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The impact of next-generation sequencing on genomics
Open accessAbstract
This article reviews basic concepts, general applications, and the potential impact of next-generation sequencing (NGS) technologies on genomics, with particular reference to currently available and possible future platforms and bioinformatics. NGS technologies have demonstrated the capacity to sequence DNA at unprecedented speed, thereby enabling previously unimaginable scientific achievements and novel biological applications. But, the massive data produced by NGS also presents a significant challenge for data storage, analyses, and management solutions. Advanced bioinformatic tools are essential for the successful application of NGS technology. As evidenced throughout this review, NGS technologies will have a striking impact on genomic research and the entire biological field. With its ability to tackle the unsolved challenges unconquered by previous genomic technologies, NGS is likely to unravel the complexity of the human genome in terms of genetic variations, some of which may be confined to susceptible loci for some common human conditions. The impact of NGS technologies on genomics will be far reaching and likely change the field for years to come.
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“Following completion of the HGP, a new approach, genome-wide association study (GWAS), was widely applied to genomics.”
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“The core philosophy of massive parallel sequencing used in next-generation sequencing (NGS) is adapted from shotgun sequencing (Venter et al., 2003; Margulies et al., 2005; Shendure et al., 2005).”
Sequencing technologies – the next generation
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“Since then, several additional diploid human genomes have been sequenced with NGS utilizing a variety of related techniques to rapidly sequence genomes with varying degrees of coverage (Ley et al., 2008; Wang et al., 2008; Ahn et al., 2009; Kim et al., 2009; Yngvadottir et al., 2009; Metzker, 2010).”
BackgroundInfluentialNext-generation DNA sequencing
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“NGS technologies have increased the speed and throughput capacities of DNA sequencing and, as a result, dramatically reduced overall sequencing costs (Mardis, 2006, 2009; Schuster, 2008; Shendure and Ji, 2008; Ng et al., 2009a; Tucker et al., 2009; Metzker, 2010).”
BackgroundSOAP: Short oligonucleotide alignment program
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“Benchmarks comparing ELAND with other popular NGS software, such as MAQ, BLAST (Basic Local Alignment Search Tool), SOAP (Short Oligonucleotide Alignment Program) (Li et al., 2008b), and SeqMap (Jiang and Wong, 2008), etc. (Table 3), generally place ELAND as one of the fastest available programs.”
MethodDe novo assembly of human genomes with massively parallel short read sequencing
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“Individual human genomes (one Asian and one African) have been successfully sequenced and assembled using the Illumina Genome Analyzer (read lengths ranged from 35 to 75 basepairs) with a modified SOAP program, SOAPdenovo (Li et al., 2010).”
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“Benchmarks comparing ELAND with other popular NGS software, such as MAQ, BLAST (Basic Local Alignment Search Tool), SOAP (Short Oligonucleotide Alignment Program) (Li et al., 2008b), and SeqMap (Jiang and Wong, 2008), etc. (Table 3), generally place ELAND as one of the fastest available programs.”
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“Nano-technologies have long been considered a cutting-edge technology for single-molecule DNA sequencing (Iqbal et al., 2007; Branton et al., 2008) and several nanopore sequencing concepts and technologies are currently under development.”
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“Other third-generation platforms under development make use of nanophotonic visualization chamber, ion semiconductor, electron microscopy, a variety of nanotechnologies like nanopores (Oxford Nanopore Technologies), nanochannels (BioNanomatrix/nanoAnalyzer), nanoparticles (GE Global Research), nanoballs (Complete Geno…”
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“These platforms use specific methods for quality assessment, alignment, assembly, and further processing (87), which are specific for noncoding RNA (88).”
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“…to handle sequence alignment, sequence assembly, detection of variation, sequence annotation and data analysis has been an essential tool for the effective and accurate application of NGS technologies to answering genetic and biological questions (see review by Zhang et al. 2011 for details).”
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“…be easy to obtain transcriptome datasets with far higher throughput by using de Bruijn graphs and pair-end sequencing, which means that low abundance mRNAs can be detected at a cost of only 1% of traditional expressed sequence tag (EST) library technology (Huang & Marth, 2008; Zhang et al., 2011).”
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“On the other hand, Sanger sequencing cannot sequence DNA fragments larger than 2 kb.(47) Therefore, complete sequencing of the RHD gene using NGS was the preferred method, which provided a complete sequence of the gene in most samples, with high coverage that allowed accurate variant calling.”
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“As a consequence, it has brought about a revolution in genomics and molecular biology, where it is able to sequence complete genomes, exomes, and specified regions of DNA with remarkable efficiency [10–12].”
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“read, deep, or massively parallel sequencing techniques that have recently been developed revolutionized sequencing capabilities and launched the “next generation” in genomics (21).”
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“More recently, next-generation sequencing (NGS) platforms have been used to generate enormous amounts of genome and transcriptome sequences [6-10].”
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“Next generation sequencing not only prompts the efficiency of genomic research [23] but also facilitates the construction of genomic libraries for populations [24].”
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“…fragments of DNA created using random fragmentation (enzymatically or sonification) and ligated with custom linkers, amplification-done by PCR (emulsion PCR or bridge PCR), sequencing-DNA sequenced using “sequencing by synthesis” or “sequencing by ligation” (Zhang et al., 2011; Ari and Arikan, 2016).”
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“The falling costs of traditional DNA sequencing and the development of next-generation sequencing technologies is leading to an accelerated number of complete genome sequences [1].”
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“) can significantly affect where the primer(s) can bind, and subsequently what regions of the genome are amplified [243-246].”
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“However, there is a tremendous expense associated with NGS as well as considerable difficulty in interpreting the output, which restrict its application (Zhang et al., 2011).”
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“To date, RNA-seq technology has been an effective tool to generate genome-wide transcriptome profiles and obtain substantial SSRs, especially for species whose genome has not been sequenced (Garg & Jain, 2013; Zhang et al., 2011; Xiao et al., 2013).”
MethodRHCE genotyping using next generation sequencing: Allele specific reference sequences
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Current Status and Challenges of DNA Sequencing
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Potential of Bioinformatics as functional genomics tool: an overview
Katara, P. (2014) · Network Modeling Analysis in Health Informatics and Bioinformatics · doi:10.1007/s13721-014-0052-3 · Cited by 9
“To store, handling and analysis of these genome datasets, advanced computing and data mining methods are required which are provided by the bioinformatics (Yang et al. 2009; Zhang et al. 2011).”
BackgroundMethodComparative Characterization of Mitogenomes From Five Orders of Cestodes (Eucestoda: Tapeworms)
Trevisan, B., Machado, D. J., Lahr, D. J. G., & Marques, F. P. L. (2021) · Frontiers in Genetics · doi:10.3389/fgene.2021.788871 · Cited by 9
Guide: a desktop application for analysing gene expression data
Choi, J. (2013) · BMC Genomics · doi:10.1186/1471-2164-14-688 · Cited by 9
“Background Next-generation sequencing technologies are having a massive impact on genomics [1], and challenging the research community with a wide range of data related issues.”
BackgroundGaspar, D., Usié, A., Leão, C., Guimarães, S. M. F., Pires, A. E., Matos, C., Ramos, A. M., & Ginja, C. (2023) · Frontiers in Genetics · doi:10.3389/fgene.2023.1109490 · Cited by 8
“, 2014) provides unprecedented opportunities for understanding the genomic basis for livestock phenotypic variability, including complex production traits (Zhang et al., 2011; Ghosh et al., 2018).”
BackgroundPast and future impact of next‐generation sequencing in head and neck cancer
Sethi, N., MacLennan, K., Wood, H. M., & Rabbitts, P. H. (2015) · Head & Neck · doi:10.1002/hed.24085 · Cited by 8
“This reaction produces a light signal proportional to the nucleotides detected by a camera and converted to sequencing “reads” by a computer.(11) The use of this to sequence an individual’s complete genome was published in 2008.”
BackgroundMethodEvolving Gene Targets and Technology in Influenza Detection
Malanoski, A. P., & Lin, B. (2013) · Molecular Diagnosis & Therapy · doi:10.1007/s40291-013-0040-9 · Cited by 8
“The principles of NGS and various platforms are explained in detail in various reviews [179–182].”
BackgroundModeling the next generation sequencing read count data for DNA copy number variant study
Ji, T., & Chen, J. (2015) · Statistical Applications in Genetics and Molecular Biology · doi:10.1515/sagmb-2014-0054 · Cited by 8
A comprehensive view of the web-resources related to sericulture
Singh, D., Chetia, H., Kabiraj, D., Sharma, S., Kumar, A., Sharma, P., Deka, M., & Bora, U. (2016) · Database · doi:10.1093/database/baw086 · Cited by 8
A Study on Optimizing MarkDuplicate in Genome Sequencing Pipeline
Zhao, Q. (2018) · International Conference on Bioinformatics Research and Applications (ICBRA) · doi:10.1145/3309129.3309134 · Cited by 8
“Except for ADAM, there are many other platform dealing with next generation sequencing (NGS) [20][21] data.”
BackgroundPersonalized medicine and the clinical laboratory
Pinho, J. R. R., Sitnik, R., & Mangueira, C. L. P. (2014) · Einstein (São Paulo) · doi:10.1590/s1679-45082014rw2859 · Cited by 8
“(1) New generation sequencing methodologies have now been incorporated into clinical laboratories, as they allow the simultaneous analysis of large regions of the genome and even the whole genome sequence, enabling the concurrent identification of different mutations in several genes.(2,3) Personalized medicine assays…”
BackgroundMethodLott, M. J., Hose, G. C., & Power, M. L. (2014) · Experimental Parasitology · doi:10.1016/j.exppara.2014.06.011 · Cited by 8
Toward Applications of Genomics and Metabolic Modeling to Improve Algal Biomass Productivity
Salehi‐Ashtiani, K., Koussa, J., Dohai, B., Chaiboonchoe, A., Cai, H., Dougherty, K., Nelson, D. R., Jijakli, K., & Khraiwesh, B. (2015) · Biofuel and biorefinery technologies · doi:10.1007/978-3-319-16640-7_10 · Cited by 8
“The main limitation of NGS has been that the relatively short read length (50–500 bp) introduces inaccuracy in the assembly of sequences (Zhang et al. 2011).”
BackgroundReiman, A., Pandey, S., Lloyd, K. L., Dyer, N. P., Khan, M., Crockard, M. A., Latten, M. J., Watson, T. L., Cree, I. A., & Grammatopoulos, D. K. (2016) · Annals of Clinical Biochemistry International Journal of Laboratory Medicine · doi:10.1177/0004563216629170 · Cited by 8
“NGS platforms have boosted the throughput and enhanced the sequencing speed and accuracy resulting in reduction in sequencing cost.(10) Moreover, bench-top nextgeneration DNA sequencers such as Ion Torrent PGM (Life Technologies, NY, US) and MiSeq (Illumina, California, US) have become an attractive option for clinica…”
BackgroundKim, A., Nguyen, T. L., & Kim, D. (2017) · doi:10.1002/9781119152125.ch5 · Cited by 8
Lu, C.-Y., Liu, Z., Arif, M., Alam, T., & Qiu, W. (2024) · Frontiers in Genetics · doi:10.3389/fgene.2024.1513938 · Cited by 7
The ARES Project: Network Architecture for Delivering and Processing Genomics Data
Femminella, M., Reali, G., Valocchi, D., & Nunzi, E. (2014) · IEEE Symposium on Network Cloud Computing and Applications (NCCA) · doi:10.1109/ncca.2014.12 · Cited by 7
“The rationale of using genome files as case study is based on the increasing scientific and societal need to utilize human genome data and the parallel development in sequencing technology that has made human genome sequencing on large scale affordable [21].”
BackgroundGenotyping of human neutrophil antigens (HNA) from whole genome sequencing data
Chu, H., Lin, H., Tsao, T. T.-H., Chang, C.-F., Hsiao, W., Yeh, T.-J., Chang, C., Liu, Y.-W., Wang, T., Yang, K.-C., et al. (2013) · BMC Medical Genomics · doi:10.1186/1755-8794-6-31 · Cited by 7
“for more detailed and precise investigation of total variants of genes [15].”
BackgroundCardiomyocyte microvesicles: proinflammatory mediators after myocardial ischemia?
Siegel, P. M., Schmich, J., Barinov, G., Bojti, I., Vedecnik, C., Simanjuntak, N. R., Bode, C., Moser, M., Peter, K., & Diehl, P. (2020) · Journal of Thrombosis and Thrombolysis · doi:10.1007/s11239-020-02156-x · Cited by 7
Landscape Genomics in Livestock
Pariset, L., Joost, S., Gargani, M., & Valentini, A. (2012) · InTech eBooks · doi:10.5772/32927 · Cited by 6
Chunwongse, C., Phumichai, C., Tongyoo, P., Juejun, N., & Chunwongse, J. (2015) · DOAJ (DOAJ: Directory of Open Access Journals) · Cited by 7
Advances in genetics and genomics: use and limitations in achieving malaria elimination goals
Gunawardena, S., & Karunaweera, N. D. (2015) · Pathogens and Global Health · doi:10.1179/2047773215y.0000000015 · Cited by 8
Zhao, W., Chen, J. J., Foley, S. L., Wang, Y., Zhao, S., Basinger, J., & Zou, W. (2015) · Biomarkers in Medicine · doi:10.2217/bmm.15.88 · Cited by 8
QTLs identified for Biofortification Traits in Wheat: A ReviewPreprint
Devi, P., Kaushik, P., & Saini, D. K. (2019) · Preprints.org · doi:10.20944/preprints201908.0120.v1 · Cited by 6
Bashar, S., Kothakota, N. J., & Jena, B. R. (2024) · Current Forensic Science · doi:10.2174/0126664844274727231218061037 · Cited by 6
The role of artificial intelligence and machine learning in NGS
Ouanes, K. (2024) · Elsevier eBooks · doi:10.1016/b978-0-323-99144-5.00002-0 · Cited by 6
Clue to a New Deafness Gene: A Large Chinese Nonsyndromic Hearing Loss Family Linked to DFNA4
Zong, L., Lu, C., Zhao, Y., Li, Q., Han, D., Wei–yan, Y., Shen, Y., Zheng, Q., & Wang, Q. (2012) · Journal of genetics and genomics/Journal of Genetics and Genomics · doi:10.1016/j.jgg.2012.11.002 · Cited by 6
“With the development of next generation sequencing technology in recent years (Zhang et al., 2011), target next-generation sequencing of the critical region would be an appropriate choice for us to identify the causal gene of family Z002.”
BackgroundOsmylated DNA, a novel concept for sequencing DNA using nanopores
Kanavarioti, A. (2015) · Nanotechnology · doi:10.1088/0957-4484/26/13/134003 · Cited by 6
Bioinformatics as Applied to Medicine
Papadopoulou, P., Lytras, M. D., & Marouli, C. (2017) · Advances in bioinformatics and biomedical engineering book series · doi:10.4018/978-1-5225-2607-0.ch001 · Cited by 6
PAN2HGENE–tool for comparative analysis and identifying new gene products
de Oliveira, M. S., Alves, J. T. C., de Sá, P. H. C. G., & Veras, A. A. D. O. (2021) · PLoS ONE · doi:10.1371/journal.pone.0252414 · Cited by 6
“However, the emergence of these tools led to an additional challenge of handling large volumes of data, affirming the need to develop efficient ways for storage and management of data [1].”
BackgroundLiu, Y., Wang, J., Wu, S., & Yang, J. (2022) · PLoS ONE · doi:10.1371/journal.pone.0266162 · Cited by 6
“Next-generation sequencing technology (NGS) has been widely used in genomic studies [1].”
Method[RNA-Seq and genuine traditional Chinese medicine].
Wang, X., Song, J., Xie, C., Han, J.-P., & Chen, S. (2014) · PubMed · Cited by 6
Metadata
- Authors
- Zhang, J., Chiodini, R., Badr, A., & Zhang, G.
- Affiliations
- Texas Tech University Health Sciences Center (US)
- Beijing Normal University (CN)
- Corresponding author
- Zhang, Jun
- Venue
- Journal of Genetics and Genomics
- Publisher
- Elsevier BV
- Published
- 2011-03
- Volume
- 38
- Issue
- 3
- Pages
- 95-109
- ISSN
- 1873-5533 (ISSN-L)
- 1673-8527
- PMC
- PMC3076108
- OpenAlex
- W2083854815
- Cited by
- 577
- References
- 98
- Citations by year
- 2026: 10 · 2025: 11 · 2024: 32 · 2023: 22 · 2022: 23 · 2021: 34 · 2020: 45 · 2019: 50 · 2018: 39 · 2017: 38 · 2016: 47 · 2015: 52 · 2014: 50 · 2013: 44 · 2012: 64
- FWCI
- 4.94
- Type
- journal article
- Language
- en
- Open access
- green
- www.ncbi.nlm.nih.gov
- Locations
- Journal of genetics and genomics/Journal of Genetics and Genomics (publishedVersion)
- PubMed (publishedVersion)
- Europe PMC (PubMed Central) (acceptedVersion)
- PubMed Central (acceptedVersion)
- Funders
- National Institute of Neurological Disorders and Stroke (R21NS061191)
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Genomics and Phylogenetic Studies
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Genetics, Bioinformatics, and Biomedical Research
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Genetics › Genomics and Rare Diseases
- Keywords
- next-generation sequencing, genomics, sequencing platforms, bioinformatics software, genomic data storage, genetic variation, human genome, sequencing data analysis
- MeSH terms
- Humans, Software, Genetic Variation, Sequence Alignment, Sequence Analysis, DNA, Computational Biology, Genomics, Nanotechnology, Precision Medicine
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