Non-invasive prenatal testing for fetal chromosomal abnormalities by low-coverage whole-genome sequencing of maternal plasma DNA: review of 1982 consecutive cases in a single center

OBJECTIVE

To review the performance of non-invasive prenatal testing (NIPT) by low-coverage whole-genome sequencing of maternal plasma DNA at a single center.

METHODS

The NIPT result and pregnancy outcome of 1982 consecutive cases were reviewed. NIPT was based on low coverage (0.1×) whole-genome sequencing of maternal plasma DNA. All subjects were contacted for pregnancy and fetal outcome.

RESULTS

Of the 1982 NIPT tests, a repeat blood sample was required in 23 (1.16%). In one case, a conclusive report could not be issued, probably because of an abnormal vanished twin fetus. NIPT was positive for common trisomies in 29 cases (23 were trisomy 21, four were trisomy 18 and two were trisomy 13); all were confirmed by prenatal karyotyping (specificity=100%). In addition, 11 cases were positive for sex-chromosomal abnormalities (SCA), and nine cases were positive for other aneuploidies or deletion/duplication. Fourteen of these 20 subjects agreed to undergo further investigations, and the abnormality was found to be of fetal origin in seven, confined placental mosaicism (CPM) in four, of maternal origin in two and not confirmed in one. Overall, 85.7% of the NIPT-suspected SCA were of fetal origin, and 66.7% of the other abnormalities were caused by CPM. Two of the six cases suspected or confirmed to have CPM were complicated by early-onset growth restriction requiring delivery before 34 weeks. Fetal outcome of the NIPT-negative cases was ascertained in 1645 (85.15%). Three chromosomal abnormalities were not detected by NIPT, including one case each of a balanced translocation, unbalanced translocation and triploidy. There were no known false negatives involving the common trisomies (sensitivity=100%).

CONCLUSIONS

Low-coverage whole-genome sequencing of maternal plasma DNA was highly accurate in detecting common trisomies. It also enabled the detection of other aneuploidies and structural chromosomal abnormalities with high positive predictive value.

The value of TRUS in the staging of rectal carcinoma before and after radiotherapy and comparison with the staging postoperative pathology

AIM

To compare the effectiveness of transrectal ultrasonography (TRUS) with that of postoperative pathological examination in staging rectal carcinoma before surgery and before and after radiotherapy.

MATERIALS AND METHODS

A prospective study was undertaken comprising 62 patients with stage T3 or T4 rectal carcinoma confirmed by endoscopic biopsy.

RESULTS

TRUS showed significant differences (p < 0.01) in tumour echogenicity and volume, border delineation, local invasion, and draining lymph node involvement before and after radiotherapy, and significant reduction in blood flow resistance index after radiotherapy but no difference (p > 0.05) in the classification of tumour blood flow. In ultrasonographic assessments, 53 of the 62 cases (85.5%) showed lower T stages after radiotherapy. TRUS showed an accuracy of 94.1% for T2 cases, 77.3% for T3 cases, and 83.3% for T4 cases, and an overall accuracy of 87.1% in comparison with the results of postoperative pathological examination.

CONCLUSION

TRUS is expected to play a vital role in the accurate preoperative staging of rectal carcinoma with the increasing utilization of adjuvant radiotherapy in rectal carcinoma and to contribute to the assessment of treatment.

Nox4 and redox signaling mediate TGF-β-induced endothelial cell apoptosis and phenotypic switch

Transforming growth factor-β (TGF-β) triggers apoptosis in endothelial cells, while the mechanisms underlying this action are not entirely understood. Using genetic and pharmacological tools, we demonstrated that TGF-β induced a moderate apoptotic response in human cultured endothelial cells, which was dependent upon upregulation of the Nox4 NADPH oxidase and production of reactive oxygen species (ROS). In contrast, we showed that ectopic expression of Nox4 via viral vectors (vNox4) produced an antiapoptotic effect. TGF-β caused ROS-dependent p38 activation, whereas inhibition of p38 blunted TGF-β-induced apoptosis. However, vNox4, but not TGF-β, activated Akt, and inhibition of Akt attenuated the antiapoptotic effect of vNox4. Akt activation induced by vNox4 was accompanied by inactivation of the protein tyrosine phosphatase-1B (PTP1B) function and enhanced vascular endothelial growth factor receptor (VEGFR)-2 phosphorylation. Moreover, we showed that TGF-β enhanced Notch signaling and increased expression of the arterial marker EphrinB2 in a redox-dependent manner. In summary, our results suggest that Nox4 and ROS have pivotal roles in mediating TGF-β-induced endothelial apoptosis and phenotype specification. Redox mechanisms may influence endothelial cell functions by modulating p38, PTP1B/VEGFR/Akt and Notch signaling pathways.

Population pharmacogenetic-based pharmacokinetic modeling of efavirenz, 7-hydroxy- and 8-hydroxyefavirenz

The purpose of this study was to determine the demographic and pharmacogenetic covariates that influence the disposition of efavirenz (EFV) and its major metabolites. A population pharmacokinetic (PK) model was developed from a randomized, cross-over, drug-interaction study in healthy male Korean subjects (n = 17). Plasma concentrations of EFV and its hydroxy-metabolites (0-120 hours) were measured by LC/MS/MS. Genomic DNA was genotyped for variants in the cytochrome P450 (CYP) 2A6, 2B6, 3A5, and MDR1 genes. A PK model was built in a stepwise procedure using nonlinear mixed effect modeling in NONMEM 7. The covariate model was built using the generalized additive modeling and forward selection-backward elimination. Model-based simulations were performed to predict EFV steady-state concentrations following 200, 400, and 600 mg daily oral dose among different CYP2B6 genotypes. The final model included only CYP2B6 genotype as a covariate that predicts EFV clearance through the formation of 8-OH EFV that represented 65% to 80% of EFV clearance. The total clearance of EFV in CYP2B6*6/*6 genotype was ∼30% lower than CYP2B6*1/*1 or CYP2B6*1/*6 alleles (P < .001). Clopidogrel reduced both formation and elimination clearances of 8-OH EFV by 22% and 19%, respectively (P = .033 and .041). Other demographics and genotype of accessory CYP pathways did not predict EFV or metabolites PK. CYP2B6 genotype was the only significant predictor of EFV disposition. The developed model may serve as the foundation for further exploration of pharmacogenetic-based dosing of EFV.

MSC-seeded dense collagen scaffolds with a bolus dose of VEGF promote healing of large bone defects

The functional repair of large skeletal defects remains a significant challenge to orthopaedic surgeons due to the lack of effective strategies to promote bone regeneration, particularly in the elderly. This study investigated the potential use of bone marrow derived mesenchymal stromal cells (MSC) in a dense collagen scaffold with a bolus dose of vascular endothelial growth factor (VEGF) to repair a defect in the femoral diaphysis of mice. MSC isolated from bone marrow of 4-month-old donor mice were seeded in type I collagen gels that were then compressed to form scaffolds with a fibrillar density similar to osteoid. The cells remained metabolically active in scaffolds incubated in vitro for up to 15 days and differentiated into osteoblasts that deposited calcium-phosphate mineral into the scaffold, which was quantified using micro-computed tomographic (micro-CT) imaging. When implanted in a 1 mm x 3 mm unicortical defect the MSC-loaded scaffolds were rapidly mineralised and integrated into host bone with administration of 10 ng of recombinant VEGF injected into the femoral canal at 4 days postoperative. Empty scaffolds and MSC-seeded scaffolds implanted in defects that did not receive a bolus dose of VEGF did not mineralise or integrate with native bone. The approach with MSC, hydrogels and a biologic factor already approved for human use warrants further pre-clinical investigation with a large animal model.

Association between KCNQ1 genetic variants and QT interval in a Chinese population

AIM

There is a close link between electrocardiographic ventricular repolarization QT parameters and Type 2 diabetes. The aim of the present study was to assess the effects of QT-related and diabetes-related variants in KCNQ1 on QT interval in a Chinese population.

METHODS

We recruited 2415 patients with Type 2 diabetes and 1163 subjects with normal glucose regulation in the present study. QT interval was obtained and the heart rate-corrected QT interval (QTc) was calculated using Bazett's formula. Four single nucleotide polymorphisms in KCNQ1 were selected (rs12296050, rs12576239, rs2237892 and rs2237895) and genotyped.

RESULTS

In participants with normal glucose regulation, the minor allele T of rs12296050 was associated with a 3.46-ms QTc prolongation under an additive model (P = 0.0109, empirical P = 0.0498). In patients with Type 2 diabetes, we did not find any association for the single nucleotide polymorphisms.

CONCLUSIONS

Our findings indicate that KCNQ1 is associated with QT interval in a Chinese population with normal glucose regulation.

Establishing a conceptual model for photochemical ozone pollution in subtropical Hong Kong

Photochemical ozone (O₃) formation is related to its precursors and meteorological conditions. A conceptual model of O₃ air pollution is developed based on the analysis of data obtained at Tung Chung (TC) in Hong Kong. By comparing meteorological parameters between O₃ and non-O₃ episode days, it was found that high temperatures, strong solar radiation, low wind speeds and relative humidity, northeasterly and/or northwesterly prevailing winds were favorable for the O₃ formation, while tropical cyclones were most conducive to the occurrence of O₃ episodes. Backward trajectories simulation and graphical illustration of O₃ pollution suggested that super-regional (i.e. central and eastern China) and regional (i.e. Pearl River Delta, southern China) transport was another factor that contributed to high O₃ levels in Hong Kong. The photochemical O₃ formation, generally VOC-limited in Hong Kong, was controlled by a small number of volatile organic compounds (VOCs). Furthermore, the positive matrix factorization (PMF) simulation suggested that solvent usage and vehicular emissions are the major contributors to ambient VOCs in Hong Kong. Finally, this paper presents recommendations for further O₃ research and implementation of O₃ control strategies.

Photochemical trajectory modeling of ozone concentrations in Hong Kong

In this study, tropical cyclones over the East and South China Seas were found to be the most predominant weather conditions associated with the occurrence of high ozone (O3) episodes in Hong Kong in 2005-2009. A photochemical trajectory model coupled with Master Chemical Mechanism (MCM) was adapted to simulate the O3 concentrations during two O3 pollution episodes. The results agreed well with the observed data. A representative backward air mass trajectory was used to determine the contribution of each volatile organic compound (VOC) to the O3 levels. After taking into account both reactivity and mass emission of each VOC, 10 species were found to be the key O3 precursors in Hong Kong. Further analysis identified solvent related products accounting for 70% of the modeled O3 concentration in Hong Kong. The results highlight the importance of considering together reactivity and source sector emissions in developing targeted VOC reduction for O3 abatement strategies.

Genome-wide association study in a Chinese population identifies a susceptibility locus for type 2 diabetes at 7q32 near PAX4

AIMS/HYPOTHESIS

Most genetic variants identified for type 2 diabetes have been discovered in European populations. We performed genome-wide association studies (GWAS) in a Chinese population with the aim of identifying novel variants for type 2 diabetes in Asians.

METHODS

We performed a meta-analysis of three GWAS comprising 684 patients with type 2 diabetes and 955 controls of Southern Han Chinese descent. We followed up the top signals in two independent Southern Han Chinese cohorts (totalling 10,383 cases and 6,974 controls), and performed in silico replication in multiple populations.

RESULTS

We identified CDKN2A/B and four novel type 2 diabetes association signals with p < 1 × 10(-5) from the meta-analysis. Thirteen variants within these four loci were followed up in two independent Chinese cohorts, and rs10229583 at 7q32 was found to be associated with type 2 diabetes in a combined analysis of 11,067 cases and 7,929 controls (p meta = 2.6 × 10(-8); OR [95% CI] 1.18 [1.11, 1.25]). In silico replication revealed consistent associations across multiethnic groups, including five East Asian populations (p meta = 2.3 × 10(-10)) and a population of European descent (p = 8.6 × 10(-3)). The rs10229583 risk variant was associated with elevated fasting plasma glucose, impaired beta cell function in controls, and an earlier age at diagnosis for the cases. The novel variant lies within an islet-selective cluster of open regulatory elements. There was significant heterogeneity of effect between Han Chinese and individuals of European descent, Malaysians and Indians.

CONCLUSIONS/INTERPRETATION

Our study identifies rs10229583 near PAX4 as a novel locus for type 2 diabetes in Chinese and other populations and provides new insights into the pathogenesis of type 2 diabetes.

Rapid diagnosis of the economically important fruit fly, Bactrocera correcta (Diptera: Tephritidae) based on a species-specific barcoding cytochrome oxidase I marker

The guava fruit fly, Bactrocera correcta (Bezzi) (Diptera: Tephritidae), is an invasive pest of fruit and vegetable crops that primarily inhabits Southeast Asia and which has the potential to become a major threat within both the Oriental and Australian oceanic regions as well as California and Florida. In light of the threat posed, it is important to develop a rapid, accurate and reliable method to identify B. correcta in quarantine work in order to provide an early warning to prevent its widespread invasion. In the present study, we describe a species-specific polymerase chain reaction assay for the diagnosis of B. correcta using mitochondrial DNA cytochrome oxidase I (mtDNA COI) barcoding genes. A B. correcta-specific primer pair was designed according to variations in the mtDNA COI barcode sequences among 14 fruit fly species. The specificity and sensitivity of the B. correcta-specific primer pair was tested based on the presence or absence of a band in the gel profile. A pair of species-specific B. correcta primers was successfully designed and named BCOR-F/BCOR-R. An ∼280 bp fragment was amplified from specimens belonging to 17 geographical populations and four life stages of B. correcta, while no such diagnostic bands were present in any of the 14 other related fruit fly species examined. Sensitivity test results demonstrated that successful amplification can be obtained with as little as 1 ng μl⁻¹ of template DNA. The species-specific PCR analysis was able to successfully diagnose B. correcta, even in immature life stages, and from adult body parts. This method proved to be a robust single-step molecular technique for the diagnosis of B. correcta with respect to potential plant quarantine.

Nanostructured high-strength molybdenum alloys with unprecedented tensile ductility

The high-temperature stability and mechanical properties of refractory molybdenum alloys are highly desirable for a wide range of critical applications. However, a long-standing problem for these alloys is that they suffer from low ductility and limited formability. Here we report a nanostructuring strategy that achieves Mo alloys with yield strength over 800 MPa and tensile elongation as large as ~ 40% at room temperature. The processing route involves a molecular-level liquid-liquid mixing/doping technique that leads to an optimal microstructure of submicrometre grains with nanometric oxide particles uniformly distributed in the grain interior. Our approach can be readily adapted to large-scale industrial production of ductile Mo alloys that can be extensively processed and shaped at low temperatures. The architecture engineered into such multicomponent alloys offers a general pathway for manufacturing dispersion-strengthened materials with both high strength and ductility.

Industrial flue gas desulfurization waste may offer an opportunity to facilitate SANI® application for significant sludge minimization in freshwater wastewater treatment

This paper reports an exploratory study on the use of a sulfite-rich industrial effluent to enable the integration of a sulfite-sulfide-sulfate cycle to the conventional carbon and nitrogen cycles in wastewater treatment to achieve sludge minimization through the non-sludge-producing Sulfate reduction, Autotrophic denitrification and Nitrification Integrated (SANI) process. A laboratory-scale sulfite reduction reactor was set up for treating sulfite-rich synthetic wastewater simulating the wastewater from industrial flue gas desulfurization (FGD) units. The results indicated that the sulfite reduction reactor can be started up within 11 d, which was much faster than that using sulfate. Thiosulfate was found to be the major sulfite reduction intermediate, accounting for about 30% of the total reduced sulfur in the reactor effluent, which may enable additional footprint reduction of the autotrophic denitrification reactor in the SANI process. This study indicated that it was possible to make use of the FGD effluent for applying the FGD-SANI process in treating freshwater-based sewage.

Genetic variants of LPIN1 indicate an association with Type 2 diabetes mellitus in a Chinese population

AIMS

Metabolic disorders are independent risk factors for the development of Type 2 diabetes. The aim of the study is to test the association of LPIN1 variants with Type 2 diabetes and clinical characteristics in large samples of the Chinese population.

METHODS

In the first stage, 15 single nucleotide polymorphisms within the LPIN1 region were selected and genotyped in 3700 Chinese Han participants. In the second stage, the single nucleotide polymorphisms showing significant association or trends towards association were genotyped in an additional 3122 samples for replication. Meta-analyses and genotype-phenotype association studies were performed after combining the data from the two stages.

RESULTS

In the first stage, we detected that rs16857876 was significantly associated with Type 2 diabetes with an odds ratio of 0.806 (95% CI 0.677-0.958, P = 0.015), while rs11695610 showed a trend with Type 2 diabetes (odds ratio 0.846, 95% CI 0.709-1.009, P = 0.062). In the second stage, a similar effect of rs11695610 on Type 2 diabetes was observed (odds ratio 0.849, 95% CI 0.700-1.030, P = 0.096). The meta-analyses combining the information from the two stages showed a significant effect of rs11695610 on Type 2 diabetes with an odds ratio of 0.847 (95% CI 0.744-0.965, P = 0.012). Finally, the phenotype-genotype association analyses showed that rs11695610 was associated with 2-h plasma glucose (P = 0.040) and triglyceride levels (P = 0.034).

CONCLUSIONS

Our data implied that common single nucleotide polymorphisms within the LPIN1 region were associated with Type 2 diabetes and metabolic traits in the Chinese population.

High intensity focused ultrasound ablation of goat liver in vivo: Pathologic changes of portal vein and the "heat-sink" effect

The purpose of this study was to evaluate pathological changes of the portal vein (PV) and the effects on main branches of the hepatic PV during HIFU (high-intensity focused ultrasound) sonication when liver tissue adjacent to the main branches of hepatic PV was ablated. Normal liver tissue at 0mm, 5mm, 10mm away from the hepatic portal vein in 50 healthy goats was ablated with magnetic resonance image-guided HIFU (MRgHIFU). MRI showed a non-perfusion region at the target area but did not show any significant changes of the PV immediately after HIFU. The histological examination 1 day after HIFU showed coagulative necrosis at the target area, revealed deep-dyed swelling collagen (CS) fibers and vessel wall fracture (VWF) in the PV adjacent to the target area; however, no CS or VWF was observed in the PV 1 week after HIFU ablation. The energy required to ablate the foci at 0mm was 21% more than that at 10mm from the PV (p<0.05); the energy needed to ablate foci 5mm away from the PV was 10% more than that at 10mm from the PV (p<0.05). We concluded that minor injury of the hepatic portal vein may occur when ablating the adjacent liver tissue, and the acoustic energy deposition is related to the distance to the portal vein.

Association between KCNQ1 genetic variants and obesity in Chinese patients with type 2 diabetes

AIMS/HYPOTHESIS

There is evidence of overlap between susceptibility loci for type 2 diabetes and obesity. The aim of this study is to explore the association between the established type 2 diabetes locus KCNQ1 and obesity in Han Chinese.

METHODS

We recruited 6,667 and 6,606 diabetic case-control samples from Shanghai and Hong Kong, respectively. Of the samples, 7.5% and 6.3% were excluded because of genotyping failure or data missing in the association analyses of rs2237892 and rs2237895 with obesity/BMI, respectively.

RESULTS

We found that rs2237892 was associated with lower BMI and lower incidence of overweight/obesity in diabetic patients from Hong Kong (BMI, β = -0.0060 per diabetes risk C allele for log(10)BMI [95% CI -0.0088, -0.0032; p = 2.83 × 10(-5)]; overweight/obesity, OR 0.880 for C allele [95% CI 0.807, 0.960; p = 0.004]) and in the meta-analysis of cases from the two regions (BMI, combined β = -0.0048 per C allele for log(10)BMI [95% CI -0.0070, -0.0026; p = 2.20 × 10(-5)]; overweight/obesity, combined OR 0.890 for C allele [95% CI 0.830, 0.955; p = 0.001]). rs2237895 was also related to decreased BMI (combined β = -0.0042 per diabetes risk C allele for log(10)BMI [95% CI -0.0062, -0.0022; p = 4.30 × 10(-5)]). A significant association with waist circumference was detected for rs2237892 in the pooled analyses (β = -0.0026 per C allele for log(10)[waist circumference] [95% CI -0.0045, -0.0007; p = 0.007]). However, neither an association with the risk of being overweight or obese nor associations with quantitive traits were detected for rs2237892 or rs2237895 in controls.

CONCLUSION

Our findings indicate that KCNQ1 is associated with obesity in Chinese patients with type 2 diabetes.

Mechanisms involved in the p62-73 idiopeptide-modulated delay of lupus nephritis in SNF(1) mice

The F(1) progeny of the (SWR × NZB) cross develop a lupus-like disease with high serum titers of autoantibodies, and increased frequency and severity of immune complex-mediated glomerulonephritis in females. In previous work, we found that an idiotypic peptide corresponding to aa62-73 (p62-73) of the heavy chain variable region of autoantibody 540 (Id(LN)F(1)) induced the proliferation of p62-73 idiotype-reactive T cell clones. Further, monthly immunization of pre-nephritic SNF(1) female mice with p62-73 resulted in decreased nephritis and prolonged life spans. Here we show that this treatment modulated proliferative responses to Id(LN)F(1) antigen, including a reduction in the population of idiopeptide-presenting antigen-presenting cells (APCs), as early as two weeks after immunization (10 weeks of age). Th1-type cytokine production was increased at 12 weeks of age. The incidence and severity of nephritis was reduced by 14 weeks compared to controls. Clinical indicators of nephritis, specifically histological evidence of glomerulonephritis and urine protein levels, were reduced by 20 weeks. Together these data suggest that events involved in the mechanism(s) whereby p62-73 immunization delayed nephritis occurred early after immunization, and involved modulation of APCs, B and T cell populations.

Fluoroscopically guided nose tube drainage of mediastinal abscesses in post-operative gastro-oesophageal anastomotic leakage

OBJECTIVE

The aim of this study was to retrospectively evaluate the technical success rates and clinical effectiveness of fluoroscopically guided nose tube drainage of mediastinal abscesses and a nasojejunum feeding tube in post-operative gastro-oesophageal anastomotic leakage (GEAL).

METHODS

From January 2006 to June 2011, 18 cases of post-operative GEAL with mediastinal abscesses after oesophagectomy with intrathoracic oesophagogastric anastomotic procedures for oesophageal and cardiac carcinoma were treated by insertion of a nose drainage tube and nasojejunum feeding tube under fluoroscopic guidance. We evaluated the feasibility of two-tube insertion to facilitate leakage site closure and complete resolution of the abscess, and the patients' nutritional benefit was also evaluated by checking the serum albumin level between pre- and post-enteral feeding via the feeding tube.

RESULTS

The two tubes were placed successfully under fluoroscopic guidance in 18 patients (100%). The procedure time for two-tube insertion ranged from 20 to 40 min (mean 30 min). 17 patients (94%) achieved leakage site closure after two-tube insertion and had a good tolerance of two tubes in the nasal cavity. The serum albumin level was significant, increased from pre-enteral feeding (2.49 ± 0.42 g dl(-1)) to the post-enteral feeding (3.58 ± 0.47 g dl(-1)) via the feeding tube (p<0.001). The duration of follow-up ranged from 1 to 49 months (mean 19 months).

CONCLUSION

The insertion of nose tube drainage and a nasojejunum feeding tube under fluoroscopic guidance is safe, and it provides effective relief from mediastinal abscesses in GEAL after oesophagectomy. Moreover, our findings indicate that two-tube insertion may be used as a selective procedure to treat mediastinal abscesses in post-operative GEAL. Advances in knowledge Directive drainage of mediastinal abscesses in post-operative GEAL may be an effective treatment.