Noninvasive prenatal diagnosis of 21-Hydroxylase deficiency using target capture sequencing of maternal plasma DNA.

Here, we aimed to validate a noninvasive method using capture sequencing for prenatal diagnosis of congenital adrenal hyperplasia due to 21-Hydroxylase deficiency (21-OHD). Noninvasive prenatal diagnosis (NIPD) of 21-OHD was based on 14 plasma samples collected from 12 families, including four plasma sample collected during the first trimester. Targeted capture sequencing was performed using genomic DNA from the parents and child trios to determine the pathogenic and wild-type alleles associated with the haplotypes. Maternal plasma DNA was also sequenced to determine the fetal inheritance of the allele using hidden Markov model-based haplotype linkage analysis. The effect of fetal DNA fraction and sequencing depth on the accuracy of NIPD was investigated. The lower limit of fetal DNA fraction was 2% and the threshold mean sequence depth was 38, suggesting potential advantage if used in early gestation. The CYP21A2 genotype of the fetus was accurately determined in all the 14 plasma samples as early as day 1 and 8 weeks of gestation. Results suggest the accuracy and feasibility of NIPD of 21-OHD using a small target capture region with a low threshold for fetal DNA fraction and sequence depth. Our method is cost-effective and suggests diagnostic applications in clinical practice

Rapid, low-input, low-bias construction of shotgun fragment libraries by high-density in vitro transposition

© The Authors, 2010. This article is distributed under the terms of the Creative Commons Attribution License. The definitive version was published in Genome Biology 11 (2010): R119, doi:10.1186/gb-2010-11-12-r119.We characterize and extend a highly efficient method for constructing shotgun fragment libraries in which transposase catalyzes in vitro DNA fragmentation and adaptor incorporation simultaneously. We apply this method to sequencing a human genome and find that coverage biases are comparable to those of conventional protocols. We also extend its capabilities by developing protocols for sub-nanogram library construction, exome capture from 50 ng of input DNA, PCR-free and colony PCR library construction, and 96-plex sample indexing.This work was supported in part by grants from the National Institutes of Health/National Heart Lung and Blood Institute (R01 HL094976 to JS), the National Institutes of Health/National Human Genome Research Institute (R21 HG004749 to JS), the National Institutes of Health/National Institute of Allergy and Infectious Disease Northwest Regional Center of Excellence for Biodefense and Emerging Infectious Diseases at the University of Washington (3U54AI05714), the Ministry of Science and Technology of China, 863 program (2006AA02A301), and an NSF Graduate Research Fellowship (to JOK)

Comprehensive comparison of three commercial human whole-exome capture platforms

BackgroundExome sequencing, which allows the global analysis of protein coding sequences in the human genome, has become an effective and affordable approach to detecting causative genetic mutations in diseases. Currently, there are several commercial human exome capture platforms; however, the relative performances of these have not been characterized sufficiently to know which is best for a particular study.ResultsWe comprehensively compared three platforms: NimbleGen's Sequence Capture Array and SeqCap EZ, and Agilent's SureSelect. We assessed their performance in a variety of ways, including number of genes covered and capture efficacy. Differences that may impact on the choice of platform were that Agilent SureSelect covered approximately 1,100 more genes, while NimbleGen provided better flanking sequence capture. Although all three platforms achieved similar capture specificity of targeted regions, the NimbleGen platforms showed better uniformity of coverage and greater genotype sensitivity at 30- to 100-fold sequencing depth. All three platforms showed similar power in exome SNP calling, including medically relevant SNPs. Compared with genotyping and whole-genome sequencing data, the three platforms achieved a similar accuracy of genotype assignment and SNP detection. Importantly, all three platforms showed similar levels of reproducibility, GC bias and reference allele bias.ConclusionsWe demonstrate key differences between the three platforms, particularly advantages of solutions over array capture and the importance of a large gene target set

Strong anthropogenic control of secondary organic aerosol formation from isoprene in Beijing

Isoprene-derived secondary organic aerosol (iSOA) is a significant contributor to organic carbon (OC) in some forested regions, such as tropical rainforests and the Southeastern US. However, its contribution to organic aerosol in urban areas that have high levels of anthropogenic pollutants is poorly understood. In this study, we examined the formation of anthropogenically influenced iSOA during summer in Beijing, China. Local isoprene emissions and high levels of anthropogenic pollutants, in particular NOx and particulate SO2-4 , led to the formation of iSOA under both high- A nd low-NO oxidation conditions, with significant heterogeneous transformations of isoprene-derived oxidation products to particulate organosulfates (OSs) and nitrooxyorganosulfates (NOSs). Ultra-high-performance liquid chromatography coupled to high-resolution mass spectrometry was combined with a rapid automated data processing technique to quantify 31 proposed iSOA tracers in offline PM2.5 filter extracts. The co-elution of the inorganic ions in the extracts caused matrix effects that impacted two authentic standards differently. The average concentration of iSOA OSs and NOSs was 82.5 ngm-3, which was around 3 times higher than the observed concentrations of their oxygenated precursors (2-methyltetrols and 2-methylglyceric acid). OS formation was dependant on both photochemistry and the sulfate available for reactive uptake, as shown by a strong correlation with the product of ozone (O3) and particulate sulfate (SO2-4). A greater proportion of high-NO OS products were observed in Beijing compared with previous studies in less polluted environments. The iSOA-derived OSs and NOSs represented 0.62% of the oxidized organic aerosol measured by aerosol mass spectrometry on average, but this increased to ∼ 3% on certain days. These results indicate for the first time that iSOA formation in urban Beijing is strongly controlled by anthropogenic emissions and results in extensive conversion to OS products from heterogenous reactions

From hyper- to hypoinsulinemia and diabetes: effect of KCNH6 on insulin secretion

Glucose-stimulated insulin secretion from islet β cells is mediated by K channels. However, the role of non-K K channels in insulin secretion is largely unknown. Here, we show that a non-K K channel, KCNH6, plays a key role in insulin secretion and glucose hemostasis in humans and mice. KCNH6 p.P235L heterozygous mutation co-separated with diabetes in a four-generation pedigree. Kcnh6 knockout (KO) or Kcnh6 p.P235L knockin (KI) mice had a phenotype characterized by changing from hypoglycemia with hyperinsulinemia to hyperglycemia with insulin deficiency. Islets from the young KO mice had increased intracellular calcium concentration and increased insulin secretion. However, islets from the adult KO mice not only had increased intracellular calcium levels but also had remarkable ER stress and apoptosis, associated with loss of β cell mass and decreased insulin secretion. Therefore, dysfunction of KCNH6 causes overstimulation of insulin secretion in the short term and β cell failure in the long term.Yang et al. show that KCNH6 plays a key role in insulin secretion and glucose hemostasis in humans and mice. Dysfunction of KCNH6 results in a hyperinsulinemia phenotype in the short term and hypoinsulinemia and diabetes in the long term

Impact of HO2 aerosol uptake on radical levels and O3 production during summertime in Beijing

The impact of heterogeneous uptake of HO2 on aerosol surfaces on radical concentrations and the O3 production regime in Beijing in summertime was investigated. The uptake coefficient of HO2 onto aerosol surfaces, γHO2 , was calculated for the AIRPRO campaign in Beijing, in summer 2017, as a function of measured aerosol soluble copper concentration, [Cu2+]eff, aerosol liquid water content, [ALWC], and particulate matter concentration, [PM]. An average γHO2 across the entire campaign of 0.070 ± 0.035 was calculated, with values ranging from 0.002 to 0.15, and found to be significantly lower than the value of γHO2 = 0.2, commonly used in modelling studies. Using the calculated γHO2 values for the summer AIRPRO campaign, OH, HO2 and RO2 radical concentrations were modelled using a box model incorporating the Master Chemical Mechanism (v3.3.1), with and without the addition of γHO2 , and compared to the measured radical concentrations. The rate of destruction analysis showed the dominant HO2 loss pathway to be HO2 + NO for all NO concentrations across the summer Beijing campaign, with HO2 uptake contributing < 0.3 % to the total loss of HO2 on average. This result for Beijing summertime would suggest that under most conditions encountered, HO2 uptake onto aerosol surfaces is not important to consider when investigating increasing O3 production with decreasing [PM] across the North China Plain. At low [NO], however, i.e. < 0.1 ppb, which was often encountered in the afternoons, up to 29 % of modelled HO2 loss was due to HO2 uptake on aerosols when calculated γHO2 was included, even with the much lower γHO2 values compared to γHO2 = 0.2, a result which agrees with the aerosol-inhibited O3 regime recently proposed by Ivatt et al. (2022). As such it can be concluded that in cleaner environments, away from polluted urban centres where HO2 loss chemistry is not dominated by NO but where aerosol surface area is high still, changes in PM concentration and hence aerosol surface area could still have a significant effect on both overall HO2 concentration and the O3 production regime. Using modelled radical concentrations, the absolute O3 sensitivity to NOx and volatile organic compounds (VOCs) showed that, on average across the summer AIRPRO campaign, the O3 production regime remained VOC-limited, with the exception of a few days in the afternoon when the NO mixing ratio dropped low enough for the O3 regime to shift towards being NOx -limited. The O3 sensitivity to VOCs, the dominant regime during the summer AIRPRO campaign, was observed to decrease and shift towards a NOx -sensitive regime both when NO mixing ratio decreased and with the addition of aerosol uptake. This suggests that if [NOx ] continues to decrease in the future, ozone reduction policies focussing solely on NOx reductions may not be as efficient as expected if [PM] and, hence, HO2 uptake to aerosol surfaces continue to decrease. The addition of aerosol uptake into the model, for both the γHO2 calculated from measured data and when using a fixed value of γHO2 = 0.2, did not have a significant effect on the overall O3 production regime across the campaign. While not important for this campaign, aerosol uptake could be important for areas of lower NO concentration that are already in a NOx -sensitive regime

Key role of NO3 radicals in the production of isoprene nitrates and nitrooxyorganosulfates in Beijing

The formation of isoprene nitrates (IsN) can lead to significant secondary organic aerosol (SOA) production and they can act as reservoirs of atmospheric nitrogen oxides. In this work, we estimate the rate of production of IsN from the reactions of isoprene with OH and NO3 radicals during the summertime in Beijing. While OH dominates the loss of isoprene during the day, NO3 plays an increasingly important role in the production of IsN from the early afternoon onwards. Unusually low NO concentrations during the afternoon resulted in NO3 mixing ratios of ca. 2 pptv at approximately 15:00, which we estimate to account for around a third of the total IsN production in the gas phase. Heterogeneous uptake of IsN produces nitrooxyorganosulfates (NOS). Two mono-nitrated NOS were correlated with particulate sulfate concentrations and appear to be formed from sequential NO3 and OH oxidation. Di- and tri-nitrated isoprene-related NOS, formed from multiple NO3 oxidation steps, peaked during the night. This work highlights that NO3 chemistry can play a key role in driving biogenic–anthropogenic interactive chemistry in Beijing with respect to the formation of IsN during both the day and night

Evaluating the sensitivity of radical chemistry and ozone formation to ambient VOCs and NOxin Beijing

Measurements of OH, HO2, complex RO2 (alkene-and aromatic-related RO2) and total RO2 radicals taken during the integrated Study of AIR Pollution PROcesses in Beijing (AIRPRO) campaign in central Beijing in the summer of 2017, alongside observations of OH reactivity, are presented. The concentrations of radicals were elevated, with OH reaching up to 2:8 × 107 molecule cm-3, HO2 peaking at 1 × 109 molecule cm-3 and the total RO2 concentration reaching 5:5×109 molecule cm-3. OH reactivity (k.OH/) peaked at 89 s-1 during the night, with a minimum during the afternoon of 22s-1 on average. An experimental budget analysis, in which the rates of production and destruction of the radicals are compared, highlighted that although the sources and sinks of OH were balanced under high NO concentrations, the OH sinks exceeded the known sources (by 15 ppbvh-1) under the very low NO conditions (< 0:5ppbv) experienced in the afternoons, demonstrating a missing OH source consistent with previous studies under high volatile organic compound (VOC) emissions and low NO loadings. Under the highest NO mixing ratios (104 ppbv), the HO2 production rate exceeded the rate of destruction by 50ppbvh-1, whilst the rate of destruction of total RO2 exceeded the production by the same rate, indicating that the net propagation rate of RO2 to HO2 may be substantially slower than assumed. If just 10 % of the RO2 radicals propagate to HO2 upon reaction with NO, the HO2 and RO2 budgets could be closed at high NO, but at low NO this lower RO2 to HO2 propagation rate revealed a missing RO2 sink that was similar in magnitude to the missing OH source. A detailed box model that incorporated the latest Master Chemical Mechanism (MCM3.3.1) reproduced the observed OH concentrations well but over-predicted the observed HO2 under low concentrations of NO (< 1ppbv) and under-predicted RO2 (both the complex RO2 fraction and other RO2 types which we classify as simple RO2) most significantly at the highest NO concentrations. The model also under-predicted the observed k.OH/consistently by 10s-1 across all NOx levels, highlighting that the good agreement for OH was fortuitous due to a cancellation of missing OH source and sink terms in its budget. Including heterogeneous loss of HO2 to aerosol surfaces did reduce the modelled HO2 concentrations in line with the observations but only at NO mixing ratios < 0:3ppbv. The inclusion of Cl atoms, formed from the photolysis of nitryl chloride, enhanced the modelled RO2 concentration on several mornings when the Cl atom concentration was calculated to exceed 1 × 104 atoms cm-3 and could reconcile the modelled and measured RO2 concentrations at these times. However, on other mornings, when the Cl atom concentration was lower, large under-predictions in total RO2 remained. Furthermore, the inclusion of Cl atom chemistry did not enhance the modelled RO2 beyond the first few hours after sunrise and so was unable to resolve the modelled under-prediction in RO2 observed at other times of the day. Model scenarios, in which missing VOC reactivity was included as an additional reaction that converted OH to RO2, highlighted that the modelled OH, HO2 and RO2 concentrations were sensitive to the choice of RO2 product. The level of modelled to measured agreement for HO2 and RO2 (both complex and simple) could be improved if the missing OH reactivity formed a larger RO2 species that was able to undergo reaction with NO, followed by isomerisation reactions reforming other RO2 species, before eventually generating HO2. In this work an a-pinene-derived RO2 species was used as an example. In this simulation, consistent with the experimental budget analysis, the model underestimated the observed OH, indicating a missing OH source. The model uncertainty, with regards to the types of RO2 species present and the radicals they form upon reaction with NO (HO2 directly or another RO2 species), leads to over an order of magnitude less O3 production calculated from the predicted peroxy radicals than calculated from the observed peroxy radicals at the highest NO concentrations. This demonstrates the rate at which the larger RO2 species propagate to HO2, to another RO2 or indeed to OH needs to be understood to accurately simulate the rate of ozone production in environments such as Beijing, where large multifunctional VOCs are likely present