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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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Cites
Initial sequencing and analysis of the human genome
International Human Genome Sequencing Consortium, Whitehead Institute for Biomedical Research, C. F. G. R., Lander, E. S., Linton, L. M., Birren, B., Nusbaum, C., Zody, M. C., Baldwin, J., Devon, K., Dewar, K., et al. (2001) · Nature · doi:10.1038/35057062 · Cited by 24,216
The sequence of the human genome
Venter, J. C., Adams, M. D., Myers, E. W., Li, P. W., Mural, R. J., Sutton, G. G., Smith, H. O., Yandell, M., Evans, C. A., Holt, R. A., et al. (2001) · Science · doi:10.1126/science.1058040 · Cited by 13,909
Self-citationFinding the missing heritability of complex diseases
Manolio, T. A., Collins, F. S., Cox, N. J., Goldstein, D. B., Hindorff, L. A., Hunter, D. J., McCarthy, M. I., Ramos, E. M., Cardon, L. R., Chakravarti, A., et al. (2009) · Nature · doi:10.1038/nature08494 · Cited by 8,336 · cited 9×
“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
Metzker, M. L. (2010) · Nature Reviews Genetics · doi:10.1038/nrg2626 · Cited by 7,066 · cited 4×
“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
Shendure, J., & Ji, H. (2008) · Nature Biotechnology · doi:10.1038/nbt1486 · Cited by 4,509 · cited 2×
“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.”
MethodDe novo assembly of human genomes with massively parallel short read sequencing
Li, R., Zhu, H., Ruan, J., Qian, W., Fang, X., Shi, Z., Li, Y., Li, S., Shan, G., Kristiansen, K., et al. (2010) · Genome Research · doi:10.1101/gr.097261.109 · Cited by 2,926 · cited 1×
“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).”
MethodMapping short DNA sequencing reads and calling variants using mapping quality scores
Li, H., Ruan, J., & Durbin, R. (2008) · Genome Research · doi:10.1101/gr.078212.108 · Cited by 2,638 · 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.”
MethodThe potential and challenges of nanopore sequencing
Branton, D., Deamer, D. W., Marziali, A., Bayley, H., Benner, S. A., Butler, T. J., Ventra, M. D., Garaj, S., Hibbs, A. H., Huang, X. C., et al. (2008) · Nature Biotechnology · doi:10.1038/nbt.1495 · Cited by 2,534 · cited 1×
“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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Diken, E., Özer, T., Arıkan, M., Emrence, Z., Öner, E. T., Üstek, D., & Arğa, K. Y. (2015) · SpringerPlus · doi:10.1186/s40064-015-1184-3 · Cited by 49
“In this context, next generation sequencing (NGS) technologies play an important role since they provide high-throughput genomic data, including whole genome sequences (WGS), at unprecedented speed with relatively low cost (Gov and Arga 2014; Zhang et al. 2011).”
BackgroundNext Generation Sequence Analysis and Computational Genomics Using Graphical Pipeline Workflows
Torri, F., Dinov, I. D., Zamanyan, A., Hobel, S., Genco, A., Petrosyan, P., Clark, A. P., Liu, Z., Eggert, P., Pierce, J., et al. (2012) · Genes · doi:10.3390/genes3030545 · Cited by 51
“Also, alternative annotation tools and strategies have been proposed [55] to retrieve information and test hypotheses about the functional role of variants present by chance in any single human genome or enriched in the genome of people affected by a psychiatric disease [56,57].”
BackgroundImputation-Based Genomic Coverage Assessments of Current Human Genotyping Arrays
Nelson, S. C., Doheny, K. F., Pugh, E., Romm, J., Ling, H., Laurie, C. A., Browning, S. R., Weir, B. S., & Laurie, C. C. (2013) · G3 Genes Genomes Genetics · doi:10.1534/g3.113.007161 · Cited by 48
Vasudevan, K., Ragupathi, N. K. D., Jacob, J. J., & Veeraraghavan, B. (2019) · Genomics · doi:10.1016/j.ygeno.2019.04.006 · Cited by 49
Expanding DNA diagnostic panel testing: is more better?
Klee, E. W., Hoppman‐Chaney, N. L., & Ferber, M. J. (2011) · Expert Review of Molecular Diagnostics · doi:10.1586/erm.11.58 · Cited by 48
MutMap: a versatile tool for identification of mutant loci and mapping of genes
Tribhuvan, K. U., Sandhya, S., Kumar, K., Sevanthi, A. M., & Gaikwad, K. (2018) · Indian Journal of Plant Physiology · doi:10.1007/s40502-018-0417-1 · Cited by 47
Spengler, M., Adler, M., & Niemeyer, C. M. (2015) · The Analyst · doi:10.1039/c5an00822k · Cited by 47
Precone, V., Monaco, V. D., Esposito, M. V., Palma, F. D. E. D., Ruocco, A., Salvatore, F., & D’Argenio, V. (2015) · BioMed Research International · doi:10.1155/2015/161648 · Cited by 51
“The study of entire genomes is faster and cheaper with NGS techniques than with conventional Sanger sequencing [13, 14].”
Cousins, M. M., Ou, S., Wawer, M. J., Munshaw, S., Swan, D. A., Magaret, C. A., Mullis, C. E., Serwadda, D., Porcella, S. F., Gray, R. H., et al. (2012) · Journal of Clinical Microbiology · doi:10.1128/jcm.01460-12 · Cited by 46
Role of Microorganisms in Soil Genesis and Functions
Kaviya, N., Upadhayay, V. K., Singh, J., Khan, A. A., Panwar, M., & Singh, A. V. (2019) · Springer eBooks · doi:10.1007/978-981-13-6480-8_2 · Cited by 50
Advances in Nano Based Biosensors for Food and Agriculture
Arora, K. (2018) · Environmental chemistry for a sustainable world · doi:10.1007/978-3-319-70166-0_1 · Cited by 45
Genetics of common complex kidney stone disease: insights from genome-wide association studies
Pálsson, R., Indridason, Ó. S., Edvardsson, V. O., & Oddsson, Á. (2018) · Urolithiasis · doi:10.1007/s00240-018-1094-2 · Cited by 46
The Genetic Diagnosis of Neurodegenerative Diseases and Therapeutic Perspectives
Casallas, J. C. G., & Bustos, R. (2018) · Brain Sciences · doi:10.3390/brainsci8120222 · Cited by 49
“It is then possible to observe which variants are shared with other members of a (target) family [14,15].”
BackgroundRamadan, M., Hetta, . F., Saleh, M. M., Ali, M. E., Ahmed, A. A., & Salah, M. (2021) · Scientific Reports · doi:10.1038/s41598-021-84529-7 · Cited by 46
Ancient DNA: the next generation - chapter and verse
Linderholm, A. E. (2015) · Biological Journal of the Linnean Society · doi:10.1111/bij.12616 · Cited by 49
Bailén, M., Bressa, C., Larrosa, M., & González-Soltero, R. (2019) · Journal of Microbiological Methods · doi:10.1016/j.mimet.2019.105811 · Cited by 44
Ciocan, C. A., Jurj, A. M., Buse, M., Gulei, D., Braicu, C., Ráduly, L., Cojocneanu, R., Pruteanu, L.-L., Iuga, C. A., Coza, O. F., et al. (2019) · International Journal of Molecular Sciences · doi:10.3390/ijms20102576 · Cited by 43
“SNPs present a central function in diseases with a genetic background and also in pharmacogenomics where investigation targets the individual patient responses to drugs [17].”
MethodRosado, T., Dias, L., Lança, M., Nogueira, C., Santos, R., Martins, M. R., Candeias, A., Mirão, J. P., & Caldeira, A. T. (2020) · MicrobiologyOpen · doi:10.1002/mbo3.1030 · Cited by 43
Recent Advancements in the Technologies Detecting Food Spoiling Agents
Saini, R. V., Vaid, P., Saini, N. K., Siwal, S. S., Gupta, V. K., Thakur, V. K., & Saini, A. K. (2021) · Journal of Functional Biomaterials · doi:10.3390/jfb12040067 · Cited by 42
“The first genomic analysis of Aspergillus flavus identified more than 7000 unique Expressed Sequence Tags (EST) [161], and, subsequently, the functional genomes of the scale of ~12,000 were identified [162].”
BackgroundKey issues review: evolution on rugged adaptive landscapes
Obolski, U., Ram, Y., & Hadany, L. (2017) · Reports on Progress in Physics · doi:10.1088/1361-6633/aa94d4 · Cited by 42
“However, the technological leaps in molecular biology methods towards the end of the 20th century and the beginning of the 21st century, most notably the genomic revolution [79, 80], have significantly changed the research of adaptive landscapes.”
BackgroundRetreatment Predictions in Odontology by means of CBR Systems
Nieves, L. C., Aliaga, I. J., Paz, J. F. D., Barbero, Á. E. G., Bajo, J., González, G. V., & Corchado, J. M. (2016) · Computational Intelligence and Neuroscience · doi:10.1155/2016/7485250 · Cited by 41
“Bioinformatics can be applied to various fields of medicine, although it is normally used in fields associated with genetic expressions [1, 2], protein analysis [3], sequencing [4], and so forth.”
BackgroundGhosh, M., Sharma, N., Singh, A. K., Gera, M., Pulicherla, K. K., & Jeong, D. K. (2018) · Critical Reviews in Biotechnology · doi:10.1080/07388551.2018.1451819 · Cited by 44
“This creates an electrical trace unique to each nucleotide [38], varying depending on whether the nanopore is blocked by an A, C, G, T, or a section of DNA that includes more than one of these bases (kmer) [39].”
BackgroundComplete RHD next-generation sequencing: establishment of reference RHD alleles
Tounsi, W. A., Madgett, T. E., & Avent, N. D. (2018) · Blood Advances · doi:10.1182/bloodadvances.2018017871 · Cited by 40
“20,21 22-24 NGS is used in HLA testing, 25 which creates a strong impetus to introduce NGS for BGG. 26 31-33 For these databases, reference sequences for all blood group genes are critical to allow effective BGG. 26 Different studies have aimed to use NGS in BGG using a variety of approaches.”
MethodCommon applications of next-generation sequencing technologies in genomic research
Lee, C., Chiu, Y., Wang, L.-B., Kuo, Y.-L., Chuang, E. Y.-Y., Lai, L., & Tsai, M. (2013) · Translational Cancer Research · doi:10.21037/962 · Cited by 40
“The read alignment in genomics, also called reference-based assembly (11), is utilized by read alignment tools ( Table 2 ) to align several hundred or thousand millions of reads back to an existing reference genome.”
MethodPersonalized Medicine: What’s in it for Rare Diseases?
Halfmann, S. S. G., Mählmann, L., Leyens, L., Reumann, M., & Brand, A. M. (2017) · Advances in experimental medicine and biology · doi:10.1007/978-3-319-67144-4_22 · Cited by 40
Abdu-Aljabar, R. D., & Awad, O. A. (2021) · IOP Conference Series Materials Science and Engineering · doi:10.1088/1757-899x/1076/1/012048 · Cited by 40
Kanagal‐Shamanna, R., Singh, R. R., Routbort, M. J., Patel, K. P., Medeiros, L. J., & Luthra, R. (2016) · Expert Review of Molecular Diagnostics · doi:10.1586/14737159.2016.1142374 · Cited by 40
“The software parameters can be optimized using files containing known variants [11,40,51].”
MethodMichils, G., Hollants, S., Dehaspe, L., Houdt, J. V., Bidet, Y., Uhrhammer, N. A., Bignon, Y., Vermeesch, J. R., Cuppens, H., & Matthijs, G. (2012) · Journal of Molecular Diagnostics · doi:10.1016/j.jmoldx.2012.05.006 · Cited by 39
Genetics of leprosy: Expected and unexpected developments and perspectives
Sauer, M. E. D., Salomão, H., Ramos, G. B., D’Espindula, H. R. S., Rodrigues, R. S. A., Macedo, W. C., Sindeaux, R., & Mira, M. T. (2014) · Clinics in Dermatology · doi:10.1016/j.clindermatol.2014.10.001 · Cited by 40
Comprehensive and accurate genome analysis at scale using DRAGEN accelerated algorithmsPreprint
Behera, S., Catreux, S., Rossi, M., Truong, S., Huang, Z., Ruehle, M., Visvanath, A., Parnaby, G., Roddey, C., Onuchic, V., et al. (2024) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2024.01.02.573821 · Cited by 39
Study of tree shrew biology and models: A booming and prosperous field for biomedical research
Yao, Y., Lü, L., Ni, R., Bi, R., Chen, C., Chen, J., Fuchs, E., Gorbatyuk, M., Lei, H., Li, H., et al. (2024) · 动物学研究 · doi:10.24272/j.issn.2095-8137.2024.199 · Cited by 41
“Advances in sequencing technologies (De Coster et al., 2021; Hook & Timp, 2023; Zhang et al., 2011) now allow researchers to determine the genome sequences of wild animals and non-model organisms, providing crucial insights into their genetic backgrounds, which is essential for their use as…”
BackgroundAnalysis of the transcriptome of the Indonesian coelacanth Latimeria menadoensis
Pallavicini, A., Canapa, A., Barucca, M., Alföldi, J., Biscotti, M. A., Buonocore, F., Moro, G. D., Palma, F. D., Fausto, A. M., Forconi, M., et al. (2013) · BMC Genomics · doi:10.1186/1471-2164-14-538 · Cited by 38
“The advent of NGS technologies has had an outstanding impact on many fields of biology, including genetics [45], functional and comparative genomics [46,47] and molecular ecology [48].”
BackgroundAdibah, A. B., Saidin, S., Hanim, M. Z. H., Munir, M. Z. B., Ghani, I. F. A., & Azizah, M. N. S. (2020) · LWT · doi:10.1016/j.lwt.2020.109585 · Cited by 38
Small RNA transcriptome investigation based on next-generation sequencing technology
Linglin, Z., Li, X., Liu, Q., Zhao, F., & Wu, J. (2011) · Journal of genetics and genomics/Journal of Genetics and Genomics · doi:10.1016/j.jgg.2011.08.006 · Cited by 37
“Due to an increased throughput and a reduced cost, next-generation sequencing (NGS) technology, such as Roche 454, ABI SOLiD and Illumina Solexa, represents an attractive alternative to traditional methods for a wide range of applications (Zhang et al., 2011).”
MethodNext generation sequencing in cardiovascular diseases
Faìta, F. (2012) · World Journal of Cardiology · doi:10.4330/wjc.v4.i10.288 · Cited by 37
Bacterial Genomics in Infectious Disease and the Clinical Pathology Laboratory
Olsen, R. J., Long, S. W., & Musser, J. M. (2012) · Archives of Pathology & Laboratory Medicine · doi:10.5858/arpa.2012-0025-ra · Cited by 36
Syme, R. A., Tan, K., Hane, J. K., Dodhia, K. N., Stoll, T. M., Hastie, M. L., Furuki, E., Ellwood, S. R., Williams, A., Tan, Y., et al. (2016) · PLoS ONE · doi:10.1371/journal.pone.0147221 · Cited by 36
“may be overcome by a complementary chemistry [33, 34].”
BackgroundWang, D., Yang, T., Liu, R., Li, N., Wang, X., Sarker, A., Zhang, X., Li, R., Pu, Y., Guan, L., et al. (2020) · The Crop Journal · doi:10.1016/j.cj.2020.04.007 · Cited by 36
DNA ‐analysis to monitor fisheries and aquaculture: Too costly?
Martinsohn, J. T., Raymond, P. W., Knott, T., Glover, K. A., Nielsen, E. E., Eriksen, L., Ogden, R., Casey, J., & Guillén, J. (2018) · Fish and Fisheries · doi:10.1111/faf.12343 · Cited by 39
Genome-wide miRNA-profiling of aflatoxin B1-induced hepatic injury using deep sequencing
Yang, W., Lian, J., Feng, Y., Srinivas, S., Guo, Z., Zhong, H., Zhuang, Z., & Wang, S. (2014) · Toxicology Letters · doi:10.1016/j.toxlet.2014.01.021 · Cited by 34
Decoding the microbial universe with metagenomics: a brief insight
Chaudhari, H. G., Prajapati, S., Wardah, Z. H., Raol, G. G., Prajapati, V., Patel, R. K., Shati, A. A., Alfaifi, M. Y., Elbehairi, S. E. I., & Sayyed, R. Z. (2023) · Frontiers in Genetics · doi:10.3389/fgene.2023.1119740 · Cited by 31
“The unincorporated nucleotides are then washed off, and the fluorescent labels on the strand are chemically erased, allowing for the insertion of the next base (T. D. Harris et al., 2008; Zhang et al., 2011).”
BackgroundImpacts of low coverage depths and post-mortem DNA damage on variant calling: a simulation study
Parks, M., & Lambert, D. M. (2015) · BMC Genomics · doi:10.1186/s12864-015-1219-8 · Cited by 30
“throughput platforms [56], and their combination of throughput and read length are well-suited to aDNA sequencing [57].”
BackgroundZhang, X., Wang, Y., Li, S., An, X., Pei, G., Huang, Y., Fan, H., Mi, Z., Zhang, Z., Wang, W., et al. (2015) · BMC Genomics · doi:10.1186/s12864-015-1612-3 · Cited by 31
“The florescent light signals were detected using a genome analyzer, which was used for base calling [25].”
MethodKhan, I. A. (2021) · Heliyon · doi:10.1016/j.heliyon.2021.e07903 · Cited by 31
Laurie, M. T., Bertout, J. A., Taylor, S. D., Burton, J. N., Shendure, J., & Bielas, J. H. (2013) · BioTechniques · doi:10.2144/000114063 · Cited by 31
Coutant, S., Cabot, C., Lefebvre, A., Léonard, M., Prieur-Gaston, É., Campion, D., Thierry Lecroq, B., & Dauchel, H. (2012) · BMC Bioinformatics · doi:10.1186/1471-2105-13-s14-s9 · Cited by 35
“…their expression levels, identifying DNA-protein interactions or chromatin modifications, surveying the species diversity in an environmental sample, all these tasks are now tackled with large-scale sequencing and require computer intensive bioinformatic analyses [5-7], although different.”
Backgroundde Melo, F., Milanesi, F. C., Angst, P. D. M., & Oppermann, R. V. (2020) · Archives of Oral Biology · doi:10.1016/j.archoralbio.2020.104776 · Cited by 31
BIND – An algorithm for loss-less compression of nucleotide sequence data
Bose, T., Mohammed, M. H., Dutta, A., & Mande, S. S. (2012) · Journal of Biosciences · doi:10.1007/s12038-012-9230-6 · Cited by 30
“Data generated using NGS platforms have been speculated to contain the scientific breakthroughs of the future (Metzker 2010; Zhang et al. 2011).”
BackgroundSequencing of plant genomes – a review
Türktaş, M., Kurtoğlu, K. Y., Dorado, G., Zhang, B., Hernández, P., & Ünver, T. (2015) · TURKISH JOURNAL OF AGRICULTURE AND FORESTRY · doi:10.3906/tar-1409-93 · Cited by 30
“Thus, the length distribution of contigs, the average and largest contig sizes, and N50 and N80 sizes are considered as the major indicators of a sequence assessment (Zhang et al., 2011a).”
BackgroundSeafood Species Identification Using DNA Sequencing
Hellberg, R. S. R., Pollack, S. J., & Hanner, R. (2016) · Elsevier eBooks · doi:10.1016/b978-0-12-801592-6.00006-1 · Cited by 30
MicroRNA signatures from multidrug-resistant Mycobacterium tuberculosis
Ren, N., Gao, G., Sun, Y., Zhang, L., Wang, H., Hua, W., Wan, K., & Li, X. (2015) · Molecular Medicine Reports · doi:10.3892/mmr.2015.4262 · Cited by 29
“However, as the quantities of sequence data increase exponentially, an analysis bottle-neck remains (31).”
Machine learning meets genome assembly
Padovani, K., Setúbal, J. C., de Carvalho, A. C. P. L. F., Oliveira, G., Château, A., & Alves, R. C. D. O. (2018) · Briefings in Bioinformatics · doi:10.1093/bib/bby072 · Cited by 28
Dietary non-coding RNAs from plants: Fairy tale or treasure?
Sundaram, G. M. (2019) · Non-coding RNA Research · doi:10.1016/j.ncrna.2019.02.002 · Cited by 28
“This can, in fact, be attributed to the evolution of DNA sequencing technologies from earlier methods such as sanger sequencing and shot gun approach to massively parallel sequencing, adopted by sequencing platforms recently [2].”
MethodShademan, B., Avci, Ç. B., Nikanfar, M., & Nourazarian, A. (2020) · NeuroMolecular Medicine · doi:10.1007/s12017-020-08601-7 · Cited by 30
Genetic epidemiology with a Capital E, ten years after
Khoury, M. J., GWINN, M. L., Clyne, M., & Yu, W. (2011) · Genetic Epidemiology · doi:10.1002/gepi.20634 · Cited by 27
“…epidemiology has flourished, encouraged to a large extent by the completion of the human genome project [Collins et al., 2003] and the HapMap project [International HapMap, 2005, 2007], as well as the emergence of next-generation sequencing and other ‘‘omic’’ technologies [Zhang et al., 2011].”
BackgroundMethodApplications of Next-Generation Sequencing for Large-Scale Pathogen Diagnoses in Soybean
Díaz-Cruz, G. A., Smith, C. M., Wiebe, K. F., Villanueva, S. M. P., Klonowski, A. R., & Cassone, B. J. (2019) · Plant Disease · doi:10.1094/pdis-05-18-0905-re · Cited by 27
Moses, M., Mtolera, M. S. P., Chauka, L. J., Lopes, F. A., de Koning, D., Houston, R. D., & Palaiokostas, C. (2019) · Aquaculture International · doi:10.1007/s10499-019-00472-5 · Cited by 27
“High-throughput sequencing has revolutionized the field of genetics, enabling costeffective discovery and characterization of molecular polymorphisms (Mardis 2008a, b; Zhang et al. 2011; Koboldt et al. 2013; Attia and Saeed 2016).”
Fonseca, A., Ramalhete, S., Mestre, A., das Neves, R. P., Marreiros, A., Castelo‐Branco, P., & Roberto, V. P. (2021) · Aging · doi:10.18632/aging.203556 · Cited by 29
Solvated protein–DNA docking using HADDOCK
van Dijk, M., Visscher, K. M., Kastritis, P. L., & Bonvin, A. M. J. J. (2013) · Journal of Biomolecular NMR · doi:10.1007/s10858-013-9734-x · Cited by 26
“In the last decade, numerous genomics (Collins et al. 2003; Zhang et al. 2011), proteomics (Pandey and Mann 2000; Renuse et al. 2011) and interactomics (Collura and Boissy 2007; Cusick et al. 2005) efforts have enriched our understanding of the biomolecular world we live in.”
BackgroundZhang, Y., Huang, Y., He, Q., Luo, J., Zhu, L., Lu, S., Liu, J., Huang, P., Zeng, X., & Liang, S. (2015) · Journal of Biological Chemistry · doi:10.1074/jbc.m114.635458 · Cited by 27
Yan, Q., Zhang, G., Zhang, X., & Huang, L. (2024) · Metabolites · doi:10.3390/metabo14050272 · Cited by 26
“With the rapid development of sequencing technologies, large amounts of omic datasets have been generated; these technologies include next-generation sequencing (NGS) [6], single-molecule real-time sequencing (SMRT) [7], chromatography and mass spectrometry technologies [8], and bioinformatic tools.”
BackgroundSelf-citationMcGaughran, A. (2020) · BMC Genomics · doi:10.1186/s12864-020-6594-0 · Cited by 26
Ramadan, M., Solyman, S. M., Yones, M., Abdallah, Y., Halaby, H., & Hanora, A. (2019) · OMICS A Journal of Integrative Biology · doi:10.1089/omi.2019.0011 · Cited by 27
“…sequencing have revolutionized the era of microbiome revealing vastly greater bacterial diversity and providing deeper understanding about the relation between community members and the degree of symbiosis provoked on skin with AD (Byrd et al., 2017; Metzker, 2005; Zhang et al., 2011).”
A review of the molecular profile of benign and malignant odontogenic lesions
Duarte‐Andrade, F. F., Vitório, J. G., Pereira, T. D. S. F., Gomes, C. C., & Gomez, R. S. (2020) · Oral Surgery Oral Medicine Oral Pathology and Oral Radiology · doi:10.1016/j.oooo.2019.12.017 · Cited by 25
Enhancing Physical and Thermodynamic Properties of DNA Storage Sets With End-Constraint
Wu, J., Zheng, Y., Wang, B., & Zhang, Q. (2021) · IEEE Transactions on NanoBioscience · doi:10.1109/tnb.2021.3121278 · Cited by 26
“Continuous bases could lead to errors in the process of decoding continuous bases and cause unmanageable hybridization reactions of the whole sequence [36], [37], so run-length limit constraint (RLL) is used to limit its occurrence [38].”
MethodAdamopoulos, P. G., Theodoropoulou, M. C., & Scorilas, A. (2018) · Annals of Translational Medicine · doi:10.21037/atm.2018.06.32 · Cited by 25
Drögemöller, B. I., Wright, G. E. B., Niehaus, D. J. H., Emsley, R. A., & Warnich, L. (2011) · Pharmacogenomics · doi:10.2217/pgs.11.119 · Cited by 24
Choi, S. K., Go, J. H., Kim, E. K., Lee, H., Lee, W. M., Cho, C.-S., & Han, K. (2016) · Genomics & Informatics · doi:10.5808/gi.2016.14.3.78 · Cited by 25
“Next-generation sequencing (NGS) technology has made genetic and molecular studies effective, with more reliable results achieved [4].”
BackgroundGenetics of leprosy: Expected—and unexpected—developments and perspectives
Sauer, M. E. D., Salomão, H., Ramos, G. B., D’Espindula, H. R. S., Rodrigues, R. S. A., Macedo, W. C., Sindeaux, R., & Mira, M. T. (2015) · Clinics in Dermatology · doi:10.1016/j.clindermatol.2015.10.005 · Cited by 24
Ishishita, S., Tsuboi, K., Ohishi, N., Tsuchiya, K., & Matsuda, Y. (2015) · Scientific Reports · doi:10.1038/srep09435 · Cited by 23
Role of Next-Generation Sequencing (NGS) in Understanding the Microbial Diversity
Dubey, A., Malla, M. A., & Kumar, A. (2022) · Springer eBooks · doi:10.1007/978-981-16-6005-4_16 · Cited by 22
Emerging Tools for Synthetic Genome Design
Lee, B.-R., Cho, S., Song, Y., Kim, S. C., & Cho, B. (2013) · Molecules and Cells · doi:10.1007/s10059-013-0127-5 · Cited by 22
“NGS methods analyze various sizes and types of DNA libraries more accurately, rapidly, and cheaply in a highthroughput fashion (Mardis, 2011; Metzker, 2010; Pareek et al., 2011; Shendure and Lieberman Aiden, 2012; Soon et al., 2013; Zhang et al., 2011).”
MethodMicrobial Comparative Genomics: An Overview of Tools and Insights Into The Genus Corynebacterium
Ali, A. (2013) · Journal of Bacteriology & Parasitology · doi:10.4172/2155-9597.1000167 · Cited by 22
“This technology has dominated the market for almost two decades, and was responsible for the release of the first complete bacterial genome in 1995 [1,23].”
BackgroundMethodInfluentialAdvances in legume research in the genomics era
Egan, A. N., & Vatanparast, M. (2019) · Australian Systematic Botany · doi:10.1071/sb19019 · Cited by 22
Tounsi, W. A., Lenis, V. P. E., Tammi, S., Sainio, S., Haimila, K., Avent, N. D., & Madgett, T. E. (2022) · Clinical Chemistry · doi:10.1093/clinchem/hvac075 · Cited by 21
Radhouani, H., Pinto, L., Poeta, P. A. C. Q. D., & Igrejas, G. (2012) · Journal of Proteomics · doi:10.1016/j.jprot.2011.12.035 · Cited by 25
“[85] Zhang J, Chiodini R, Badr A, Zhang G.”
BackgroundInfluentialReQON: a Bioconductor package for recalibrating quality scores from next-generation sequencing data
Cabanski, C. R., Cavin, K., Bizon, C., Wilkerson, M. D., Parker, J. S., Wilhelmsen, K. C., Perou, C. M., Marron, J. S., & Hayes, D. N. (2012) · BMC Bioinformatics · doi:10.1186/1471-2105-13-221 · Cited by 25
“This sequencing error rate is machine, run and sample specific, but it occurs at a rate of approximately 1/1000 [2], resulting in tens of millions of errors in a single experiment.”
BackgroundNext-generation sequencing: a frameshift in skeletal dysplasia gene discovery
Lazarus, S., Zankl, A., & Duncan, E. L. (2013) · Osteoporosis International · doi:10.1007/s00198-013-2443-1 · Cited by 21
“Some of the reads may not be mappable if they do not align uniquely to one location in the genome [36]; again, paired-end reads improve specificity of alignment as both reads have to map within a very short distance of each other.”
BackgroundA novel procedure on next generation sequencing data analysis using text mining algorithm
Zhao, W., Chen, J. J., Perkins, R., Wang, Y., Liu, Z., Hong, H., Tong, W., & Zou, W. (2016) · BMC Bioinformatics · doi:10.1186/s12859-016-1075-9 · Cited by 23
“Most of these tools are used for the general categories, such as sequence alignment, genome assembly and annotation, and genetic variation detection [8].”
MethodSun, Y., Zhang, X., Wang, Y., Day, R. W., Yang, H., & Zhang, Z. (2019) · Scientific Reports · doi:10.1038/s41598-019-56150-2 · Cited by 21
Global mutational profiling of formalin-fixed human colon cancers from a pathology archive
Adams, M. D., Veigl, M. L., Wang, Z., Molyneux, N., Sun, S., Guda, K., Yu, X., Markowitz, S. D., & Willis, J. E. (2012) · Modern Pathology · doi:10.1038/modpathol.2012.121 · Cited by 20
Gondal, M. N., & Chaudhary, S. U. (2021) · Frontiers in Oncology · doi:10.3389/fonc.2021.712505 · Cited by 19
“Rapid advancements in molecular biology research, particularly in high-throughput genomics (23), transcriptomics (24), and proteomics (25) have resulted in the generation of big data on spatiotemporal measurements of scale-specific biomolecules (Figure 1A) in physiological as well as pathological contexts (26, 27).”
BackgroundCousins, M. M., Donnell, D. J., & Eshleman, S. H. (2012) · Journal of Molecular Diagnostics · doi:10.1016/j.jmoldx.2012.08.008 · Cited by 20
Nguyen, T. K., & Lim, J.-H. (2019) · Horticulture Environment and Biotechnology · doi:10.1007/s13580-019-00160-6 · Cited by 20
Cancer Predisposition Syndromes Associated With Pediatric High-Grade Gliomas
Ceglie, G., Baldo, G. D., Agolini, E., Rinelli, M., Cacchione, A., Bufalo, F. D., Vinci, M., Carta, R., Boccuto, L., Miele, E., et al. (2020) · Frontiers in Pediatrics · doi:10.3389/fped.2020.561487 · Cited by 21
“These revolutionary technological advances have drastically reduced sequencing costs and shortened the turnaround time, increasing the detection rate (68).”
BackgroundNguyen‐Vo, T., Trinh, Q. H., Nguyen, L., Nguyen-Hoang, P.-U., Rahardja, S., & Nguyen, B. P. (2022) · BMC Genomics · doi:10.1186/s12864-022-08829-6 · Cited by 19
“Recently, with the extensive growth of the next-generation sequencing (NGS) technology [16], a large number of genomes have been sequenced to provide a huge source of genome data for in silico discovery [17–22].”
BackgroundLigterink, W., Joosen, R. V. L., & Hilhorst, H. W. M. (2012) · Seed Science Research · doi:10.1017/s0960258511000328 · Cited by 19
“…genome, such as Arabidopsis and tomato, but recent and future developments in secondand third-generation sequencing technologies (Metzker, 2010; Zhang et al., 2011) will open the path towards a successful implementation of genetical genomics approaches for non-model organisms (Varshney et al.,…”
BackgroundToxin Diversity Revealed by a Transcriptomic Study of Ornithoctonus huwena
Zhang, Y., Huang, Y., He, Q., Liu, J., Luo, J., Zhu, L., Lu, S., Huang, P., Chen, X., Zeng, X., et al. (2014) · PLoS ONE · doi:10.1371/journal.pone.0100682 · Cited by 19
“The 454 Life Sciences pyrosequencing technology is commonly used due to its highthroughput and accuracy comparable to traditional Sanger sequencing [21,22].”
MethodDubé, C., Planes, S., Zhou, Y., Berteaux‐Lecellier, V., & Boissin, É. (2017) · PeerJ · doi:10.7717/peerj.2936 · Cited by 19
“, with no genetic information available) (Zhang et al., 2011), with a good representativeness of loci across the genome (Martin et al.”
BackgroundOsunmakinde, C. O., Selvarajan, R., Sibanda, T., Mamba, B. B., & Msagati, T. A. M. (2018) · Viruses · doi:10.3390/v10080429 · Cited by 20
“The main setback of this technology is that it is a low throughput, thereby limiting it as a means for diagnosis, and is labour intensive and slow [181,183].”
BackgroundMethodPan-Genome Analysis Reveals Host-Specific Functional Divergences in Burkholderia gladioli
Lee, H., Park, J., Jung, H., & Seo, Y. (2021) · Microorganisms · doi:10.3390/microorganisms9061123 · Cited by 20
“Rapid advances in next-generation sequencing (NGS) technology have drastically reduced the cost of genome sequencing, thereby accelerating the development of comparative genomics through numerous genomes of various organisms [7].”
BackgroundEverything at once: Comparative analysis of the genomes of bacterial pathogens
Laing, C., Zhang, Y., Thomas, J. E., & Gannon, V. P. J. (2011) · Veterinary Microbiology · doi:10.1016/j.vetmic.2011.06.014 · Cited by 19
Hadooping the genome: The impact of big data tools on biology
Stevens, H. (2016) · BioSocieties · doi:10.1057/s41292-016-0003-6 · Cited by 20
“As such, the most significant early uses of NGS technology were in performing genome-wide searches for human variation and the most critical challenges were in finding faster algorithms for performing alignment and mapping of short reads (Zhang et al , 2011).”
BackgroundKang, B. H., Kim, W. J., Chowdhury, S., Moon, C. Y., Kang, S., Kim, S., Jo, S., Jun, T., Kim, K. D., & Ha, B. (2023) · International Journal of Molecular Sciences · doi:10.3390/ijms24054762 · Cited by 18
“Recently, the development of high-throughput sequencing technologies, such as nextgeneration sequencing (NGS), has made it possible to better understand plant genomes, which is essential for understanding complex traits, including those associated with salt stress [26].”
BackgroundEl estudio de la biodiversidad en la era de la secuenciación masiva
Escalante, A. E., Jardón‐Barbolla, L., Ramírez‐Barahona, S., & Eguiarte, L. E. (2015) · Revista Mexicana de Biodiversidad · doi:10.7550/rmb.43498 · Cited by 23
“This goal can be accomplished in different ways, depending on the scale at which the analysis is conducted (Mardis, 2008; Metzker, 2010; Neale and Kremer, 2011; Zhang et al., 2011).”
The humankind genome: from genetic diversity to the origin of human diseases
Belizário, J. E. (2013) · Genome · doi:10.1139/gen-2013-0125 · Cited by 19
O'Brien, M. A., Costin, B. N., & Miles, M. F. (2012) · International review of neurobiology · doi:10.1016/b978-0-12-398323-7.00005-7 · Cited by 18
PromoterLCNN: A Light CNN-Based Promoter Prediction and Classification Model
Hernández, D., Jara, N., Araya, M., Durán, R. E., & Buil-Aranda, C. (2022) · Genes · doi:10.3390/genes13071126 · Cited by 17
“, RNA-seq, systematic genomic evolution of ligands by exponential enrichment) [9–11] still does not compare to the explosive amount of genomic data generated during the last decade [12,13].”
BackgroundNext-Generation Sequencing Trends among Adult Patients with Select Advanced Tumor Types
Ferreira‐Gonzalez, A., Hocum, B. T., Ko, G., Shuvo, S. A., Appukkuttan, S., & Babajanyan, S. (2024) · Journal of Molecular Diagnostics · doi:10.1016/j.jmoldx.2024.01.005 · Cited by 17
Forensic use of human mitochondrial DNA: A review
Cavalcanti, P. D., Nogueira, T. L. S., de Carvalho, E. F., & Da, S. (2024) · Anais da Academia Brasileira de Ciências · doi:10.1590/0001-3765202420231179 · Cited by 20
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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