Variant analysis of SARS-CoV-2 strains with phylogenetic analysis and the Coronavirus Antiviral and Resistance Database

Aims: This study determined SARS-CoV-2 variations by phylogenetic and virtual phenotyping analyses. Materials & methods: Strains isolated from 143 COVID-19 cases in Turkey in April 2021 were assessed. Illumina NexteraXT library preparation kits were processed for next-generation ]sequencing. Phylogenetic (neighbor-joining method) and virtual phenotyping analyses (Coronavirus Antiviral and Resistance Database [CoV-RDB] by Stanford University) were used for variant analysis. Results: B.1.1.7–1/2 (n = 103, 72%), B.1.351 (n = 5, 3%) and B.1.525 (n = 1, 1%) were identified among 109 SARS-CoV-2 variations by phylogenetic analysis and B.1.1.7 (n = 95, 66%), B.1.351 (n = 5, 4%), B.1.617 (n = 4, 3%), B.1.525 (n = 2, 1.4%), B.1.526-1 (n = 1, 0.6%) and missense mutations (n = 15, 10%) were reported by CoV-RDB. The two methods were 85% compatible and B.1.1.7 (alpha) was the most frequent SARS-CoV-2 variation in Turkey in April 2021. Conclusion: The Stanford CoV-RDB analysis method appears useful for SARS-CoV-2 lineage surveillance.

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Whole Chloroplast Genomes reveals the uniqueness of Bolivian native cacao (Theobroma cacao) from the northern part of Bolivia

10.1101/2021.04.16.440153 ◽

2021 ◽

Author(s):

Marcia Gumiel ◽

Oscar M Rollano-Penaloza ◽

Carmelo Peralta-Rivero ◽

Leslie Tejeda ◽

Valeria D. Palma Encinas ◽

...

Keyword(s):

Phylogenetic Analysis ◽

Next Generation Sequencing ◽

Theobroma Cacao ◽

Phylogenetic Trees ◽

Plastid Genome ◽

Next Generation ◽

Center Of Origin ◽

Chloroplast Genomes ◽

Geographical Locations ◽

Generation Sequencing

We report the complete chloroplast sequences of two varieties of Theobroma cacao collected in the Bolivian Amazonia using Next-Generation Sequencing. Comparisons made between these two chloroplast genomes and the Belizean reference plastid genome identified 19 and 22 nucleotide variants. The phylogenetic analysis reported three main T. cacao clades belonging to the Forastero, Criollo and Trinitario groups. The Bolivian Native Cacao varieties were located inside the Trinitario group forming their unique branch. The Bolivian Native Cacao branch reveals a possible new subpopulation different from the well-characterized T. cacao subpopulations. The phylogenetic trees showed that the relationships among the T. cacao varieties were consistent with their geographical locations placing the Cacao Center of Origin in Western Amazon. The data presented here will contribute to the usage of ultrabarcoding to distinguish different T. cacao varieties and to identify native cacaos from introduced cacaos. Thus helping in the conservation of local native varieties of T. cacao.

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Clinical results and importance of next-generation sequencing (NGS) in detecting targeted mutations in the treatment of metastatic Lung Cancer: Single center initial results

Medical Science and Discovery ◽

10.36472/msd.v6i12.330 ◽

2019 ◽

Vol 6 (12) ◽

pp. 327-332

Author(s):

Cem Mirili ◽

Çiğdem Kahraman ◽

Ali Yılmaz ◽

Mehmet Bilici ◽

Salim Başol Tekin ◽

...

Keyword(s):

Lung Cancer ◽

Next Generation Sequencing ◽

Genetic Variants ◽

Genetic Variant ◽

Clinical Results ◽

Clinical Effects ◽

Next Generation ◽

Variant Analysis ◽

Next Generation Sequencing Ngs ◽

Generation Sequencing

Objective: In Lung cancer (LC), which is one of the most deadly cancers, longer survival has been achieved with targeted agents. For this reason, it is important to find the patients who are suitable for targeted therapies. Next-generation sequencing (NGS) is a method that allows multiple genetic variants to be detected simultaneously by performing massive parallel DNA sequencing at the same time. We wanted to reveal the clinical effects and benefits of genetic variant analysis with NGS for our patients. Material and Methods: Patients with stage 4 non-squamous and not otherwise specified (NOS) Non-small cell LC who underwent genetic variant analysis with NGS were included in the study, retrospectively. Results: Total of the 51 patients, 41 (80.4%) were male and the median age was 64 (35-85) years. According to TNM, 21 (41.2%) patients were stage 4A, 30 (58.8%) patients were stage 4B and 39 (76.5%) patients had adenocarcinoma and 12 (23.5%) had NOS histology. NGS analyzes were performed in median 14 days (8-43) and determined 24 pathogenic variants in 17 (%25) patients: 9EGFR (%17,6), 6PIKC3A (%11,7), 5KRAS (%9,8), 2PTEN (%3,9), 1BRAF (%1,9), 1MET (%1,6) (7 of them concomitantly). Cytotoxic chemotherapy was recommended in 41, anti-EGFR agents in 8 (afatinib in 4, erlotinib in 4 patients) patients and anti-BRAF+MEK inhibitor agent (dabrafenib+trametinib) in 1 patient. Conclusion: With the NGS, in just two weeks, both target and resistance genetic variants of our patients were detected at the same time and individualized treatments were applied. In this way, both time and cost were saved.

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Robust Sub-nanomolar Library Preparation for High Throughput Next Generation Sequencing

BMC Genomics ◽

10.1186/s12864-018-4677-y ◽

2018 ◽

Vol 19 (1) ◽

Cited By ~ 7

Author(s):

Wells W. Wu ◽

Je-Nie Phue ◽

Chun-Ting Lee ◽

Changyi Lin ◽

Lai Xu ◽

...

Keyword(s):

Next Generation Sequencing ◽

High Throughput ◽

Library Preparation ◽

Next Generation ◽

Generation Sequencing

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Sample Preparation, Standards, and Library Preparation for Next Generation Sequencing

Next Generation Sequencing in Forensic Science ◽

10.4324/9781003196464-3 ◽

2021 ◽

pp. 31-45

Author(s):

Kelly M. Elkins ◽

Cynthia B. Zeller

Keyword(s):

Next Generation Sequencing ◽

Sample Preparation ◽

Library Preparation ◽

Next Generation ◽

Generation Sequencing

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A Benchmark of Structural Variant Analysis Tools for Next Generation Sequencing Data

International Journal of Systems Biology and Biomedical Technologies ◽

10.4018/ijsbbt.2013100106 ◽

2013 ◽

Vol 2 (4) ◽

pp. 86-98

Author(s):

Chatzinikolaou Panagiotis ◽

Makris Christos ◽

Dimitrios Vlachakis ◽

Sophia Kossida

Keyword(s):

Next Generation Sequencing ◽

Level Structure ◽

Atomic Level ◽

Protein Sequencing ◽

Next Generation Sequencing Data ◽

Next Generation ◽

Sequencing Data ◽

Variant Analysis ◽

Generation Sequencing

In language of genetics and biochemistry, sequencing is the determination of an unbranched biopolymer's primary structure. A sequence is a symbolic linear depiction, result of sequencing. This sequence is a succinct summary of the most of the sequenced molecule's atomic-level structure. (Most known is DNA-sequencing, RNA-sequencing, Protein-sequencing and Next-Generation-sequencing)

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