Diagnostic utility and reporting recommendations for clinical DNA methylation episignature testing in genetically undiagnosed rare diseases.

PURPOSE: This study aims to assess the diagnostic utility and provide reporting recommendations for clinical DNA methylation episignature testing based on the cohort of patients tested through the EpiSign Clinical Testing Network. METHODS: The EpiSign assay utilized unsupervised clustering techniques and a support vector machine-based classification algorithm to compare each patient's genome-wide DNA methylation profile with the EpiSign Knowledge Database, yielding the result that was reported. An international working group, representing distinct EpiSign Clinical Testing Network health jurisdictions, collaborated to establish recommendations for interpretation and reporting of episignature testing. RESULTS: Among 2399 cases analyzed, 1667 cases underwent a comprehensive screen of validated episignatures, imprinting, and promoter regions, resulting in 18.7% (312/1667) positive reports. The remaining 732 referrals underwent targeted episignature analysis for assessment of sequence or copy-number variants (CNVs) of uncertain significance or for assessment of clinical diagnoses without confirmed molecular findings, and 32.4% (237/732) were positive. Cases with detailed clinical information were highlighted to describe various utility scenarios for episignature testing. CONCLUSION: Clinical DNA methylation testing including episignatures, imprinting, and promoter analysis provided by an integrated network of clinical laboratories enables test standardization and demonstrates significant diagnostic yield and clinical utility beyond DNA sequence analysis in rare diseases.

Synthetic Control of the Defect Structure and Hierarchical Extra-Large-/Small-Pore Microporosity in Aluminosilicate Zeolite SWY.

The SWY-type aluminosilicate zeolite, STA-30, has been synthesized via different routes to understand its defect chemistry and solid acidity. The synthetic parameters varied were the gel aging, the Al source, and the organic structure directing agent. All syntheses give crystalline materials with similar Si/Al ratios (6-7) that are stable in the activated K,H-form and closely similar by powder X-ray diffraction. However, they exhibit major differences in the crystal morphology and in their intracrystalline porosity and silanol concentrations. The diDABCO-C82+ (1,1'-(octane-1,8-diyl)bis(1,4-diazabicyclo[2.2.2]octan)-1-ium)-templated STA-30 samples (but not those templated by bisquinuclidinium octane, diQuin-C82+) possess hierarchical microporosity, consisting of noncrystallographic extra-large micropores (13 Å) that connect with the characteristic swy and gme cages of the SWY structure. This results in pore volumes up to 30% greater than those measured in activated diQuin-C8_STA-30 as well as higher concentrations of silanols and fewer Brønsted acid sites (BASs). The hierarchical porosity is demonstrated by isopentane adsorption and the FTIR of adsorbed pyridine, which shows that up to 77% of the BASs are accessible (remarkable for a zeolite that has a small-pore crystal structure). A structural model of single can/d6r column vacancies is proposed for the extra-large micropores, which is revealed unambiguously by high-resolution scanning transmission electron microscopy. STA-30 can therefore be prepared as a hierarchically porous zeolite via direct synthesis. The additional noncrystallographic porosity and, subsequently, the amount of SiOHs in the zeolites can be enhanced or strongly reduced by the choice of crystallization conditions.

DNA methylation episignature for Witteveen-Kolk syndrome due to SIN3A haploinsufficiency.

PURPOSE: Witteveen-Kolk syndrome (WITKOS) is a rare, autosomal dominant neurodevelopmental disorder caused by heterozygous loss-of-function alterations in the SIN3A gene. WITKOS has variable expressivity that commonly overlaps with other neurodevelopmental disorders. In this study, we characterized a distinct DNA methylation epigenetic signature (episignature) distinguishing WITKOS from unaffected individuals as well as individuals with other neurodevelopmental disorders with episignatures and described 9 previously unpublished individuals with SIN3A haploinsufficiency. METHODS: We studied the phenotypic characteristics and the genome-wide DNA methylation in the peripheral blood samples of 20 individuals with heterozygous alterations in SIN3A. A total of 14 samples were used for the identification of the episignature and building of a predictive diagnostic biomarker, whereas the diagnostic model was used to investigate the methylation pattern of the remaining 6 samples. RESULTS: A predominantly hypomethylated DNA methylation profile specific to WITKOS was identified, and the classifier model was able to diagnose a previously unresolved test case. The episignature was sensitive enough to detect individuals with varying degrees of phenotypic severity carrying SIN3A haploinsufficient variants. CONCLUSION: We identified a novel, robust episignature in WITKOS due to SIN3A haploinsufficiency. This episignature has the potential to aid identification and diagnosis of individuals with WITKOS.

Functional correlation of genome-wide DNA methylation profiles in genetic neurodevelopmental disorders.

An expanding range of genetic syndromes are characterized by genome-wide disruptions in DNA methylation profiles referred to as episignatures. Episignatures are distinct, highly sensitive, and specific biomarkers that have recently been applied in clinical diagnosis of genetic syndromes. Episignatures are contained within the broader disorder-specific genome-wide DNA methylation changes, which can share significant overlap among different conditions. In this study, we performed functional genomic assessment and comparison of disorder-specific and overlapping genome-wide DNA methylation changes related to 65 genetic syndromes with previously described episignatures. We demonstrate evidence of disorder-specific and recurring genome-wide differentially methylated probes (DMPs) and regions (DMRs). The overall distribution of DMPs and DMRs across the majority of the neurodevelopmental genetic syndromes analyzed showed substantial enrichment in gene promoters and CpG islands, and under-representation of the more variable intergenic regions. Analysis showed significant enrichment of the DMPs and DMRs in gene pathways and processes related to neurodevelopment, including neurogenesis, synaptic signaling and synaptic transmission. This study expands beyond the diagnostic utility of DNA methylation episignatures by demonstrating correlation between the function of the mutated genes and the consequent genomic DNA methylation profiles as a key functional element in the molecular etiology of genetic neurodevelopmental disorders.

Novel diagnostic DNA methylation episignatures expand and refine the epigenetic landscapes of Mendelian disorders.

Overlapping clinical phenotypes and an expanding breadth and complexity of genomic associations are a growing challenge in the diagnosis and clinical management of Mendelian disorders. The functional consequences and clinical impacts of genomic variation may involve unique, disorder-specific, genomic DNA methylation episignatures. In this study, we describe 19 novel episignature disorders and compare the findings alongside 38 previously established episignatures for a total of 57 episignatures associated with 65 genetic syndromes. We demonstrate increasing resolution and specificity ranging from protein complex, gene, sub-gene, protein domain, and even single nucleotide-level Mendelian episignatures. We show the power of multiclass modeling to develop highly accurate and disease-specific diagnostic classifiers. This study significantly expands the number and spectrum of disorders with detectable DNA methylation episignatures, improves the clinical diagnostic capabilities through the resolution of unsolved cases and the reclassification of variants of unknown clinical significance, and provides further insight into the molecular etiology of Mendelian conditions.

Near complete deletion of KMT2D in a college student.

Pathogenic variants in KMT2D are typically associated with Kabuki syndrome (KS), a rare multisystem disorder. KS is characterized by facial dysmorphisms, intellectual disability, skeletal and dermatoglyphic differences, and poor growth. Seventy percent of individuals with clinically diagnosed KS have a confirmed pathogenic variant in KMT2D or less commonly KDM6A. The majority of mutations found in KMT2D are de novo nonsense or frameshift, with deletions and duplications rarely reported in the literature. Here, we present the case of near complete deletion of KMT2D in a college student with normal intelligence discovered via exome sequencing and EpiSign methylation testing. This case provides evidence that large deletions in KMT2D are compatible with normal intelligence and presents EpiSign as a method for discovering molecular causes of KS not identified by traditional molecular testing.

Clinical epigenomics: genome-wide DNA methylation analysis for the diagnosis of Mendelian disorders.

PURPOSE: We describe the clinical implementation of genome-wide DNA methylation analysis in rare disorders across the EpiSign diagnostic laboratory network and the assessment of results and clinical impact in the first subjects tested. METHODS: We outline the logistics and data flow between an integrated network of clinical diagnostics laboratories in Europe, the United States, and Canada. We describe the clinical validation of EpiSign using 211 specimens and assess the test performance and diagnostic yield in the first 207 subjects tested involving two patient subgroups: the targeted cohort (subjects with previous ambiguous/inconclusive genetic findings including genetic variants of unknown clinical significance) and the screening cohort (subjects with clinical findings consistent with hereditary neurodevelopmental syndromes and no previous conclusive genetic findings). RESULTS: Among the 207 subjects tested, 57 (27.6%) were positive for a diagnostic episignature including 48/136 (35.3%) in the targeted cohort and 8/71 (11.3%) in the screening cohort, with 4/207 (1.9%) remaining inconclusive after EpiSign analysis. CONCLUSION: This study describes the implementation of diagnostic clinical genomic DNA methylation testing in patients with rare disorders. It provides strong evidence of clinical utility of EpiSign analysis, including the ability to provide conclusive findings in the majority of subjects tested.

Techniques for direct experimental evaluation of structure-transport relationships in disordered porous solids.

Determining structure-transport relationships is critical to optimising the activity and selectivity performance of porous pellets acting as heterogeneous catalysts for diffusion-limited reactions. For amorphous porous systems determining the impact of particular aspects of the void space on mass transport often requires complex characterization and modelling steps to deconvolve the specific influence of the feature in question. These characterization and modelling steps often have limited accuracy and precision. It is the purpose of this work to present a case-study demonstrating the use of a more direct experimental evaluation of the impact of pore network features on mass transport. The case study evaluated the efficacy of the macropores of a bidisperse porous foam structure on improving mass transport over a purely mesoporous system. The method presented involved extending the novel integrated gas sorption and mercury porosimetry method to include uptake kinetics. Results for the new method were compared with those obtained by the alternative NMR cryodiffusometry technique, and found to lead to similar conclusions. It was found that the experimentally-determined degree of influence of the foam macropores was in line with expectations from a simple resistance model for a disconnected macropore network.

Improving sensitivity and accuracy of pore structural characterisation using scanning curves in integrated gas sorption and mercury porosimetry experiments.

Gas sorption scanning curves are increasingly used as a means to supplement the pore structural information implicit in boundary adsorption and desorption isotherms to obtain more detailed pore space descriptors for disordered solids. However, co-operative adsorption phenomena set fundamental limits to the level of information that conventional scanning curve experiments can deliver. In this work, we use the novel integrated gas sorption and mercury porosimetry technique to show that crossing scanning curves are obtained for some through ink-bottle pores within a disordered solid, thence demonstrating that their shielded pore bodies are undetectable using conventional scanning experiments. While gas sorption alone was not sensitive enough to detect these pore features, the integrated technique was, and, thence, this synergistic method is more powerful than the two individual techniques applied separately. The integrated method also showed how the appropriate filling mechanism equation (e.g. meniscus geometry for capillary condensation equations), to use to convert filling pressure to pore size, varied with position along the adsorption branch, thereby enabling avoidance of the further systematic error introduced into PSDs by assuming a single filling mechanism for disordered solids.

Simulation of nonwetting phase entrapment within porous media using magnetic resonance imaging.

Models representing the pore structures of amorphous, mesoporous silica pellets have been constructed using magnetic resonance images of the materials. Using magnetic resonance imaging (MRI), maps of the macroscopic (approximately 0.01-1 mm) spatial distribution of porosity and pore size were obtained. The nature and key parameters of the physical mechanism for mercury retraction, during porosimetry experiments on the silica materials, were determined using integrated gas sorption experiments. Subsequent simulations of mercury porosimetry within the structural models derived from MRI have been used to successfully predict, a priori, the point of the onset of structural hysteresis and the final levels of mercury entrapment for the silicas. Hence, a firm understanding of the physical processes of mercury retraction and entrapment in these amorphous silica materials has been established.

Characterization of Macroscopic Structural Disorder in Porous Media Using Mercury Porosimetry.

A new structural model for the interpretation of mercury porosimetry data for samples having a bimodal pore size distribution is presented. The morphology of the macropore network of a porous solid has been studied using a combination of mercury porosimetry and NMR techniques. The model consists of a lattice-based network of pore bodies and pore necks. The model enables assessment of the spatial geometric distribution of the directly accessible macropore network of a porous material having a bimodal pore size distribution. A methodology that can be used to determine the spatial distribution of the critical pore neck diameters controlling access to the macroporous void space has also been described. This method was used to provide a map of the local critical macropore neck distribution over macroscopic length scales for an alumina tablet that is not possible with other techniques. Copyright 2001 Academic Press.