Bioinformatics: Identification of Markers from Next-Generation Sequence Data

Due to the development of high-throughput DNA sequencing technology, genome-sequencing costs have been significantly reduced, which has led to a number of revolutionary advances in the genetics industry. However, the problem is that compared to the decrease in time and cost needed for DNA sequencing, the management of such large volumes of data is still an issue. Therefore, this research proposes Blockchain Applied FASTQ and FASTA Lossless Compression (BAQALC), a lossless compression algorithm that allows for the efficient transmission and storage of the immense amounts of DNA sequence data that are being generated by Next Generation Sequencing (NGS). Also, security and reliability issues exist in public sequence databases. For methods, compression ratio comparisons were determined for genetic biomarkers corresponding to the five diseases with the highest mortality rates according to the World Health Organization. The results showed an average compression ratio of approximately 12 for all the genetic datasets used. BAQALC performed especially well for lung cancer genetic markers, with a compression ratio of 17.02. BAQALC performed not only comparatively higher than widely used compression algorithms, but also higher than algorithms described in previously published research. The proposed solution is envisioned to contribute to providing an efficient and secure transmission and storage platform for next-generation medical informatics based on smart devices for both researchers and healthcare users.

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Transcriptome Profile of Next Generation Sequence Data Related to Inflammation on Nasopharyngeal Carcinoma Cases in Indonesia

Asian Pacific Journal of Cancer Prevention ◽

10.31557/apjcp.2020.21.9.2763 ◽

2020 ◽

Vol 21 (9) ◽

pp. 2763-2769

Author(s):

Digdo Sudigyo ◽

Gisti Rahmawati ◽

Dicka Setiasari ◽

Risky Poluan ◽

Salsabila Sesotyosari ◽

...

Keyword(s):

Nasopharyngeal Carcinoma ◽

Sequence Data ◽

Next Generation ◽

Transcriptome Profile

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Development of single nucleotide polymorphism markers in the large and complex rubber tree genome using next-generation sequence data

Molecular Breeding ◽

10.1007/s11032-016-0534-3 ◽

2016 ◽

Vol 36 (8) ◽

Cited By ~ 11

Author(s):

Livia Moura de Souza ◽

Guilherme Toledo-Silva ◽

Claudio Benicio Cardoso-Silva ◽

Carla Cristina da Silva ◽

Isabela Aparecida de Araujo Andreotti ◽

...

Keyword(s):

Single Nucleotide Polymorphism ◽

Sequence Data ◽

Rubber Tree ◽

Next Generation ◽

Nucleotide Polymorphism ◽

Single Nucleotide

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Reply to "Internet-Based Solutions for Analysis of Next-Generation Sequence Data"

Journal of Clinical Microbiology ◽

10.1128/jcm.01393-13 ◽

2013 ◽

Vol 51 (9) ◽

pp. 3163-3163

Author(s):

N. L. Sherry ◽

T. P. Stinear ◽

B. P. Howden

Keyword(s):

Sequence Data ◽

Next Generation

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Validation of variants using cost effective highresolution melting (HRM) analysis predicted from target re-sequencing in Eucalyptus

Acta Botanica Croatica ◽

10.37427/botcro-2020-019 ◽

2020 ◽

Vol 79 (2) ◽

pp. 105-113

Author(s):

Abdul Bari Muneera Parveen ◽

Divya Lakshmanan ◽

Modhumita Ghosh Dasgupta

Keyword(s):

Next Generation Sequencing ◽

Large Scale ◽

Sequence Data ◽

Cost Effective ◽

Nucleotide Polymorphisms ◽

Next Generation ◽

Time Saving ◽

Hrm Analysis ◽

The Cost ◽

Generation Sequencing

The advent of next-generation sequencing has facilitated large-scale discovery and mapping of genomic variants for high-throughput genotyping. Several research groups working in tree species are presently employing next generation sequencing (NGS) platforms for marker discovery, since it is a cost effective and time saving strategy. However, most trees lack a chromosome level genome map and validation of variants for downstream application becomes obligatory. The cost associated with identifying potential variants from the enormous amount of sequence data is a major limitation. In the present study, high resolution melting (HRM) analysis was optimized for rapid validation of single nucleotide polymorphisms (SNPs), insertions or deletions (InDels) and simple sequence repeats (SSRs) predicted from exome sequencing of parents and hybrids of Eucalyptus tereticornis Sm. ? Eucalyptus grandis Hill ex Maiden generated from controlled hybridization. The cost per data point was less than 0.5 USD, providing great flexibility in terms of cost and sensitivity, when compared to other validation methods. The sensitivity of this technology in variant detection can be extended to other applications including Bar-HRM for species authentication and TILLING for detection of mutants.

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Metagenomic analysis using next-generation sequencing of pathogens in bronchoalveolar lavage fluid from pediatric patients with respiratory failure

Scientific Reports ◽

10.1038/s41598-019-49372-x ◽

2019 ◽

Vol 9 (1) ◽

Cited By ~ 7

Author(s):

Suguru Takeuchi ◽

Jun-ichi Kawada ◽

Kazuhiro Horiba ◽

Yusuke Okuno ◽

Toshihiko Okumura ◽

...

Keyword(s):

Respiratory Failure ◽

Next Generation Sequencing ◽

Bronchoalveolar Lavage ◽

Bronchoalveolar Lavage Fluid ◽

Pediatric Patients ◽

Respiratory Infections ◽

Sequence Data ◽

Lavage Fluid ◽

Next Generation ◽

Generation Sequencing

Abstract Next-generation sequencing (NGS) has been applied in the field of infectious diseases. Bronchoalveolar lavage fluid (BALF) is considered a sterile type of specimen that is suitable for detecting pathogens of respiratory infections. The aim of this study was to comprehensively identify causative pathogens using NGS in BALF samples from immunocompetent pediatric patients with respiratory failure. Ten patients hospitalized with respiratory failure were included. BALF samples obtained in the acute phase were used to prepare DNA- and RNA-sequencing libraries. The libraries were sequenced on MiSeq, and the sequence data were analyzed using metagenome analysis tools. A mean of 2,041,216 total reads were sequenced for each library. Significant bacterial or viral sequencing reads were detected in eight of the 10 patients. Furthermore, candidate pathogens were detected in three patients in whom etiologic agents were not identified by conventional methods. The complete genome of enterovirus D68 was identified in two patients, and phylogenetic analysis suggested that both strains belong to subclade B3, which is an epidemic strain that has spread worldwide in recent years. Our results suggest that NGS can be applied for comprehensive molecular diagnostics as well as surveillance of pathogens in BALF from patients with respiratory infection.

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