DNA Sequencing Resolves Misdiagnosed and Rare Genetic Disorders

Performance Evaluation of SpliceAI for the Prediction of Splicing of NF1 Variants

Genes ◽

10.3390/genes12091308 ◽

2021 ◽

Vol 12 (9) ◽

pp. 1308

Author(s):

Changhee Ha ◽

Jong-Won Kim ◽

Ja-Hyun Jang

Keyword(s):

Dna Sequencing ◽

Sensitivity And Specificity ◽

In Silico ◽

Genetic Disorders ◽

Area Under The Curve ◽

Neurofibromatosis Type ◽

Prediction Algorithm ◽

In Silico Prediction ◽

Web Based

Neurofibromatosis type 1, characterized by neurofibromas and café-au-lait macules, is one of the most common genetic disorders caused by pathogenic NF1 variants. Because of the high proportion of splicing mutations in NF1, identifying variants that alter splicing may be an essential issue for laboratories. Here, we investigated the sensitivity and specificity of SpliceAI, a recently introduced in silico splicing prediction algorithm in conjunction with other in silico tools. We evaluated 285 NF1 variants identified from 653 patients. The effect on variants on splicing alteration was confirmed by complementary DNA sequencing followed by genomic DNA sequencing. For in silico prediction of splicing effects, we used SpliceAI, MaxEntScan (MES), and Splice Site Finder-like (SSF). The sensitivity and specificity of SpliceAI were 94.5% and 94.3%, respectively, with a cut-off value of Δ Score > 0.22. The area under the curve of SpliceAI was 0.975 (p < 0.0001). Combined analysis of MES/SSF showed a sensitivity of 83.6% and specificity of 82.5%. The concordance rate between SpliceAI and MES/SSF was 84.2%. SpliceAI showed better performance for the prediction of splicing alteration for NF1 variants compared with MES/SSF. As a convenient web-based tool, SpliceAI may be helpful in clinical laboratories conducting DNA-based NF1 sequencing.

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Clinical Utility of Rapid Exome Sequencing Combined With Mitochondrial DNA Sequencing in Critically Ill Pediatric Patients With Suspected Genetic Disorders

Frontiers in Genetics ◽

10.3389/fgene.2021.725259 ◽

2021 ◽

Vol 12 ◽

Author(s):

Xuejun Ouyang ◽

Yu Zhang ◽

Lijuan Zhang ◽

Jixuan Luo ◽

Ting Zhang ◽

...

Keyword(s):

Mitochondrial Dna ◽

Differential Diagnosis ◽

Dna Sequencing ◽

Exome Sequencing ◽

Critically Ill ◽

Clinical Utility ◽

Pediatric Patients ◽

Genetic Disorders ◽

Mitochondrial Diseases ◽

Mtdna Mutation

Genetic disorders are a frequent cause of hospitalization, morbidity and mortality in pediatric patients, especially in the neonatal or pediatric intensive care unit (NICU/PICU). In recent years, rapid genome-wide sequencing (exome or whole genome sequencing) has been applied in the NICU/PICU. However, mtDNA sequencing is not routinely available in rapid genetic diagnosis programs, which may fail to diagnose mtDNA mutation-associated diseases. Herein, we explored the clinical utility of rapid exome sequencing combined with mtDNA sequencing in critically ill pediatric patients with suspected genetic disorders. Rapid clinical exome sequencing (CES) was performed as a first-tier test in 40 critically ill pediatric patients (aged from 6 days to 15 years) with suspected genetic conditions. Blood samples were also collected from the parents for trio analysis. Twenty-six patients presented with neuromuscular abnormalities or other systemic abnormalities, suggestive of suspected mitochondrial diseases or the necessity for a differential diagnosis of other diseases, underwent rapid mtDNA sequencing concurrently. A diagnosis was made in 18 patients (45.0%, 18/40); three cases with de novo autosomal dominant variants, ten cases with homozygous or compound heterozygous variants, three cases with hemizygous variants inherited from mother, three cases with heterozygous variants inherited from either parent, and one case with a mtDNA mutation. The 18 patients were diagnosed with metabolic (n = 7), immunodeficiency (n = 4), cardiovascular (n = 2), neuromuscular (n = 2) disorders, and others. Genetic testing reports were generated with a median time of 5 days (range, 3–9 days). Thirteen patients that were diagnosed had an available medical treatment and resulted in a positive outcome. We propose that rapid exome sequencing combined with mitochondrial DNA sequencing should be available to patients with suspected mitochondrial diseases or undefined clinical features necessary for making a differential diagnosis of other diseases.

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Imaging polymers, proteins and dna in aqueous solutions with the atomic force microscope

Proceedings, annual meeting, Electron Microscopy Society of America ◽

10.1017/s0424820100152136 ◽

1989 ◽

Vol 47 ◽

pp. 32-33

Author(s):

S.A.C. Gould ◽

B. Drake ◽

C.B. Prater ◽

A.L. Weisenhorn ◽

S.M. Lindsay ◽

...

Keyword(s):

Amino Acids ◽

Dna Sequencing ◽

Aqueous Solutions ◽

Atomic Force Microscope ◽

Piezoelectric Crystal ◽

Atomic Force ◽

Structure Of Molecules ◽

Optical Lever

The atomic force microscope (AFM) is an instrument that can be used to image many samples of interest in biology and medicine. Images of polymerized amino acids, polyalanine and polyphenylalanine demonstrate the potential of the AFM for revealing the structure of molecules. Images of the protein fibrinogen which agree with TEM images demonstrate that the AFM can provide topographical data on larger molecules. Finally, images of DNA suggest the AFM may soon provide an easier and faster technique for DNA sequencing.The AFM consists of a microfabricated SiO2 triangular shaped cantilever with a diamond tip affixed at the elbow to act as a probe. The sample is mounted on a electronically driven piezoelectric crystal. It is then placed in contact with the tip and scanned. The topography of the surface causes minute deflections in the 100 μm long cantilever which are detected using an optical lever.

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