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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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Self-citationFinding the missing heritability of complex diseases
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“Following completion of the HGP, a new approach, genome-wide association study (GWAS), was widely applied to genomics.”
BackgroundInfluentialGenome sequencing in microfabricated high-density picolitre reactors
Margulies, M., Egholm, M., Altman, W. E., Attiya, S., Bader, J. S., Bemben, L. A., Berka, J., Braverman, M. S., Chen, Y.-J., Chen, Z., et al. (2005) · Nature · doi:10.1038/nature03959 · Cited by 7,693 · cited 1×
“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
Li, R., Li, Y., Kristiansen, K., & Wang, J. (2008) · Bioinformatics · doi:10.1093/bioinformatics/btn025 · Cited by 3,597 · cited 2×
“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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“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.”
Background
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“Although available NGS technologies utilize quite diverse chemistry and base incorporation ⁄ detection tools, they share two main steps: library fragmentation ⁄ amplicon library preparation and detection of the incorporated nucleotides (Glenn 2011; Zhang et al. 2011).”
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Fabregat, A., Sidiropoulos, K., Viteri, G., Forner, O., Marín-García, P., Arnau, V., D’Eustachio, P., Stein, L. D., & Hermjakob, H. (2017) · BMC Bioinformatics · doi:10.1186/s12859-017-1559-2 · Cited by 884
“Since the size of the data samples is constantly increasing [2, 3], Reactome offers a set of pathway analysis tools which aim to deal with this scenario and yet provide reliable and accurate results with interactive (seconds) response time for genome-wide datasets.”
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Self-citationDual RNA-seq of pathogen and host
Westermann, A. J., Gorski, S. A., & Vogel, J. (2012) · Nature Reviews Microbiology · doi:10.1038/nrmicro2852 · Cited by 782
A spectral approach integrating functional genomic annotations for coding and noncoding variants
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“The tremendous progress in massively parallel sequencing technologies enables investigators to efficiently obtain genetic information down to single base resolution on a genome-wide scale [1, 2, 3].”
BackgroundTranscriptome analysis using next-generation sequencing
Mutz, K.-O., Heilkenbrinker, A., Lönne, M., Walter, J., & Stahl, F. (2012) · Current Opinion in Biotechnology · doi:10.1016/j.copbio.2012.09.004 · Cited by 547
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“The agent is able to (1) provide an interface for DICOM, HL7, HTTP, and XDS standard and nonstandardized data; (2) synchronize metadata on local PACS and RIS; (3) cache images and data received from local PACS, RIS, any input tool, or another agent; (4) archive image data with compression and multitier storage, backup…”
BackgroundMicroparticles: major transport vehicles for distinct microRNAs in circulation
Diehl, P., Fricke, A., Sander, L., Stamm, J., Bassler, N., Htun, N., Ziemann, M., Helbing, T., El‐Osta, A., Jowett, J. B. M., et al. (2012) · Cardiovascular Research · doi:10.1093/cvr/cvs007 · Cited by 484
“NGS is a promising method for miRNA studies as it has major advantages in comparison to microarrays, including higher sensitivity, wider miRNA spectrum that can be analysed and the ability of de novo sequencing of so far unknown miRNAs.(22,23) We could demonstrate that MP contain a significantly distinct miRNA pattern…”
Assuring the quality of next-generation sequencing in clinical laboratory practice
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Using Genomics to Track Global Antimicrobial Resistance
Hendriksen, R. S., Bortolaia, V., Tate, H. P., Tyson, G. H., Aarestrup, F. M., & McDermott, P. F. (2019) · Frontiers in Public Health · doi:10.3389/fpubh.2019.00242 · Cited by 461
Malla, M. A., Dubey, A., Kumar, A., Yadav, S., Hashem, A., & Allah, E. F. A. (2019) · Frontiers in Immunology · doi:10.3389/fimmu.2018.02868 · Cited by 366
Allali, I., Arnold, J. W., Roach, J., Cadenas, M. B., Butz, N., Hassan, H. M., Koci, M., Ballou, A., Mendoza, M., Ali, R., et al. (2017) · BMC Microbiology · doi:10.1186/s12866-017-1101-8 · Cited by 298
Diversity and Plasticity of Sex Determination and Differentiation in Fishes
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“Recently, access to detailed genomic information of animals by using next-generation sequencing has become easier [Zhang et al., 2011].”
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Salipante, S. J., SenGupta, D. J., Cummings, L. A., Land, T. A., Hoogestraat, D. R., & Cookson, B. T. (2015) · Journal of Clinical Microbiology · doi:10.1128/jcm.03385-14 · Cited by 306
Analysis of plant microbe interactions in the era of next generation sequencing technologies
Knief, C. (2014) · Frontiers in Plant Science · doi:10.3389/fpls.2014.00216 · Cited by 267
“A detailed description of second generation sequencing platforms and principles can be found in dedicated reviews (e.g., Voelkerding et al., 2009; Metzker, 2010; Glenn, 2011; Pareek et al., 2011; Zhang et al., 2011; Liu et al., 2012; Shokralla et al., 2012; Mardis, 2013; Morey et al., 2013).”
BackgroundAspergillus derived mycotoxins in food and the environment: Prevalence, detection, and toxicity
Navale, V. D., Vamkudoth, K. R., Ajmera, S., & Dhuri, V. C. (2021) · Toxicology Reports · doi:10.1016/j.toxrep.2021.04.013 · Cited by 264
Next Generation Sequencing Technologies: The Doorway to the Unexplored Genomics of Non-Model Plants
Unamba, C. I. N., Nag, A., & Sharma, R. K. (2015) · Frontiers in Plant Science · doi:10.3389/fpls.2015.01074 · Cited by 236
Unraveling plant–microbe interactions: can multi-species transcriptomics help?
Schenk, P. M., Carvalhais, L. C., & Kazan, K. (2011) · Trends in biotechnology · doi:10.1016/j.tibtech.2011.11.002 · Cited by 227
Sicilia, C. B., Silvestre, S., Haslam, R. P., & Michaelson, L. V. (2017) · Plant Science · doi:10.1016/j.plantsci.2017.07.017 · Cited by 224
Massively parallel sequencing techniques for forensics: A review
Bruijns, B., Tiggelaar, R. M., & Gardeniers, H. J. G. E. (2018) · Electrophoresis · doi:10.1002/elps.201800082 · Cited by 204
SUPER-FOCUS: a tool for agile functional analysis of shotgun metagenomic data
Silva, G. G. Z., Green, K. T., Dutilh, B. E., & Edwards, R. A. (2015) · Bioinformatics · doi:10.1093/bioinformatics/btv584 · Cited by 194
“Here, we introduce SUPER-FOCUS, SUbsystems Profile by databasE Reduction using FOCUS, an agile homology-based approach using a reduced reference database to report the subsystems present in metagenomic datasets and profile their abundances.”
MethodDeePromoter: Robust Promoter Predictor Using Deep Learning
Oubounyt, M., Louadi, Z., Tayara, H., & Chong, K. T. (2019) · Frontiers in Genetics · doi:10.3389/fgene.2019.00286 · Cited by 198
“Recently, with the development of the next-generation sequencing (NGS) (Behjati and Tarpey, 2013) more genes of different organisms have been sequenced and their gene elements have been computationally explored (Zhang et al., 2011).”
BackgroundMicrobial Biodiversity and Bioremediation Assessment Through Omics Approaches
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“It produces a massively parallel analysis from multiple samples where small sections of DNA are ligated with adaptors for random reads during DNA amplification which provides enormous data within a short duration (Zhang et al., 2011).”
BackgroundA post-assembly genome-improvement toolkit (PAGIT) to obtain annotated genomes from contigs
Swain, M., Tsai, I. J., Assefa, S. A., Newbold, C., Berriman, M., & Otto, T. D. (2012) · Nature Protocols · doi:10.1038/nprot.2012.068 · Cited by 183
“Furthermore, the types of error can be influenced by the characteristics of different sequencing technologies 7,8 .”
BackgroundBioinformatics for Clinical Next Generation Sequencing
Oliver, G. R., Hart, S. N., & Klee, E. W. (2014) · Clinical Chemistry · doi:10.1373/clinchem.2014.224360 · Cited by 188
Next-generation sequencing technology in clinical virology
Capobianchi, M. R., Giombini, E., & Rozera, G. (2012) · Clinical Microbiology and Infection · doi:10.1111/1469-0691.12056 · Cited by 164
“The continuous and dynamic development of NGS represents an unprecedented opportunity for metagenomic applications, and is expanding our capacity to analyse microbial communities from a variety of habitats and environments [3,11].”
BackgroundPlant pathogen nanodiagnostic techniques: forthcoming changes?
Khiyami, M. A., Almoammar, H., Awad, Y. M., Alghuthaymi, M. A., & Abd-Elsalam, K. A. (2014) · Biotechnology & Biotechnological Equipment · doi:10.1080/13102818.2014.960739 · Cited by 159
Whole exome and whole genome sequencing
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“The microbial genomics today has progressed from the long drawnout individual genome sequencing projects in the past to a level of technological advancement, where sequencing and comparing the genomes of several strains of a single pathogen is accomplished in a very short period of time [1, 2].”
BackgroundlncRNome: a comprehensive knowledgebase of human long noncoding RNAs
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“The appropriate value for a SNP threshold is context-specific and will be affected by study-specific factors such as strain diversity in the setting [31, 43] , the definition of a quality read, the extent of within-host diversity [15, 22, 25, 31, 38] and the number of amplification steps [1, [44] [45] [46] [47] (Addit…”
BackgroundWang, B., Kumar, V., Olson, A. J., & Ware, D. (2019) · Frontiers in Genetics · doi:10.3389/fgene.2019.00384 · Cited by 147
“One of the most important applications of NGS is to identify mutations, including single nucleotide polymorphisms (SNP), small insertions/deletions (INDELs), structural variations, e.g., translocations, inversions, and copy number variations (CNV) (Zhang et al., 2011; Bahassi el and Stambrook, 2014; Wadapurkar and Vya…”
BackgroundAdvances in monitoring soil microbial community dynamic and function
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“This platform generates the best data quality as a result of its sequencing-by-ligation approach (Zhang et al. 2011).”
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Behera, S., Catreux, S., Rossi, M., Truong, S., Huang, Z., Ruehle, M., Visvanath, A., Parnaby, G., Roddey, C., Onuchic, V., et al. (2025) · Nature Biotechnology · doi:10.1038/s41587-024-02382-1 · Cited by 137
Tierney, L., Linde, J., Müller, S., Brunke, S., Molina, J. C., Hube, B., Schöck, U., Guthke, R., & Kuchler, K. (2012) · Frontiers in Microbiology · doi:10.3389/fmicb.2012.00085 · Cited by 131
“These technologies now allow for the parallel sequencing of millions of nucleotide sequences simultaneously (Wang et al., 2009; Zhang et al., 2011).”
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“Transcriptome sequencing was conducted using a combination of 454 and Illumina technologies (Zhang et al. 2011).”
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“, Illumina’s HiSeq200 V3 chemistry kit) (Clark et al., 2011; Zhang et al., 2011).”
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“Raw sequencing reads were initially processed with GenomeQuest tools [12].”
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“Aside from sequencing entire genomes—an approach that is becoming increasingly feasible (Allendorf et al. 2010; Seeb et al. 2011; Zhang et al. 2011)—the use of DNA markers to amplify random genomic regions remains the most accessible and widely used method of elucidating the distribution of genetic…”
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“Advancement in molecular profiling technologies have enabled rapid whole genome sequencing, with better resolution that provides researchers the opportunity to scan for known genomic mutations, as well as identify novel genomic aberrations specific to different subsets of gastric carcinoma patients (26-28).”
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“(2014), new introgression lines with high yields and fiber quality were developed as a result of interspecific hybridization between G. hirsutum and G. barbadense (Zhang, 2011).”
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“007, Helicos Heliscope, and the system of Pacific Biosystems (reviewed by Metzker 2010; Zhang et al. 2011).”
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Wood, S., Smith, K. F., Banks, J. C., Tremblay, L. A., Rhodes, L., Mountfort, D., Cary, S. C., & Pochon, X. (2013) · New Zealand Journal of Marine and Freshwater Research · doi:10.1080/00288330.2012.745885 · Cited by 97
“Although available platforms utilise quite diverse chemistry and base incorporation/detection tools, they all share two main steps: library preparation (fragmentation or amplicon preparation); and detection of the incorporated nucleotide (Zhang et al. 2011).”
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“Consequently, these technologies have reached unprecedented levels of acceptance and implementation and are actively replacing classical technologies, such as Sanger sequencing, hybridization-based arrays, fluorescence in situ hybridization, qualitative real-time PCR, and PCR-coupled with fragment analysis platforms […”
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Lahlali, R., Ibrahim, D. S. S., Belabess, Z., Roni, M. Z. K., Radouane, N., Vicente, C. S. L., Menéndez, E., Mokrını, F., Barka, E. A., Mota, M. G. D. M. E., et al. (2021) · Heliyon · doi:10.1016/j.heliyon.2021.e08142 · Cited by 93
“gonucleotides of the complementary probe that hybridize to the primer (Zhang et al., 2011).”
BackgroundOmoyinmi, E., Standing, A. S. I., Keylock, A., Price-Kuehne, F. E., Gomes, S. M., Rowczenio, D. M., Nanthapisal, S., Cullup, T., Nyanhete, R., Ashton, E., et al. (2017) · PLoS ONE · doi:10.1371/journal.pone.0181874 · Cited by 82
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Using Metagenomics to Connect Microbial Community Biodiversity and Functions
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The emerging roles of NGS in clinical oncology and personalized medicine
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The Core Human Microbiome: Does It Exist and How Can We Find It? A Critical Review of the Concept
Sharon, I., Quijada, N. M., Pasolli, E., Fabbrini, M., Vitali, F., Agamennone, V., Dötsch, A., Selberherr, E., Grau, J. H., Meixner, M., et al. (2022) · Nutrients · doi:10.3390/nu14142872 · Cited by 83
“This is due to the short length of the sequenced variable regions, typically at the level of genus at most [91], and precludes distinguishing between closely related species [92,93].”
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Molecular Approaches to Studying Microbial Communities: Targeting the 16S Ribosomal RNA Gene
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Halvade: scalable sequence analysis with MapReduce
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“For example, modern Illumina systems can generate several hundreds of gigabases per run (Zhang et al., 2011) with a high accuracy.”
BackgroundTracking the best reference genes for RT-qPCR data normalization in filamentous fungi
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“With the rapid development of novel technologies, there are a number of assays that can be considered and these have been reviewed elsewhere (Krueger et al. 2012; Zhou et al. 2011; Zhang et al. 2011; Ku et al. 2011).”
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“As a matter of fact, due to the advances in genome sequencing technologies [6, 7], these methods represent the only practical strategy to keep up with the rapid accumulation of sequence information [8, 9].”
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“Recent improvements in next generation sequencing technologies (e.g. Zhang et al. 2011) have made the study of nonmodel organisms’ genomes more accessible, allowing for the first time the evaluation of multiple aspects of their genomic variation (e.g. Nekrutenko & Taylor 2012).”
BackgroundSakai, H., Kanamori, H., Arai-Kichise, Y., Shibata-Hatta, M., Ebana, K., Oono, Y., Kurita, K., Fujisawa, H., Katagiri, S., Mukai, Y., et al. (2014) · DNA Research · doi:10.1093/dnares/dsu006 · Cited by 67
“sativa, thereafter, new reference sequences from additional rice cultivars are needed, although chromosomal mapping and de novo assembly of the NGS reads are still challenging.(21,22) RicecultivarKasalathbelongsto the indica subspecies or aus group of O.”
BackgroundDiMeX: A Text Mining System for Mutation-Disease Association Extraction
Mahmood, A. S. M. A., Wu, T.-J., Mazumder, R., & Vijay‐Shanker, K. (2016) · PLoS ONE · doi:10.1371/journal.pone.0152725 · Cited by 67
“Rapidly evolving sequencing technologies [1,2] have led to a dramatic rise in the number of published articles reporting associations between genomic variations and diseases.”
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“Next generation sequencing (NGS) provides large sequencing datasets at a fast sequencing speed and more lately at an affordable price [20].”
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“For nonmodel species, de novo assembly presents additional challenges for SNP discovery and genotyping including spurious SNP calls as a result of collapsing paralogs into unique loci (Zhang et al. 2011).”
BackgroundNanotechnology for the Detection and Diagnosis of Plant Pathogens
Kashyap, P. L., Rai, P., Sharma, S., Chakdar, H., Kumar, S., Pandiyan, K., & Srivastava, A. K. (2016) · Sustainable agriculture reviews · doi:10.1007/978-3-319-39306-3_8 · Cited by 67
Current Status and Future Opportunities of Omics Tools in Mycotoxin Research
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“These novel technologies generate a massive throughput at a considerably lower per base cost than traditional Sanger sequencing, and obviate the need for laborious cloning procedures [6–8].”
BackgroundScrutinizing Virus Genome Termini by High-Throughput Sequencing
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“The florescent light signals were detected by the Genome Analyzer, which performed basecalling [20].”
MethodDiagnostic Cancer Genome Sequencing and the Contribution of Germline Variants
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“…variants and quantification of gene expression (Meijer et al. 2005; Aanes et al. 2011; Coppe et al. 2010; Fu et al. 2011; Vesterlund et al. 2011; Zhang et al. 2011b), other applications such as SNP identification (Canovas et al. 2010; Yang et al. 2011), allele-specific gene expression (Degner…”
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“NGS technologies now allow large quantities of high-quality DNA sequence data to be generated at modest cost (Zhang et al., 2001).”
BackgroundHeterozygous rare genetic variants in non-syndromic early-onset obesity
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Soil Microbiome Study Based on DNA Extraction: A Review
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“The found data is then analyzed, usually using tools available on the web [97,98].”
BackgroundMethodInfluentialNext generation analytic tools for large scale genetic epidemiology studies of complex diseases
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“The average next generation sequencing experiment generates terabytes of data [Zhang et al., 2011].”
MethodIonita‐Laza, I., Capanu, M., Rubeis, S. D., McCallum, K., & Buxbaum, J. D. (2014) · PLoS Genetics · doi:10.1371/journal.pgen.1004729 · Cited by 56
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“Recently the next generation DNA sequencing technology has come of age [6].”
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“The changing epidemiology of emerging infectious diseases, with more frequent novel outbreaks and faster spread adds to the fact that efficiency in outbreak control and response relies on timely and global access to MGR [1–3].”
A Tidal Wave of Inevitable Data? Assetization in the Consumer Genomics Testing Industry
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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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