-12 the score point difference=2.64, 95% CI=1.88-3.40, p<0.001). No significant differences in odor identification was found between NTG (groups G+ and G-) and healthy subjects (groups H(+) and H-; score point difference=-0.14, 95% CI=-0.9-0.62, p=0.72). CONCLUSIONS: Subjects with a PVD can identify odors significantly better than those without a PVD.