Twelve years of assessing the quality of preimplantation genetic testing for monogenic disorders

Objective

Genomics Quality Assessment has provided external quality assessments (EQAs) for preimplantation genetic testing (PGT) for 12 years for eight monogenic diseases to identify sub-optimal PGT strategies, testing and reporting of results, which can be shared with the genomics community to aid optimised standards of PGT services for couples.

Method

The EQAs were provided in two stages to mimic end-to-end protocols. Stage 1 involved DNA feasibility testing of a couple undergoing PGT and affected proband. Participants were required to report genotyping results and outline their embryo testing strategy. Lymphoblasts were distributed for mock embryo testing for stage 2. Submitted clinical reports and haplotyping results were assessed against peer-ratified criteria. Performance was monitored to identify poor performance.

Results

The most common testing methodology was short tandem repeat linkage analysis (59%); however, the adoption of single nucleotide polymorphism-based platforms was observed and a move from blastomere to trophectoderm testing. There was a variation in testing strategies, assigning marker informativity and understanding test limitations, some clinically unsafe. Critical errors were reported for genotyping and interpretation.

Conclusion

EQA provides an overview of the standard of preimplantation genetic testing-M clinical testing and identifies areas of improvement for accurate detection of high-risk embryos.     

The possible origin of Zostera noltii in the Canary Islands and guidelines for restoration

Seagrasses and their habitat are declining worldwide. Zostera noltii in the Canary Islands has been drastically reduced, mainly by anthropogenic disturbance, to three small surviving patches in a single harbor in Lanzarote. A previous genetic study, using neutral microsatellite markers, revealed that these patches consist of a single clonal individual. Here, an assignment test, using microsatellite data, was used to locate the most likely population of origin from a set of possible donor populations. Our results show that the Moulay Bousselham population in northern Morocco is assigned as the most likely population of origin (88%), although the probability of being at one generation time distance is low (2.7%). This result, however, allows locating the most closely related stands that may be the most successful donor populations for future restoration based on shoot or seed transplantation.     

Begging calls and parental feeding decisions in tree swallows (Tachycineta bicolor)

We conducted playback experiments to examine how parent tree swallows (Tachycineta bicolor) use nestling begging calls to distribute feedings to individuals within broods. In a first study, we used a paired-choice test to determine if parents discriminated between the taped begging calls of nestlings deprived of food and those of nestlings that had been recently fed. Our results showed that parents directed their first feeding attempt towards model nestlings near speakers playing deprived calls significantly more often than to models near speakers playing fed calls. They also made more feeding attempts overall to models with deprived calls. In the second study, we varied call rate and amplitude to examine which call features parents might use to discriminate begging calls. Parents directed significantly more first feeding attempts and more feeding attempts overall towards non-begging nestlings near speakers playing high call rates than to nestlings near speakers playing low call rates. They did not, however, discriminate between calls differing in amplitude. Previous studies have shown that parent birds use begging calls to regulate overall feeding rates to the brood. Our results suggest that parent tree swallows also use begging calls when feeding individual nestlings and, in particular, prefer calls associated with increased levels of nestling hunger. Received: 14 February 2000 / Revised: 6 October 2000 / Accepted: 16 October 2000     

Anaerobic treatment of atrazine bearing wastewater.

Performance of mixed microbial anaerobic culture in treating synthetic waste-water with high Chemical Oxygen Demand (COD) and varying atrazine concentration was studied. Performance of hybrid reactors with wood charcoal as adsorbent, with a dose of 10 g/l and 40 g/l, along with the microbial mass was also studied. All the reactors were operated in sequential mode with Hydraulic Retention Time (HRT) of 5 days. In all the cases, COD removal after 5 days was found to be above 81%. Initial COD was above 1,000 mg/l. From a hybrid reactor COD removal after 2 days was observed to be 90%. Atrazine reduction after 5 days by microbial mass alone was 43.8%, 40% and 33.2% with an initial concentration of 0.5, 1.0 and 2.0 mg/l respectively. MLSS on all the cases were almost same. Increasing MLSS concentration by about 2 fold did not increase the atrazine removal efficiency significantly. Maximum atrazine removal was observed to be 64% from the hybrid reactor with 10 g/l of wood charcoal and 69.4% from the reactor with 40 g/l of wood charcoal. Atrazine removal from the hybrid reactors after 15 days were observed to be 35.7% and 38.7%, which showed that the higher dose of wood charcoal in hybrid reactor did not improve the atrazine removal efficiency significantly. Specific methanogenic activity test showed no inhibitory effect of atrazine on methane producing bacteria. The performance of anaerobic microorganisms in removing atrazine with no external carbon source and inorganic nitrogen source was studied in batch mode. With an initial concentration of 1.0 mg/l, reduction of atrazine by the anaerobic microorganisms in absence of external carbon source after 35 days was observed to be 61.8% where as in absence of external carbon and inorganic nitrogen source the reduction was only 44.2% after 150 days. Volatilization loss of atrazine was observed to be insignificant.     

Prenatal DNA Sequencing: Clinical,Counseling, and Diagnostic Laboratory Considerations

Clinical diagnostic laboratories are producing next-generation sequencing-based test results that are becoming increasingly incorporated into patient care. Whole genome and exome sequencing on fetal material derived from amniocytes, chorionic villi, or products of conception is starting to be offered clinically in specialized centers, but it has not yet become routine practice. The technical, interpretation, and ethical challenges are greatest in the area of prenatal medicine because the fetus has a limited health history, and the physical examination is only indirectly available via prenatal sonography. Here, we provide an overview of these challenges and highlight the clinical utility, reporting, and counseling issues associated with prenatal DNA sequencing. Future considerations are also discussed. © 2017 John Wiley & Sons, Ltd.     

The Chartherm process,what’s in the name?

Earlier research has identified the Chartherm process (Thermya, France) as a candidate for the best available technology to treat chromated copper arsenate (CCA) impregnated wood waste. This paper presents the working principle, the characteristics and the current state-of-knowledge related to the process, illustrating clearly the differences with pyrolysis and carbonisation processes. To emphasise the specific nature of the process, it has been given its own name ‘chartherisation’. The avoidance of tar and dioxin release, the role of the solid matrix in the metal behaviour and the separation process are described. Furthermore, the possible benefits of working at elevated pressure are discussed, based on the experience with charcoal production from coal and biomass. This paper shows that more fundamental research is needed to understand and model all mechanisms contributing to the characteristic nature of chartherisation, in order to control the dynamic behaviour and tune the operating conditions in the reactor on the quality of the products requested.     

Fetal magnetocardiography using optically pumped magnetometers: a more adaptable and less expensive alternative?

Fetal magnetocardiography provides the requisite precision for diagnostic measurement of electrophysiological events in the fetal heart. Despite its significant benefits, this technique with current cryogenic based sensors has been limited to few centers, due to high cost of maintenance. In this study, we show that a less expensive non-cryogenic alternative, optically pumped magnetometers, can provide similar electrophysiological and quantitative characteristics when subjected to direct comparison with the current technology. Further research can potentially increase its clinical use for fetal magnetocardiography. © 2016 John Wiley & Sons, Ltd.