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PubMed1996

Unique properties of cardiac action potentials recorded with voltage-sensitive dyes.

INTRODUCTION: Optical mapping with voltage-sensitive dyes has made it possible to record cardiac action potentials with high spatial resolution that is unattainable by conventional techniques. Optically recorded signals possess distinct properties that differ importantly from electrograms recorded with extracellular electrodes or action potentials recorded with microelectrode techniques. Despite the growing application of optical mapping to cardiac electrophysiology, relatively little quantitative information is available regarding the characteristics of optical action potentials recorded from cardiac tissue. METHODS AND RESULTS: A high-resolution optical mapping system and microelectrode techniques were used to determine the characteristics of guinea pig ventricular action potentials recorded with the voltage-sensitive dye di-4-ANEPPS. The effects of optical magnification, tissue-light interaction, sampling rate, voltage resolution, spatial resolution, and cardiac motion on action potential signal characteristics were determined. The optical action potential signal represents the relative change in transmembrane potential arising from a volume of cells, where the area of a recording site is determined by optical magnification and detector area, and the depth of recording is determined by system optics and the visible light transmission characteristics of cardiac muscle. Using photographic lenses, the depth of tissue contributing to the signal is < 250 microns. The action potential plateau and final repolarization can be accurately reconstructed from data digitized at modest sampling rates (450 to 750 Hz), since the frequency content of optical action potentials is band-limited to approximately 150 Hz. However, faster sampling rates are needed to depict the subtle details of the action potential upstroke. In addition to temporal resolution, it is essential to achieve sufficient dynamic range and voltage resolution to accurately represent the time course of membrane potential change. Voltage resolution is inversely related to the square of spatial resolution, hence, there exists an inherent trade-off between increased spatial resolution and diminished voltage resolution. Cardiac motion, which can otherwise limit spatial resolution as well as signal fidelity, can be effectively reduced using mechanical stabilization of the heart without distorting action potential characteristics. CONCLUSIONS: Optical mapping with voltage-sensitive dyes provides high-fidelity multisite action potential recording with flexible spatial resolution. When recording cardiac action potentials with voltage-sensitive dyes, the interdependence of temporal, spatial, and voltage resolutions must be carefully considered.

Action Potentials↗
PubMed1997

A new method for straightening DNA molecules for optical restriction mapping.

We have developed an improved method of straightening DNA molecules for use in optical restriction mapping. The DNA was straightened on 3-aminopropyltriethoxysilane-coated glass slides using surface tension generated by a moving meniscus. In our method the meniscus motion was controlled mechanically, which provides advantages of speed and uniformity of the straightened molecules. Variation in the affinity of the silanized surfaces for DNA was compensated by precoating the slide with single-stranded non-target blocking DNA. A small amount of MgCl2 added to the DNA suspension increased the DNA-surface affinity and was necessary for efficient restriction enzyme digestion of the straightened surface-bound DNA. By adjusting the amounts of blocking DNA and MgCl2, we prepared slides that contained many straight parallel DNA molecules. Straightened lambda phage DNA (48 kb) bound to a slide surface was digested by EcoRI restriction endonuclease, and the resulting restriction fragments were imaged by fluorescence microscopy using a CCD camera. The observed fragment lengths showed excellent agreement with their predicted lengths.

Bacteriophage lambda↗
PubMed2006

An algorithm for assembly of ordered restriction maps from single DNA molecules.

The restriction mapping of a massive number of individual DNA molecules by optical mapping enables assembly of physical maps spanning mammalian and plant genomes; however, not through computational means permitting completely de novo assembly. Existing algorithms are not practical for genomes larger than lower eukaryotes due to their high time and space complexity. In many ways, sequence assembly parallels map assembly, so that the overlap-layout-consensus strategy, recently shown effective in assembling very large genomes in feasible time, sheds new light on solving map construction issues associated with single molecule substrates. Accordingly, we report an adaptation of this approach as the formal basis for de novo optical map assembly and demonstrate its computational feasibility for assembly of very large genomes. As such, we discuss assembly results for a series of genomes: human, plant, lower eukaryote and bacterial. Unlike sequence assembly, the optical map assembly problem is actually more complex because restriction maps from single molecules are constructed, manifesting errors stemming from: missing cuts, false cuts, and high variance of estimated fragment sizes; chimeric maps resulting from artifactually merged molecules; and true overlap scores that are "in the noise" or "slightly above the noise." We address these problems, fundamental to many single molecule measurements, by an effective error correction method using global overlap information to eliminate spurious overlaps and chimeric maps that are otherwise difficult to identify.

Algorithms↗
PubMed2025

Optical Genome Mapping in Myelodysplastic Syndromes: Clinical Value and Limitations Derived From a Cohort of 236 Patients.

Identification of cytogenetic abnormalities is critical for the classification and risk stratification of myelodysplastic syndromes (MDS). Optical genome mapping (OGM) is an emerging cytogenomic platform that enables high-resolution genome-wide cytogenetic analysis. We analyzed bone marrow specimens of 236 MDS patients, 149 newly diagnosed and 87 with relapsed/refractory disease, using OGM, conventional karyotyping, and next-generation sequencing analysis. OGM and karyotyping showed concordant results in 68% of cases, including 34% with normal findings by both assays. OGM provided additional information in 27% of patients. Common abnormalities detected exclusively by OGM included chromoanagenesis (n = 33), KMT2A partial tandem duplication (n = 7), and MECOM rearrangement (n = 4). These OGM findings led to disease reclassification and/or changes in risk stratification in 14 patients (9.4%) with newly diagnosed MDS. In contrast, OGM failed to detect small clones or subclones in 5% of patients, resulting in risk group changes in 2% of newly diagnosed MDS patients. We conclude that OGM enhances the cytogenetic assessment of MDS in approximately 25% of patients and leads to a change in disease classification and/or risk stratification in approximately 10% of patients. However, low sensitivity for detecting small clones or subclones remains a limitation of OGM.

Humans↗
PubMed2002

Enhanced method for the reconstruction of zero-dispersion wavelength maps of optical fibers by measurement of continuous-wave four-wave mixing efficiency.

The zero-dispersion wavelength map of an optical fiber can be obtained from measurement of end-to-end four-wave mixing efficiency at various wavelengths. A fast and unambiguous algorithm for reconstruction of the zero-dispersion wavelength map of an optical fiber by measurement of four-wave mixing efficiency is proposed. This method can produce high-resolution results in a few seconds. We also study the limitations of this technique that are due to polarization-mode dispersion (PMD). Simple practical rules to avoid the effects of PMD in such measurements are established.

Journal Article↗
PubMed2025

Optical genome mapping improves clinical interpretation of constitutional copy-number gains and reduces their VUS burden.

PURPOSE: Genomic structure of copy-number gains is critical for their clinical interpretation but cannot be determined by chromosomal microarray (CMA) analysis, which does not provide information about chromosomal location and orientation of multiplied regions. We thus hypothesized that in CMA testing gains have higher probability than losses to be classified as variants of uncertain significance (VUS) and that structural information from optical genome mapping (OGM) may improve their interpretation. METHODS: Using a &#x3c7;2 test, we assessed the association between classification of copy-number variants as VUS and their type (gains vs losses) in a cohort of 4073 CMA cases. Thirty-three VUS gains involving disease-associated genes were characterized by OGM to evaluate if OGM data enable their more conclusive clinical interpretation. RESULTS: The proportion of variants reported as VUS compared with likely pathogenic/pathogenic was significantly higher for gains than losses, confirming their increased VUS burden. OGM successfully determined genomic structure for all 33 copy-number gains, showing that 26 of 33 were tandem duplications and 7 of 33 were complex rearrangements. Structural information facilitated clinical interpretation in majority of the cases; it supported benign nature for 27 of 33 gains and was inconclusive or supported pathogenic role for 6 of 33. An estimated 20% of reported VUS gains would not have been reportable if we had OGM data. CONCLUSION: We illustrate a specific advantage of OGM compared with CMA: in addition to detecting both copy-number variants and balanced rearrangements, OGM improves clinical interpretation of copy-number gains by providing structural information and is thus expected to significantly decrease their VUS burden.

Humans↗
PubMed2001

Reproducibility of retinal mapping using optical coherence tomography.

OBJECTIVE: To assess the reproducibility of retinal thickness measurement using commercially available mapping software of optical coherence tomography (OCT). METHODS: Six radial scans, 6 mm long and centered on the fixation point, were performed on 10 eyes of 10 healthy volunteers and 10 eyes of 10 diabetic patients with clinically significant macular edema. Retinal thickness was measured automatically using the mapping software of OCT in the 9 macular Early Treatment Diabetic Retinopathy Study areas and in a central area 500 microm in diameter. Measurement reproducibility was tested by means of 3 series of scans performed by 2 different observers on 2 different days. Results were assessed by their repeatability and intraclass correlation coefficients (ICCs). RESULTS: In healthy subjects, intraobserver, interobserver, and intervisit reproducibility of retinal thickness measurements were excellent, with a repeatability coefficient of less than 7 microm and ICCs of greater than 0.89. In diabetic patients, the repeatability coefficient was less than 21 microm in all areas of the macula except one, with an ICC of greater than 0.98. Relative variations in measurements were small in both healthy and diabetic subjects, with reproducibilities of +/- 5% and +/- 6%, respectively. CONCLUSION: Retinal mapping software of OCT allows reproducible measurement of retinal thickness in both healthy subjects and diabetic patients with macular edema.

Adult↗
PubMed2026

Optical genome mapping enhanced by refined variant interpretation in pediatric acute lymphoblastic leukemia.

Reliable detection of structural variants (SVs) and copy number variations (CNVs) is crucial in the contemporary diagnostics of pediatric B-cell acute lymphoblastic leukemia (B-ALL). However, limitations of commonly used conventional and molecular cytogenetic methods may hinder the accurate genetic characterization of patients. Optical genome mapping (OGM) offers a reliable alternative by enabling high-resolution, genome-wide detection of CNVs and SVs. Chromosomal aberrations were screened using OGM in 51 children with B-ALL. The results were compared with those of karyotyping, fluorescence in situ hybridization (FISH), digital multiplex ligation-dependent probe amplification (digitalMLPA), and targeted RNA sequencing (RNA-seq). OGM data showed high congruency with karyotyping and FISH findings, detecting clinically relevant variants beyond G-banding results and unraveling a complex KMT2A fusion undetected by FISH. Gene fusions involved in complex ETV6::RUNX1 translocations, but not detected by RNA-seq, were confirmed using FISH. Normalization of OGM copy number values with DNA-index-improved concordance with FISH-derived copy numbers in near-tri/tetraploid cases. In the peripheral regions of OGM variants (fringe-zones), a novel evaluation strategy called 'FriZone' was applied, which significantly improved the concordance between OGM and digitalMLPA. In addition, a co-segregation analysis revealed strong associations between ETV6::RUNX1 fusion and deletions of ETV6, RAG2, and NR3C2. OGM uncovered complex rearrangements undetected by widely used methods in 15% of cases, improving genetic classification and risk stratification in 10% of the patients. The FriZone analysis and normalization by DNA-index provide a refined, more accurate approach to OGM variant interpretation, facilitating the efficient application of OGM in clinical diagnostics. &#xa9; 2026 The Author(s). The Journal of Pathology published by John Wiley & Sons Ltd on behalf of The Pathological Society of Great Britain and Ireland.

Humans↗
PubMed2026

Integrating Optical Genome Mapping into the Genetic Diagnostic Algorithm: Clinical Utility in Unresolved Autosomal Recessive Disorders from a Large Cohort.

INTRODUCTION: The identification of precise genetic etiologies is indispensable for the clinical management of monogenic disorders. However, conventional diagnostic methods and exome sequencing (ES) frequently fail to identify complex structural variations (SVs), leaving the genetic basis unexplained in approximately 30-60% of suspected cases. Optical genome mapping (OGM) emerges as a high-resolution technology capable of detecting cryptic SVs inaccessible to standard methodologies. METHODS: In this study, we evaluated the clinical utility of integrating OGM into the diagnostic algorithm for unresolved monogenic diseases. Following negative or inconclusive results from standard ES pipelines, OGM was applied to a targeted subset of patients (n = 7) selected from a comprehensive clinical cohort of 1,257 individuals with suspected genetic disorders. RESULTS: The integration of OGM identified candidate SVs that may represent the second allelic alteration in two distinct cases; however, confirmation through parental segregation analysis remains pending. Specifically, OGM identified an intronic insertion in the TTLL5 gene and a deletion in a putative regulatory region approximately 400 kb upstream of the NMNAT1 gene, both of which were missed by prior diagnostic testing. CONCLUSION: Our findings suggest that OGM has potential value in investigating the missing heritability of autosomal recessive disorders. By detecting candidate SVs invisible to conventional methods, OGM may warrant consideration as a complementary diagnostic approach following inconclusive ES; however, larger cohorts and confirmatory functional studies are needed to establish its clinical utility.

Autosomal recessive disorders↗
PubMed2006

Measurements of electrophysiological effects of components of acute ischemia in Langendorff-perfused rat hearts using voltage-sensitive dye mapping.

INTRODUCTION: This study was carried out to evaluate optical mapping in the presence of cytochalasin-D as a method for measuring electrophysiological responses in general, and in particular the responses to acute ischemia in the Langendorff-perfused rat heart. Cytochalasin-D is commonly used to reduce contraction for the purpose of suppressing motion artifacts in voltage-sensitive dye recordings of cardiac membrane potential. METHODS AND RESULTS: Observations using optical mapping were complemented by recordings of the surface electrogram to provide information independent of the optical measurements. Perfusion of Langendorff-perfused rat hearts with 3 microM cytochalasin-D resulted in a 24% prolongation of the QT interval of surface electrograms indicating that cytochalasin-D prolongs the rat ventricular action potential. Individual components of the electrophysiological response to acute ischemia were globally induced as follows: (1) opening of K(ATP) channels was induced by perfusion of 2 micro M P-1,075, (2) accumulation of extracellular K(+) was simulated by increasing perfusate [K(+)] to 12 mM, and (3) acidosis was simulated by reducing perfusate pH to 6.5. The responses to these interventions could be reliably documented using optical recordings, as well as from surface electrograms. Whole-cell patch clamp measurements on isolated rat ventricular myocytes indicate that cytochalasin-D produces an approximately 2.5-fold increase in P-1,075-induced I(K,ATP). CONCLUSION: These results provide the necessary background information for interpreting electrophysiological measurements during acute ischemia in the presence of cytochalasin-D.

Action Potentials↗
PubMed2025

Optical Genome Mapping Is a Powerful Diagnostic Tool in Non-Hodgkin Lymphoma.

Non-Hodgkin lymphoma (NHL) is a diverse and heterogeneous group of hematological malignancies. These lymphomas arise from the clonal proliferation of either B/T or natural killer lymphocytes, and their correct classification relies partly on identifying characteristic structural variants and copy number alterations. Current standard-of-care technologies for detecting these genomic features, chromosome banding analysis (CBA) and fluorescent in situ hybridization (FISH), are labor intensive and have specific limitations. CBA has low resolution and relies on viable cell culture, whereas the targeted approach of FISH does not provide the whole genome view required for comprehensive disease characterization. This highlights the need for higher-resolution nontargeted genomic methods. Previous studies have evaluated optical genome mapping (OGM) as a whole genome alternative for cytogenomic characterization in NHL diagnostics but were restricted in number and to cases with peripheral blood and/or bone marrow invasion. Here, we selected a comprehensive cohort of 110 NHL cases (79 B-NHL and 31 T-NHL/natural killer-NHL) derived from different types of tissue biopsies, all with established histopathological diagnoses. Seventy-eight samples were genomically well characterized at diagnosis by CBA and FISH. The remaining 32 cases were included because of previous CBA failure, although FISH data were available for 20 cases. OGM provided informative results in 94% of the cohort, with a high concordance rate of 97.6% compared with CBA/FISH in detecting clinically relevant aberrations. The 2 variants that were missed were both present at the detection threshold of OGM. In contrast, OGM successfully resolved 26 samples with previous CBA failure and detected 3 additional disease-defining events, resulting in diagnostic reclassification of 1 patient. Finally, OGM identified novel recurrent aberrations that warrant further investigation into their pathogenetic implications. To conclude, OGM robustly detects clinically relevant structural variants and copy number alterations and presents a promising alternative to CBA and FISH in routine diagnostic evaluation of NHL.

Humans↗
PubMed2026

[Optical genome mapping analysis of a Chinese pedigree with a complex balanced translocation involving four chromosomes].

OBJECTIVE: To explore the genetic characteristics of a complex balanced translocation involving four non-homologous chromosomes in a Chinese pedigree using optical genomic mapping (OGM). METHODS: A woman with primary infertility and her family members who presented at the Prenatal Diagnosis Center of the Sixth Affiliated Hospital of Sun Yat-sen University in October 2021 were selected as study subjects. Comprehensive analysis and verification of chromosomal abnormalities were conducted through conventional G-band karyotyping analysis, single nucleotide polymorphism microarray (SNP array) and OGM. This study was approved by the Medical Ethics Committee of the hospital (Ethics No.: E2022210). RESULTS: G-band karyotyping analysis indicated that the proband, her father, and younger brother have all carried a complex translocation involving four chromosomes. SNP array analysis revealed a duplication of approximately 21.63 Mb in the 9p24.1-p21.1 region in the proband's younger brother, while no abnormality was detected in other family members. OGM confirmed that the complex balanced translocation has involved chromosomes 5, 8, 9, and 10. CONCLUSION: The proband has harbored a complex balanced translocation. OGM has demonstrated certain advantages in characterization of complex chromosomal structural abnormalities.

Humans↗
PubMed2005

Full-field strain mapping by optical correlation of micrographs acquired during deformation.

Optical correlation is an emerging strain-mapping technique that allows full-field surface strain mapping by comparing the images of the same region before, during and after deformation. The fundamental aspects of optical correlation are presented, with emphasis on the applicability of the technique to the analysis of micrographs obtained during in situ deformation studies. Without considering specific algorithms, this paper discusses important practical issues such as accuracy and spatial resolution and how these are affected by image quality and other experimental difficulties. The technique was used to analyse image sequences obtained during in situ deformation tensile tests on two very different materials: antler bone and ferritic steel. As the technique does not require patterns or coatings to be applied on the surface of interest, the strain maps obtained could be used to relate strain heterogeneity to the underlying microstructure.

Animals↗
PubMed1997

Optically imaged maps of orientation preference in primary visual cortex of cats and ferrets.

Feature maps in the cerebral cortex constitute orderly representations of response features created within the cortex; an example is the mapping of orientation-selective neurons in visual cortex. We have compared the properties of orientation maps in area 17 of cats and ferrets, obtained by optical imaging of intrinsic signals. Orientation maps in both species contain a quasi-periodic distribution of iso-orientation domains that are organized into a lattice of pinwheels. However, the spatial density of orientation domains and of pinwheels in ferret area 17 is nearly twice that in cat area 17. The ferret map also contains more discontinuities, or fractures, where orientation changes abruptly. The size of orientation domains scales with interdomain spacing, so that the ratio of the two is approximately the same in both species. Consistent with this finding, the orientation tuning width of individual pixels is similar in the two. The magnitude of orientation preference, however, is much lower in ferret compared to cat. The greater incidence of fractures in ferret appears to be due to proportionately greater overlap between domains of different orientations, particularly along fracture lines that link pinwheel centers. We hypothesize that a key determinant of orientation maps, the relationship between orientation domain size and spacing, expresses an anatomical link between sizes of thalamocortical arbors and horizontal intracortical connections in area 17.

Animals↗
PubMed1999

Accuracy of Orbscan total optical power maps in detecting refractive change after myopic laser in situ keratomileusis.

PURPOSE: To determine whether the refractive change obtained using the Orbscan-derived total optical power (TOP) map is in concordance with the manifest refractive change produced by laser in situ keratomileusis (LASIK). SETTING: LASIK Vision Canada, Vancouver, BC, Canada (an ambulatory surgical center for refractive surgery). METHODS: Twenty eyes of 10 consecutive bilateral LASIK patients were included in the study. Orbscan topographical analysis and manifest refraction were performed preoperatively and at least 1 month postoperatively. The change in manifest refraction (corrected to the corneal plane) before and after LASIK was correlated with the corneal power change averaged within the 2.0, 3.0, 4.0, and 5.0 mm diameter zones of TOP and axial power maps. RESULTS: The central 4.0 mm zone TOP map gave the best correlation between manifest refractive change and Orbscan-measured corneal power change (r2 = 0.835, P < .004). The correlation was higher with TOP maps than with anterior axial power maps. CONCLUSION: The corneal power change measured by the Orbscan TOP maps correlated highly with the changes in manifest refraction after LASIK.

Cornea↗
PubMed2003

Failure to form a stable topographic map during optic nerve regeneration: abnormal activity-dependent mechanisms.

Visually evoked responses in the optic tectum are mediated by glutamate receptors. During development, there is a switch from N-methyl-d-aspartate (NMDA)- to alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid (AMPA)-mediated activity as the retinotectal map refines and visual function ensues. A similar pattern is seen in goldfish as the map refines during optic nerve regeneration. Here we examined glutamate receptors during optic nerve regeneration in the lizard, Ctenophorus ornatus, in which an imprecise retinotopic map forms transiently but degrades, leaving animals blind via the experimental eye. Receptor function was examined using NMDA and AMPA/kainate antagonists during in vitro tectal recording of visually evoked post-synaptic extracellular responses. Expression of NR1 (NMDA) and GluR2 (AMPA) receptor subtypes was examined immunohistochemically. In unoperated control animals, responses were robust and AMPA/kainate receptor-mediated. When the imprecise map was present, responses were difficult to evoke and insecure; periods of spontaneous activity as well as inactivity were also noted. Although AMPA/kainate-mediated activity persisted and GluR2 immunoreactivity increased transiently, NMDA receptor-mediated activity was also consistently detected and NR1 expression increased. In the long term, when the map had degraded, responses were readily evoked and predominantly AMPA/kainate receptor-mediated although some NMDA-mediated activity and NR1 expression remained. We suggest that the asynchronous activity reaching the optic tectum results in an inability to recapitulate the appropriate functional sequences of expression of NMDA and AMPA/kainate receptors necessary to refine the retinotectal map.

Animals↗
PubMed2001

Visualization and functional characterization of the developing murine cardiac conduction system.

The cardiac conduction system is a complex network of cells that together orchestrate the rhythmic and coordinated depolarization of the heart. The molecular mechanisms regulating the specification and patterning of cells that form this conductive network are largely unknown. Studies in avian models have suggested that components of the cardiac conduction system arise from progressive recruitment of cardiomyogenic progenitors, potentially influenced by inductive effects from the neighboring coronary vasculature. However, relatively little is known about the process of conduction system development in mammalian species, especially in the mouse, where even the histological identification of the conductive network remains problematic. We have identified a line of transgenic mice where lacZ reporter gene expression delineates the developing and mature murine cardiac conduction system, extending proximally from the sinoatrial node to the distal Purkinje fibers. Optical mapping of cardiac electrical activity using a voltage-sensitive dye confirms that cells identified by the lacZ reporter gene are indeed components of the specialized conduction system. Analysis of lacZ expression during sequential stages of cardiogenesis provides a detailed view of the maturation of the conductive network and demonstrates that patterning occurs surprisingly early in embryogenesis. Moreover, optical mapping studies of embryonic hearts demonstrate that a murine His-Purkinje system is functioning well before septation has completed. Thus, these studies describe a novel marker of the murine cardiac conduction system that identifies this specialized network of cells throughout cardiac development. Analysis of lacZ expression and optical mapping data highlight important differences between murine and avian conduction system development. Finally, this line of transgenic mice provides a novel tool for exploring the molecular circuitry controlling mammalian conduction system development and should be invaluable in studies of developmental mutants with potential structural or functional conduction system defects.

Animals↗