scholarly journals Single-molecule optical mapping enables quantitative measurement of D4Z4 repeats in facioscapulohumeral muscular dystrophy (FSHD)

2019 ◽  
Vol 57 (2) ◽  
pp. 109-120 ◽  
Author(s):  
Yi Dai ◽  
Pidong Li ◽  
Zhiqiang Wang ◽  
Fan Liang ◽  
Fan Yang ◽  
...  
Keyword(s):  
Muscular Dystrophy ◽  
Single Molecule ◽  
Quantitative Measurement ◽  
Optical Mapping ◽  
Small Sample Size ◽  
Human Subjects ◽  
Facioscapulohumeral Muscular Dystrophy ◽  
Small Sample ◽  
Segmental Duplications ◽  
Control Subjects

PurposeFacioscapulohumeral muscular dystrophy (FSHD) is a common adult muscular dystrophy. Over 95% of FSHD cases are associated with contraction of the D4Z4 tandem repeat (~3.3 kb per unit) at 4q35 with a specific genomic configuration (haplotype) called 4qA. Molecular diagnosis of FSHD typically requires pulsed-field gel electrophoresis with Southern blotting. We aim to develop novel genomic and computational methods for characterising D4Z4 repeat numbers in FSHD.MethodsWe leveraged a single-molecule optical mapping platform that maps locations of restriction enzyme sites on high molecular weight (>150 kb) DNA molecules. We developed bioinformatics methods to address several challenges, including the differentiation of 4qA with 4qB alleles, the differentiation of 4q35 and 10q26 segmental duplications, the quantification of repeat numbers with different enzymes that may or may not have recognition sites within D4Z4 repeats. We evaluated the method on 25 human subjects (13 patients, 3 individual control subjects, 9 control subjects from 3 families) labelled by the Nb.BssSI and/or Nt.BspQI enzymes.ResultsWe demonstrated that the method gave a direct quantitative measurement of repeat numbers on D4Z4 repeats with 4qA allelic configuration and the levels of postzygotic mosaicism. Our method had high concordance with Southern blots from several cohorts on two platforms (Bionano Saphyr and Bionano Irys), but with improved quantification of repeat numbers.ConclusionWhile the study is limited by small sample size, our results demonstrated that single-molecule optical mapping is a viable approach for more refined analysis on genotype-phenotype relationships in FSHD, especially when postzygotic mosaicism is present.

scholarly journals Single-molecule optical mapping enables accurate molecular diagnosis of facioscapulohumeral muscular dystrophy (FSHD)

2018 ◽  
Author(s):  
Yi Dai ◽  
Pidong Li ◽  
Zhiqiang Wang ◽  
Fan Liang ◽  
Fan Yang ◽  
...  
Keyword(s):  
Muscular Dystrophy ◽  
Molecular Diagnosis ◽  
Single Molecule ◽  
Optical Mapping ◽  
Genetic Diagnosis ◽  
Turnaround Time ◽  
Facioscapulohumeral Muscular Dystrophy ◽  
Copy Number Loss ◽  
Bioinformatics Pipeline ◽  
Repeat Array

ABSTRACTFacioscapulohumeral Muscular Dystrophy (FSHD) is a common adult muscular dystrophy in which the muscles of the face, shoulder blades and upper arms are among the most affected. FSHD is the only disease in which “junk” DNA is reactivated to cause disease, and the only known repeat array-related disease where fewer repeats cause disease. More than 95% of FSHD cases are associated with copy number loss of a 3.3kb tandem repeat (D4Z4 repeat) at the subtelomeric chromosomal region 4q35, of which the pathogenic allele contains less than 10 repeats and has a specific genomic configuration called 4qA. Currently, genetic diagnosis of FSHD requires pulsed-field gel electrophoresis followed by Southern blot, which is labor-intensive, semi-quantitative and requires long turnaround time. Here, we developed a novel approach for genetic diagnosis of FSHD, by leveraging Bionano Saphyr single-molecule optical mapping platform. Using a bioinformatics pipeline developed for this assay, we found that the method gives direct quantitative measurement of repeat numbers, can differentiate 4q35 and the highly paralogous 10q26 regions, can determine the 4qA/4qB allelic configuration, and can quantitate levels of post-zygotic mosaicism. We evaluated this approach on 5 patients (including two with post-zygotic mosaicism) and 2 patients (including one with post-zygotic mosaicism) from two separate cohorts, and had complete concordance with Southern blots, but with improved quantification of repeat numbers resolved between haplotypes. We concluded that single-molecule optical mapping is a viable approach for molecular diagnosis of FSHD and may be applied in clinical diagnostic settings once more validations are performed.

scholarly journals Rapid prenatal diagnosis of Facioscapulohumeral Muscular Dystrophy 1 by combined Bionano optical mapping and karyomapping

2019 ◽  
Vol 40 (3) ◽  
pp. 317-323 ◽  
Author(s):  
Yuting Zheng ◽  
Lingrong Kong ◽  
Hui Xu ◽  
Yongjie Lu ◽  
Xuechao Zhao ◽  
...  
Keyword(s):  
Prenatal Diagnosis ◽  
Muscular Dystrophy ◽  
Optical Mapping ◽  
Facioscapulohumeral Muscular Dystrophy

Evaluation of speech outcomes in oral and oropharyngeal cancers

2009 ◽  
Vol 27 (15_suppl) ◽  
pp. e17039-e17039
Author(s):  
R. C. Dwivedi
Keyword(s):  
Primary Closure ◽  
Acoustic Analysis ◽  
Small Sample Size ◽  
Human Subjects ◽  
Small Sample ◽  
Cross Sectional ◽  
Perceptual Evaluation ◽  
Retrospective Nature

e17039 Background: The aim of the study was to review the literature on oral and oropharyngeal cancers for speech outcomes over the last 8 years. Study design: Systematic review of published studies between 2000 and 2008. Methods: A comprehensive literature search for speech outcomes was performed on PUBMED/MEDLINE, EMBASE, CINAHL, and Science citation index from 2000 to 2008 using the key words- speech, voice, articulation, acoustic analysis etc in oral and oropharyngeal cancers. The reference lists from the selected relevant articles were also inspected and any other pertinent publications were added to the final review. Articles published in all languages on human subjects, and all types of studies were included. Sixty eight articles satisfied the inclusion criterion and their findings were tabulated, analysed and evaluate based on the modality used for evaluation - questionnaire evaluation (QE), perceptual evaluation (PE) and acoustic analysis (AE). Results: 39/68 studies used questionnaires; 30/68 used PE and 2/68 used acoustic analysis. Questionnaires with PE were used in 5 studies. Thirty three/ 68 were retrospective, 28/68 prospective and 7/68 were cross-sectional studies. The finds suggest that the Frequency and quality of abnormal phonation depends on postoperative deficits. Oral (vs. oropharyngeal) cancers, advanced (vs. early), associated comorbidities (vs. without comorbidities), flap reconstruction (vs. primary closure), irradiated (vs. non-irradiated) and Mandibulotomy (vs. without mandibulotomy) have poor speech outcome. Preservation of Tip of tongue and FOM, lateral type excision, smaller excision, greater tongue mobility, primary closure and younger patients have better speech outcome. Conclusions: No validated scoring system for PE has been used; QE needs to be done with speech/ dysarthria specific questionnaires. Most studies suffered because of their retrospective nature, single modality evaluation, small sample size and short duration of follow-up. There is a clear paucity of acoustic analysis studies in oral and oropharyngeal literature and further longitudinal studies are needed. No significant financial relationships to disclose.

scholarly journals Gamma estimator of Jarzynski equality for recovering binding energies from noisy dynamic data sets

2020 ◽  
Vol 11 (1) ◽  
Author(s):  
Zhifeng Kuang ◽  
Kristi M. Singh ◽  
Daniel J. Oliver ◽  
Patrick B. Dennis ◽  
Carole C. Perry ◽  
...  
Keyword(s):  
Free Energy ◽  
Single Molecule ◽  
Fundamental Problem ◽  
Small Sample Size ◽  
Small Sample ◽  
Binding Energies ◽  
External Work ◽  
Work Distribution ◽  
Jarzynski Equality ◽  
The Mean

Abstract A fundamental problem in thermodynamics is the recovery of macroscopic equilibrated interaction energies from experimentally measured single-molecular interactions. The Jarzynski equality forms a theoretical basis in recovering the free energy difference between two states from exponentially averaged work performed to switch the states. In practice, the exponentially averaged work value is estimated as the mean of finite samples. Numerical simulations have shown that samples having thousands of measurements are not large enough for the mean to converge when the fluctuation of external work is above 4 kBT, which is easily observable in biomolecular interactions. We report the first example of a statistical gamma work distribution applied to single molecule pulling experiments. The Gibbs free energy of surface adsorption can be accurately evaluated even for a small sample size. The values obtained are comparable to those derived from multi-parametric surface plasmon resonance measurements and molecular dynamics simulations.

scholarly journals Nanopore-based single molecule sequencing of the D4Z4 array responsible for facioscapulohumeral muscular dystrophy

2017 ◽  
Vol 7 (1) ◽  
Author(s):  
Satomi Mitsuhashi ◽  
So Nakagawa ◽  
Mahoko Takahashi Ueda ◽  
Tadashi Imanishi ◽  
Martin C. Frith ◽  
...  
Keyword(s):  
Muscular Dystrophy ◽  
Single Molecule ◽  
Facioscapulohumeral Muscular Dystrophy ◽  
Single Molecule Sequencing ◽  
D4z4 Array

scholarly journals The Effect of Implanted Functional Electrical Stimulation on Gait Performance in Stroke Survivors: A Systematic Review

Sensors ◽  
2021 ◽  
Vol 21 (24) ◽  
pp. 8323
Author(s):  
Gu Eon Kang ◽  
Rebecca Frederick ◽  
Brandon Nunley ◽  
Lawrence Lavery ◽  
Yasin Dhaher ◽  
...  
Keyword(s):  
Systematic Review ◽  
Electrical Stimulation ◽  
Functional Electrical Stimulation ◽  
Small Sample Size ◽  
Human Subjects ◽  
Small Sample ◽  
Cochrane Library ◽  
Therapeutic Effects ◽  
Stroke Survivors ◽  
Gait Performance

The emerging literature suggests that implantable functional electrical stimulation may improve gait performance in stroke survivors. However, there is no review providing the possible therapeutic effects of implanted functional electrical stimulation on gait performance in stroke survivors. We performed a web-based, systematic paper search using PubMed, the Cochrane Library, and EMBASE. We limited the search results to human subjects and papers published in peer-reviewed journals in English. We did not restrict demographic or clinical characteristics. We included 10 papers in the current systematic review. Across all included studies, we found preliminary evidence of the potential therapeutic effects of functional electrical stimulation on walking endurance, walking speed, ankle mobility, and push-off force in stroke survivors. However, due to the heterogeneity between the included studies, small sample size, and lack of randomized controlled trials, more studies are critically needed to confirm whether implanted functional electrical stimulation can improve gait performance in stroke survivors.

scholarly journals Nanopore-based single molecule sequencing of the D4Z4 array responsible for facioscapulohumeral muscular dystrophy

2017 ◽  
Author(s):  
Satomi Mitsuhashi ◽  
So Nakagawa ◽  
Mahoko Takahashi Ueda ◽  
Tadashi Imanishi ◽  
Martin C Frith ◽  
...  
Keyword(s):  
Muscular Dystrophy ◽  
Single Molecule ◽  
Gc Content ◽  
Facioscapulohumeral Muscular Dystrophy ◽  
Repeat Sequence ◽  
Reference Sequence ◽  
Sequencing Data ◽  
Bac Clone ◽  
D4z4 Repeat ◽  
D4z4 Array

AbstractSubtelomeric macrosatellite repeats are difficult to sequence using conventional sequencing methods owing to the high similarity among repeat units and high GC content. Sequencing these repetitive regions is challenging, even with recent improvements in sequencing technologies. Among these repeats, a haplotype carrying a particular sequence and shortening of the D4Z4 array on human chromosome 4q35 causes one of the most prevalent forms of muscular dystrophy with autosomal-dominant inheritance, facioscapulohumeral muscular dystrophy (FSHD). Here, we applied a nanopore-based ultra-long read sequencer to sequence a BAC clone containing 13 D4Z4 repeats and flanking regions. We successfully obtained the whole D4Z4 repeat sequence, including the pathogenic gene DUX4 in the last D4Z4 repeat. The estimated sequence accuracy of the total repeat region was 99.8% based on a comparison with the reference sequence. Errors were typically observed between purine or between pyrimidine bases. Further, we analyzed the D4Z4 sequence from publicly available ultra-long whole human genome sequencing data obtained by nanopore sequencing. This technology may be a new tool for studying D4Z4 repeats and pathomechanism of FSHD in the future and has the potential to widen our understanding of subtelomeric regions.

scholarly journals Genome mapping resolves structural variation within segmental duplications associated with microdeletion/microduplication syndromes

2020 ◽  
Author(s):  
Yulia Mostovoy ◽  
Feyza Yilmaz ◽  
Stephen K. Chow ◽  
Catherine Chu ◽  
Chin Lin ◽  
...  
Keyword(s):  
Single Molecule ◽  
Structural Variation ◽  
Optical Mapping ◽  
Genome Mapping ◽  
Sequence Similarity ◽  
Chromosomal Rearrangements ◽  
Population Level ◽  
Segmental Duplications ◽  
Microdeletion Syndromes ◽  
Genomic Disorders

AbstractSegmental duplications (SDs) are a class of long, repetitive DNA elements whose paralogs share a high level of sequence similarity with each other. SDs mediate chromosomal rearrangements that lead to structural variation in the general population as well as genomic disorders associated with multiple congenital anomalies, including the 7q11.23 (Williams-Beuren Syndrome, WBS), 15q13.3, and 16p12.2 microdeletion syndromes. These three genomic regions, and the SDs within them, have been previously analyzed in a small number of individuals. However, population-level studies have been lacking because most techniques used for analyzing these complex regions are both labor- and cost-intensive. In this study, we present a high-throughput technique to genotype complex structural variation using a single molecule, long-range optical mapping approach. We identified novel structural variants (SVs) at 7q11.23, 15q13.3 and 16p12.2 using optical mapping data from 154 phenotypically normal individuals from 26 populations comprising 5 super-populations. We detected several novel SVs for each locus, some of which had significantly different prevalence between populations. Additionally, we refined the microdeletion breakpoints located within complex SDs in two patients with WBS, one patient with 15q13.3, and one patient with 16p12.2 microdeletion syndromes. The population-level data presented here highlights the extreme diversity of large and complex SVs within SD-containing regions. The approach we outline will greatly facilitate the investigation of the role of inter-SD structural variation as a driver of chromosomal rearrangements and genomic disorders.

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