Implementation of non-invasive prenatal testing by semiconductor sequencing in a genetic laboratory

Objectives: To implement non-invasive prenatal testing (NIPT) for fetal aneuploidies with semiconductor sequencing in an academic cytogenomic laboratory and to evaluate the first 15-month experience on clinical samples. Methods: We validated a NIPT protocol for cell-free fetal DNA sequencing from maternal plasma for the detection of trisomy 13, 18 and 21 on a semiconductor sequencing instrument. Fetal DNA fraction calculation for all samples and several quality parameters were implemented in the workflow. One thousand eighty-one clinical NIPT samples were analysed, following the described protocol. Results: Non-invasive prenatal testing was successfully implemented and validated on 201 normal and 74 aneuploid samples. From 1081 clinical samples, 17 samples showed an abnormal result: 14 trisomy 21 samples, one trisomy 18 and one trisomy 16 were detected. Also a maternal copy number variation on chromosome 13 was observed, which could potentially lead to a false positive trisomy 13 result. One sex discordant result was reported, possibly attributable to a vanishing twin. Moreover, our combined fetal fraction calculation enabled a more reliable risk estimate for trisomy 13, 18 and 21. Conclusions: Non-invasive prenatal testing for trisomy 21, 18 and 13 has a very high specificity and sensitivity. Because of several biological phenomena, diagnostic invasive confirmation of abnormal results remains required

Glucose metabolism during bovine preimplantation development: analysis of gene expression in single oocytes and embryos.

peer reviewedGlucose metabolism of the bovine embryo is low during the first cleavages and increases sharply after the major resumption of the genome (8-16 cells). The mRNA level for genes involved in glucose metabolism was tested by RT-PCR on individual oocytes and embryos at different stages of development. These genes were: glucose transport GLUT-1, hexokinase (HK), glucose-6-phosphatase-dehydrogenase (G6PDH), and glucose-phosphate-isomerase (GPI); actin was used as a reference transcript. RT-PCR results revealed three types of oocytes or embryos: positive with a PCR signal for each transcript considered, nul with no signal for any transcript, and heterogeneous with a PCR signal for some transcripts and none for others. The number of nul and heterogeneous samples was higher for slow than for fast-cleaving embryos (81% vs. 36%), and the proportion of positive embryos increased significantly at the 16-cell and morula stages (P < 0.002), suggesting a correlation between mRNA content and developmental capacity. In positive embryos, GLUT-1 level was reduced by half during maturation and fertilization. Actin and hexokinase mRNA levels decreased during the first cleavages, but significantly increased at the 16-cell and morula stages, respectively. GPI transcript remained stable throughout development, whereas there was a significant rise for G6PDH at the 4-cell stage, perhaps due to a polyadenylation process. Finally, the absence or decrease in intensity of several transcripts at the blastocyst stage suggests suboptimal culture conditions

Impact of chronic somatoform and osteoarthritis pain on conscious and preconscious cognitive processing

The study investigates the impact of chronic pain (CP) on conscious and preconscious cognitive processes and on guessing behavior, and examines the mediating effect of a depressive state. Twenty-eight patients with CP due to hip osteoarthritis, 32 patients with a somatoform disorder including pain symptoms, and 31 participants who did not have CP were examined within the framework of a modified Process-Dissociation-Procedure. Neutral, health threatening and general threatening stimuli were presented acoustically in a lexical decision task. Parameters of conscious processing, preconscious processing, and of chance were estimated by a multinomial modelling procedure. CP-patients with osteoarthritis showed the lowest level of conscious processing and the highest level of guessing behavior. Patients with somatoform pain tended to react preconsciously to health threatening stimuli but overall showed a profile similar to that of controls who did not have CP. The impact of the threatening quality of stimuli on different levels of cognitive processing was weak. Depression did not mediate between the experience of pain and estimates of conscious and preconscious processing. Perspective: The impact of CP on preconscious and conscious cognitive processing depends on types and causes of pain. The experience of CP caused by inflammation or physical damage tends to reduce the probability of conscious processing and to provoke memory biases. CP in the context of a somatoform disorder seems to have less impact on cognitive functions

A Rank-Based Nonparametric Method for Mapping Quantitative Trait Loci in Outbred Half-Sib Pedigrees: Application to Milk Production in a Granddaughter Design

We describe the development of a multipoint nonparametric quantitative trait loci mapping method based on the Wilcoxon rank-sum test applicable to outbred half-sib pedigrees. The method has been evaluated on a simulated dataset and its efficiency compared with interval mapping by using regression. It was shown that the rank-based approach is slightly inferior to regression when the residual variance is homoscedastic normal; however, in three out of four other scenarios envisaged, i.e., residual variance heteroscedastic normal, homoscedastic skewed, and homoscedastic positively kurtosed, the latter outperforms the former one. Both methods were applied to a real data set analyzing the effect of bovine chromosome 6 on milk yield and composition by using a 125-cM map comprising 15 microsatellites and a granddaughter design counting 1158 Holstein-Friesian sires

Short-term prospective memory deficits in chronic back pain patients

Objective: Chronic pain, particularly low back pain, is widespread. Although a great deal is known about the impact that this has on quality of life and physical activity, relatively little has been established regarding the more cognitive effects of pain. This study aims to find out whether individuals with chronic pain experience memory deficits in prospective memory (PM), the process of remembering to do things at some future point in time. Examples of PM include remembering to keep an appointment, such as a visit to a clinic, or to perform a particular task, such as paying a bill on time. Methods: The PM of 50 participants with chronic pain was compared with 50 pain-free participants. Each participant completed the Prospective Memory Questionnaire, which assesses three aspects of prospective memory (short-term habitual, long-term episodic, and internally cued), and records the use of strategies to aid remembering. Results: In comparison to those not in pain, participants with chronic pain had significantly impaired short-term prospective memory, an effect which was evident even after co-varying use of analgesics and other drugs. Conclusions: These findings provide new insights into prospective memory dysfunction in people with chronic pain. Possible mechanisms for this dysfunction are discussed and suggestions for future research given

Pressure Dependence of the Frequency Permeability Spectra of Soft Ferrite Composite Materials: A Method of Measuring the Natural Ferromagnetic Resonance Frequency

International audienceExperimental studies on the complex susceptibility of soft magnetic composite materials (magnetostrictive Ni-Zn and Ni-Zn-Co spinels) in their region of ferrimagnetic resonance (FMR) show that the FMR is an increasing function of the applied pressure. It is shown that powders could advantageously replace their sintered materials counterpart to measure without any ambiguity the natural ferrimagnetic resonance (NFMR) frequencies of bulk materials. It is also shown that such soft ferrite composites can be realized in order to shift FMR to higher values, and to obtain low magnetic losses up to 900 MHz. High frequencies applications can be envisaged

Influence de ferrites de Ni-Zn dans la miniaturisation d'antennes pour applications DVB-H.

National audienceCette étude se situe dans la problématique de la miniaturisation d'antennes dans le domaine de fréquences 470-862MHz, correspondant à la norme DVB-H. Dans cet objectif les propriétés magnétostrictives de ferrites de Ni-Zn sont mises à profit pour étendre jusqu'à 1 GHz leur potentialité d'application comme substrats d'antennes. Les matériaux réalisés présentent des tangentes de pertes magnétiques qui restent inférieures à 5.10-2 dans la gamme de fréquence 100MHZ-1GHz, avec une perméabilité constante et un indice optique proche de 3 pour le matériau présenté Cette valeur pourra être aisément augmentée jusqu'à 4,5 environ. Ces propriétés prédisposent ces matériaux aux applications dans le domaine UHF

Fitting and validating the genomic evaluation model to Polish Holstein-Friesian cattle

The aim of the study was to fit the genomic evaluation model to Polish Holstein-Friesian dairy cattle. A training data set for the estimation of additive effects of single nucleotide polymorphisms (SNPs) consisted of 1227 Polish Holstein-Friesian bulls. Genotypes were obtained by the use of Illumina BovineSNP50 Genotyping BeadChip. Altogether 29 traits were considered: milk-, fat- and protein- yields, somatic cell score, four female fertility traits, and 21 traits describing conformation. The prediction of direct genomic values was based on a mixed model containing deregressed national proofs as a dependent variable and random SNP effects as independent variables. The correlations between direct genomic values and conventional estimated breeding values estimated for the whole data set were overall very high and varied between 0.98 for production traits and 0.78 for non return rates for cows. For the validation data set of 232 bulls the corresponding correlations were 0.38 for milk-, 0.37 for protein-, and 0.32 for fat yields, while the correlations between genomic enhanced breeding values and conventional estimated breeding values for the four traits were: 0.43, 0.44, 0.31, and 0.35. This model was able to pass the interbull validation criteria for genomic selection, which indicates that it is realistic to implement genomic selection in Polish Holstein-Friesian cattle

Dominance and parent-of-origin effects of coding and non-coding alleles at the acylCoA-diacylglycerol-acyltransferase (DGAT1) gene on milk production traits in German Holstein cows

<p>Abstract</p> <p>Background</p> <p>Substantial gene substitution effects on milk production traits have formerly been reported for alleles at the K232A and the promoter VNTR loci in the bovine acylCoA-diacylglycerol-acyltransferase 1 (<it>DGAT1</it>) gene by using data sets including sires with accumulated phenotypic observations of daughters (breeding values, daughter yield deviations). However, these data sets prevented analyses with respect to dominance or parent-of-origin effects, although an increasing number of reports in the literature outlined the relevance of non-additive gene effects on quantitative traits.</p> <p>Results</p> <p>Based on a data set comprising German Holstein cows with direct trait measurements, we first confirmed the previously reported association of <it>DGAT1 </it>promoter VNTR alleles with milk production traits. We detected a dominant mode of effects for the <it>DGAT1 </it>K232A and promoter VNTR alleles. Namely, the contrasts between the effects of heterozygous individuals at the <it>DGAT1 </it>loci differed significantly from the midpoint between the effects for the two homozygous genotypes for several milk production traits, thus indicating the presence of dominance. Furthermore, we identified differences in the magnitude of effects between paternally and maternally inherited <it>DGAT1 </it>promoter VNTR – K232A haplotypes indicating parent-of-origin effects on milk production traits.</p> <p>Conclusion</p> <p>Non-additive effects like those identified at the bovine <it>DGAT1 </it>locus have to be accounted for in more specific QTL detection models as well as in marker assisted selection schemes. The <it>DGAT1 </it>alleles in cattle will be a useful model for further investigations on the biological background of non-additive effects in mammals due to the magnitude and consistency of their effects on milk production traits.</p