Human Genome Sequencing Using Unchained Base Reads on Self-Assembling DNA Nanoarrays

Initial sequencing and analysis of the human genome

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The sequence of the human genome

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Genome sequencing in microfabricated high-density picolitre reactors

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Next-generation DNA sequencing

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A second generation human haplotype map of over 3.1 million SNPs

The International HapMap Consortium (2007) · Nature · doi:10.1038/nature06258 · Cited by 4,438

Accurate whole human genome sequencing using reversible terminator chemistry

Bentley, D. R., Balasubramanian, S., Swerdlow, H. P., Smith, G. P., Milton, J., Brown, C. G., Hall, K. P., Evers, D. J., Barnes, C. L., Bignell, H. R., et al. (2008) · Nature · doi:10.1038/nature07517 · Cited by 3,684

The complete genome of an individual by massively parallel DNA sequencing

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The Diploid Genome Sequence of an Individual Human

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Mutation detection and single-molecule counting using isothermal rolling-circle amplification

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DNA sequencing of a cytogenetically normal acute myeloid leukaemia genome

Ley, T. J., Mardis, E. R., Ding, L., Fulton, B., McLellan, M. D., Chen, K., Dooling, D. J., Dunford-Shore, B. H., McGrath, S. D., Hickenbotham, M. T., et al. (2008) · Nature · doi:10.1038/nature07485 · Cited by 1,434

Single-cell Stereo-seq reveals induced progenitor cells involved in axolotl brain regeneration

Wei, X., Fu, S., Li, H., Liu, Y., Wang, S., Feng, W., Yang, Y., Liu, X., Zeng, Y.-Y., Cheng, M., et al. (2022) · Science · doi:10.1126/science.abp9444 · Cited by 311

The effects of hepatitis B virus integration into the genomes of hepatocellular carcinoma patientsPreprint

Jiang, Z., Jhunjhunwala, S., Liu, J., Haverty, P. M., Kennemer, M. I., Guan, Y., Lee, W., Carnevali, P., Stinson, J., Johnson, S. L., et al. (2012) · Genome Research · doi:10.1101/gr.133926.111 · Cited by 330

On the accumulation of deleterious mutations during range expansions

Peischl, S., Dupanloup, I., Kirkpatrick, M., & Excoffier, L. (2013) · Molecular Ecology · doi:10.1111/mec.12524 · Cited by 317

A reference human genome dataset of the BGISEQ-500 sequencer

Huang, J., Liang, X., Xuan, Y., Geng, C., Li, Y., Lu, H., Qu, S., Mei, X., Chen, H., Yu, T., et al. (2017) · GigaScience · doi:10.1093/gigascience/gix024 · Cited by 313

Comparative performance of the BGISEQ-500 vs Illumina HiSeq2500 sequencing platforms for palaeogenomic sequencing

Mak, S. S. T., Gopalakrishnan, S., Carøe, C., Geng, C., Liu, S., Sinding, M.-H. S., Kuderna, L. F. K., Zhang, W., Fu, S., Vieira, F. G., et al. (2017) · GigaScience · doi:10.1093/gigascience/gix049 · Cited by 317

Integrated multi-omics of the human gut microbiome in a case study of familial type 1 diabetes

Heintz-Buschart, A., May, P., Laczny, C. C., Lebrun, L. A., Bellora, C., Krishna, A., Wampach, L., Schneider, J. G., Hogan, A., de Beaufort, C., et al. (2016) · Nature Microbiology · doi:10.1038/nmicrobiol.2016.180 · Cited by 316

Whole-genome sequencing reveals important role for TBK1 and OPTN mutations in frontotemporal lobar degeneration without motor neuron disease

Pottier, C., Bieniek, K. F., Finch, N., van de Vorst, M., Baker, M., Perkersen, R., Brown, P., Ravenscroft, T., van Blitterswijk, M., Nicholson, A. M., et al. (2015) · Acta Neuropathologica · doi:10.1007/s00401-015-1436-x · Cited by 312

Truncating mutations of MAGEL2 cause Prader-Willi phenotypes and autism

Schaaf, C. P., Gonzalez‐Garay, M. L., Xia, F., Potocki, L., Gripp, K. W., Zhang, B., Peters, B. A., McElwain, M. A., Drmanac, R., Beaudet, A. L., et al. (2013) · Nature Genetics · doi:10.1038/ng.2776 · Cited by 303

Increased L1 Retrotransposition in the Neuronal Genome in Schizophrenia

Bundo, M., Toyoshima, M., Okada, Y., Akamatsu, W., Ueda, J., Nemoto-Miyauchi, T., Sunaga, F., Toritsuka, M., Ikawa, D., Kakita, A., et al. (2014) · Neuron · doi:10.1016/j.neuron.2013.10.053 · Cited by 321

Hybridization-based in situ sequencing (HybISS) for spatially resolved transcriptomics in human and mouse brain tissue

Gyllborg, D., Langseth, C. M., Qian, X., Choi, E., Salas, S. M., Hilscher, M. M., Lein, E. S., & Nilsson, M. F. (2020) · Nucleic Acids Research · doi:10.1093/nar/gkaa792 · Cited by 308

The role of replicates for error mitigation in next-generation sequencing

Robasky, K., Lewis, N. E., & Church, G. M. (2013) · Nature Reviews Genetics · doi:10.1038/nrg3655 · Cited by 316

Next-Generation Sequencing and Emerging Technologies

Kumar, K. R., Cowley, M. J., & Davis, R. L. (2019) · Seminars in Thrombosis and Hemostasis · doi:10.1055/s-0039-1688446 · Cited by 327

Recessive mutations in a distal PTF1A enhancer cause isolated pancreatic agenesis

Weedon, M. N., Cebola, I., Patch, A., Flanagan, S. E., Franco, E. D., Caswell, R. C., Rodríguez‐Seguí, S. A., Shaw-Smith, C. J., Cho, C. H.-H., Allen, H. L., et al. (2013) · Nature Genetics · doi:10.1038/ng.2826 · Cited by 305

Denoising DNA deep sequencing data—high-throughput sequencing errors and their correction

Laehnemann, D., Borkhardt, A., & McHardy, A. C. (2015) · Briefings in Bioinformatics · doi:10.1093/bib/bbv029 · Cited by 304

Recurrent DGCR8, DROSHA, and SIX Homeodomain Mutations in Favorable Histology Wilms Tumors

Walz, A. L., Ooms, A. H. A. G., Gadd, S., Gerhard, D. S., Smith, M. A., Auvil, J. M. G., Meerzaman, D. M., Chen, Q., Hsu, C. H., Yan, C., et al. (2015) · Cancer Cell · doi:10.1016/j.ccell.2015.01.003 · Cited by 288

Whole-genome sequencing identifies recurrent somatic NOTCH2 mutations in splenic marginal zone lymphoma

Kiel, M. J., Velusamy, T., Betz, B. L., Zhao, L., Weigelin, H. C., Chiang, M. Y., Huebner-Chan, D. R., Bailey, N. G., Yang, D. T., Bhagat, G., et al. (2012) · The Journal of Experimental Medicine · doi:10.1084/jem.20120910 · Cited by 294

MOSAIK: A Hash-Based Algorithm for Accurate Next-Generation Sequencing Short-Read Mapping

Lee, W.-P., Strömberg, M. P., Ward, A. N., Stewart, C., Garrison, E. P., & Marth, G. (2014) · PLoS ONE · doi:10.1371/journal.pone.0090581 · Cited by 281

Cytosolic 5′‐nucleotidase 1A autoimmunity in sporadic inclusion body myositis

Larman, H. B., Salajegheh, M. K., Nazareno, R., Lam, T., Sauld, J. F. K., Steen, H., Kong, S. W., Pinkus, J. L., Amato, A. A., Elledge, S. J., et al. (2012) · Annals of Neurology · doi:10.1002/ana.23840 · Cited by 281

Uncovering an Organ’s Molecular Architecture at Single-Cell Resolution by Spatially Resolved Transcriptomics

Liao, J., Lu, X., Shao, X., Zhu, L., & Fan, X. (2020) · Trends in biotechnology · doi:10.1016/j.tibtech.2020.05.006 · Cited by 282

A missense mutation in TFRC, encoding transferrin receptor 1, causes combined immunodeficiency

Jabara, H. H., Boyden, S. E., Chou, J., Ramesh, N., Massaad, M. J., Benson, H., Bainter, W., Fraulino, D., Rahimov, F., Sieff, C., et al. (2016) · Nature Genetics · doi:10.1038/ng.3465 · Cited by 279

A method for calculating probabilities of fitness consequences for point mutations across the human genome

Gulko, B., Hubisz, M. J., Gronau, I., & Siepel, A. C. (2015) · Nature Genetics · doi:10.1038/ng.3196 · Cited by 276

Genomic architecture of autism from comprehensive whole-genome sequence annotation

Trost, B., Thiruvahindrapuram, B., Chan, A. J. S., Engchuan, W., Higginbotham, E. J., Howe, J., Loureiro, L. O., Reuter, M. S., Roshandel, D., Whitney, J., et al. (2022) · Cell · doi:10.1016/j.cell.2022.10.009 · Cited by 287

Deleterious- and Disease-Allele Prevalence in Healthy Individuals: Insights from Current Predictions, Mutation Databases, and Population-Scale Resequencing

Xue, Y., Chen, Y., Ayub, Q., Huang, N., Ball, E. V., Mort, M. E., Phillips, A. D., Shaw, K., Stenson, P. D., Cooper, D. N., et al. (2012) · The American Journal of Human Genetics · doi:10.1016/j.ajhg.2012.10.015 · Cited by 286

Leveraging big data analytics in healthcare enhancement: trends, challenges and opportunities

Rehman, A., Naz, S., & Razzak, I. (2021) · Multimedia Systems · doi:10.1007/s00530-020-00736-8 · Cited by 312

Population genetic inference from genomic sequence variationPreprint

Pool, J. E., Hellmann, I., Jensen, J. D., & Nielsen, R. (2010) · Genome Research · doi:10.1101/gr.079509.108 · Cited by 273

Mutations in the Gene PRRT2 Cause Paroxysmal Kinesigenic Dyskinesia with Infantile Convulsions

Lee, H.-Y., Huang, Y., Bruneau, N., Roll, P., Roberson, E. D. O., Hermann, M., Quinn, E. A., Maas, J., Edwards, R. H., Ashizawa, T., et al. (2012) · Cell Reports · doi:10.1016/j.celrep.2011.11.001 · Cited by 268

Metagenomics next-generation sequencing tests take the stage in the diagnosis of lower respiratory tract infections

Diao, Z., Han, D., Zhang, R., & Li, J. (2021) · Journal of Advanced Research · doi:10.1016/j.jare.2021.09.012 · Cited by 279

Bioinformatics challenges for personalized medicine

Fernald, G. H., Capriotti, E., Daneshjou, R., Karczewski, K. J., & Altman, R. B. (2011) · Bioinformatics · doi:10.1093/bioinformatics/btr295 · Cited by 268

Mouse regulatory DNA landscapes reveal global principles of cis-regulatory evolution

Vierstra, J. D., Rynes, E., Sandstrom, R. S., Zhang, M., Canfield, T. K., Hansen, R. S., Stehling-Sun, S., Sabo, P. J., Byron, R., Humbert, R., et al. (2014) · Science · doi:10.1126/science.1246426 · Cited by 263

High‐Throughput Metagenomics for Identification of Pathogens in the Clinical Settings

Li, N., Cai, Q., Miao, Q., Song, Z., Fang, Y., & Hu, B. (2020) · Small Methods · doi:10.1002/smtd.202000792 · Cited by 265

Uganda Genome Resource Enables Insights into Population History and Genomic Discovery in Africa

Gurdasani, D., Carstensen, T., Fatumo, S., Chen, G., Franklin, C. S., Prado-Martinez, J., Bouman, H. J., Abascal, F., Haber, M., Tachmazidou, I., et al. (2019) · Cell · doi:10.1016/j.cell.2019.10.004 · Cited by 255

Accurate whole-genome sequencing and haplotyping from 10 to 20 human cells

Peters, B. A., Kermani, B. G., Sparks, A. B., Alferov, O., Hong, P., Alexeev, A., Jiang, Y., Dahl, F., Tang, Y. T., Haas, J., et al. (2012) · Nature · doi:10.1038/nature11236 · Cited by 251

Higher Levels of Neanderthal Ancestry in East Asians than in Europeans

Wall, J. D., Yang, M. A., Jay, F., Kim, S. K., Durand, E. Y., Stevison, L. S., Gignoux, C., Woerner, A., Hammer, M. F., & Slatkin, M. (2013) · Genetics · doi:10.1534/genetics.112.148213 · Cited by 249

A survey of error-correction methods for next-generation sequencing

Yang, X. F., Chockalingam, S. P., & Aluru, S. (2012) · Briefings in Bioinformatics · doi:10.1093/bib/bbs015 · Cited by 249

Optimized filtering reduces the error rate in detecting genomic variants by short-read sequencing

Reumers, J., Rijk, P. D., Zhao, H., Liekens, A. M. L., Smeets, D., Cleary, J., Loo, P. V., Bossche, M. J. A. V. D., Catthoor, K., Sabbe, B., et al. (2011) · Nature Biotechnology · doi:10.1038/nbt.2053 · Cited by 239

Mutations in SPRTN cause early onset hepatocellular carcinoma, genomic instability and progeroid features

Lessel, D., Vaz, B., Halder, S., Lockhart, P. J., Marinovic‐Terzić, I., López-Mosqueda, J., Philipp, M., Sim, J. C. H., Smith, K. R., Oehler, J., et al. (2014) · Nature Genetics · doi:10.1038/ng.3103 · Cited by 234

Analysis of High-Throughput Ancient DNA Sequencing Data

Kircher, M. (2012) · Methods in Molecular Biology · doi:10.1007/978-1-61779-516-9_23 · Cited by 236

Efficient and unique cobarcoding of second-generation sequencing reads from long DNA molecules enabling cost-effective and accurate sequencing, haplotyping, and de novo assemblyPreprint

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Clinical Implications of the Cancer Genome

MacConaill, L. E., & Garraway, L. A. (2010) · Journal of Clinical Oncology · doi:10.1200/jco.2009.27.4944 · Cited by 234

Comparison of Exome and Genome Sequencing Technologies for the Complete Capture of Protein‐Coding Regions

Lelieveld, S. H., Spielmann, M., Mundlos, S., Veltman, J. A., & Gilissen, C. (2015) · Human Mutation · doi:10.1002/humu.22813 · Cited by 217

A public resource facilitating clinical use of genomes

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Next-Generation Sequencing — An Overview of the History, Tools, and “Omic” Applications

Kulski, J. K. (2016) · InTech eBooks · doi:10.5772/61964 · Cited by 248

Genetic Signatures Reveal High-Altitude Adaptation in a Set of Ethiopian Populations

Huerta‐Sánchez, E., DeGiorgio, M., Pagani, L., Tarekegn, A., Ekong, R., Antão, T., Cardona, A., Montgomery, H., Cavalleri, G. L., Robbins, P. A., et al. (2013) · Molecular Biology and Evolution · doi:10.1093/molbev/mst089 · Cited by 223

Ancestry and Disease in the Age of Genomic Medicine

Rotimi, C. N., & Jorde, L. B. (2010) · New England Journal of Medicine · doi:10.1056/nejmra0911564 · Cited by 221

Tracing the Route of Modern Humans out of Africa by Using 225 Human Genome Sequences from Ethiopians and Egyptians

Pagani, L., Schiffels, S., Gurdasani, D., Danecek, P., Scally, A., Chen, Y., Xue, Y., Haber, M., Ekong, R., Oljira, T., et al. (2015) · The American Journal of Human Genetics · doi:10.1016/j.ajhg.2015.04.019 · Cited by 216

The Predictive Capacity of Personal Genome Sequencing

Roberts, N. J., Vogelstein, J. T., Parmigiani, G., Kinzler, K. W., Vogelstein, B., & Velculescu, V. E. (2012) · Science Translational Medicine · doi:10.1126/scitranslmed.3003380 · Cited by 216

Conservation of trans-acting circuitry during mammalian regulatory evolution

Stergachis, A. B., Neph, S., Sandstrom, R., Haugen, E., Reynolds, A. P., Zhang, M., Byron, R., Canfield, T., Stelhing-Sun, S., Lee, K., et al. (2014) · Nature · doi:10.1038/nature13972 · Cited by 212

Smartphone‐based clinical diagnostics: towards democratization of evidence‐based health care

Hernández-Neuta, I., Neumann, F., Brightmeyer, J., Tis, T. B., Madaboosi, N., Wei, Q., Özcan, A., & Nilsson, M. F. (2018) · Journal of Internal Medicine · doi:10.1111/joim.12820 · Cited by 207

Benchmarking challenging small variants with linked and long reads

Wagner, J., Olson, N. D., Harris, L. N., McDaniel, J., Khan, Z., Farek, J., Mahmoud, M., Stankovic, A., Kovacevic, V., Yoo, B., et al. (2022) · Cell Genomics · doi:10.1016/j.xgen.2022.100128 · Cited by 205

New observations on maternal age effect on germline de novo mutations

Wong, W. S. W., Solomon, B. D., Bodian, D. L., Kothiyal, P., Eley, G. D., Huddleston, K., Baker, R., Thach, D., Iyer, R. K., Vockley, J. G., et al. (2016) · Nature Communications · doi:10.1038/ncomms10486 · Cited by 200

Novel MYBL1 Gene Rearrangements with Recurrent MYBL1–NFIB Fusions in Salivary Adenoid Cystic Carcinomas Lacking t(6;9) Translocations

Mitani, Y., Liu, B., Rao, P. H., Borra, V. J., Zafereo, M., Weber, R. S., Kies, M. S., Lozano, G., Futreal, P. A., Caulı́n, C., et al. (2015) · Clinical Cancer Research · doi:10.1158/1078-0432.ccr-15-2867-t · Cited by 201

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

Inactivation of IL11 Signaling Causes Craniosynostosis, Delayed Tooth Eruption, and Supernumerary Teeth

Nieminen, P., Morgan, N. V., Fenwick, A. L., Parmanen, S., Veistinen, L., Mikkola, M. L., van der Spek, P. J., Giraud, A. S., Judd, L. M., Arte, S., et al. (2011) · The American Journal of Human Genetics · doi:10.1016/j.ajhg.2011.05.024 · Cited by 200

Genome and transcriptome sequencing of lung cancers reveal diverse mutational and splicing eventsPreprint

Liu, J., Lee, W., Jiang, Z., Chen, Z., Jhunjhunwala, S., Haverty, P. M., Gnad, F., Guan, Y., Gilbert, H., Stinson, J., et al. (2012) · Genome Research · doi:10.1101/gr.140988.112 · Cited by 208

The genomic landscape of high hyperdiploid childhood acute lymphoblastic leukemia

Paulsson, K. M., Lilljebjörn, H., Biloglav, A., Olsson, L., Rissler, M., Castor, A., Barbany, G., Fogelstrand, L., Nordgren, A., Sjögren, H., et al. (2015) · Nature Genetics · doi:10.1038/ng.3301 · Cited by 206

Mutations in STX1B, encoding a presynaptic protein, cause fever-associated epilepsy syndromes

Schubert, J., Siekierska, A., Langlois, M., May, P., Huneau, C., Becker, F., Muhle, H., Suls, A., Lemke, J. R., de Kovel, C. G. F., et al. (2014) · Nature Genetics · doi:10.1038/ng.3130 · Cited by 193

Sequencing an Ashkenazi reference panel supports population-targeted personal genomics and illuminates Jewish and European origins

Carmi, S., Hui, K. Y., Kochav, E., Liu, X., Xue, J., Grady, F., Guha, S., Upadhyay, K., Ben-Avraham, D., Mukherjee, S., et al. (2014) · Nature Communications · doi:10.1038/ncomms5835 · Cited by 188

Genomic landscape and genetic heterogeneity in gastric adenocarcinoma revealed by whole-genome sequencing

Wong, S. S., Kim, K., Ting, J. C., Yu, K., Fu, J., Liu, S., Cristescu, R., Nebozhyn, M., Gong, L., Yue, Y. G., et al. (2014) · Nature Communications · doi:10.1038/ncomms6477 · Cited by 190

From Mouse to Human: Evolutionary Genomics Analysis of Human Orthologs of Essential Genes

Georgi, B., Voight, B. F., & Bućan, M. (2013) · PLoS Genetics · doi:10.1371/journal.pgen.1003484 · Cited by 183

A Model-Based Approach for Identifying Signatures of Ancient Balancing Selection in Genetic Data

DeGiorgio, M., Lohmueller, K. E., & Nielsen, R. (2014) · PLoS Genetics · doi:10.1371/journal.pgen.1004561 · Cited by 179

Next-Generation Sequencing of Duplication CNVs Reveals that Most Are Tandem and Some Create Fusion Genes at Breakpoints

Newman, S., Hermetz, K. E., Weckselblatt, B., & Rudd, M. K. (2015) · The American Journal of Human Genetics · doi:10.1016/j.ajhg.2014.12.017 · Cited by 191

Variant Annotation and Functional Prediction: SnpEff

Cingolani, P. (2012) · Methods in molecular biology · doi:10.1007/978-1-0716-2293-3_19 · Cited by 193

Validation of a Next-Generation Sequencing Assay for Clinical Molecular Oncology

Cottrell, C. E., Al‐Kateb, H., Bredemeyer, A. J., Duncavage, E. J., Spencer, D. H., Abel, H., Lockwood, C. M., Hagemann, I. S., O’Guin, S. M., Burcea, L. C., et al. (2013) · Journal of Molecular Diagnostics · doi:10.1016/j.jmoldx.2013.10.002 · Cited by 187

Isothermal amplifications – a comprehensive review on current methods

Glökler, J., Lim, T. S., Ida, J., & Frohme, M. (2021) · Critical Reviews in Biochemistry and Molecular Biology · doi:10.1080/10409238.2021.1937927 · Cited by 189

The clinical context of copy number variation in the human genome

Lee, C., & Scherer, S. W. (2010) · Expert Reviews in Molecular Medicine · doi:10.1017/s1462399410001390 · Cited by 188

Comprehensive Genetic Landscape of Uveal Melanoma by Whole-Genome Sequencing

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Genetic alterations of JAK/STAT cascade and histone modification in extranodal NK/T-cell lymphoma nasal type

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Effects of sequence variation on differential allelic transcription factor occupancy and gene expressionPreprint

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DNA Dendrimer: An Efficient Nanocarrier of Functional Nucleic Acids for Intracellular Molecular Sensing

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A novel Fanconi anaemia subtype associated with a dominant-negative mutation in RAD51

Ameziane, N., May, P., Haitjema, A., van de Vrugt, H. J., van Rossum-Fikkert, S. E., Ristić, D., Williams, G. J., Balk, J. A., Rockx, D., Li, H., et al. (2015) · Nature Communications · doi:10.1038/ncomms9829 · Cited by 173

PDE3A mutations cause autosomal dominant hypertension with brachydactyly

Maass, P. G., Aydin, A., Luft, F. C., Schächterle, C., Weise, A., Stricker, S., Lindschau, C., Vaegler, M., Qadri, F., Toka, H. R., et al. (2015) · Nature Genetics · doi:10.1038/ng.3302 · Cited by 166

Evidence for recent, population-specific evolution of the human mutation rate

Harris, K. (2015) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1418652112 · Cited by 165

Identification by whole-genome resequencing of gene defect responsible for severe hypercholesterolemia

Rios, J. J., Stein, E. A., Shendure, J., Hobbs, H. H., & Cohen, J. C. (2010) · Human Molecular Genetics · doi:10.1093/hmg/ddq352 · Cited by 164

De novo truncating mutations in ASXL3 are associated with a novel clinical phenotype with similarities to Bohring-Opitz syndrome

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Systems genomics evaluation of the SH-SY5Y neuroblastoma cell line as a model for Parkinson’s disease

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Personalized Medicine: Marking a New Epoch in Cancer Patient Management

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Whole Genome Sequencing Increases Molecular Diagnostic Yield Compared with Current Diagnostic Testing for Inherited Retinal Disease

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Natural Selection Affects Multiple Aspects of Genetic Variation at Putatively Neutral Sites across the Human Genome

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Human Genome Sequencing Using Unchained Base Reads on Self-Assembling DNA

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Genome sequencing on nanoballs

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