Clinical outcome of subchromosomal events detected by whole-genome noninvasive prenatal testing

Objective

A novel algorithm to identify fetal microdeletion events in maternal plasma has been developed and used in clinical laboratory‐based noninvasive prenatal testing. We used this approach to identify the subchromosomal events 5pdel, 22q11del, 15qdel, 1p36del, 4pdel, 11qdel, and 8qdel in routine testing. We describe the clinical outcomes of those samples identified with these subchromosomal events.

Methods

Blood samples from high‐risk pregnant women submitted for noninvasive prenatal testing were analyzed using low coverage whole genome massively parallel sequencing. Sequencing data were analyzed using a novel algorithm to detect trisomies and microdeletions.

Results

In testing 175 393 samples, 55 subchromosomal deletions were reported. The overall positive predictive value for each subchromosomal aberration ranged from 60% to 100% for cases with diagnostic and clinical follow‐up information. The total false positive rate was 0.0017% for confirmed false positives results; false negative rate and sensitivity were not conclusively determined.

Conclusion

Noninvasive testing can be expanded into the detection of subchromosomal copy number variations, while maintaining overall high test specificity. In the current setting, our results demonstrate high positive predictive values for testing of rare subchromosomal deletions. © 2015 The Authors. Prenatal Diagnosis published by John Wiley & Sons Ltd.

What's already known about this topic?

Circulating cell free DNA is a powerful clinical tool that can detect whole chromosomal aneuploidies in a fetus as early as 10 weeks with high specificity and high sensitivity. Subchromosomal events in the fetus have been shown to be detected via ccfDNA via whole genome sequencing.

What does this study add?

This study shows that ccfDNA whole genome analysis for fetal subchromosomal aneuploidies including clinically significant microdeletions can be tested clinically with high specificity and high positive predictive value (PPV).

Influence of Solid Phase and Formulation Processing on Stability of Abbott-232 Tablet Formulations

Abbott-232 is a chemically stable, highly water soluble non-hygroscopic compound selected for development as a potent uroselective alpha(1A) agonist. An anhydrate, a monohydrate, and an amorphous phase were isolated. The anhydrate was chosen for formulation development based on solid-state characterization. Excipients for immediate release (IR) tablet formulations were selected according to compatibility studies. However, the prototype IR tablets designed for clinical trials were found to be chemically unstable. Thus, process-induced phase transformation was investigated as the likely cause of the observed instability. Since the drug loading in the formulations was low (1%), model granulations containing 30% drug were evaluated to test this hypothesis. Investigation using a variety of analytical techniques indicated that the observed degradation was, indeed, a result of a solution-mediated phase transformation from anhydrate to amorphous Abbott-232 during wet granulation. A new direct compression formulation was, therefore, developed to prevent the solution-mediated process induced phase transition. Since the drug loading was low, a polarized light microscope (PLM) method was used to evaluate the solid phase in the new formulation. PLM confirmed that the original anhydrate form remained unchanged in tablets manufactured by the dry process. Stability studies confirmed that both IR and extended release (ER) tablets of Abbott-232 were successfully developed for clinical trials using direct compression.

Exploiting plant somatic radiation hybrids for physical mapping of expressed sequence tags

Methods are described for the optimisation of the generation of radiation hybrids suitable for physical mapping of a plant (barley) genome. A combination of PCR-based technologies, involving the use of whole genome, mixed primer and hemi-nested primer amplifications, can greatly extend their utility for the physical mapping of expressed sequence tags (ESTs). Using panels of hybrids and ESTs, donor DNA retention and individual marker retention frequencies for the expressed portion of the barley genome in the hybrids were estimated.

Metabolic responses of cultured cells to oxygenated perfluorocarbon

Protoplast-derived cells of albino Petunia hybrida cv. Comanche were used as a model, nonphotosynthetic, eukaryotic plant system to study changes in (1) the rate of oxygen consumption as measured by a Clark-type oxygen microelectrode, (2) mitochondrial membrane potential (MMP) as assessed by Rhodamine 123 fluorescence, and (3) intracellular activities of superoxide dismutases (SOD, EC 1.15.1.1) and catalases (CAT, EC 1.11.1.6), following culture for up to 14 d in aqueous nutrient medium overlaying oxygen-gassed perfluorodecalin (Flutec PP5; F2 Chemicals, Preston, UK). The mean (+/- s.e.m., n = 7) rate of oxygen consumption of Petunia cells after 24 h of culture in the presence of oxygenated PFC was 14.3 +/- 1.6 mol O2 ml(-1) min(-1), compared to 9.7 +/- 0.8 micromol O2 ml(-1) min(-1) for untreated (control) cells (P < 0.05). Similarly, the culture of cells with oxygenated PFC for 24 h resulted in a significant (P < 0.05) increase of over 50% in the mean MMP, compared to the control. Culture of protoplasts with oxygenated PFC also produced significant (P < 0.05) increases in both mean SOD and CAT activities after 3-7 d of culture, the former comparable to that reported previously for protoplasts of Salpiglossis sinuata cultured with oxygenated PFC.

A preliminary study of mental and physical practice on the kayak wet exit skill

Outdoor activities and high-risk water sports often create anxiety in participants who feel concern about danger. Relaxation and imagery, often used to enhance training, can improve performance of skills in a variety of sports. The aim of this study was to establish whether Mental Practice, Physical Practice, Combined Mental and Physical Practice, or No Practice would affect the acquisition of skill for a kayak wet exit. 60 postprimary girls aged 11-16 yr., competent swimmers but without previous experience in kayaking, gave their informed consent to be in the study. Each participant was randomly assigned to one of the four experimental groups. Following their practice periods, each group performed three kayak wet exit attempts (unseen by others); these were videotaped for later analysis by an observer. The participant and an independent observer, who was blind to the allocation of practice group, then used a 6-point rating scale to assess each performance. Participants' and the observer's ratings were analysed by separate Kruskal-Wallis one-way analysis of variance which indicated a significant practice effect. Subsequent chi-squared tests indicated significantly different distributions of groups, showing Physical Practice superior to No Practice and Mental Practice. While physical practice remained effective in improving technique, combinations of mental and physical practice were better than no practice.

Determination of erythromycin and related substances in enteric-coated tablet formulations by reversed-phase liquid chromatography

An isocratic method for the identification and quantitation of erythromycin and related substances in enteric-coated tablet formulations using high-performance liquid chromatography (HPLC) with ultraviolet (UV) detection at 205 nm is described. A novel method for sample preparation using a molecular weight centrifuge filter to reduce the interferences observed from polymeric tablet coating material is also presented. Erythromycin HPLC assays are best run at high pH; therefore, various polymer columns were evaluated. The resulting HPLC method that was developed has several advantages over current pharmacopeial assay methods for enteric-coated erythromycin tablets. Comparative data from both methods for the same batch of EryTab tablets are presented. The method can also be applied to various other erythromycin formulations, including particle-coated tablets, erythromycin stearate tablets, and erythromycin ethylsuccinate suspensions and fermentation broths. A C18 Polymeric column is used with a mobile phase composition of 0.02 M potassium phosphate dibasic buffer (pH 9): acetonitrile (60:40) and flow rate of 1 mL/min. This method is more sensitive, specific, and rugged than the pharmacopeial method.

Drug release from spray layered and coated drug-containing beads: effects of pH and comparison of different dissolution methods

Based on dissolution profiles of three model drugs on spray layered beads with the same percentage of Aquacoat coating, it was concluded that in vitro dissolution of oral controlled-release formulations should be performed in both gastric and intestinal media for ionizable drugs. Ketoprofen (weak acid, pKa 4.8), nicardipine HCl (salt of weak organic base, pKa 8.6), and acetaminophen (very weak organic acid, pKa 9.7, not ionized at physiologic pH) provided different dissolution characteristics in enzyme-free simulated gastric fluid (pH 1.4) and enzyme-free simulated intestinal fluid (pH 7.4), indicating that the rate of drug release was pH dependent and related to drug ionization even though the solubility of the coating (ethylcellulose) is pH independent. In acidic media, ketoprofen release from the beads containing low-level coating (3%) was slower than that of nicardipine HCl, with the opposite holding true in basic media. Acetaminophen was released at approximately the same rate in both acidic and basic media. A comparison of drug release profiles for nicardipine HCl nude beads was also investigated among three different dissolution methods: USP dissolution apparatus I (basket method, 50 rpm), USP dissolution apparatus II (paddle method, 50 rpm), and USP dissolution apparatus III (Bio-Dis, Van-Kel Industries, 5 and 10 dpm). Release profiles obtained from all methods were similar, indicating that the three dissolution methods were comparable.

Multiple-layer compression-coated tablets: formulation and humidity studies of novel chewable amoxicillin/clavulanate tablet formulations

The purpose of this study was to produce novel multiple-layer, compression-coated, chewable tablet formulations containing amoxicillin trihydrate, and clavulanic acid as potassium clavulanate, and to test in vitro dissolution characteristics and the effect of humidity stability compared to Augmentin chewable tablets as a reference. Double- and triple-layer tablets were manufactured on a laboratory scale by multiple-layer dry compression, and dissolution profiles of both active ingredients were determined. Tablets were subjected to stability evaluation in laboratory-scale humidity tanks maintained at constant humidity. Assay of content was determined by HPLC or UV spectroscopy. Physical characteristics of the powder mixture, such as angle of repose, and of tablets for hardness and friability, were also determined. Chewable tablets showed similar dissolution profiles in vitro for both active ingredients, compared to the marketed reference, Augmentin. The stability of clavulanic acid, but not amoxicillin, was increased in the novel triple or bilayer formulation. The tablets showed suitable friability, hardness, and angle of repose for starting materials to suggest that industrial scale-up is feasible. This approach to formulation of drugs containing multiple or moisture-sensitive ingredients has been shown to increase the stability of the central core drug without changing the dissolution pattern of the active ingredients. This formulation is expected to be bioequivalent in vivo based on these in vitro results.

Carbon dioxide-gassed fluorocarbon enhances micropropagation of rose (Rosa chinesis Jacq.)

The inert perfluorochemical (PFC) liquid, perfluorodecalin (Flutec PP6), has been used to increase the CO₂ supply to cultured shoots of Rosa chinensis Jacq. cv. Baby Love. Culture of shoots in semi-solid medium overlaying CO₂-gassed PFC (2 mbar; 5 min repeated every 7 days) for up to 42 days, increased biomass as reflected by significant (P<0.01) increases in shoot number, number of leaves per shoot and mean shoot fresh weight. Additionally, there were significant (P<0.01) increases in the number of roots and their fresh and dry weights following a further 10 days of culture on rooting medium prior to transfer of plants to the glasshouse. Treatment of cultured rose shoots with CO₂-gassed PFC also significantly reduced (P<0.01) the accumulation of phenolic compounds in roots. The total chlorophyll of aerial parts was unaffected, although total protein in shoots and roots was significantly (P<0.01) lower than in the control. The biotechnological implications of this novel cultural régime are discussed for the micropropagation of woody species.

Changes in cell biochemistry in response to culture of protoplasts with oxygenated perfluorocarbon

Superoxide dismutase (superoxide oxidoreductase; EC 1.15.1.1; SOD) was measured in enzymatically isolated protoplasts of Salpiglossis sinuata following culture in aqueous nutrient medium overlaying oxygen-gassed perfluorodecalin (Flutec PP6; BNFL Fluorochemicals, UK). SOD was extracted from harvested, lysed protoplast-derived cells after 1, 3, 7 and 14 days of culture and assayed spectrophotometrically. Protoplasts cultured with oxygenated PFC (+/- s.e.m, n = 5) showed significant increases in mean SOD activity to 4.2 +/- 0.1 U after 1 day (P < 0.05) and 9.3 +/- 0.7 U after 3 days (P < 0.01), with a fall in mean SOD after 7 days (5.1 +/- 0.9 U), similar to control. The decrease in SOD after 7 days correlated closely with a progressive fall in pO2 in the PFC phase over the same period. In contrast, control protoplasts (medium alone) or protoplasts cultured in medium overlaying non-oxygenated PFC showed no significant changes in mean SOD activity over the 14-day culture assessment period.

Beneficial effects of oxygenated fluorocarbon on the in vitro culture of protoplasts and cell electrofusion products

Electrofused Passiflora protoplasts (P. edulis, P. giberti) were plated in KPR medium overlaying oxygen-gassed perfluorodecalin (Flutec PP6). Oxygenated PFC significantly (P < 0.05) enhanced protoplast division, as reflected by an increase in mean plating efficiency of up to 62% (P < 0.05) over 14 days. After 21 days of culture, the liquid phase containing dividing protoplast-derived cells, was removed from the PFC surface and overlaid onto MS-based agar medium for callus proliferation. Forty days later, protoplast-derived calli were transferred to one of two regeneration protocols, previously determined using unfused parental protoplasts. Calli derived from electrofusion-treated protoplasts exhibited organogenesis or somatic embryogenesis, depending on the regeneration procedure. The regeneration efficiency after 121 days for protoplasts initially cultured with oxygenated PFC was over 2-fold greater (P < 0.01) than control. These results indicate that oxygenated PFC can enhance growth and regeneration of protoplasts and their fusion products.

Perfluorochemicals and cell biotechnology

Perfluorochemical (PFC) liquids have properties, especially high gas solubility, which make these compounds useful in medicine and biotechnology. PFCs are being employed to facilitate respiratory gas supply to both prokaryotic and eukaryotic cells and, in some systems, to improve biomass production and yields of commercially-important cellular products. Animal (including human) and plant cells have also been cultured at the interface between PFC liquids and aqueous culture medium, while fluorocarbon polymers have been employed as gaspermeable membranes in eukaryotic cell cultures. This paper presents an overview of the applications and beneficial effects of PFCs in microbial, animal and plant culture systems. PFCs have been compared with other physical and chemical options for manipulating respiratory gas supply to cultured cells. PFC-facilitated improvements in cell culture technology will have increasingly important biotechnological implications.

Preservation of viable biological samples for experiments in space laboratories

Standard viable preservation methods for biological samples using low temperatures have been investigated concerning their storage capabilities under higher temperature levels than usual. For a representative set of organism classes (plants, mammalian cells, arthropods and aquatic invertebrates), the minimum appropriate storage conditions have been identified by screening storage temperatures at -196 degrees, -80 degrees, -20 degrees, +4 degrees, +20 degrees/25 degrees C for periods from 2 days to 4 weeks. For storage below 0 degree C, as a typical cryopreservative, dimethylsulfoxide (DMSO) was used. For some samples, the addition of trehalose (as cryopreservative) and the use of a nitrogen atmosphere were investigated. After storage, the material was tested for vitality. The findings demonstrated that acceptable preservation can be achieved under higher storage temperatures than are typically applied. Small, dense cultured plant cells survive for 21 d when moderately cooled (+4 degrees to -20 degrees C); addition of trehalose enhances viability at -20 degrees C. For mammalian cells, the results show that human lymphocytes can be preserved for 3 d at 25 degrees C, 7 d at 4 degrees C and 28 d at -80 degrees C. Friend leukaemia virus transformed cells can be stored for 3 d at 25 degrees C, 14 d at 4 degrees C and 28 d at -80 degrees C. Hybridoma cells can be kept 7 d at 4 degrees C and 28 d at -20 degrees C or -80 degrees C. Model arthropod systems are well preserved for 2 weeks if maintained at lower temperatures that vary depending on the species and/or stage of development; e.g., 12 degrees C for Drosophila imagoes and 4-6 degrees C for Artemia nauplii. For aquatic invertebrates such as sea urchins, embryonic and larval stages can be preserved for several weeks at +6 degrees C, whereas sperm and eggs can best be stored at + 4 degrees C for up to 5 d at maximum. These results enhance the range of feasible space experiments with biological systems. Moreover, for typical terrestrial preservation methods, considerable modification potential is identified.

Case where a Seton was introduced between the fractured extremities of a Femur, which had not united in the usual manner; with some observations on the methods which have been employed to produce reunion in fractured bones

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