Application of Next-generation Sequencing in Clinical Molecular Diagnostics

Seifi, Morteza; Ghasemi, Asghar; Raeisi, Sina; Heidarzadeh, Siamak

doi:10.1590/1678-4324-2017160414

Cited by 2 publications

(5 citation statements)

References 70 publications

(128 reference statements)

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“…Among the SGS technologies, Illumina has been reported to offer a big variety of benchtop and production scale NGS instruments and they are the most popular [ 2 ] among the clients. The instruments are more economical [ 1 ] and are among the platforms that have the highest throughput [ 67 , 68 ]. The Ion Torrent instruments are more automatic in the sense that in addition to automation in NGS data generation and analysis they provide automation in library preparation as well.…”

Section: Discussionmentioning

confidence: 99%

“…Although Roche 454 was one of the most popular instruments, now they have been discontinued [ 45 – 47 ]. Some studies have reported that Roche instruments are more error prone and costly and have low throughput as compared to other NGS instruments [ 67 , 71 ]. The GenapSys is lightweight, low-priced, and easy to use, even good for beginners in the genomic filed.…”

Section: Discussionmentioning

confidence: 99%

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A Comprehensive Review of Performance of Next-Generation Sequencing Platforms

Pervez

Hasnain

Abbas

et al. 2022

BioMed Research International

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Background. Next-generation sequencing methods have been developed and proposed to investigate any query in genomics or clinical activity involving DNA. Technical advancement in these sequencing methods has enhanced sequencing volume to several billion nucleotides within a very short time and low cost. During the last few years, the usage of the latest DNA sequencing platforms in a large number of research projects helped to improve the sequencing methods and technologies, thus enabling a wide variety of research/review publications and applications of sequencing technologies. Objective. The proposed study is aimed at highlighting the most fast and accurate NGS instruments developed by various companies by comparing output per hour, quality of the reads, maximum read length, reads per run, and their applications in various domains. This will help research institutions and biological/clinical laboratories to choose the sequencing instrument best suited to their environment. The end users will have a general overview about the history of the sequencing technologies, latest developments, and improvements made in the sequencing technologies till now. Results. The proposed study, based on previous studies and manufacturers’ descriptions, highlighted that in terms of output per hour, Nanopore PromethION outperformed all sequencers. BGI was on the second position, and Illumina was on the third position. Conclusion. The proposed study investigated various sequencing instruments and highlighted that, overall, Nanopore PromethION is the fastest sequencing approach. BGI and Nanopore can beat Illumina, which is currently the most popular sequencing company. With respect to quality, Ion Torrent NGS instruments are on the top of the list, Illumina is on the second position, and BGI DNB is on the third position. Secondly, memory- and time-saving algorithms and databases need to be developed to analyze data produced by the 3rd- and 4th-generation sequencing methods. This study will help people to adopt the best suited sequencing platform for their research work, clinical or diagnostic activities.

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Section: Discussionmentioning

confidence: 99%

Section: Discussionmentioning

confidence: 99%

A Comprehensive Review of Performance of Next-Generation Sequencing Platforms

Pervez

Hasnain

Abbas

et al. 2022

BioMed Research International

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“…Although there is a wide spectrum of DNA variations in a human genome such as insertions/ deletions (indels), substitutions, and arrangements (inversions and translocations), which some of them like substitutions and small indels cannot be detected by routine sequencing methods, researchers, with the advent of NGS technology, can capture a range of novel mutations and disease causing genes by investigation of the full genome or exome without bias [35]. For instance, by applying the WES, the causal variants of Miller syndrome, as the first rare Mendelian disorder, were identified [36]. Although WES encompasses the protein-coding regions of the genome, they may not be completely covered due to the presence of the high GC content and repetitive sequences, which are poorly sequenced [35,36].…”

Section: Detection Of Gene Variationsmentioning

confidence: 99%

“…For instance, by applying the WES, the causal variants of Miller syndrome, as the first rare Mendelian disorder, were identified [36]. Although WES encompasses the protein-coding regions of the genome, they may not be completely covered due to the presence of the high GC content and repetitive sequences, which are poorly sequenced [35,36].…”

Section: Detection Of Gene Variationsmentioning

confidence: 99%

“…Cancers are induced by a broad spectrum of genomic alterations including point mutations, deletions, insertions, copy number alterations, and structural variations, which can be somatic or inheritable. Therefore, genomics and transcriptomics (RNA) data of cancer cells and structures with new DNA sequencing technologies (NGS) coupled with powerful bioinformatic tools provide opportunities to understand pathogenesis, diagnosis, management, treatment of disease, and improvement of the personalized treatment strategies [36,37]. These technologies have the potential ability to identify the novel mutations and alterations in the cancer genome through whole-genome and whole-exome methods in order to distinguish the somatic and germ line variants by comparing these changes with those of normal samples [38].…”

Section: Oncologymentioning

confidence: 99%

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Strategies, Quality Control and Clinical Applications of Next Generation Sequencing

Khorshidi

Palangi

2018

Multidiscip Cancer Investig

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DNA sequencing is one of the great valuable techniques in molecular biology, which can be used to detect the sequence of nucleotides in a DNA fragment. The high-throughput sequencing known as Next Generation Sequencing (NGS) revolutionized genomic research and molecular biology; therefore, the whole human genome can be sequenced with a low cost in several days. NGS technology is similar to the traditional method, Sanger, which detects small DNA fragments by emitted signals at the time of synthesis of each fragment (from the DNA template), but the difference is that NGS can determine the massive simultaneous sequencing in a few days with high accuracy and the results are directly detected without the need for electrophoresis. In fact, NGS technology combines a variety of steps such as sample preparation, fragmentation of the sample of the studied genome, attachment of adapter to the ends of the fragments, imaging, and data analyses. In recent years, NGS technology continuously expanded the range of applications in different fields by reducing costs, increasing rates, and improving the quality of the data. The current review provided the potential applications of the NGS technology by emphasizing the diagnosis of the genetic diseases, identification of several types of cancers, prenatal screening, epigenetic modifications, personalized medicine, and identification of pathogens.

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Application of Next-generation Sequencing in Clinical Molecular Diagnostics

Abstract: Next-generation sequencing (NGS) is the catch all terms that used to explain

Cited by 2 publications

References 70 publications

A Comprehensive Review of Performance of Next-Generation Sequencing Platforms

A Comprehensive Review of Performance of Next-Generation Sequencing Platforms

Strategies, Quality Control and Clinical Applications of Next Generation Sequencing

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