A Next-Generation Sequencing Primer—How Does It Work and What Can It Do?

Alekseyev, Yuriy O.; Fazeli, Roghayeh; Shi, Yang; Basran, Raveen K.; Maher, Thomas A.; Miller, Nancy S.; Remick, Daniel G.

doi:10.1177/2374289518766521

Cited by 72 publications

(45 citation statements)

References 140 publications

(158 reference statements)

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“…Molecular genetics testing was performed using a Massively Parallel Sequencing assay developed for clinical genetics testing of PCD at the UNC hospitals Molecular Genetics Laboratory (Figure ). The test consists of screening the complete coding region and splice‐site junctions for the 35 genes associated with PCD as well as two genes ( CFTR and RAG1 ) that have overlapping phenotypes.…”

Section: Methodsmentioning

confidence: 99%

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The prevalence of the defining features of primary ciliary dyskinesia within a cri du chat syndrome cohort

Sanders

Leigh

Chao

et al. 2018

Pediatric Pulmonology

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Background Primary ciliary dyskinesia (PCD) and cri du chat syndrome (CdCS) are distinct disorders that can co‐occur due to a common genetic locus on chromosome 5p. Chronic respiratory symptoms associated with PCD can occur in CdCS and are typically attributed to hypotonia, dysphagia, and aspiration. The prevalence of PCD among individuals with CdCS is not known. Methods An online survey assessing common features of PCD was distributed to members of the 5P Minus Society, a cri du chat patient advocacy group. Respondents who met criteria for elevated risk of PCD (at least 3 symptoms or other features highly suggestive of PCD) were offered PCD genetic testing. Results For the 123 respondents (median age 10.1 years with IQR 5.5‐17.3 years; from 33 U.S. states and 10 other countries) chronic respiratory symptoms associated with PCD were prevalent, including unexplained neonatal respiratory distress, year‐round nasal congestion beginning in infancy, and year‐round, wet cough beginning in infancy in 35%, 32%, and 20% of respondents, respectively. Fifteen respondents (12%) met criteria for elevated risk for PCD and completed genetic analysis; however, none were diagnostic for PCD. A PCD clinical center evaluated an additional subject with CdCS who met criteria for likely PCD and had negative genetics, but had diagnostic electron microscopy of the respiratory cilia (missing outer dynein arms). Conclusion Clinicians should be aware of the genetic connection between CdCS and PCD. Non‐informative genetic testing does not rule out PCD. CdCS patients with chronic respiratory symptoms may benefit from referral to specialized PCD diagnostic centers.

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Section: Methodsmentioning

confidence: 99%

“…Parallel Sequencing 15,16 assay developed for clinical genetics testing of PCD at the UNC hospitals Molecular Genetics Laboratory 17 (Figure 1).…”

Section: Molecular Genetics Testing Was Performed Using a Massivelymentioning

confidence: 99%

The prevalence of the defining features of primary ciliary dyskinesia within a cri du chat syndrome cohort

Sanders

Leigh

Chao

et al. 2018

Pediatric Pulmonology

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“…Although the limited approach of Sanger sequencing is costly and inefficient for large-scale genomic sequencing, it remains the most widely accepted means to validate variants identified by NGS methodologies, particularly for clinically reportable findings. 86 Targeted gene panels typically focus on sequencing genes that are known to be causative of or associated with a given phenotype. While they can be convenient and are commonly used, the gene lists are often too restrictive, can rapidly become out of date, and can miss unanticipated findings.…”

Section: Comparison Of Sequencing Approachesmentioning

confidence: 99%

Next-Generation Sequencing and Emerging Technologies

Kumar

Cowley

Davis

2019

Semin Thromb Hemost

196

160

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Genetic sequencing technologies are evolving at a rapid pace with major implications for research and clinical practice. In this review, the authors provide an updated overview of next-generation sequencing (NGS) and emerging methodologies. NGS has tremendously improved sequencing output while being more time and cost-efficient in comparison to Sanger sequencing. The authors describe short-read sequencing approaches, such as sequencing by synthesis, ion semiconductor sequencing, and nanoball sequencing. Third-generation long-read sequencing now promises to overcome many of the limitations of short-read sequencing, such as the ability to reliably resolve repeat sequences and large genomic rearrangements. By combining complementary methods with massively parallel DNA sequencing, a greater insight into the biological context of disease mechanisms is now possible. Emerging methodologies, such as advances in nanopore technology, in situ nucleic acid sequencing, and microscopy-based sequencing, will continue the rapid evolution of this area. These new technologies hold many potential applications for hematological disorders, with the promise of precision and personalized medical care in the future.

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“…Sixth, data analysis. Data analysis includes the quality evaluation of the sequence, alignment to reference sequence to identify some possible variations such as single nucleotide polymorphism (SNP) or insertiondeletion (indel) identification, phylogenetic or metagenomic analysis, as well as the identification, interpretation, and classification of pathogenic variants [122,123].…”

Section: Next-generation Sequencingmentioning

confidence: 99%

Molecular Tools for Gene Analysis in Fission Yeast

Herrera-Camacho¹,

Millán-Pérez-Peña²,

Sosa-Jurado³

et al. 2020

Biochemical Analysis Tools - Methods for Bio-Molecules Studies

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Schizosaccharomyces pombe or fission yeast has been called micromammal due to the potential application of the knowledge derived from the yeast in the physiology of higher eukaryotes. Fission yeast has been consolidated as an excellent model for the study of highly conserved cellular processes. The possibility of using haploid or diploid strains facilitates the analysis of the dominant or recessive phenotype of an allele as well as its function, making it a model of first choice for the development of any investigation in eukaryotes cells. With a growing community that employs fission yeast as a model system for the study of numerous cellular processes, it has motivated the simultaneous development of molecular tools that facilitate the study of genes and proteins in the yeast. In this review, we present the most used molecular techniques in fission yeast for the analysis of genes, its characterization, as well as the determination of its function.

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A Next-Generation Sequencing Primer—How Does It Work and What Can It Do?

Cited by 72 publications

References 140 publications

The prevalence of the defining features of primary ciliary dyskinesia within a cri du chat syndrome cohort

The prevalence of the defining features of primary ciliary dyskinesia within a cri du chat syndrome cohort

Next-Generation Sequencing and Emerging Technologies

Molecular Tools for Gene Analysis in Fission Yeast

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