Estimating summary statistics for electronic health record laboratory data for use in high-throughput phenotyping algorithms

We study the question of how to represent or summarize raw laboratory data taken from an electronic health record (EHR) using parametric model selection to reduce or cope with biases induced through clinical care. It has been previously demonstrated that the health care process (Hripcsak and Albers, 2012, 2013), as defined by measurement context (Hripcsak and Albers, 2013; Albers et al., 2012) and measurement patterns (Albers and Hripcsak, 2010, 2012), can influence how EHR data are distributed statistically (Kohane and Weber, 2013; Pivovarov et al., 2014). We construct an algorithm, PopKLD, which is based on information criterion model selection (Burnham and Anderson, 2002; Claeskens and Hjort, 2008), is intended to reduce and cope with health care process biases and to produce an intuitively understandable continuous summary. The PopKLD algorithm can be automated and is designed to be applicable in high-throughput settings; for example, the output of the PopKLD algorithm can be used as input for phenotyping algorithms. Moreover, we develop the PopKLD-CAT algorithm that transforms the continuous PopKLD summary into a categorical summary useful for applications that require categorical data such as topic modeling. We evaluate our methodology in two ways. First, we apply the method to laboratory data collected in two different health care contexts, primary versus intensive care. We show that the PopKLD preserves known physiologic features in the data that are lost when summarizing the data using more common laboratory data summaries such as mean and standard deviation. Second, for three disease-laboratory measurement pairs, we perform a phenotyping task: we use the PopKLD and PopKLD-CAT algorithms to define high and low values of the laboratory variable that are used for defining a disease state. We then compare the relationship between the PopKLD-CAT summary disease predictions and the same predictions using empirically estimated mean and standard deviation to a gold standard generated by clinical review of patient records. We find that the PopKLD laboratory data summary is substantially better at predicting disease state. The PopKLD or PopKLD-CAT algorithms are not meant to be used as phenotyping algorithms, but we use the phenotyping task to show what information can be gained when using a more informative laboratory data summary. In the process of evaluation our method we show that the different clinical contexts and laboratory measurements necessitate different statistical summaries. Similarly, leveraging the principle of maximum entropy we argue that while some laboratory data only have sufficient information to estimate a mean and standard deviation, other laboratory data captured in an EHR contain substantially more information than can be captured in higher-parameter models.

Intellectual developmental disorder with cardiac arrhythmia syndrome in a child with compound heterozygous GNB5 variants

Identification of a novel compound heterozygous of GNB5 in a patient with intellectual developmental disorder with cardiac arrhytmia (IDDCA), from non-consaguineous family. Three-dimensional modelling and in silico predictions suggest that GNB5 variants are causative of the phenotype, extending the number of IDDCA patients so far identified.

Multimodality Imaging of Vertebrobasilar Dolichoectasia: Clinical Presentations and Imaging Spectrum

Vertebrobasilar dolichoectasia (VBD) is characterized by ectasia, elongation, and tortuosity of the vertebrobasilar arteries, with a high degree of variability in clinical presentation. The disease origin is believed to involve degeneration of the internal elastic lamina, thinning of the media secondary to reticular fiber deficiency, and smooth muscle atrophy. The prevalence of VBD is variable, ranging from 0.05% to 18%. Most patients with VBD are asymptomatic and their VBD is detected incidentally; however, it is important to recognize that the presence of symptoms, which can lead to clinically significant morbidity and sometimes mortality, may influence clinical management. The most important clinical presentations of VBD are vascular events, such as ischemic stroke and catastrophic intracranial hemorrhage, or progressive compressive symptoms related to compression of adjacent structures, including the cranial nerves, brainstem, or third ventricle, causing hydrocephalus. The imaging diagnostic criteria for computed tomography and magnetic resonance (MR) imaging include three quantitative measures of basilar artery morphology: laterality score, height of bifurcation, and basilar artery diameter. The authors review the relevant anatomy and disease origin of VBD; pertinent imaging findings, including intraluminal thrombus and relation to the cranial nerves; and imaging pitfalls, such as the hyperintense vessel sign on MR images and artifacts related to slow flow in the dolichoectatic vessel. In addition, clinical manifestations, the role of radiology in diagnosis and management of this condition, and available management options are reviewed. (©)RSNA, 2016.

20: NASOPHARYNX MICROBIOME COMPOSITION VARIES OVER TIME IN PEDIATRIC ASTHMA

Purpose of Study

The application of next-generation sequencing (NGS) technology has shown that microbial communities in the respiratory airways (i.e., the microbiome) play a significant role in the onset, development and severity of asthma. However, little is known about their temporal dynamics (i.e., microbial succession), which poses a significant obstacle to identifying pulmotypes of disease and assessing inter-patient variation. Here, we couple NGS and 16S rRNA data to characterize the nasopharynx microbiome of children with asthma and determine its stability over time.

Methods Used

We collected nasal washes from 40 children with asthma enrolled in the AsthMaP-2 Project from two consecutive visits, six months apart. Total DNA was extracted and sequenced for the 16S-V4 rRNA gene region (∼250 bp) using the MySeq Illumina platform. Reads were analyzed in Mothur using the SILVAv119 reference database. Alpha diversity metrics and phylogenetic and count-base distance community indexes of beta diversity were compared across samples and time points. PCoA and NJ clustering analysis were used to assess community relatedness. Differences in alpha diversity and OTU abundance between sample pairs across time points were also compared.

Summary of Results

A mean of 27,479 clean 16S sequences corresponding to an average of 173 OTUs were sequenced and detected per sample, respectively. Representatives of Moraxella, Corynebacterium, Prevotella, Staphylococcus, Alloiococcus, Streptococcus, Peptoniphilus, Fusobacterium, and Haemophilus accounted for 36 to 99% of the reads across samples. These genera have been previously found in the nasopharynx of asthmatic and healthy children. A total of 61 OTUs from these genera were present in at least 50% of the samples (i.e., the nasal core microbiome). Significant differences in core microbiome composition were detected between sample pairs, but no directional trend (increase or decrease) was observed across sample pairs. Samples were randomly ordinated and did not cluster together.

Conclusions

Our analysis of nasal microbiomes in 40 asthmatic children revealed significant differences in composition within individuals over six months. Future cross-sectional microbiome studies need to be aware of short span temporal dynamics in nasal microbiota.

ZONE BEHAVIOR OF ENZYMES : ILLUSTRATED BY THE EFFECT OF DISSOCIATION CONSTANT AND DILUTION ON THE SYSTEM CHOLINESTERASE-PHYSOSTIGMINE

1. The kinetics of the reversible combination of one enzyme center with one molecule of a substrate or inhibitor is treated as a true bimolecular instead of a pseudomonomolecular reaction. The general equations describing such a reaction are presented and analyzed algebraically and graphically. 2. A new term, "specific concentration," is introduced to denote the concentration of reactants in units equal to the dissociation constant. Its use makes the kinetic equations universally applicable to all reversible systems of the given type. 3. It is shown that such a system exhibits three "zones" of behavior. Each zone is characterized and shown to exhibit significant differences in the function relating the concentrations of the components of the system at equilibrium. The zone boundaries are rigorously defined in terms of the specific enzyme concentration, for the mathematical error tolerable with a given experimental accuracy; and approximate boundaries for practical use are proposed. 4. The classical treatment of enzyme kinetics is shown to be a limiting case valid only for low specific enzyme concentrations (zone A) and to be inapplicable in a number of systems whose dissociation constants are very small or whose molar enzyme concentrations are very great, and in which, therefore, the specific enzyme concentrations are large. See Table I for a summary of zone differences. 5. In an enzyme system containing substrate or inhibitor, dilution before determination of reaction velocities is shown to be a crucial operation, entailing large changes in the fraction of enzyme in the form of a complex. The changes in fractional activity or inhibition with dilution are shown to be a function of specific enzyme concentration, the dilution factor, and the fraction of enzyme initially in the form of complex. Equations are given permitting the calculation of the state of the system at any concentration. The errors introduced into physiological work by failure to take the dilution effect into account are pointed out. 6. Experimental data are presented showing that the system composed of serum cholinesterase and physostigmine behaves as predicted by the dilution effect equations. 7. Two other conclusions of practical pharmacological importance are drawn from the theory of zone behavior: (a) The finding that a biological response is a linear function of the dose of a drug does not necessarily mean that the reaction is irreversible, but only that if reversible, the reactant with which the drug combines has a high specific concentration. (b) If a tissue enzyme has a high specific concentration, all reversible inhibitors will be equally potent in combining with it, regardless of their relative potency in dilute systems; provided only that their dissociation constants are within certain broad limits. 8. It is shown how the type of analysis here applied to bimolecular reactions can be applied in toto to systems of the type E + nX ⇋ EX_n, where n molecules of substrate or inhibitor unite with one enzyme center. The zone boundaries and the magnitude of the dilution effect change with n, but the general characteristics of the zones are the same for all values of n. 9. Since the analysis is based only on mass law assumptions, it is applicable to any system that is formally analogous to the one here treated.

THE MECHANISM OF ENZYME-INHIBITOR-SUBSTRATE REACTIONS : ILLUSTRATED BY THE CHOLINESTERASE-PHYSOSTIGMINE-ACETYLCHOLINE SYSTEM

The mechanism of enzyme-inhibitor-substrate reactions has been analyzed from a theoretical standpoint and illustrated by data from the system cholinesterase-physostigmine-acetylcholine. This treatment is by no means limited to a single system but should be generally applicable to others of similar type. Competitive enzyme-inhibitor-substrate systems show the same characteristic "zones of behavior" already demonstrated for non-competitive systems by Straus and Goldstein. These zones, three in number, determine the mathematical function which relates activity of an enzyme to concentration of an added substrate or inhibitor or both. The effects of suboptimal substrate concentration in such systems have been considered, and the errors arising from various common simplifications of the descriptive equations have been pointed out. The zone behavior phenomenon has been shown to be useful in determining the number of molecules of substrate or inhibitor combining reversibly with a single enzyme center. The kinetics of competitive inhibition, dilution effect, combination of inhibitor or substrate with enzyme, and destruction of inhibitor or substrate by enzyme have been analyzed and experimentally verified, and absolute velocity constants have been determined. Theoretical conclusions have been discussed from the standpoint of their physiological significance. Specifically, it has been shown that: 1. The inhibition of cholinesterase by physostigmine is competitive. A single molecule of physostigmine or acetylcholine combines with one center of cholinesterase—n = 1; and the mechanism n = 2 has been. excluded. Numerical values of the constants for this system are as follows: K_I = 3.11 x 10^–8k₁ (combination) = 8.3 x 10⁵k₂ (dissociation) = 0.026 K_S = 1.25 x 10^–3k₃ (combination) = 260 k₄ (dissociation) = 0.32 2. No definitive value can be assigned to E, the molar concentration of enzyme centers, but in 4.54 per cent dog serum, E < 1.8 x 10^–8 (E_I' < 0.58). The system therefore operates in (or nearly in) zone A at this concentration. 3. Competitive displacement of inhibitor by substrate and vice versa introduces considerable error in the usual 20 minute determination of the activity of an inhibited enzyme, unless properly corrected for. 4. Dissociation of the enzyme-inhibitor complex on dilution proceeds moderately slowly so that the full corrections for dilution cannot be applied unless time has been allowed for full dissociation. 5. Combination of physostigmine with cholinesterase is slow at all but large concentrations of inhibitor. 6. The destruction of physostigmine or acetylcholine by cholinesterase follows the predicted curve; k_D for the destruction of physostigmine is found to be > 0.00182; k_D for acetylcholine destruction is > 3500. There is no reason to assume inhibition of destruction by excess substrate or inhibitor. 7. The common assumption that enzymatic activity follows (or nearly follows) a monomolecular course is true only under limited conditions, which have been here defined. It is not valid, as a rule, for the enzymatic destruction of an inhibitor (e.g., physostigmine) and its application to such a case may lead to erroneous conclusions about the reaction mechanism.

Expanding CEP290 mutational spectrum in ciliopathies

Ciliopathies are an expanding group of rare conditions characterized by multiorgan involvement, that are caused by mutations in genes encoding for proteins of the primary cilium or its apparatus. Among these genes, CEP290 bears an intriguing allelic spectrum, being commonly mutated in Joubert syndrome and related disorders (JSRD), Meckel syndrome (MKS), Senior-Loken syndrome and isolated Leber congenital amaurosis (LCA). Although these conditions are recessively inherited, in a subset of patients only one CEP290 mutation could be detected. To assess whether genomic rearrangements involving the CEP290 gene could represent a possible mutational mechanism in these cases, exon dosage analysis on genomic DNA was performed in two groups of CEP290 heterozygous patients, including five JSRD/MKS cases and four LCA, respectively. In one JSRD patient, we identified a large heterozygous deletion encompassing CEP290 C-terminus that resulted in marked reduction of mRNA expression. No copy number alterations were identified in the remaining probands. The present work expands the CEP290 genotypic spectrum to include multiexon deletions. Although this mechanism does not appear to be frequent, screening for genomic rearrangements should be considered in patients in whom a single CEP290 mutated allele was identified.