Translating genetic and functional data into clinical practice: a series of 223 families with myotonia.

High-throughput DNA sequencing is increasingly employed to diagnose single gene neurological and neuromuscular disorders. Large volumes of data present new challenges in data interpretation and its useful translation into clinical and genetic counselling for families. Even when a plausible gene is identified with confidence, interpretation of the clinical significance and inheritance pattern of variants can be challenging. We report our approach to evaluating variants in the skeletal muscle chloride channel ClC-1 identified in 223 probands with myotonia congenita as an example of these challenges. Sequencing of CLCN1, the gene that encodes CLC-1, is central to the diagnosis of myotonia congenita. However, interpreting the pathogenicity and inheritance pattern of novel variants is notoriously difficult as both dominant and recessive mutations are reported throughout the channel sequence, ClC-1 structure-function is poorly understood and significant intra- and interfamilial variability in phenotype is reported. Heterologous expression systems to study functional consequences of CIC-1 variants are widely reported to aid the assessment of pathogenicity and inheritance pattern. However, heterogeneity of reported analyses does not allow for the systematic correlation of available functional and genetic data. We report the systematic evaluation of 95 CIC-1 variants in 223 probands, the largest reported patient cohort, in which we apply standardized functional analyses and correlate this with clinical assessment and inheritance pattern. Such correlation is important to determine whether functional data improves the accuracy of variant interpretation and likely mode of inheritance. Our data provide an evidence-based approach that functional characterization of ClC-1 variants improves clinical interpretation of their pathogenicity and inheritance pattern, and serve as reference for 34 previously unreported and 28 previously uncharacterized CLCN1 variants. In addition, we identify novel pathogenic mechanisms and find that variants that alter voltage dependence of activation cluster in the first half of the transmembrane domains and variants that yield no currents cluster in the second half of the transmembrane domain. None of the variants in the intracellular domains were associated with dominant functional features or dominant inheritance pattern of myotonia congenita. Our data help provide an initial estimate of the anticipated inheritance pattern based on the location of a novel variant and shows that systematic functional characterization can significantly refine the assessment of risk of an associated inheritance pattern and consequently the clinical and genetic counselling.

Experimental power spectral density analysis for mid- to high-spatial frequency surface error control.

The control of surface errors as a function of spatial frequency is critical during the fabrication of modern optical systems. A large-scale surface figure error is controlled by a guided removal process, such as computer-controlled optical surfacing. Smaller-scale surface errors are controlled by polishing process parameters. Surface errors of only a few millimeters may degrade the performance of an optical system, causing background noise from scattered light and reducing imaging contrast for large optical systems. Conventionally, the microsurface roughness is often given by the root mean square at a high spatial frequency range, with errors within a 0.5×0.5 mm local surface map with 500×500 pixels. This surface specification is not adequate to fully describe the characteristics for advanced optical systems. The process for controlling and minimizing mid- to high-spatial frequency surface errors with periods of up to ∼2-3 mm was investigated for many optical fabrication conditions using the measured surface power spectral density (PSD) of a finished Zerodur optical surface. Then, the surface PSD was systematically related to various fabrication process parameters, such as the grinding methods, polishing interface materials, and polishing compounds. The retraceable experimental polishing conditions and processes used to produce an optimal optical surface PSD are presented.

Subaperture stitching tolerancing for annular ring geometry.

Subaperture stitching is an economical way to extend small-region, high-resolution interferometric metrology to cover large-aperture optics. Starting from system geometry and measurement noise knowledge, this work derives an analytical expression for how noise in an annular ring of subapertures leads to large-scale errors in the computed stitched surface. These errors scale as sin(πp/M)(-2) where p is the number of sine periods around the annular full-aperture and M is the number of subaperture measurements. Understanding how low-spatial-frequency surface errors arise from subaperture noise is necessary for tolerancing systems which use subaperture stitching.

Generalized sine condition.

The classic Abbe sine condition relates pupil distortion to aberrations with linear field dependence such as coma. This paper provides a fully generalized form of the sine condition that does not use any symmetry. It accurately predicts the change in aberration in the presence of field independent and pupil aberrations. The definitions of the image, object, and coordinate system are completely arbitrary. The relationship is verified using ray trace simulations of a number of systems that have varying degrees of complexity. The potential applications are discussed.

Instrument transfer function of slope measuring deflectometry systems.

Slope measuring deflectometry (SMD) systems are developing rapidly in testing freeform optics. They measure the surface slope using a camera and an incoherent source. The principle of the test is mainly discussed in geometric optic domain. The system response as a function of spatial frequency or instrument transfer function (ITF) has yet to be studied thoroughly. Through mathematical modeling, simulation, and experiment we show that the ITF of an SMD system is very close to the modulation transfer function of the camera used. Furthermore, the ITF can be enhanced using a deconvolution filter. This study will lead to more accurate measurements in SMD and will show the physical optics nature of these tests.

Application of a synthetic extended source for interferometry.

This paper presents the design of a synthetic extended source (SES) that reduces coherent noise in interferometric measurements. The SES uses a fully coherent source for data acquisition to preserve high-contrast interferograms. Multiple measurements are made while the point source is translated according to a prescribed trajectory. The average of the measurements has the effect of using a source with a distribution defined by the trajectory. Thus, the optical system uses a coherent point source, but the data combination synthesizes the behavior of an extended source. A parametric model to quantify measurement noise due to diffraction from small particles is developed and used to evaluate SES designs. Experimental results are shown that validate the modeling. An example of a practical working SES implemented in a custom SPSI interferometer is provided.

Binary pattern deflectometry.

Deflectometry is widely used to accurately calculate the slopes of any specular reflective surface, ranging from car bodies to nanometer-level mirrors. This paper presents a new deflectometry technique using binary patterns of increasing frequency to retrieve the surface slopes. Binary Pattern Deflectometry allows almost instant, simple, and accurate slope retrieval, which is required for applications using mobile devices. The paper details the theory of this deflectometry method and the challenges of its implementation. Furthermore, the binary pattern method can also be combined with a classic phase-shifting method to eliminate the need of a complex unwrapping algorithm and retrieve the absolute phase, especially in cases like segmented optics, where spatial algorithms have difficulties. Finally, whether it is used as a stand-alone or combined with phase-shifting, the binary patterns can, within seconds, calculate the slopes of any specular reflective surface.

Alignment of a three-mirror anastigmat using the sine condition test.

Continuing to develop the sine condition test (SCTest), we show how violations of the generalized sine condition can be used to align a three-mirror anastigmat (TMA). This paper shows how the linear aberrations measured using the sine condition, along with aberrations that have constant field dependence, can be used to align a system. We discuss the design of the test hardware needed to align a TMA and the procedure for alignment. Using simulation, we then investigate the behavior of the alignment SCTest for various levels of mirror misalignment, mirror fabrication errors, and misalignment of the test equipment. All of these tests show that the alignment SCTest can successfully align an optical system.

Development of a portable deflectometry system for high spatial resolution surface measurements.

The Slope-Measuring Portable Optical Test System (SPOTS) is a new, portable, high-resolution, deflectometry device that achieves mid to high (20 to 1000 cyc/m) spatial frequency optical surface metrology with very little filtering and very little noise. Using a proof of concept system, we achieved 1 nm RMS surface accuracy for mid to high spatial frequencies, and 300 nrad RMS slope precision. SPOTS offers a turnkey solution for measuring errors on a wide variety of optical surfaces including the large mirrors fabricated at The University of Arizona. This paper defines and discusses SPOTS, including the principles of operation, measurement modes, design, performance, error analysis, and experimental results.

Diffractive optics calibrator: measurement of etching variations for binary computer-generated holograms.

We present a new device, the diffractive optics calibrator (DOC), for measuring etching variations of computer-generated holograms (CGHs). The intensity distribution of the far-field diffraction pattern is captured and fitted to a parametric model to obtain local etching parameters such as the duty cycle, etching depth, and grating period. The sensitivity of each etching parameter is analyzed, and design choices are provided. For the wavefront created by the CGH, the DOC is capable of measuring variations in these parameters that cause 1 nm peak-to-valley phase errors. System performance is verified by measurements from a phase shift Fizeau interferometer. This device will be used primarily for quality control of the CGHs. The measurement results can be used to evaluate the fabrication performance and guide future design. DOC is also capable of generating an induced phase error map for calibration. Such calibration is essential for measuring free-form aspheric surfaces with 1 nm root-mean-square accuracy.

Orthonormal curvature polynomials over a unit circle: basis set derived from curvatures of Zernike polynomials.

Zernike polynomials are an orthonormal set of scalar functions over a circular domain, and are commonly used to represent wavefront phase or surface irregularity. In optical testing, slope or curvature of a surface or wavefront is sometimes measured instead, from which the surface or wavefront map is obtained. Previously we derived an orthonormal set of vector polynomials that fit to slope measurement data and yield the surface or wavefront map represented by Zernike polynomials. Here we define a 3-element curvature vector used to represent the second derivatives of a continuous surface, and derive a set of orthonormal curvature basis functions that are written in terms of Zernike polynomials. We call the new curvature functions the C polynomials. Closed form relations for the complete basis set are provided, and we show how to determine Zernike surface coefficients from the curvature data as represented by the C polynomials.

Correlation-based smoothing model for optical polishing.

A generalized model is developed to quantitatively describe the smoothing effects from different polishing tools used for optical surfaces. The smoothing effect naturally corrects mid-to-high spatial frequency errors that have features small compared to the size of the polishing lap. The original parametric smoothing model provided a convenient way to compare smoothing efficiency of different polishing tools for the case of sinusoidal surface irregularity, providing the ratio of surface improvement via smoothing to the bulk material removal. A new correlation-based smoothing model expands the capability to quantify smoothing using general surface data with complex irregularity. For this case, we define smoothing as a band-limited correlated component of the change in the surface and original surface. Various concepts and methods, such as correlation screening, have been developed and verified to manipulate the data for the calculation of smoothing factor. Data from two actual polishing runs from the Giant Magellan Telescope off-axis segment and the Large Synoptic Survey Telescope monolithic primary-tertiary mirror were processed, and a quantitative evaluation for the smoothing efficiency of a large pitch lap and a conformal lap with polishing pads is provided.

Nongenomic actions of progesterone and 17ß-estradiol on the chloride conductance of skeletal muscle.

INTRODUCTION: Myotonia congenita, caused by mutations in ClC-1, tends to be more severe in men and is often exacerbated by pregnancy. METHODS: We performed whole-cell patch clamp of mouse muscle chloride currents in the absence/presence of 100 µM progesterone or 17ß-estradiol. RESULTS: 100 µM progesterone rapidly and reversibly shifted the ClC-1 activation curve of mouse skeletal muscle (V50 changed from -52.6 ± 9.3 to +35.5 ± 6.7; P < 0.01) and markedly reduced chloride currents at depolarized potentials. 17ß-estradiol at the same concentration had a similar but smaller effect (V50 change from -57.2 ± 7.6 to -40.5 ± 9.8; P < 0.05). 1 µM progesterone produced no significant effect. CONCLUSIONS: Although the data support the existence of a nongenomic mechanism in mammalian skeletal muscle through which sex hormones at high concentration can rapidly modulate ClC-1, the influence of hormones on muscle excitability in vivo remains an open question.

Analysis of wavefront errors introduced by encoding computer-generated holograms.

The fabrication of computer-generated holograms (CGH) by e-beam or laser-writing machine specifically requires using polygon segments to approximate the continuously smooth fringe pattern of an ideal CGH. Wavefront phase errors introduced in this process depend on the size of the polygon segments and the shape of the fringes. In this paper, we propose a method for estimating the wavefront error and its spatial frequency, allowing optimization of the polygon sizes for required measurement accuracy. This method is validated with computer simulation and direct measurements from an interferometer.

Design and optimization of the sine condition test for measuring misaligned optical systems.

By taking a new look at an old concept, we have shown in our previous work how the Abbe sine condition can be used to measure linearly field-dependent aberrations in order to verify the alignment of optical systems. In this paper, we expand on this method and discuss the design choices involved in implementing the sine condition test (SCTest). Specifically, we discuss the two illumination options for the test: point source with a grating or flat-panel display, and we discuss the tradeoffs of the two approaches. Additionally, experimental results are shown using a flat-panel display to measure linearly field-dependent aberrations. Last, we elaborate on how to implement the SCTest on more complex optical systems, such as a three-mirror anastigmat and a double Gauss imaging lens system.

Measuring rough optical surfaces using scanning long-wave optical test system. 1. Principle and implementation.

Current metrology tools have limitations when measuring rough aspherical surfaces with 1-2 µm root mean square roughness; thus, the surface cannot be shaped accurately by grinding. To improve the accuracy of grinding, the scanning long-wave optical test system (SLOTS) has been developed to measure rough aspherical surfaces quickly and accurately with high spatial resolution and low cost. It is a long-wave infrared deflectometry device consisting of a heated metal ribbon and an uncooled thermal imaging camera. A slope repeatability of 13.6 µrad and a root-mean-square surface accuracy of 31 nm have been achieved in the measurements of two 4 inch spherical surfaces. The shape of a rough surface ground with 44 µm grits was also measured, and the result matches that from a laser tracker measurement. With further calibration, SLOTS promises to provide robust guidance through the grinding of aspherics.

Refined exercise testing can aid DNA-based diagnosis in muscle channelopathies.

OBJECTIVE: To improve the accuracy of genotype prediction and guide genetic testing in patients with muscle channelopathies we applied and refined specialized electrophysiological exercise test parameters. METHODS: We studied 56 genetically confirmed patients and 65 controls using needle electromyography, the long exercise test, and short exercise tests at room temperature, after cooling, and rewarming. RESULTS: Concordant amplitude-and-area decrements were more reliable than amplitude-only measurements when interpreting patterns of change during the short exercise tests. Concordant amplitude-and-area pattern I and pattern II decrements of >20% were 100% specific for paramyotonia congenita and myotonia congenita, respectively. When decrements at room temperature and after cooling were <20%, a repeat short exercise test after rewarming was useful in patients with myotonia congenita. Area measurements and rewarming distinguished true temperature sensitivity from amplitude reduction due to cold-induced slowing of muscle fiber conduction. In patients with negative short exercise tests, symptomatic eye closure myotonia predicted sodium channel myotonia over myotonia congenita. Distinctive "tornado-shaped" neuromyotonia-like discharges may be seen in patients with paramyotonia congenita. In the long exercise test, area decrements from pre-exercise baseline were more sensitive than amplitude decrements-from-maximum-compound muscle action potential (CMAP) in patients with Andersen-Tawil syndrome. Possible ethnic differences in the normative data of the long exercise test argue for the use of appropriate ethnically-matched controls. INTERPRETATION: Concordant CMAP amplitude-and-area decrements of >20% allow more reliable interpretation of the short exercise tests and aid accurate DNA-based diagnosis. In patients with negative exercise tests, specific clinical features are helpful in differentiating sodium from chloride channel myotonia. A modified algorithm is suggested.

Use of thermal sieve to allow optical testing of cryogenic optical systems.

Full aperture testing of large cryogenic optical systems has been impractical due to the difficulty of operating a large collimator at cryogenic temperatures. The Thermal Sieve solves this problem by acting as a thermal barrier between an ambient temperature collimator and the cryogenic system under test. The Thermal Sieve uses a set of thermally controlled baffles with array of holes that are lined up to pass the light from the collimator without degrading the wavefront, while attenuating the thermal background by nearly 4 orders of magnitude. This paper provides the theory behind the Thermal Sieve system, evaluates the optimization for its optical and thermal performance, and presents the design and analysis for a specific system.

Non-null full field X-ray mirror metrology using SCOTS: a reflection deflectometry approach.

In a previous paper, the University of Arizona (UA) has developed a measurement technique called: Software Configurable Optical Test System (SCOTS) based on the principle of reflection deflectometry. In this paper, we present results of this very efficient optical metrology method applied to the metrology of X-ray mirrors. We used this technique to measure surface slope errors with precision and accuracy better than 100 nrad (rms) and ~200 nrad (rms), respectively, with a lateral resolution of few mm or less. We present results of the calibration of the metrology systems, discuss their accuracy and address the precision in measuring a spherical mirror.

Novel insights into the pathomechanisms of skeletal muscle channelopathies.

The nondystrophic myotonias and primary periodic paralyses are an important group of genetic muscle diseases characterized by dysfunction of ion channels that regulate membrane excitability. Clinical manifestations vary and include myotonia, hyperkalemic and hypokalemic periodic paralysis, progressive myopathy, and cardiac arrhythmias. The severity of myotonia ranges from severe neonatal presentation causing respiratory compromise through to mild later-onset disease. It remains unclear why the frequency of attacks of paralysis varies greatly or why many patients develop a severe permanent fixed myopathy. Recent detailed characterizations of human genetic mutations in voltage-gated muscle sodium (gene: SCN4A), chloride (gene: CLCN1), calcium (gene: CACNA1S), and inward rectifier potassium (genes: KCNJ2, KCNJ18) channels have resulted in new insights into disease mechanisms, clinical phenotypic variation, and therapeutic options.