Critical assessment of variant prioritization methods for rare disease diagnosis within the rare genomes project.

BACKGROUND: A major obstacle faced by families with rare diseases is obtaining a genetic diagnosis. The average "diagnostic odyssey" lasts over five years and causal variants are identified in under 50%, even when capturing variants genome-wide. To aid in the interpretation and prioritization of the vast number of variants detected, computational methods are proliferating. Knowing which tools are most effective remains unclear. To evaluate the performance of computational methods, and to encourage innovation in method development, we designed a Critical Assessment of Genome Interpretation (CAGI) community challenge to place variant prioritization models head-to-head in a real-life clinical diagnostic setting. METHODS: We utilized genome sequencing (GS) data from families sequenced in the Rare Genomes Project (RGP), a direct-to-participant research study on the utility of GS for rare disease diagnosis and gene discovery. Challenge predictors were provided with a dataset of variant calls and phenotype terms from 175 RGP individuals (65 families), including 35 solved training set families with causal variants specified, and 30 unlabeled test set families (14 solved, 16 unsolved). We tasked teams to identify causal variants in as many families as possible. Predictors submitted variant predictions with estimated probability of causal relationship (EPCR) values. Model performance was determined by two metrics, a weighted score based on the rank position of causal variants, and the maximum F-measure, based on precision and recall of causal variants across all EPCR values. RESULTS: Sixteen teams submitted predictions from 52 models, some with manual review incorporated. Top performers recalled causal variants in up to 13 of 14 solved families within the top 5 ranked variants. Newly discovered diagnostic variants were returned to two previously unsolved families following confirmatory RNA sequencing, and two novel disease gene candidates were entered into Matchmaker Exchange. In one example, RNA sequencing demonstrated aberrant splicing due to a deep intronic indel in ASNS, identified in trans with a frameshift variant in an unsolved proband with phenotypes consistent with asparagine synthetase deficiency. CONCLUSIONS: Model methodology and performance was highly variable. Models weighing call quality, allele frequency, predicted deleteriousness, segregation, and phenotype were effective in identifying causal variants, and models open to phenotype expansion and non-coding variants were able to capture more difficult diagnoses and discover new diagnoses. Overall, computational models can significantly aid variant prioritization. For use in diagnostics, detailed review and conservative assessment of prioritized variants against established criteria is needed.

Mechanochemically Induced Solid-State Transformations of Levofloxacin.

Levofloxacin hemihydrate (LVXh) is a complex fluoroquinolone drug that exists in both hydrated and anhydrous/dehydrated forms. Due to the complexity of such a compound, the primary aim of this study was to investigate the amorphization capabilities and solid-state transformations of LVXh when exposed to mechanical treatment using ball milling. Spray drying was utilized as a comparative method for investigating the capabilities of complete LVX amorphous (LVXam) formation. The solid states of the samples produced were comprehensively characterized by powder X-ray diffraction, thermal analysis, infrared spectroscopy, Rietveld method, and dynamic vapor sorption. The kinetics of the process and the quantification of phases at different time points were conducted by Rietveld refinement. The impact of the different mills, milling conditions, and parameters on the composition of the resulting powders was examined. A kinetic investigation of samples produced using both mills disclosed that it was in fact possible to partially amorphize LVXh upon mechanical treatment. It was discovered that LVXh first transformed to the anhydrous/dehydrated form γ (LVXγ), as an intermediate phase, before converting to LVXam. The mechanism of LVXam formation by ball milling was successfully revealed, and a new method of forming LVXγ and LVXam by mechanical forces was developed. Spray drying from water depicted that complete amorphization of LVXh was possible. The amorphous form of LVX had a glass transition temperature of 80 °C. The comparison of methods highlighted that the formation of LVXam is thus both mechanism- and process-dependent. Dynamic vapor sorption studies of both LVXam samples showed comparable stability properties and crystallized to the most stable hemihydrate form upon analysis. In summary, this work contributed to the detailed understanding of solid-state transformations of essential fluoroquinolones while employing greener and more sustainable manufacturing methods.

Mechanochemical ignition of self-propagating reactions in equimolar Al-Ni powder mixtures and multilayers.

This work addresses a long standing question in the field of mechanochemistry, namely the role of mesostructure in the initiation of self-propagating high-temperature reactions in exothermic chemical systems, commonly referred to as ignition. In an attempt to find robust evidence in this regard, we compare the ignition behaviour of equimolar Al-Ni powder mixtures and equimolar Al-Ni multilayers. To achieve the best possible control of experimental conditions and allowing high reproducibility, we used elemental powders sieved in the range between 20 µm and 44 µm, and multilayers with bi-layer thickness between 10 nm and 800 nm. We carried out systematic ball milling experiments involving pristine powder mixtures and multilayers as well as a mix of pristine material and material prone to ignition suitably prepared. Experimental findings suggest that pristine powder mixtures and multilayers with bi-layer thickness of 240 nm have analogous ignition behaviour. Along the same lines, data suggest that pristine powder mixtures undergo ignition when they attain a mesostructure similar to that of multilayers with bi-layer thickness of 10 nm.

A kinetic study of mechanically activated atom exchange: the effect of milling frequency and ball mass.

This study investigates the mechanochemical reaction of hydrogen isotope exchange between solid benzoic acid and liquid heavy water. The systematic change of milling conditions revealed that the reaction rate scales with the milling frequency and the mass of the milling balls. The ball size being always the same, faster reactions stem from the use of higher milling frequencies and heavier balls. The kinetic curves are described by a kinetic model that accounts for the statistical, deformational and chemical factors involved in mechanochemical transformations. The results indicate that the reaction is driven by the generation of a new interface area caused by the deformation of the solid reactants.

Mechanochemical reaction kinetics scales linearly with impact energy.

Inelastic collisions of the milling media in ball milling provide energy to the reaction mixture required for chemical transformations. However, movement of the milling media also results in physical mixing of reactants, which may enable a chemical reaction too. Separating the two contributions is challenging and gaining a direct insight into the purely mechanochemically driven reactivity is accordingly hindered. Here, we have applied in situ reaction monitoring by Raman spectroscopy to a suitable, purely mechanically activated, chemical reaction and combined kinetic analysis with numerical simulations to access experimentally unattainable milling parameters. The breadth of milling conditions allows us to establish a linear relationship between the reaction rate and the energy dose received by the sample. Consequently, different kinetic profiles in time scale to the same profile when plotted against the energy dose, which increases with the ball mass, the average ball velocity and the frequency of impacts, but decreases with the hardness of the milling media due to more elastic collisions. The fundamental relationship between kinetics and energy input provides the basis for planning and optimisation of mechanochemical reactions and is essential for transferability of mechanochemical reactions across different milling platforms.

Mechanochemical Reactions from Individual Impacts to Global Transformation Kinetics.

Typically induced by the mechanical processing of powders in ball mills, mechanochemical transformations are considered to result from the application of mechanical force to solid reactants. However, the undeniable deep connection between the dynamic compaction of powders during impacts and the overall transformation degree has yet to be disclosed. In the present work, we show that the square planar bis(dibenzoylmethanato)NiII coordination compound undergoes trimerization when its powder experiences even a single ball impact. Based on systematic experiments with individual ball impacts and analysis by Raman spectroscopy, we provide here quantitative mapping of the transformation in the powder compact and deduce bulk reaction kinetics from multiple individual impacts.

A phenomenological kinetic equation for mechanochemical reactions involving highly deformable molecular solids.

With its ability to enable solvent-free chemical reactions, mechanochemistry promises to open new and greener synthetic routes to chemical products of industrial interest. Its practical exploitation requires understanding the relationships between processing variables, powders' mechanical behaviour, and chemical reactivity. To this aim, rationalizing experimental kinetics is of paramount importance. In this work, we propose a phenomenological kinetic model that could help experimentalists to disentangle the mechanical, chemical, and statistical factors underlying mechanochemical reactions. The model takes into account the statistical nature of ball milling and relates the global kinetic curve that can be obtained experimentally to the deformation and chemical processes that occur on the mesoscopic and microscopic scales during individual impacts. We show that our model equations can satisfactorily best fit experimental datasets, providing information on the underlying mechanochemistry.

Kinetics of mechanochemical transformations.

The use of mechanical forces to activate and drive chemical transformations in solid particulate is attracting remarkable interest in the light of its promising application in a wide spectrum of strategic areas ranging from materials science to fine chemical synthesis and pharmaceutical ingredient production. The capability of enabling solventless processes and fabricating unique materials inaccessible otherwise has made mechanochemistry one of the ten chemical innovations with the highest potential of changing the world. As in the past, so again now, the development of reliable technologies based on mechanochemical transformations cannot be separated from the understanding of the underlying mechanisms, their description and their control. To this aim, in this work we propose a kinetic model that relates macroscopic and microscopic scales while accounting for the statistical nature of the mechanical processing of powder. We discuss several specific case studies and develop the pertinent kinetic equations, showing how they can be used to best fit the experimental data and obtain insight into the microscopic features of mechanical activation.

Phenomenological Inferences on the Kinetics of a Mechanically Activated Knoevenagel Condensation: Understanding the "Snowball" Kinetic Effect in Ball Milling.

We focus on understanding the kinetics of a mechanically activated Knoevenagel condensation conducted in a ball mill, that is characterized by sigmoidal kinetics and the formation of a rubber-like cohesive intermediate state coating the milling ball. The previously described experimental findings are explained using a phenomenological kinetic model. It is assumed that reactants transform into products already at the very first collision of the ball with the wall of the jar. The portion of reactants that are transformed into products during each oscillation is taken to be a fraction of the amount of material that is trapped between the ball and the wall of the jar. This quantity is greater when the reaction mixture transforms from its initial powder form to the rubber-like cohesive coating on the ball. Further, the amount of reactants processed in each collision varies proportionally with the total area of the layer coating the ball. The total area of this coating layer is predicted to vary with the third power of time, thus accounting for the observed dramatic increase of the reaction rate. Supporting experiments, performed using a polyvinyl acetate adhesive as a nonreactive but cohesive material, confirm that the coating around the ball grows with the third power of time.

Hepatocellular carcinoma in thalassaemia: an update of the Italian Registry.

The risk of developing hepatocellular carcinoma (HCC) in patients with thalassaemia is increased by transfusion-transmitted infections and haemosiderosis. All Italian Thalassaemia Centres use an ad hoc form to report all diagnoses of HCC to the Italian Registry. Since our last report, in 2002, up to December 2012, 62 new cases were identified, 52% of whom were affected by thalassaemia major (TM) and 45% by thalassaemia intermedia (TI). Two had sickle-thalassaemia (ST). The incidence of the tumour is increasing, possibly because of the longer survival of patients and consequent longer exposure to the noxious effects of the hepatotropic viruses and iron. Three patients were hepatitis B surface antigen-positive, 36 patients showed evidence of past infection with hepatitis B virus (HBV). Fifty-four patients had antibodies against hepatitis C virus (HCV), 43 of whom were HCV RNA positive. Only 4 had no evidence of exposure either to HCV or HBV. The mean liver iron concentration was 8 mg/g dry weight. Therapy included chemoembolization, thermoablation with radiofrequency and surgical excision. Three patients underwent liver transplant, 21 received palliative therapy. As of December 2012, 41 patients had died. The average survival time from HCC detection to death was 11·5 months (1·4-107·2 months). Ultrasonography is recommended every 6 months to enable early diagnosis of HCC, which is crucial to decrease mortality.

Machine Learning-Supported Diagnosis of Small Blue Round Cell Sarcomas Using Targeted RNA Sequencing.

Small blue round cell sarcomas (SBRCSs) are a heterogeneous group of tumors with overlapping morphologic features but markedly varying prognosis. They are characterized by distinct chromosomal alterations, particularly rearrangements leading to gene fusions, whose detection currently represents the most reliable diagnostic marker. Ewing sarcomas are the most common SBRCSs, defined by gene fusions involving EWSR1 and transcription factors of the ETS family, and the most frequent non-EWSR1-rearranged SBRCSs harbor a CIC rearrangement. Unfortunately, currently the identification of CIC::DUX4 translocation events, the most common CIC rearrangement, is challenging. Here, we present a machine-learning approach to support SBRCS diagnosis that relies on gene expression profiles measured via targeted sequencing. The analyses on a curated cohort of 69 soft-tissue tumors showed markedly distinct expression patterns for SBRCS subgroups. A random forest classifier trained on Ewing sarcoma and CIC-rearranged cases predicted probabilities of being CIC-rearranged >0.9 for CIC-rearranged-like sarcomas and <0.6 for other SBRCSs. Testing on a retrospective cohort of 1335 routine diagnostic cases identified 15 candidate CIC-rearranged tumors with a probability >0.75, all of which were supported by expert histopathologic reassessment. Furthermore, the multigene random forest classifier appeared advantageous over using high ETV4 expression alone, previously proposed as a surrogate to identify CIC rearrangement. Taken together, the expression-based classifier can offer valuable support for SBRCS pathologic diagnosis.

Extending the Hammett correlation to mechanochemical reactions.

Using Raman in situ monitoring and mechanochemistry-specific kinetic analysis, we find a correlation between the reaction probability and the Hammett constants in a model mechanochemical reaction of imine formation, indicating that the body of knowledge developed in physical-organic chemistry could be transferable to ball milling reactions in the solid state.

Mechanochemical effects underlying the mechanically activated catalytic hydrogenation of carbon monoxide.

In this work, we highlight and measure the intensity of mechanochemical effects at work in the hydrogenation of carbon monoxide by comparing the activity of a supported Co-Fe catalyst subjected, respectively, to ball milling and simple powder agitation. Paying due regard to the discontinuous nature of ball milling, we show that mechanochemical hydrogenation proceeds at significantly higher rate and disclose its connection with individual impacts. Experimental evidence suggests that the enhanced catalytic activity we observe can be ascribed to local processes affecting the amount of powder that gets involved in individual impacts.

Critical assessment of variant prioritization methods for rare disease diagnosis within the Rare Genomes Project.

Background: A major obstacle faced by rare disease families is obtaining a genetic diagnosis. The average "diagnostic odyssey" lasts over five years, and causal variants are identified in under 50%. The Rare Genomes Project (RGP) is a direct-to-participant research study on the utility of genome sequencing (GS) for diagnosis and gene discovery. Families are consented for sharing of sequence and phenotype data with researchers, allowing development of a Critical Assessment of Genome Interpretation (CAGI) community challenge, placing variant prioritization models head-to-head in a real-life clinical diagnostic setting. Methods: Predictors were provided a dataset of phenotype terms and variant calls from GS of 175 RGP individuals (65 families), including 35 solved training set families, with causal variants specified, and 30 test set families (14 solved, 16 unsolved). The challenge tasked teams with identifying the causal variants in as many test set families as possible. Ranked variant predictions were submitted with estimated probability of causal relationship (EPCR) values. Model performance was determined by two metrics, a weighted score based on rank position of true positive causal variants and maximum F-measure, based on precision and recall of causal variants across EPCR thresholds. Results: Sixteen teams submitted predictions from 52 models, some with manual review incorporated. Top performing teams recalled the causal variants in up to 13 of 14 solved families by prioritizing high quality variant calls that were rare, predicted deleterious, segregating correctly, and consistent with reported phenotype. In unsolved families, newly discovered diagnostic variants were returned to two families following confirmatory RNA sequencing, and two prioritized novel disease gene candidates were entered into Matchmaker Exchange. In one example, RNA sequencing demonstrated aberrant splicing due to a deep intronic indel in ASNS, identified in trans with a frameshift variant, in an unsolved proband with phenotype overlap with asparagine synthetase deficiency. Conclusions: By objective assessment of variant predictions, we provide insights into current state-of-the-art algorithms and platforms for genome sequencing analysis for rare disease diagnosis and explore areas for future optimization. Identification of diagnostic variants in unsolved families promotes synergy between researchers with clinical and computational expertise as a means of advancing the field of clinical genome interpretation.

Renal function in patients with ß-thalassaemia major: a long-term follow-up study.

BACKGROUND: Little information is available about the kidney's involvement in patients with ß-thalassaemia major (TM). In particular, there are no studies reporting the outcome of renal function over time. METHODS: In this retrospective study, we evaluated the changes in estimated glomerular filtration rate (eGFR) in 81 adult patients with TM followed for 10 years. Only patients who had an eGFR of >90 mL/min/1.73 m(2) at presentation were admitted to the study. All patients were regularly followed for at least 10 years. RESULTS: At 10 years, 66 patients showed a mild decline in eGFR that remained, however, within a normal range (from 119.9 to 113.6 mL/min/1.73 m(2), P = 0.636). In the remaining 15 patients (18.5%), eGFR decreased to <90 mL/min (from 98.1 to 78.2 mL/min/1.73 m(2); P = 0.004). The repeated-measures models showed that the decline in eGFR over time was significantly higher (P = 0.0068) in patients with baseline phosphaturia >1000 mg/24 h (P = 0.0068), while eGFR tended to decline more rapidly in patients with baseline uricuria >700 mg/24 h than in those with lower uricuria (P = 0.0783). Univariate Cox's proportional regression models showed that abnormal levels of calcaemia were associated with the risk of kidney damage [hazard ratio (HR) 0.30, 95% confidence interval 0.09-0.97 for calcaemia 8.4-10.2 mg/dL versus HR not estimable for calcaemia <8.4 or >10.2 mg/dL]. CONCLUSIONS: In most adults with TM, the eGFR tends to remain within a normal range after 10 years. However, patients with elevated phosphaturia, elevated uricuria and/or abnormal levels of calcaemia show a significant decline in eGFR over time, suggesting that tubular damage acquired in childhood caused by either TM or its treatment may eventually result in abnormal eGFR. Further studies in a larger cohort of TM patients are needed to further elucidate the long-term impact of TM on renal function.

Chemical effects induced by the mechanical processing of granite powder.

Starting from 1970s, the use of mechanical forces to induce chemical transformations has radically changed vast areas of metallurgy and materials science. More recently, mechanochemistry has expanded to core sectors of chemistry, showing the promise to deeply innovate chemical industry while enhancing its sustainability and competitiveness. We are still far, however, from unveiling the full potential of mechanical activation. This study marks a step forward in this direction focusing on the chemical effects induced on the surrounding gaseous phase by the mechanical processing of granite. We show that fracturing granite blocks in oxygen can result in the generation of ozone. The refinement of coarse granite particles and the friction between fine ones are also effective in this regard. Combining experimental evidence related to the crushing of large granite samples by uniaxial compression and the ball milling of coarse and fine granite powders, we develop a model that relates mechanochemical ozone generation to the surface area effectively affected by fracture and frictional events taking place during individual impacts. We also extend the investigation to gaseous phases involving methane, oxygen, benzene and water, revealing that chemical transformations occur as well.

Thalassemia intermedia is associated with a proatherogenic biochemical phenotype.

OBJECTIVE: Unlike beta thalassemia major (ß-TM) in which cardiac siderosis represents the leading cause of mortality and morbidity, in beta thalassemia intermedia (ß-TI), pulmonary hypertension (PHT) and thrombosis seems to be the major cardiovascular complications. However, the mechanism underlying these complications in ß-TI is still unclear. Endothelial dysfunction, the key early event in atherogenesis, is now emerging as an important cardiovascular risk determiner in ß-TI patients. Among the factors known to affect endothelial function, iron and cholesterol merit particular consideration in ß-TI patients. Therefore, with the aim to extend our knowledge on the mechanisms connecting atherosclerosis to ß-TI, in this study, we compared lipid and iron metabolism in serum and in peripheral blood mononuclear cells (PBMCs) from ß-TI and ß-TM patients and controls. METHODS AND RESULTS: In this study the iron status and the lipid profile in serum and in peripheral blood mononuclear cells (PBMCs) of 22 adult ß-TI patients were examined, and compared with 70 adult ß-TM, and 50 age-matched controls. Despite the great variability, levels of serum iron and transferrin saturation were significantly higher in ß-TI compared to both controls and ß-TM. By contrast, transferrin and hepcidin levels were lower in ß-TI patients. Changes in serum indicators in ß-TI patients were associated with altered expressions in PBMCs of hepcidin and IL-1α, involved in some way in the regulation of iron homeostasis. In addition ß-TI exhibited a reduction of total and high density lipoprotein cholesterol in serum and of neutral cholesterol ester hydrolase in PBMCs, and an increase of cytoplasmic neutral lipids and mRNA levels of acetyl-coenzymeA:cholesterol acyltransferase. CONCLUSIONS: Taken together, these findings provide experimental support for the idea that ß-TI patients exhibit a proatherogenic biochemical phenotype which may contribute to enhance cardiovascular risk in these subjects.

Evidence for a proatherogenic biochemical phenotype in beta thalassemia minor and intermedia.

The purpose of this study was to focus on pathophysiological mechanisms linking ß-thalassemia intermedia (ß-TI) and minor (ß-TMI) with cardiovascular risk. Iron status, prooxidant-antioxidant balance and lipid profiles in serum, and lipid content in peripheral blood mononuclear cells (PBMCs) were evaluated in 20 ß-TMI subjects, 22 ß-TI patients and in 30 nonthalassemic blood donors. The mRNA levels of some genes involved in the regulation of iron and cholesterol metabolism were also determined. In ß-TI and in ß-TMI, serum iron, prooxidant-antioxidant ratio, transferrin saturation and erythropoietin levels were higher, while transferrin and hepcidin were lower compared to controls. Hepcidin and interleukin-1α mRNA levels were found to be reduced in ß-TI- and ß-TMI-PBMCs, while those of tumor necrosis factor alpha were increased. A reduction in high-density lipoprotein cholesterol in serum and an accumulation of neutral lipids coupled with increased mRNA levels of acetyl-coenzyme A:cholesterol acyltransferase and decreased neutral cholesterol ester hydrolase in PBMCs were also observed in ß-TI and ß-TMI compared to controls. Taken together, these findings provide experimental support for the idea that not only ß-TI patients but also ß-TMI have a proatherogenic biochemical phenotype which may contribute to increase their cardiovascular disease risk.

Case report: thalassemia intermedia patient with hypertension non-responsive to combined medical treatment.

Pheochromocytoma is a rare disease in the general population and, to the best of our knowledge, only one case has been reported so far in patients with hemoglobinopathies. We describe the occurrence of pheochromocytoma in a patient with thalassemia intermedia associated with Gilbert's disease and Crigler- Najjar Type 2 syndrome.

Increased survival and reversion of iron-induced cardiac disease in patients with thalassemia major receiving intensive combined chelation therapy as compared to desferoxamine alone.

Myocardial iron overload is the leading cause of death in patients with beta-thalassemia major. An intensification monotherapy with deferoxamine (DFO) as well as a combination therapy with DFO and deferiprone (DFP) reduces myocardial iron and improves cardiac function. However, the prognosis for thalassemia major patients with established cardiac disease switched from DFO monotherapy to combined DFP/DFO chelation is unknown. Twenty-eight thalassemia major patients with cardiac disease were enrolled in a prospective study lasting 42+/-6 months. Fifteen (9 high-ferritin and 6 low-ferritin) were placed on DFP/DFO (DFP, 75 mg/kg t.i.d.; DFO, 40-50mg/kg over 8-12h at night 5-7 days/week), while 13 (5 high- and 8 low-ferritin) received DFO alone. No cardiac events were observed among high-ferritin patients on combination therapy, whereas 4 cardiac events (p=0.0049), including three deaths, occurred in high-ferritin patients on DFO monotherapy. These findings demonstrate that in thalassemia major patients with well-established cardiac disease combined iron-chelation therapy with DFP/DFO is superior to DFO monotherapy.