Non-invasive prenatal testing for trisomies 21, 18 and 13: clinical experience from 146,958 pregnancies

OBJECTIVES

To report the clinical performance of massively parallel sequencing-based non-invasive prenatal testing (NIPT) in detecting trisomies 21, 18 and 13 in over 140,000 clinical samples and to compare its performance in low-risk and high-risk pregnancies.

METHODS

Between 1 January 2012 and 31 August 2013, 147,314 NIPT requests to screen for fetal trisomies 21, 18 and 13 using low-coverage whole-genome sequencing of plasma cell-free DNA were received. The results were validated by karyotyping or follow-up of clinical outcomes.

RESULTS

NIPT was performed and results obtained in 146,958 samples, for which outcome data were available in 112,669 (76.7%). Repeat blood sampling was required in 3213 cases and 145 had test failure. Aneuploidy was confirmed in 720/781 cases positive for trisomy 21, 167/218 cases positive for trisomy 18 and 22/67 cases positive for trisomy 13 on NIPT. Nine false negatives were identified, including six cases of trisomy 21 and three of trisomy 18. The overall sensitivity of NIPT was 99.17%, 98.24% and 100% for trisomies 21, 18 and 13, respectively, and specificity was 99.95%, 99.95% and 99.96% for trisomies 21, 18 and 13, respectively. There was no significant difference in test performance between the 72,382 high-risk and 40,287 low-risk subjects (sensitivity, 99.21% vs. 98.97% (P = 0.82); specificity, 99.95% vs. 99.95% (P = 0.98)). The major factors contributing to false-positive and false-negative NIPT results were maternal copy number variant and fetal/placental mosaicism, but fetal fraction had no effect.

CONCLUSIONS

Using a stringent protocol, the good performance of NIPT shown by early validation studies can be maintained in large clinical samples. This technique can provide equally high sensitivity and specificity in screening for trisomy 21 in a low-risk, as compared to high-risk, population.

Optimization of SCoT-PCR reaction system in Dactylis glomerata by orthogonal design

The effects of 5 factors (template DNA, Mg(2+), dNTPs, Taq DNA polymerase, and primer) on the polymerase chain reaction (PCR) were investigated to optimize the start codon targeted polymor-phism (SCoT)-PCR system of Dactylis glomerata L., using an orthogo-nal design L16 (4(5)). A suitable SCoT-PCR system for D. glomerata was established; the 20 μL reaction volume contained 3.0 mM Mg(2+), 0.2 mM dNTPs, 1.0 U Taq DNA polymerase, 0.2 μM primer, 20 ng tem-plate DNA, and 2 μL 10X buffer. Each factor had a different effect on the amplification reaction, and the concentration of dNTPs had the larg-est effect on the SCoT-PCR system. We tested 10 orchardgrass samples to determine and verify the stability of the reaction system. The results showed that amplified bands from diverse materials were clear, stable, and rich in polymorphisms, indicating that the optimized system was very stable.

Study of e(+)e(-)→ωχ(cJ) at center of mass energies from 4.21 to 4.42 GeV

Based on data samples collected with the BESIII detector at the BEPCII collider at nine center of mass energies from 4.21 to 4.42 GeV, we search for the production of e^{+}e^{-}→ωχ_{cJ} (J=0, 1, 2). The process e^{+}e^{-}→ωχ_{c0} is observed for the first time, and the Born cross sections at sqrt[s]=4.23 and 4.26 GeV are measured to be (55.4±6.0±5.9) and (23.7±5.3±3.5)  pb, respectively, where the first uncertainties are statistical and the second are systematic. The ωχ_{c0} signals at the other seven energies and the e^{+}e^{-}→ωχ_{c1} and ωχ_{c2} signals are not significant, and the upper limits on the cross sections are determined. By examining the ωχ_{c0} cross section as a function of center of mass energy, we find that it is inconsistent with the line shape of the Y(4260) observed in e^{+}e^{-}→π^{+}π^{-}J/ψ. Assuming the ωχ_{c0} signals come from a single resonance, we extract the mass and width of the resonance to be (4230±8±6)  MeV/c^{2} and (38±12±2)  MeV, respectively, and the statistical significance is more than 9σ.

Unsteady aerodynamic analysis for offshore floating wind turbines under different wind conditions

A free-vortex wake (FVW) model is developed in this paper to analyse the unsteady aerodynamic performance of offshore floating wind turbines. A time-marching algorithm of third-order accuracy is applied in the FVW model. Owing to the complex floating platform motions, the blade inflow conditions and the positions of initial points of vortex filaments, which are different from the fixed wind turbine, are modified in the implemented model. A three-dimensional rotational effect model and a dynamic stall model are coupled into the FVW model to improve the aerodynamic performance prediction in the unsteady conditions. The effects of floating platform motions in the simulation model are validated by comparison between calculation and experiment for a small-scale rigid test wind turbine coupled with a floating tension leg platform (TLP). The dynamic inflow effect carried by the FVW method itself is confirmed and the results agree well with the experimental data of a pitching transient on another test turbine. Also, the flapping moment at the blade root in yaw on the same test turbine is calculated and compares well with the experimental data. Then, the aerodynamic performance is simulated in a yawed condition of steady wind and in an unyawed condition of turbulent wind, respectively, for a large-scale wind turbine coupled with the floating TLP motions, demonstrating obvious differences in rotor performance and blade loading from the fixed wind turbine. The non-dimensional magnitudes of loading changes due to the floating platform motions decrease from the blade root to the blade tip.

Association of the ApoE gene polymorphism and dietary factors with cerebral infarction and circulating lipid concentrations

The aim of this study was to explore the relationship between the ApoE gene polymorphism and dietary factors with stroke and circulating lipid levels in the Chinese population. We selected 580 patients with stroke and 580 age- and gender-matched healthy controls, and examined their ApoE polymorphism genotype using the polymerase chain reaction-restriction fragment length polymorphism (PCR-RFLP) method. We also analyzed the relationship between the ApoE gene polymorphism and dietary factors as well as plasma lipid concentrations in this cohort. We detected six ApoE genotypes in the study populations, and determined that the E4 allele was positively associated with cerebral infarction (CI), whereas allele E2 was negatively associated with total cholesterol (TC) and low-density lipoprotein-cholesterol levels. The dietary habits of the subjects with descending order of average total TC and triglyceride levels were: subjects addicted to oily food > subjects addicted to sweets > subjects addicted to smoking > subjects addicted to alcohol > subjects following a vegetarian diet (P < 0.05). Our results demonstrated that the ApoE gene polymorphism was associated with a risk for CI in a Chinese population.

Isolation of new polymorphic microsatellite markers from the marbled rockfish Sebastiscus marmoratus

The marbled rockfish, Sebastiscus marmoratus, is an important commercially near-shore fish that inhabits the beach rocky bottom from Japan to the South China Sea. Eleven polymorphic microsatellite loci were developed from S. marmoratus and were used to identify polymorphisms in 30 samples from a wild population. The allele locus number ranged from 2 to 7. Polymorphism data content ranged from 0.032 to 0.751. The observed and expected heterozygosity levels were 0.0333-0.9667 and 0.0328-0.7675, respectively. Two loci, Smd1-112 and Smd2-80, deviated from Hardy-Weinberg equilibrium. These polymorphic microsatellite markers will facilitate further studies of genetic diversity and genetic differentiation of S. marmoratus.

CYP4F2 gene single nucleotide polymorphism is associated with ischemic stroke

The objective of this study was to explore the relationship between CYP4F2 gene polymorphism and ischemic stroke (IS) in the Han Chinese population. We performed a case-control study to genotype four single nucleotide polymorphisms (SNPs) (rs2108622, rs3093100, rs3093105, rs3093135) in the CYF4F2 gene. The genotype and haplotype distributions were compared between the case and control groups. We found that the GG genotype of rs2108622 in the CYP4F2 gene was associated with risk of IS (P = 0.023). Haplotype analysis indicated that the GGGT haplotype comprising rs2108622-rs3093100-rs3093105-rs3093135 was associated with IS, which suggests that the GGGT haplotype may be a risk factor for IS (P = 0.012). CYP4F2 gene polymorphism might increase the risk of IS in the Chinese population.

Development and characterization of polymorphic microsatellite loci in the sea cucumber Holothuria leucospilota

Holothuria leucospilota is a tropical holothurian species that is widely distributed in the tropical and sub-tropical India-Western Pacific Region. Eight polymorphic microsatellite loci were developed from H. leucospilota by using the protocol fast isolation by amplified fragment length polymorphism of sequences containing repeats and tested in 30 individuals from Hainan Island in China. The number of alleles was 2-6 and polymorphism information content ranged from 0.371-0.694. The levels of expected and observed heterozygosities varied from 0.3913-0.6701 and from 0.1154-0.7000, respectively. No significant linkage disequilibrium was detected for any pairwise combination of loci. Only loci YZHS1-42 deviated from Hardy-Weinberg equilibrium. These polymorphic microsatellite loci may be useful for germplasm conservation of H. leucospilota.

Cloning and characterization of a farnesyl pyrophosphate synthase from Matricaria recutita L. and its upregulation by methyl jasmonate

Matricaria recutita (L.), commonly known as chamomile, is one of the most valuable medicinal plants because it synthesizes a large number of pharmacologically active secondary metabolites known as α-bisabolol and chamazulene. Although the plant has been well characterized in terms of chemical constituents of essential oil as well as pharmacological properties, little is known about the genes responsible for biosynthesis of these compounds. In this study, we report a new full-length cDNA encoding farnesyl diphosphate synthase (FPS), a key enzyme in the pathway of biosynthesis of isoprenoids, from M. recutita. The cDNA of MrFPS comprises 1032 bp and encodes 343 amino acid residues with a calculated molecular mass of 39.4 kDa. The amino acid sequence homology and phylogenetic analysis indicated that MrFPS belongs to the plant FPS super-family and is closely related to FPS from the Asteraceae family. Expression of the MrFPS gene in Escherichia coli yielded FPS activity. Using real-time quantitative PCR, the expression pattern of the MrFPS gene was analyzed in different tissues of M. recutita as well as in response to methyl jasmonate. The expression analysis demonstrated that MrFPS expression varies in different tissues (with maximal expression in flowers and stems) and was significantly elevated in response to methyl jasmonate. This study will certainly enhance our understanding of the role of MrFPS in the biosynthesis and regulation of valuable secondary metabolites in M. recutita at a molecular level.

Isolation and characterization of novel microsatellite markers for molecular genetic diversity in Siganus fuscescens

The rabbitfish Siganus fuscescens is an economically valuable species that is widely distributed throughout the estuaries, intertidal, and offshore coasts of the Indo-Pacific and eastern Mediterranean. Ten novel microsatellite loci from the genome of S. fuscescens were developed using the fast isolation protocol with amplified fragment length polymorphism of sequences containing repeats. Polymorphisms in these 10 microsatellite markers were determined from 32 wild individuals. The number of alleles per locus and the polymorphism information content ranged from 2 to 5 and from 0.059 to 0.668, respectively. The observed and expected heterozygosities varied from 0.063 to 0.781 and from 0.062 to 0.731, respectively. Although 1 locus (LZY-X7, P < 0.005) showed significant deviation from the Hardy-Weinberg equilibrium, no deviations were detected in the other 9 loci. These microsatellite loci may be useful for further population genetic studies, conservation studies, population structure assessment, and linkage map construction of S. fuscescens.

Incidence and factors associated with nosocomial infections in a neonatal intensive care unit (NICU) of an urban children's hospital in China

OBJECTIVE

The study's aim was to assess incidence and epidemiologic profile of nosocomial infection (NI) in a NICU of China, and to identify main risk factors of NIs.

MATERIALS AND METHODS

Chi square test for discrete variables and independent t-test for continuous variables to examine the association with NI. Univariate regression model was applied to the variables to predict the NI status. Finally the multivariate model was utilized with stepwise methods included all variables in the univariate model to extrapolate the independent variables to NI.

RESULTS

Infection rate in NICU during the study period was 6.2 episodes per 100 patients. Infection density was 4.2 episodes per 1,000 patient-days. Infection rate of ventilation-related pneumonia was 3.4 episodes per 1,000 mechanical ventilation (MV) days. Central line-associated bloodstream infection rate was 5.4 episodes per 1,000 central line days. Gestational age < 32 weeks, with congenital malformation, twins or triplets, gastric tube feeding, operation, duration of prophylaxis antibiotic use, duration of probiotic use, duration of parenteral nutrition were the risk factors associated with NI in NICU. We discussed the association between intrinsic factors of infants and health care procedures with NI.

CONCLUSION

This study provided information for prevention strategies of NI, that will ultimately improve the healthcare service level.

Molecular cloning and characterization of the full-length Hsp90 gene from Matricaria recutita

Heat shock protein 90 (Hsp90) is one of the most abundant and conserved chaperone proteins and plays important roles in plant growth and responses to environmental stimuli. However, little is known regarding the sequence and function of Hsp90s in Matricaria recutita. In the present study, we cloned the full-length cDNA sequence of the hsp90 gene from this species. Using rapid amplification of cDNA ends technologies with 2 degenerate primers that were designed based on the hsp90 gene sequence from other members of Asteraceae, we isolated and characterized an Hsp90 homolog gene from M. recutita (Mr-Hsp90). The full-length Mr-hsp90 cDNA sequence, containing 2097 base pairs, encodes a protein of 698 amino acids. Based on amino acid sequence identity, Mr-Hsp90 showed high similarity to other cloned Hsp90 proteins. The Mr-Hsp90 protein was closely clustered with the Lactuca sativa in a phylogenetic tree. These results indicate that the cloned sequence of Mr-Hsp90 is a member of the Hsp90 family, which is reported for the first time in M. recutita. Next, we conducted a salt stress experiment to determine the protein's function under salt stress conditions. Survival of chamomile seedlings subjected to heat-shock pretreatment was significantly increased compared with groups that had not undergone heat-shock pretreatment in a salt stress environment. This indicates that Mr-Hsp90 plays an important role in the salt resistance of chamomile seedlings.

Survey of acrylamide levels in Chinese foods

A survey of levels of acrylamide (AA) in 349 food products obtained from the Chinese market was conducted. AA was determined by an liquid chromatography-tandem mass spectrometry (LC-MS/MS) method. The limit of detection (LOD) and the limit of quantification (LOQ) of the method in four different matrices ranged from 0.8 to 10 µg kg(-1) and from 4.0 to 25 µg kg(-1), respectively. The results from this survey indicated that AA was present in all samples except drinking water and tea. AA contents in different samples varied greatly according to the raw materials and processing conditions. The highest level of AA was found in potato products, with an average level of 1467 µg kg(-1). Preliminary estimates of AA exposure and risk assessment of AA from foods in the Chinese population were performed using a combination of data obtained in the present survey and 2002 dietary consumption survey carried out in 2002 for the Chinese population. The average dietary exposure of AA was estimated to be 0.38 µg kg(-1) body weight day(-1), which is relatively low compared with the result reported by the Food and Agricultural Organization/World Health Organization (FAO/WHO). Furthermore, the margin of exposure for neurotoxicity, reproductive toxicity, and carcinogenicity of AA was calculated to be 1318, 5250, and 787, respectively.

Survey of nitrite content in foods from north-east China

This study reports a survey of nitrite in a variety of foods consumed in north-east China and estimates the intake of nitrite for the north-east Chinese consumer. A total of 642 food categories including rice and rice products, flour and flour products, soybean and products, vegetables, fruit, preserved vegetables, cured meat products, dairy products, fish products, salt, and soy sauce were analysed for their content of nitrite. Nitrite content was quite different both between different food categories and within the same food category, ranging from not determined (n.d.) to 19.7 mg kg(-1). A great variation in the content of nitrite was found for all the food products. The average content of nitrite was highest in cured meat products (14.3 mg kg(-1)). Next to that, the nitrite content was high in the order of preserved vegetables (4.1 mg kg(-1)), soybean products (3.5 mg kg(-1)), and dairy products (1.9 mg kg(-1)). The lowest average values of nitrite were detected in soy sauce, rice and rice products, salt and fish products, the contents being 0.1, 0.3, 0.3, and 0.6 mg kg(-1). Calculations on the basis of these results and including dietary surveys show that the average intake of nitrite in north-east China from food was 0.03 mg kg(-1) body weight for an average Chinese person weighing 60 kg, and the data are lower than the established acceptable daily intake (ADI) for nitrite. Cured meat products are normally the major contributor to average nitrite intake of the north-east Chinese population. The second contributor is vegetables.

Performance improvement of flame-retarded poly(butylene terephthalate)/aluminum diethylphosphinate composites by epoxy-functional polysiloxane

An epoxy-functional polysiloxane (EPM) was employed for improving the performance of flame-retarded poly(butylene terephthalate)/aluminum diethylphosphinate (PBT/AlPi) composites. The effect was investigated by UL-94 test, limiting oxygen index, mechanical test, torque rheometer measurement, differential scanning calorimetry, dynamic mechanical analysis, and heat distortion temperature. An obvious increase in torque evolution of the PBT/AlPi composite during processing was associated with chain-extending, branching, and cross-linking reaction by the combination of EPM. The addition of 0.6 wt% EPM remarkably enhanced not only the mechanical properties but also the flame retardancy and heat resistance of the PBT/AlPi composite. A high-performance PBT/AlPi composite was developed by virtue of EPM.

Observation of e(+)e(-)→π(0)π(0)hc and a neutral charmoniumlike structure Zc(4020)(0)

Using data collected with the BESIII detector operating at the Beijing Electron Positron Collider at center-of-mass energies of sqrt[s]=4.23, 4.26, and 4.36 GeV, we observe e(+)e(-)→π(0)π(0)hc for the first time. The Born cross sections are measured and found to be about half of those of e(+)e(-)→π(+)π(-)hc within less than 2σ. In the π(0)hc mass spectrum, a structure at 4.02  GeV/c(2) is found. It is most likely to be the neutral isospin partner of the Zc(4020)(±) observed in the process of e(+)e(-)→π(+)π(-)hc being found. A fit to the π(0)hc invariant mass spectrum, with the width of the Zc(4020)(0) fixed to that of its charged isospin partner and possible interferences with non-Zc(4020)(0) amplitudes neglected, gives a mass of (4023.9±2.2±3.8)  MeV/c(2) for the Zc(4020)(0), where the first error is statistical and the second systematic.