RNA-seq analysis, targeted long-read sequencing and in silico prediction to unravel pathogenic intronic events and complicated splicing abnormalities in dystrophinopathy.

Dystrophinopathy is caused by alterations in DMD. Approximately 1% of patients remain genetically undiagnosed, because intronic variations are not detected by standard methods. Here, we combined laboratory and in silico analyses to identify disease-causing genomic variants in genetically undiagnosed patients and determine the regulatory mechanisms underlying abnormal DMD transcript generation. DMD transcripts from 20 genetically undiagnosed dystrophinopathy patients in whom no exon variants were identified, despite dystrophin deficiency on muscle biopsy, were analyzed by transcriptome sequencing. Genome sequencing captured intronic variants and their effects were interpreted using in silico tools. Targeted long-read sequencing was applied in cases with suspected structural genomic abnormalities. Abnormal DMD transcripts were detected in 19 of 20 cases; Exonization of intronic sequences in 15 cases, exon skipping in one case, aberrantly spliced and polyadenylated transcripts in two cases and transcription termination in one case. Intronic single nucleotide variants, chromosomal rearrangements and nucleotide repeat expansion were identified in DMD gene as pathogenic causes of transcript alteration. Our combined analysis approach successfully identified pathogenic events. Detection of diseasing-causing mechanisms in DMD transcripts could inform the therapeutic options for patients with dystrophinopathy.

Additional findings of tibial dysplasia in a male with orofaciodigital syndrome type XVI.

We describe the case of a male patient with orofaciodigital (OFD) syndrome type XVI with a homozygous variant of TMEM107 (p.Phe106del) and the additional findings of tibial dysplasia, which is a pivotal finding of OFD syndrome type IV. His family history included two fetuses with anencephaly with or without cleft lip/palate and polydactyly with no genetic information. Careful attention should be given to the interpretation of this rare pattern.

Simple and reliable method to simultaneously determine urinary 1- and 2-naphthol using in situ derivatization and gas chromatography-mass spectrometry for biological monitoring of naphthalene exposure in occupational health practice.

OBJECTIVES: The aim of this study was to develop and validate a simple and reliable gas chromatography-mass spectrometry (GC-MS) method to simultaneously determine urinary 1-naphthol (1-NAP) and 2-naphthol (2-NAP) for biological monitoring of occupational exposure to naphthalene. METHODS: NAPs were derivatized in situ with acetic anhydride after enzymatic hydrolysis, extracted with n-hexane, and analyzed using GC-MS. Validation of the proposed method was conducted in accordance with US Food and Drug Administration guidance. A final validation was performed by analyzing a ClinChek® -Control for phenolic compounds. RESULTS: The linearity of calibration curves was indicated by a high correlation coefficient (>0.999) in the concentration range 1-100 µg/L for each NAP. The limits of detection and quantification for each NAP were 0.30 and 1.00 µg/L, respectively. The recovery was 90.8%-98.1%. The intraday and interday accuracies, expressed as the deviation from the nominal value, were 92.2%-99.9% and 93.4%-99.9%, respectively. The intraday and interday precision, expressed as the relative standard deviation, was 0.3%-3.9% and 0.4%-4.1%, respectively. The ClinChek® values obtained using our method were sufficiently accurate. CONCLUSIONS: The proposed method is simple, reliable, and appropriate for routine analyses, and is useful for biological monitoring of naphthalene exposure in occupational health practice.

Matrix behavior during sample preparation using metabolomics analysis approach for pesticide residue analysis by GC-MS in agricultural products.

The detailed matrices and their behaviors during pesticide residue analyses were clarified using a metabolomics analysis approach. The matrix profile was investigated using two different extraction solvents, acetone and acetonitrile. Acetone extracted the matrix components with a wide range of log P(O/W) values. Components with log P(O/W) values >10, such as sterols and tocopherols, and components with log P(O/W) values <3.2 were more extracted by acetone than by acetonitrile. In contrast, components with log P(O/W) values in the range from 3.2 to 10 were extracted by both acetone and acetonitrile at the same concentration level. The study also examined the difference in the column cleanup efficiency using a solid phase extraction (SPE). Florisil, silica gel, NH(2), PSA, and GCB were selected as representative columns for pesticide residue analysis, and acetone extraction of brown rice was selected in this experiment. Most of the matrix components were removed by either column, whereas monoacylglycerols, which are the components causing the matrix effect, were not removed by any column. Understanding such a detailed matrix behavior helps to develop a better analytical method for pesticide analysis using GC-MS.

Deoxidation of fenthion sulfoxide, fenthion oxon sulfoxide and fensulfothion in gas chromatograph/mass spectrometer, and the prevention of sulfoxide deoxidation by polyethylene glycol 300.

Fenthion, fenthion sulfoxide, fenthion oxon sulfoxide and fensulfothion showed two different mass spectra in GC/MS, depending on their concentrations. The base peaks shifted to lower levels by 1 m/z at lower concentration, and no retention time shifts were observed. The "shifted base peaks" were not obtained by a general EI fragmentation. The product ion scan spectra of the "shifted base peaks" were coincident with those of molecular ions of their corresponding sulfides. These phenomena can be ascribed to the conversion of sulfoxide into sulfide by the dominant deoxidation reaction than EI fragmentation in an ion source. Adding polyethylene glycol 300 (PEG300) into a test solution prevented sulfoxide deoxidation.

Fast screening of pesticide multiresidues in aqueous samples by dual stir bar sorptive extraction-thermal desorption-low thermal mass gas chromatography-mass spectrometry.

A method for fast screening of pesticide multiresidues in aqueous samples using dual stir bar sorptive extraction-thermal desorption-low thermal mass gas chromatography-mass spectrometry (dual SBSE-TD-LTM-GC-MS) has been developed. Recovery of 82 pesticides - organochlorine, carbamate, organophosphorous, pyrethroid and others - for the SBSE was evaluated as a function of octanol-water distribution coefficients (log K(o/w): 1.7-8.35), sample volume (2-20 mL), salt addition (0-30% NaCl), and methanol addition (0-20%). The optimized method consists of a dual SBSE performed simultaneously on respectively a 20-mL sample containing 30% NaCl and a 20-mL sample without modifier (100% sample solution). One extraction with 30% NaCl is mainly targeting solutes with low K(o/w) (log K(o/w)<3.5) and another extraction with unmodified sample solution is targeting solutes with medium and high K(o/w) (log K(o/w)>3.5). After extraction, the two stir bars are placed in a single glass desorption liner and are simultaneously desorbed. The desorbed compounds are analyzed by use of LTM-GC-MS with fast temperature programming (75 degrees C min(-1)) using a 0.18 mm i.d. narrow-bore capillary column and fast scanning (10.83 scan s(-1)) using quadrupole MS. The method showed good linearity (r(2)>0.9900) and high sensitivity (limit of detection: <10 ng L(-1)) for most of the target pesticides. The method was applied to the determination of pesticides at nanograms per liter levels in river water and brewed green tea.

Simultaneous determination of 64 pesticides in river water by stir bar sorptive extraction and thermal desorption-gas chromatography-mass spectrometry.

A method for determining 68 pesticides in river water using stir bar sorptive extraction (SBSE)-thermal desorption (TD)-gas chromatography-mass spectrometry (GC-MS) is described. SBSE sampling was optimized for sample solution pH, salting-out and methanol addition. Although salting-out enhanced the ability of the method to extract most of the pesticides with low absolute recoveries, the absolute recoveries of four pesticides were not improved by salting-out. The detection limits of the method for the pesticides ranged from 0.2 to 20 ng/l. Analyte recoveries from a river water sample spiked with standards at 10 and 100 ng/l were 58.5-132.0% (RSD: 1.8-15.8%) and 61.0-121.3% (RSD: 1.4-20.2%), respectively.

Determination of 2-methylisoborneol and geosmin in aqueous samples by static headspace-gas chromatography-mass spectrometry with ramped inlet pressure.

A method for determining the earthy and musty odors 2-methylisoborneol (2-MIB) and geosmin in drinking water using static headspace-GC-MS is described. To achieve lower detection limits, split ratio was optimized with ramped inlet pressure for large headspace sampling volume. The ramped inlet pressure, which held higher pressure (higher column flow rate) only during injection, allowed us to inject 3-mL volume to GC with very low split ratio (2:1). Although sequential analysis with a stainless steel ion source often changed the mass spectrum of 2-MIB, this spectral change was eliminated by using an inert ion source with a 6 mm drawout plate. The detection limits of this method were 0.36 and 0.14 ng/L, respectively, for 2-MIB and geosmin. The repeatabilities (n = 30) were 6.6 and 4.8%, respectively, at 1 ng/L for 2-MIB and geosmin.

Simultaneous determination of alkylphenols and bisphenol A in river water by stir bar sorptive extraction with in situ acetylation and thermal desorption-gas chromatography-mass spectrometry.

A method for the determination of seven alkylphenols and bisphenol A by stir bar sorptive extraction (SBSE) with in situ derivatization-thermal desorption (TD)-gas chromatography (GC)-mass spectrometry (MS) is described. SBSE was performed with in situ acetylation and without derivatization for comparison. For 4-tert-butylphenol and bisphenol A, in situ acetylation improved the responses in SBSE-TD-GC-MS. The method detection limits ranged from 0.1 to 3.2 ng/l. The recoveries of the analytes from a river water sample spiked with standards at 10 and 100 ng/l were 85.3-105.9% (R.S.D., 3.0-11.0%) and 88.3-105.8% (R.S.D., 1.6-8.3%), respectively.