Prenatal diagnosis of fetal aneuploidies: post-genomic developments

Prenatal diagnosis of fetal aneuploidies and chromosomal anomalies is likely to undergo a profound change in the near future. On the one hand this is mediated by new technical developments, such as chromosomal microarrays, which allow a much more precise delineation of minute sub-microscopic chromosomal aberrancies than the classical G-band karyotype. This will be of particular interest when investigating pregnancies at risk of unexplained development delay, intellectual disability or certain forms of autism. On the other hand, great strides have been made in the non-invasive determination of fetal genetic traits, largely through the analysis of cell-free fetal nucleic acids. It is hoped that, with the assistance of cutting-edge tools such as digital PCR or next generation sequencing, the long elusive goal of non-invasive prenatal diagnosis for fetal aneuploidies can finally be attained

Implementing Prenatal Diagnosis Based on Cell-Free Fetal DNA: Accurate Identification of Factors Affecting Fetal DNA Yield

Objective: Cell-free fetal DNA is a source of fetal genetic material that can be used for non-invasive prenatal diagnosis. Usually constituting less than 10% of the total cell free DNA in maternal plasma, the majority is maternal in origin. Optimizing conditions for maximizing yield of cell-free fetal DNA will be crucial for effective implementation of testing. We explore factors influencing yield of fetal DNA from maternal blood samples, including assessment of collection tubes containing cell-stabilizing agents, storage temperature, interval to sample processing and DNA extraction method used.Methods: Microfluidic digital PCR was performed to precisely quantify male (fetal) DNA, total DNA and long DNA fragments (indicative of maternal cellular DNA). Real-time qPCR was used to assay for the presence of male SRY signal in samples.Results: Total cell-free DNA quantity increased significantly with time in samples stored in K(3)EDTA tubes, but only minimally in cell stabilizing tubes. This increase was solely due to the presence of additional long fragment DNA, with no change in quantity of fetal or short DNA, resulting in a significant decrease in proportion of cell-free fetal DNA over time. Storage at 4 degrees C did not prevent these changes.Conclusion: When samples can be processed within eight hours of blood draw, K(3)EDTA tubes can be used. Prolonged transfer times in K(3)EDTA tubes should be avoided as the proportion of fetal DNA present decreases significantly; in these situations the use of cell stabilising tubes is preferable. The DNA extraction kit used may influence success rate of diagnostic tests

Absolute values of the London penetration depth in YBa2Cu3O6+y measured by zero field ESR spectroscopy on Gd doped single crystals

Zero-field electron spin resonance (ESR) of dilute Gd ions substituted for Y in the cuprate superconductor YBa$_2$Cu$_3$O$_{\rm 6+y}$ is used as a novel technique for measuring the absolute value of the low temperature magnetic penetration depth $\lambda(T\to 0)$. The Gd ESR spectrum of samples with $\approx 1$ substitution was obtained with a broadband microwave technique that measures power absorption bolometrically from 0.5 GHz to 21 GHz. This ESR spectrum is determined by the crystal field that lifts the level degeneracy of the spin 7/2 Gd$^{3+}$ ion and details of this spectrum provide information concerning oxygen ordering in the samples. The magnetic penetration depth is obtained by relating the number of Gd ions exposed to the microwave magnetic field to the frequency-integrated intensity of the observed ESR transitions. This technique has allowed us to determine precise values of $\lambda$ for screening currents flowing in the three crystallographic orientations ($\hat a$, $\hat b$ and $\hat c$) in samples of Gd$_{\rm x}$Y$_{\rm 1-x}$Ba$_2$Cu$_3$O$_{6+{\rm y}}$ of three different oxygen contents ${\rm y}=0.993$ ($T_c = 89$ K), ${\rm y}=0.77$ ($T_c=75$ K) and ${\rm y}=0.52$ ($T_c=56$ K). The in-plane values are found to depart substantially from the widely reported relation $T_c\propto 1/\lambda^2$.Comment: 14 pages, 12 figures; version to appear in PR

Electrochemical detection of low-copy number salivary RNA based on specific signal amplification with a hairpin probe

We developed a technique for electrochemical detection of salivary mRNA employing a hairpin probe (HP). Steric hindrance (SH) suppresses unspecific signal and generates a signal-on amplification process for target detection. The stem-loop configuration brings the reporter end of the probe into close proximity with the surface and makes it unavailable for binding with the mediator. Target binding opens the hairpin structure of the probe, and the mediator can then bind to the accessible reporter. Horseradish peroxidase is utilized to generate electrochemical signal. This signal-on process is characterized by a low basal signal, a strong positive readout and a large dynamic range. The SH is controlled via hairpin design and electrical field. By applying electric field control to HPs, the limit of detection of RNA is about 0.4 fM, which is 10 000-fold more sensitive than conventional linear probes. Endogenous Interleukin-8 mRNA is detected with the HP, and good correlation with the quantitative PCR technique is obtained. The resultant process allows a simple setup and by reducing the number of steps it is suited for the point-of-care detection of specific nucleic acid sequences from complex body fluids such as saliva

Is standard breast-conserving therapy (BCT) in elderly breast cancer patients justified? A prospective measurement of acute toxicity according CTC-classification

<p>Abstract</p> <p>Background</p> <p>Breast conserving therapy (BCT) is an accepted treatment for early-stage breast cancer. This study aimed to measure prospectively acute radiation-related toxicity and to create a comprehensive data base for long-term temporal analyses of 3D conformal adjuvant radiotherapy. The specific aspect of age has been neglected by traditional research. Therefore, the impact of age on acute BCT toxicity should be also specifically adressed.</p> <p>Methods</p> <p>Toxicity was measured in 109 patients at initiation (t1), during radiotherapy (t2-t7), and 6 weeks after treatment completion (t8) using a new topographic module. Organ systems were recorded in 15 scales and scored according to symptom intensity (grade 0-5) based on CTC (Common Toxicity Criteria) -classification. Radiotherapy was virtually CT-based planned and applied with 6-MeV-photons. Mean total dose was 60.1 Gy. Patients were stratified by age in 3 Groups: <50, 50-60, and >60 years.</p> <p>Results</p> <p>Registered toxicity was generally low. Mean overall-grade climbed from 0.29-0.40 (t1-t7), and dropped to 0.23 (t8). Univariate analyses revealed slightly higher toxicity in older (> 60 years) versus young patients (< 50 years) in 2 scales only: breast-symmetry (p = 0.033), and arm function (p = 0.007). However, in the scale "appetite" toxicity was higher in younger (< 50 years) versus older (> 60 years) patients (p = 0.039). Toxicity differences in all other scales were not significant. Between older (> 60 years) and midaged patients (50-60 years) no significant differences in toxicity were found. This was also true for the comparison between young (< 50 years) versus midaged patient groups (50-60 years).</p> <p>Conclusion</p> <p>The treatment concept of BCT for breast cancer is generally well tolerated. The toxicity-measurement with the new topographic module is feasible. Not modified standard treatment for BC should be performed in elderly women.</p

Phase Separation Models for Cuprate Stripe Arrays

An electronic phase separation model provides a natural explanation for a large variety of experimental results in the cuprates, including evidence for both stripes and larger domains, and a termination of the phase separation in the slightly overdoped regime, when the average hole density equals that on the charged stripes. Several models are presented for charged stripes, showing how density waves, superconductivity, and strong correlations compete with quantum size effects (QSEs) in narrow stripes. The energy bands associated with the charged stripes develop in the middle of the Mott gap, and the splitting of these bands can be understood by considering the QSE on a single ladder.Comment: significant revisions: includes island phase, 16 eps figures, revte

Parkinson’s disease: evolution of cognitive impairment and CSF Aβ₁−₄₂ profiles in a prospective longitudinal study

OBJECTIVE: To evaluate the evolution of cognitive impairment in relation to cerebrospinal fluid (CSF) profiles of amyloid-β (Aβ), total-Tau and phosphorylated-Tau in Parkinson’s disease (PD). METHODS: Prospective, longitudinal, observational study up to 10 years with follow-up every 2  years. We assessed CSF profiles in 415 patients with sporadic PD (median age 66; 63% men) and 142 healthy controls (median age 62; 43% men). RESULTS: Patients with PD with low CSF Aβ₁−₄₂ levels at baseline were more often cognitively impaired than patients with intermediate and high Aβ₁−₄₂ levels. Sixty-seven per cent of the patients with low Aβ₁−₄₂ levels at baseline and normal cognition developed cognitive impairment during follow-up, compared with 41% and 37% of patients having intermediate and high CSF Aβ₁−₄₂ levels. Kaplan-Meier survival curves and Cox regression revealed that patients with low CSF Aβ₁−₄₂ levels at baseline developed cognitive impairment more frequently and earlier during follow-up. CONCLUSION: We conclude that in patients with sporadic PD, low levels of Aβ₁−₄₂ are associated with a higher risk of developing cognitive impairment earlier in the disease process at least in a subgroup of patients

Genome-wide association meta-analysis for early age-related macular degeneration highlights novel loci and insights for advanced disease

Peer reviewedPublisher PD

Single hadron response measurement and calorimeter jet energy scale uncertainty with the ATLAS detector at the LHC

The uncertainty on the calorimeter energy response to jets of particles is derived for the ATLAS experiment at the Large Hadron Collider (LHC). First, the calorimeter response to single isolated charged hadrons is measured and compared to the Monte Carlo simulation using proton-proton collisions at centre-of-mass energies of sqrt(s) = 900 GeV and 7 TeV collected during 2009 and 2010. Then, using the decay of K_s and Lambda particles, the calorimeter response to specific types of particles (positively and negatively charged pions, protons, and anti-protons) is measured and compared to the Monte Carlo predictions. Finally, the jet energy scale uncertainty is determined by propagating the response uncertainty for single charged and neutral particles to jets. The response uncertainty is 2-5% for central isolated hadrons and 1-3% for the final calorimeter jet energy scale.Comment: 24 pages plus author list (36 pages total), 23 figures, 1 table, submitted to European Physical Journal