Identification and characterization of human xylosyltransferase II promoter single nucleotide variants

Although DNA-sequencing is the most effective procedure to achieve a molecular diagnosis in genetic diseases, complementary RNA analyses are often required. Reverse-Transcription polymerase chain reaction (RT-PCR) is still a valuable option when the clinical phenotype and/or available DNA-test results address the diagnosis toward a gene of interest or when the splicing effect of a single variant needs to be assessed. We use Single-Molecule Real-Time sequencing to detect and characterize splicing defects and single nucleotide variants in well-known disease genes (DMD, NF1, TTN). After proper optimization, the procedure could be used in the diagnostic setting, simplifying the workflow of cDNA analysis.

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Identification and characterization of coding single-nucleotide polymorphisms within human protocadherin-α and -β gene clusters

Gene ◽

10.1016/j.gene.2004.11.044 ◽

2005 ◽

Vol 349 ◽

pp. 1-14 ◽

Cited By ~ 15

Author(s):

Rie Miki ◽

Kotaro Hattori ◽

Yusuke Taguchi ◽

Motoki N. Tada ◽

Tomoko Isosaka ◽

...

Keyword(s):

Single Nucleotide Polymorphisms ◽

Gene Clusters ◽

Nucleotide Polymorphisms ◽

Single Nucleotide ◽

Identification And Characterization

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Characterization of BRCA1/2 mutations in patients with family history of breast cancer in Armenia

F1000Research ◽

10.12688/f1000research.10434.1 ◽

2017 ◽

Vol 6 ◽

pp. 29 ◽

Cited By ~ 2

Author(s):

Sofi Atshemyan ◽

Andranik Chavushyan ◽

Nerses Berberian ◽

Arthur Sahakyan ◽

Roksana Zakharyan ◽

...

Keyword(s):

Breast Cancer ◽

Family History ◽

Breast Cancers ◽

Single Nucleotide ◽

History Of ◽

Different Populations ◽

Amino Acid Mutations ◽

Armenian Population ◽

Identification And Characterization

Background. Breast cancer is one of the most common cancers in women worldwide. The germline mutations of the BRCA1 and BRCA2 genes are the most significant and well characterized genetic risk factors for hereditary breast cancer. Intensive research in the last decades has demonstrated that the incidence of mutations varies widely among different populations. In this study we attempted to perform a pilot study for identification and characterization of mutations in BRCA1 and BRCA2 genes among Armenian patients with family history of breast cancer and their healthy relatives. Methods. We performed targeted exome sequencing for BRCA1 and BRCA2 genes in 6 patients and their healthy relatives. After alignment of short reads to the reference genome, germline single nucleotide variation and indel discovery was performed using GATK software. Functional implications of identified variants were assessed using ENSEMBL Variant Effect Predictor tool. Results. In total, 39 single nucleotide variations and 4 indels were identified, from which 15 SNPs and 3 indels were novel. No known pathogenic mutations were identified, but 2 SNPs causing missense amino acid mutations had significantly increased frequencies in the study group compared to the 1000 Genome populations. Conclusions. Our results demonstrate the importance of screening of BRCA1 and BRCA2 gene variants in the Armenian population in order to identity specifics of mutation spectrum and frequencies and enable accurate risk assessment of hereditary breast cancers.

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Implementation of Next Generation Sequencing-Based Liquid Biopsy for Clinical Molecular Diagnostics in Non-Small Cell Lung Cancer (NSCLC) Patients

Diagnostics ◽

10.3390/diagnostics11081468 ◽

2021 ◽

Vol 11 (8) ◽

pp. 1468

Author(s):

Elisabetta Zulato ◽

Valeria Tosello ◽

Giorgia Nardo ◽

Laura Bonanno ◽

Paola Del Bianco ◽

...

Keyword(s):

Liquid Biopsy ◽

Single Nucleotide Variants ◽

Clinical Genetic ◽

Single Nucleotide ◽

Circulating Free Dna ◽

Somatic Alterations ◽

High Consistency ◽

Nsclc Patients ◽

Actionable Variants

Genetic screening of somatic mutations in circulating free DNA (cfDNA) opens up new opportunities for personalized medicine. In this study, we aim to illustrate the implementation of NGS-based liquid biopsy in clinical practice for the detection of somatic alterations in selected genes. Our work is particularly relevant for the diagnosis and treatment of NSCLC. Beginning in 2020, we implemented the use of Roche’s Avenio ctDNA expanded panel in our diagnostic routine. In this study, we retrospectively review NGS-based clinical genetic tests performed in our laboratory, focusing on key analytical parameters. Avenio ctDNA kits demonstrated 100% sensitivity in detecting single nucleotide variants (SNVs) at >0.5% variant allele frequency (VAF), and high consistency in reproducibility. Since 2020, we performed cfDNA genotyping test in 86 NSCLC patients, and we successfully sequenced 96.5% (83/86) of samples. We observed consistency in sequencing performance based upon sequencing depth and on-target rate. At least one gene variant was identified in 52 samples (63%), and one or more actionable variants were detected in 21 out of 83 (25%) of analysed patients. We demonstrated the feasibility of implementing an NGS-based liquid biopsy assay for routine genetic characterization of metastatic NSCLC patients.

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Genomic characterization of a novel SARS-CoV-2 lineage from Rio de Janeiro, Brazil

10.1101/2020.12.23.20248598 ◽

2020 ◽

Author(s):

Carolina M Voloch ◽

Ronaldo da Silva F ◽

Luiz G P de Almeida ◽

Cynthia C Cardoso ◽

Otavio J. Brustolini ◽

...

Keyword(s):

Rio De Janeiro ◽

Neutralizing Antibodies ◽

Health Management ◽

The State ◽

Single Nucleotide Variants ◽

Single Nucleotide ◽

Viral Genomes ◽

Genomic Characterization ◽

Second Wave

AbstractIn this study, we report the sequencing of 180 new viral genomes obtained from different municipalities of the state of Rio de Janeiro from April to December 2020. We identified a novel lineage of SARS-CoV-2, originated from B.1.1.28, distinguished by five single-nucleotide variants (SNVs): C100U, C28253U, G28628U, G28975U, and C29754U. The SNV G23012A (E484K), in the receptor-binding domain of Spike protein, was widely spread across the samples. This mutation was previously associated with escape from neutralizing antibodies against SARS-CoV-2. This novel lineage emerged in late July being first detected by us in late October and still mainly restricted to the capital of the state. However, as observed for other strains it can be rapidly spread in the state. The significant increase in the frequency of this lineage raises concerns about public health management and continuous need for genomic surveillance during the second wave of infections.Article Summary LineWe identified a novel circulating lineage of SARS-CoV-2 in the state of Rio de Janeiro Brazil originated from B.1.1.28 lineage.

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