Non-invasive spectroscopic and imaging systems for prediction of beef quality in a meat processing pilot plant.

This study evaluated a range of diffuse reflectance spectroscopic (Vis-NIR spectrophotometers) and imaging (Hyperspectral imaging cameras) instruments for predicting pH, IMF and shear force values of beef in a meat processing pilot plant. A total of 364 beef striploin samples were evaluated and prediction models were developed using PLSR. Models for pH and IMF (except Vis snapshot camera) showed good fit with high Rcv2 (0.29-0.92) and low SECV values. Good prediction accuracy with high Rp2 (0.44-0.90), RPD and low SEP values was also observed. While low values of Rp2 for shear force was observed, the expected curvilinear relationship between predicted values of shear force and predicted values of pH was observed suggesting that spectroscopic measurements were able detect biophysical factors associated to these two attributes. Overall, it can be concluded that diffuse reflectance spectroscopy combined with chemometrics has a great potential to be used as an on/in-line quality monitoring system for the meat processing industry.

Diagnostic value of whole-exome sequencing in Chinese pediatric-onset neuromuscular patients.

BACKGROUND: Neuromuscular disorders (NMDs) comprise a group of heterogeneous genetic diseases with a broad spectrum of overlapping the clinical presentations that makes diagnosis challenging. Notably, the recent introduction of whole-exome sequencing (WES) is introducing rapid changes on the genetic diagnosis of NMDs. We aimed to investigate the diagnostic value of WES for pediatric-onset NMDs. METHODS: We applied integrated diagnostic approach and performed WES in 50 Chinese subjects (30 males, 20 females) with undiagnosed pediatric-onset NMDs despite previous specific tests. The patients were categorized in four subgroups according to phenotyping and investigation findings. Variants on NMDs gene list and open exome analysis for those with initial negative findings were identified. RESULTS: WES identified causative variants in ACTA1 (n = 2), POMT1, COL6A1 (n = 2), MTMR2, LMNA, SELENON, DNM2, TGFB1, MPZ, IGHMBP2, and LAMA2 in 13 patients. Two subjects have variants of uncertain significance (VUSs) in TTN and SCN11A, unlikely to be pathogenic due to incompatible phenotypes. The mean interval time from symptom onset to genetic diagnosis was 10.4 years (range from 1 month to 33 years). The overall diagnostic yield of WES in our cohort was 26%. Open exome analysis was necessary to identify the pathogenic variant in TGFB1 that caused skeletal dysplasia with neuromuscular presentation. CONCLUSION: Our study shows a clear role of WES in the pathway of integrated diagnostic approach to shorten the diagnostic odyssey in patients with rare NMDs.

Rapid whole-exome sequencing facilitates precision medicine in paediatric rare disease patients and reduces healthcare costs.

BACKGROUND: Rapid whole-exome sequencing (rWES) offers the potential for early diagnosis-predicated precision medicine. Previous evidence focused predominantly on infants from the intensive care unit (ICU). This study sought to examine the diagnostic and clinical utility, and the economic impact on clinical management of rWES in patients beyond infancy and ICU setting. METHODS: rWES was performed on a prospective cohort of patients with suspected monogenic disorder referred from territory-wide paediatric ICUs and non-ICUs in Hong Kong urging for rapid genetic diagnosis. All eligible families were invited. We aimed to achieve a rapid turnaround time (TAT) of 14 days. Clinical utility and costs associated with clinical management were assessed in diagnosed cases. Actual quantitative changes in healthcare utilisation were compared with a counterfactual diagnostic trajectory and/or with matched historical control whenever possible. FINDINGS: rWES were offered to 102 families and 32/102 (31%) patients received a molecular diagnosis, with a median TAT of 11 days. Clinical management changed in 28 of 32 diagnosed patients (88%), including but not limited to modifications in treatment, avoidance of surgeries, and informing decisions on redirection of care. Cost analysis was performed in eight patients. rWES was estimated to reduce hospital length of stay by 566 days and decrease healthcare costs by HKD$8,044,250 (GBP£796,460) for these eight patients. The net cost-savings after inclusion of rWES costs were estimated to be HKD$5,325,187 (GBP£527,246). INTERPRETATION: This study replicates the diagnostic capacity and rapid TAT of rWES in predominantly Chinese patients, and demonstrates diagnosis-predicated precision medicine and net healthcare savings. Findings were corroborated by evidence from multinational cohorts, combined as part of a meta-analysis. rWES merits consideration as a first-tier diagnostic tool for patients with urgent needs in the clinical setting. FUNDING: Health and Medical Research Fund, HKU Seed Fund for Basic Research, The Society for the Relief of Disabled Children, and Edward and Yolanda Wong Fund.

Genetic landscape of RASopathies in Chinese: Three decades' experience in Hong Kong.

RASopathies are a group of genetic disorders due to dysregulation of the RAS-MAPK signaling pathway, which is important in regulating cell growth, proliferation, and differentiation. These include Noonan syndrome (NS), Noonan syndrome with multiple lentigines (NSML), cardiofaciocutaneous (CFC) syndrome, and Costello syndrome (CS), clinical manifestations include growth retardation, developmental delay, cardiac defects, and specific dysmorphic features. There were abundant publications describing the genotype and phenotype from the Western populations. However, detailed study of RASopathies in Chinese population is lacking. We present here the largest cohort of RASopathies ever reported in Chinese populations, detailing the mutation spectrum and clinical phenotypes of these patients. The Clinical Genetic Service, Department of Health, and Queen Mary Hospital are tertiary referral centers for genetic disorders in Hong Kong. We retrospectively reviewed all the genetically confirmed cases of RASopathies, including NS, NSML, CFC syndrome, and CS, over the past 29 years (from 1989 to 2017). Analyses of the mutation spectrum and clinical phenotypes were performed. One hundred and ninety-one ethnic Chinese patients with genetically confirmed RASopathies were identified, including 148 patients with NS, 23 NSML, 12 CFC syndrome, and eight CS. We found a lower incidence of hypertrophic cardiomyopathy in individuals with NSML (27.3%), and NS caused by RAF1 mutations (62.5%). Another significant finding was for those NS patients with myeloproliferative disorder, the mutations fall within Exon 3 of PTPN11 but not only restricted to the well-known hotspots, that is, p.Asp61 and p.Thr731, which suggested that re-evaluation of the current tumor surveillance recommendation maybe warranted.

A significant inflation in TGM6 genetic risk casts doubt in its causation in spinocerebellar ataxia type 35.

Spinocerebellar ataxia 35 (SCA35) has been associated with pathogenic mutations in the gene TGM6. In a Chinese exome sequencing cohort, we identified 8 families with reported TGM6 variants sharing no features of SCA35. Considering this finding, we reviewed the public database gnomAD and found these variants to be significantly more common in the East Asians than in other ethnic groups (P < 0.0001). Gene constraint metrics showed that both missense and loss-of-function variants in TGM6 are likely to be tolerated and there is no regional constraint. By performing inflation analysis, it demonstrated that the cumulative frequency of TGM6 reported pathogenic variants is at least 111-fold inflated over disease prevalence of all autosomal dominant SCAs, indicating a high chance of misdiagnosis or low penetrance. Misclassification of benign or low penetrant variants as pathogenic is a significant problem that often results in genetic misdiagnosis. This highlights the necessity of evaluating variant pathogenicity with sequencing of genomes from diverse populations, both from asymptomatic controls and phenotypically different patients, in order to ensure accurate classification of variants.

Identifying the genetic causes for prenatally diagnosed structural congenital anomalies (SCAs) by whole-exome sequencing (WES).

BACKGROUND: Whole-exome sequencing (WES) has become an invaluable tool for genetic diagnosis in paediatrics. However, it has not been widely adopted in the prenatal setting. This study evaluated the use of WES in prenatal genetic diagnosis in fetuses with structural congenital anomalies (SCAs) detected on prenatal ultrasound. METHOD: Thirty-three families with fetal SCAs on prenatal ultrasonography and normal chromosomal microarray results were recruited. Genomic DNA was extracted from various fetal samples including amniotic fluid, chorionic villi, and placental tissue. Parental DNA was extracted from peripheral blood when available. We used WES to sequence the coding regions of parental-fetal trios and to identify the causal variants based on the ultrasonographic features of the fetus. RESULTS: Pathogenic mutations were identified in three families (n = 3/33, 9.1%), including mutations in DNAH11, RAF1 and CHD7, which were associated with primary ciliary dyskinesia, Noonan syndrome, and CHARGE syndrome, respectively. In addition, variants of unknown significance (VUSs) were detected in six families (18.2%), in which genetic changes only partly explained prenatal features. CONCLUSION: WES identified pathogenic mutations in 9.1% of fetuses with SCAs and normal chromosomal microarray results. Databases for fetal genotype-phenotype correlations and standardized guidelines for variant interpretation in prenatal diagnosis need to be established to facilitate the use of WES for routine testing in prenatal diagnosis.

Integrating Functional Analysis in the Next-Generation Sequencing Diagnostic Pipeline of RASopathies.

RASopathies are a group of heterogeneous conditions caused by germline mutations in RAS/MAPK signalling pathway genes. With next-generation sequencing (NGS), sequencing capacity is no longer a limitation to molecular diagnosis. Instead, the rising number of variants of unknown significance (VUSs) poses challenges to clinical interpretation and genetic counselling. We investigated the potential of an integrated pipeline combining NGS and the functional assessment of variants for the diagnosis of RASopathies. We included 63 Chinese patients with RASopathies that had previously tested negative for PTPN11 and HRAS mutations. In these patients, we performed a genetic analysis of genes associated with RASopathies using a multigene NGS panel and Sanger sequencing. For the VUSs, we evaluated evidence from genetic, bioinformatic and functional data. Twenty disease-causing mutations were identified in the 63 patients, providing a primary diagnostic yield of 31.7%. Four VUSs were identified in five patients. The functional assessment supported the pathogenicity of the RAF1 and RIT1 VUSs, while the significance of two VUSs in A2ML1 remained unclear. In summary, functional analysis improved the diagnostic yield from 31.7% to 36.5%. Although technically demanding and time-consuming, a functional genetic diagnostic analysis can ease the clinical translation of these findings to aid bedside interpretation.

Noonan syndrome in diverse populations.

Noonan syndrome (NS) is a common genetic syndrome associated with gain of function variants in genes in the Ras/MAPK pathway. The phenotype of NS has been well characterized in populations of European descent with less attention given to other groups. In this study, individuals from diverse populations with NS were evaluated clinically and by facial analysis technology. Clinical data and images from 125 individuals with NS were obtained from 20 countries with an average age of 8 years and female composition of 46%. Individuals were grouped into categories of African descent (African), Asian, Latin American, and additional/other. Across these different population groups, NS was phenotypically similar with only 2 of 21 clinical elements showing a statistically significant difference. The most common clinical characteristics found in all population groups included widely spaced eyes and low-set ears in 80% or greater of participants, short stature in more than 70%, and pulmonary stenosis in roughly half of study individuals. Using facial analysis technology, we compared 161 Caucasian, African, Asian, and Latin American individuals with NS with 161 gender and age matched controls and found that sensitivity was equal to or greater than 94% for all groups, and specificity was equal to or greater than 90%. In summary, we present consistent clinical findings from global populations with NS and additionally demonstrate how facial analysis technology can support clinicians in making accurate NS diagnoses. This work will assist in earlier detection and in increasing recognition of NS throughout the world.

CFTR founder mutation causes protein trafficking defects in Chinese patients with cystic fibrosis.

BACKGROUND: Cystic fibrosis (CF) is a rare condition in Asians. Since 1985, only about 30 Chinese patients have been reported with molecular confirmation. METHOD: Using our in-house next-generation sequencing (NGS) pipeline for childhood bronchiectasis, we identified disease-causing CFTR mutations in CF patients in Hong Kong. After identifying p.I1023R in multiple patients, haplotype analysis was performed with genome-wide microarray to ascertain the likelihood of this being a founder mutation. We also assessed the processing and gating activity of the mutant protein by Western hybridization and patch-clamp test. RESULTS: Molecular diagnoses were confirmed in four patients, three of whom shared a missense mutation: CFTR:c.3068T>G:p.I1023R. The results suggested that p.I1023R is a founder mutation in southern Han Chinese. In addition, the processing and gating activity of the mutant protein was assessed by gel electrophoresis and a patch-clamp test. The mutant protein exhibited trafficking defects, suggesting that the dysfunction is caused by reduced cell surface expression of the fully glycosylated proteins. CONCLUSION: Together with other previously reported mutations, the specific founder mutation presented herein suggests a unique CFTR mutation spectrum in the southern Chinese populations, and this finding has vital implications for improving molecular testing and mutation-specific treatments for Chinese patients with CF.

Before and after - Nutritional transformation of dysmorphism in a case of Costello syndrome.

Costello syndrome is a type of RASopathy mapped to HRAS gene in chromosome 11, characterized by prenatal overgrowth, postnatal failure to thrive, classic facial gestalt and multisystem involvement including cardiomyopathy and intellectual disability. We present a 7 months old child with severe failure to thrive whose "subtle" facial dysmorphism at the time eluded clinical recognition of the syndrome. It was only with optimization of his nutritional status that dysmorphic features became more apparent, which affirmed the molecular diagnosis of Costello syndrome from exome sequencing. The case illustrated how drastic failure to thrive can be in Costello syndrome, and how nutritional status can transform dysmorphic features in a child. It also highlights the importance of serial dysmorphic evaluation in difficult cases.

Mechanisms for the Generation of Two Quadruplications Associated with Split-Hand Malformation.

Germline copy-number variants (CNVs) involving quadruplications are rare and the mechanisms generating them are largely unknown. Previously, we reported a 20-week gestation fetus with split-hand malformation; clinical microarray detected two maternally inherited triplications separated by a copy-number neutral region at 17p13.3, involving BHLHA9 and part of YWHAE. Here, we describe an 18-month-old male sibling of the previously described fetus with split-hand malformation. Custom high-density microarray and digital droplet PCR revealed the copy-number gains were actually quadruplications in the mother, the fetus, and her later born son. This quadruplication-normal-quadruplication pattern was shown to be expanded from the triplication-normal-triplication CNV at the same loci in the maternal grandmother. We mapped two breakpoint junctions and demonstrated that both are mediated by Alu repetitive elements and identical in these four individuals. We propose a three-step process combining Alu-mediated replicative-repair-based mechanism(s) and intergenerational, intrachromosomal nonallelic homologous recombination to generate the quadruplications in this family.

De novo large rare copy-number variations contribute to conotruncal heart disease in Chinese patients.

Conotruncal heart anomalies (CTDs) are particularly prevalent congenital heart diseases (CHD) in Hong Kong. We surveyed large (>500 kb), rare (<1% frequency in controls) copy-number variations (CNVs) in Chinese patients with CTDs to identify potentially disease-causing variations. Adults who tested negative for 22q11.2 deletions were recruited from the adult CHD clinic in Hong Kong. Using a stringent calling criteria, high-confidence CNV calls were obtained, and a large control set comprising 3,987 Caucasian and 1,945 Singapore Chinese subjects was used to identify rare CNVs. Ten large rare CNVs were identified, and 3 in 108 individuals were confirmed to harbour de novo CNVs. All three patients were syndromic with a more complex phenotype, and each of these CNVs overlapped regions likely to be important in CHD. One was a 611 kb deletion at 17p13.3, telomeric to the Miller-Dieker syndrome (MDS) critical region, overlapping the NXN gene. Another was a 5 Mb deletion at 13q33.3, within a previously described critical region for CHD. A third CNV, previously unreported, was a large duplication at 2q22.3 overlapping the ZEB2 gene. The commonly reported 1q21.1 recurrent duplication was not observed in this Chinese cohort. We provide detailed phenotypic and genotypic descriptions of large rare genic CNVs that may represent CHD loci in the East Asian population. Larger samples of Chinese origin will be required to determine whether the genome-wide distribution differs from that found in predominantly European CHD cohorts.

Molecular excitons in a copper azadipyrrin complex.

Exciton coupling is investigated in a copper azadipyrrin complex, Cu(L-aza)2. Exciton coupling in Cu(L-aza)2 assuming a single π-π* state on the L-aza ligand fails to account for the electronic structure of Cu(L-aza)2, which displays two almost equal intensity transitions at 15 600 cm(-1) and 17 690 cm(-1). TD-UB3LYP/6-31G(d) calculations suggest multiple π-π* transitions for the L-aza ligands and simple vector addition of the transition dipoles predicts two nearly orthogonal co-planar excitonic transitions that correctly reproduce the absorption band profile. Empirical modelling of absolute resonance Raman intensities using wavepacket dynamics confirms Cu(L-aza)2 has two equal intensity orthogonal exciton transitions. The phenyl substituents at the α- and γ-positions of the pyrrole rings play a central role in determining the orientation of the transition dipoles. Consequently the π-π* transitions for the L-aza ligands are oriented towards the substituent groups and are not in the plane of the pyrrole rings. Mode displacements in the Franck-Condon (FC) region obtained from the wavepacket model suggest that pyrrole ring and phenyl modes control the exciton FC dynamics. Our results suggest that Cu(L-aza)2 is an ideal model for theoretical, computational and experimental investigations of molecular excitons in molecular systems.

Application of terahertz pulsed imaging to analyse film coating characteristics of sustained-release coated pellets.

Terahertz pulsed imaging (TPI) was employed to explore its suitability for detecting differences in the film coating thickness and drug layer uniformity of multilayered, sustained-release coated, standard size pellets (approximately 1mm in diameter). Pellets consisting of a sugar starter core and a metoprolol succinate layer were coated with a Kollicoat(®) SR:Kollicoat(®) IR polymer blend for different times giving three groups of pellets (batches I, II and III), each with a different coating thickness according to weight gain. Ten pellets from each batch were mapped individually to evaluate the coating thickness and drug layer thickness between batches, between pellets within each batch, and across individual pellets (uniformity). From the terahertz waveform the terahertz electric field peak strength (TEFPS) was used to define a circular area (approximately 0.13 mm(2)) in the TPI maps, where no signal distortion was found due to pellet curvature in the measurement set-up used. The average coating thicknesses were 46 µm, 71 µm and 114 µm, for batches I, II and III respectively, whilst no drug layer thickness difference between batches was observed. No statistically significant differences in the average coating thickness and drug layer thickness within batches (between pellets) but high thickness variability across individual pellets was observed. These results were confirmed by scanning electron microscopy (SEM). The coating thickness results correlated with the subsequent drug release behaviour. The fastest drug release was obtained from batch I with the lowest coating thickness and the slowest from batch III with the highest coating thickness. In conclusion, TPI is suitable for detailed, non-destructive evaluation of film coating and drug layer thicknesses in multilayered standard size pellets.

The impact of surface- and nano-crystallisation on the detected amorphous content and the dissolution behaviour of amorphous indomethacin.

The crystallinity and physical stability of amorphous drugs has previously been studied using different analytical techniques. However, the effect of the measurement method on observed crystallinity and its importance for critical quality attributes, such as dissolution, has not yet been widely investigated. The aim of this study was to (i) qualitatively analyse and understand the recrystallisation behaviour of amorphous indomethacin during storage, (ii) quantify the amorphous content during storage with complementary analytical techniques and (iii) investigate the relationship between observed recrystallisation behaviour and dissolution behaviour. Quench cooled indomethacin was stored and the samples were visualised by scanning electron microscopy to gain spatially resolved information about the recrystallisation behaviour. Crystallisation was quantified by Fourier transform attenuated total reflectance infrared (FT-ATR-IR) spectroscopy, differential scanning calorimetry and X-ray powder diffraction. These techniques resulted in different observed recrystallisation profiles. The physicochemical phenomena detected and sampling geometry for each technique together with the sample recrystallising from the surface and appearance of nano-crystals were used to explain the differences. The dissolution behaviour at the observed recrystallisation endpoints for the different analytical techniques revealed that FT-ATR-IR spectroscopy predicted the changes in dissolution behaviour due to crystallisation best.

Mixtures of oppositely charged polypeptides as high-performance dispersing agents for single-wall carbon nanotubes.

A new and simple strategy for the dispersion of single-wall carbon nanotubes in aqueous media is presented which does not rely on hydrophobic interactions between the polypeptidic dispersing agent and the nanotubes, and allows the surface charge of the resulting conjugate materials to be controlled.

Raman spectroscopic quantification of milk powder constituents.

Raman spectroscopy has significant potential for the quantification of food products. Milk powder is an important foodstuff and ingredient that is produced on large scale (over 20 million tonnes per annum). Raman spectroscopy, unlike near- and mid-infrared spectroscopies, has not been used extensively to quantify milk powder constituents. The effect of sample presentation on spectroscopic calibrations of protein and fat for 136 New Zealand milk powders was assessed using Raman spectroscopy. Prediction models were produced to quantify a protein concentration range of 32.19-37.65% w/w for skim milk powder, and a protein concentration range of 23.34-25.02% w/w and a fat concentration range of 26.26-29.68% w/w for whole milk powder (where ratios of prediction to deviation exceeded 2.6 with one exception). The resultant calibrations were not influenced by sample orientation; the sample temperature during data collection did affect the calibrations. Calcium fortification in the form of calcium carbonate was identified within a sub-set of samples, reinforcing the efficacy of Raman spectroscopy for identifying both crystalline and non-crystalline constituents within milk powder.

Raman spectroscopic prediction of the solid fat content of New Zealand anhydrous milk fat.

The functionality of anhydrous milk fat (AMF) is determined from solid fat content (SFC) and triacylglycerol (TG) profiles, parameters traditionally measured using nuclear magnetic resonance and high pressure liquid chromatography respectively. Raman spectroscopy coupled with partial least squares (PLS) analysis has been assessed as an alternative method for SFC and TG class quantification. Sample temperature at which the Raman spectra were collected, method of spectral preprocessing and type of PLS analysis were all investigated and found to significantly affect the resulting calibrations (as parameterized by root mean square error of cross validation). Physically heterogeneous AMF samples held at 20 °C were shown to allow reliable SFC predictions on the basis of collected Raman spectra. In contrast to SFC calibrations, physically homogenous samples in a liquid form were ideal for TG class concentration predictions, however, not all TG classes could be reliably predicted.

Analysis of sustained-release tablet film coats using terahertz pulsed imaging.

The coating quality of a batch of lab-scale, sustained-release coated tablets was analysed by terahertz pulsed imaging (TPI). Terahertz radiation (2 to 120 cm(-1)) is particularly interesting for coating analysis as it has the capability to penetrate through most pharmaceutical excipients, and hence allows non-destructive coating analysis. Terahertz pulsed spectroscopy (TPS) was employed for the determination of the terahertz refractive indices (RI) on the respective sustained-release excipients used in this study. The whole surface of ten tablets with 10 mg/cm(2) coating was imaged using the fully-automated TPI imaga2000 system. Multidimensional coating thickness or signal intensity maps were reconstructed for the analysis of coating layer thickness, reproducibility, and uniformity. The results from the TPI measurements were validated with optical microscopy imaging and were found to be in good agreement with this destructive analytical technique. The coating thickness around the central band was generally 33% thinner than that on the tablet surfaces. Bimodal coating thickness distribution was detected in some tablets, with thicker coatings around the edges relative to the centre. Aspects of coating defects along with their site, depth and size were identified with virtual terahertz cross-sections. The inter-day precision of the TPI measurement was found to be within 0.5%.

Influence of sample characteristics on quantification of carbamazepine hydrate formation by X-ray powder diffraction and Raman spectroscopy.

This study aimed to assess the suitability of two widely utilized solid state characterization techniques namely powder X-ray diffraction (XRPD) and Raman spectroscopy, in polymorph detection and quantification for carbamazepine anhydrate and dihydrate mixtures. The influences of particle size, particle morphology, mixing, and in particular, surface bias on quantitation were investigated. Binary mixtures of carbamazepine anhydrate (form III) and dihydrate were prepared and analyzed using both XRPD and Raman spectroscopy in combination with partial least squares analysis. It was found that in principle both XRPD and Raman spectroscopy could be used to build calibration models for quantitative analysis, and a satisfactory correlation between the two techniques could be achieved. However, Raman spectroscopy appeared to be a more reliable quantification method because problems such as different particle size, morphology, and special distribution of the two solid state forms of the drug seemed to have no significant influence on Raman scattering in this study. The robust nature of Raman analysis greatly facilitates the whole quantification process from the preparation of calibration models to the quantification of in situ CBZ-DH conversion.