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

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

Genome 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

Next-generation DNA sequencing

Shendure, J., & Ji, H. (2008) · Nature Biotechnology · doi:10.1038/nbt1486 · Cited by 4,509

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

Wheeler, D. A., Srinivasan, M., Egholm, M., Shen, Y., Chen, L., McGuire, A., He, W., Chen, Y.-J., Makhijani, V., Roth, G. T., et al. (2008) · Nature · doi:10.1038/nature06884 · Cited by 1,838

The Diploid Genome Sequence of an Individual Human

Levy, S., Sutton, G., Ng, P. C., Feuk, L., Halpern, A. L., Walenz, B. P., Axelrod, N., Huang, J., Kirkness, E. F., Denisov, G., et al. (2007) · PLoS Biology · doi:10.1371/journal.pbio.0050254 · Cited by 1,778

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

Lizardi, P. M., Huang, X. C., Zhu, Z., Bray‐Ward, P., Thomas, D. C., & Ward, D. C. (1998) · Nature Genetics · doi:10.1038/898 · Cited by 1,443

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

The Genome Analysis Toolkit: A MapReduce framework for analyzing next-generation DNA sequencing data

McKenna, A., Hanna, M., Banks, E., Sivachenko, A., Cibulskis, K., Kernytsky, A., Garimella, K., Altshuler, D., Gabriel, S., Daly, M., et al. (2010) · Genome Research · doi:10.1101/gr.107524.110 · Cited by 27,895

A framework for variation discovery and genotyping using next-generation DNA sequencing data

DePristo, M. A., Banks, E., Poplin, R. E., Garimella, K. V., Maguire, J., Hartl, C., Philippakis, A., del Angel, G., Rivas, M. A., Hanna, M., et al. (2011) · Nature Genetics · doi:10.1038/ng.806 · Cited by 11,457

An integrated map of genetic variation from 1,092 human genomes

The 1000 Genomes Project Consortium (2012) · Nature · doi:10.1038/nature11632 · Cited by 7,711

Sequencing technologies – the next generation

Metzker, M. L. (2010) · Nature Reviews Genetics · doi:10.1038/nrg2626 · Cited by 7,066

A statistical framework for SNP calling, mutation discovery, association mapping and population genetical parameter estimation from sequencing data

Li, H. (2011) · Bioinformatics · doi:10.1093/bioinformatics/btr509 · Cited by 6,454

Coming of age: ten years of next-generation sequencing technologies

Goodwin, S., McPherson, J. D., & McCombie, W. R. (2016) · Nature Reviews Genetics · doi:10.1038/nrg.2016.49 · Cited by 4,352

Annotation of functional variation in personal genomes using RegulomeDB

Boyle, A. P., Hong, E. L., Hariharan, M., Cheng, Y., Schaub, M. A., Kasowski, M., Karczewski, K. J., Park, J., Hitz, B. C., Weng, S., et al. (2012) · Genome Research · doi:10.1101/gr.137323.112 · Cited by 2,722

An integrated semiconductor device enabling non-optical genome sequencing

Rothberg, J. M., Hinz, W., Rearick, T. M., Schultz, J., Mileski, W., Davey, M. S., Leamon, J. H., Johnson, K., Milgrew, M. J., Edwards, M. M., et al. (2011) · Nature · doi:10.1038/nature10242 · Cited by 2,271

Accurate circular consensus long-read sequencing improves variant detection and assembly of a human genome

Wenger, A. M., Peluso, P., Rowell, W. J., Chang, P.-C., Hall, R. J., Concepcion, G. T., Ebler, J., Fungtammasan, A., Kolesnikov, A., Olson, N. D., et al. (2019) · Nature Biotechnology · doi:10.1038/s41587-019-0217-9 · Cited by 1,841

Spatiotemporal transcriptomic atlas of mouse organogenesis using DNA nanoball-patterned arrays

Chen, A., Liao, S., Cheng, M., Ma, K., Wu, L., Lai, Y., Qiu, X., Yang, J., Xu, J., Hao, S., et al. (2022) · Cell · doi:10.1016/j.cell.2022.04.003 · Cited by 1,784

Reference-based phasing using the Haplotype Reference Consortium panel

Loh, P.-R., Danecek, P., Palamara, P. F., Fuchsberger, C., A Reshef, Y., K Finucane, H., Schoenherr, S., Forer, L., McCarthy, S., Abecasis, G. R., et al. (2016) · Nature Genetics · doi:10.1038/ng.3679 · Cited by 1,723

Three-dimensional intact-tissue sequencing of single-cell transcriptional states

Wang, X., Allen, W. E., Wright, M. A., Sylwestrak, E. L., Samusik, N., Vesuna, S., Evans, K., Liu, C., Ramakrishnan, C., Liu, J., et al. (2018) · Science · doi:10.1126/science.aat5691 · Cited by 1,620

Robust Demographic Inference from Genomic and SNP Data

Excoffier, L., Dupanloup, I., Huerta‐Sánchez, E., Sousa, V. C., & Foll, M. (2013) · PLoS Genetics · doi:10.1371/journal.pgen.1003905 · Cited by 1,480

Clinical Metagenomic Next-Generation Sequencing for Pathogen Detection

Gu, W., Miller, S., & Chiu, C. Y. (2019) · Annual Review of Pathology: Mechanisms of Disease · doi:10.1146/annurev-pathmechdis-012418-012751 · Cited by 1,458

The sequence of sequencers: The history of sequencing DNA

Heather, J. M., & Chain, B. (2016) · Genomics · doi:10.1016/j.ygeno.2015.11.003 · Cited by 1,397

High-Throughput Sequencing Technologies

Reuter, J., Spacek, D. V., & Snyder, M. P. (2015) · Molecular Cell · doi:10.1016/j.molcel.2015.05.004 · Cited by 1,404

Nanopore sensors for nucleic acid analysis

Venkatesan, B. M., & Bashir, R. (2011) · Nature Nanotechnology · doi:10.1038/nnano.2011.129 · Cited by 1,287

Next-Generation Sequencing Technology: Current Trends and Advancements

Satam, H., Joshi, K., Mangrolia, U., Waghoo, S., Zaidi, G., Rawool, S., Thakare, R. P., Banday, S., Mishra, A. K., Das, G., et al. (2023) · Biology · doi:10.3390/biology12070997 · Cited by 1,299

Highly sensitive spatial transcriptomics at near-cellular resolution with Slide-seqV2

Stickels, R. R., Murray, E., Kumar, P., Li, J., Marshall, J. L., Di Bella, D. J., Arlotta, P., Macosko, E. Z., & Chen, F. (2021) · Nature Biotechnology · doi:10.1038/s41587-020-0739-1 · Cited by 1,295

MYD88 L265P Somatic Mutation in Waldenström's Macroglobulinemia

Treon, S. P., Xu, L., Yang, G., Zhou, Y., Liu, X., Cao, Y., Sheehy, P. S., Manning, R. J., Patterson, C. J., Tripsas, C. K., et al. (2012) · New England Journal of Medicine · doi:10.1056/nejmoa1200710 · Cited by 1,316

Analyzing and minimizing PCR amplification bias in Illumina sequencing libraries

Aird, D., Ross, M. G., Chen, W.-S., Danielsson, M., Fennell, T., Russ, C., Jaffe, D. B., Nusbaum, C., & Gnirke, A. (2011) · Genome Biology · doi:10.1186/gb-2011-12-2-r18 · Cited by 1,174

Somatic coding mutations in human induced pluripotent stem cells

Gore, A., Li, Z., Fung, H.-L., Young, J. E., Agarwal, S., Antosiewicz-Bourget, J., Canto, I., Giorgetti, A., Israel, M. A., Kiskinis, E., et al. (2011) · Nature · doi:10.1038/nature09805 · Cited by 1,273

The human splicing code reveals new insights into the genetic determinants of disease

Xiong, H. Y., Alipanahi, B., Lee, L. J., Bretschneider, H., Merico, D., Yuen, R. K. C., Hua, Y., Gueroussov, S., Najafabadi, H. S., Hughes, T., et al. (2014) · Science · doi:10.1126/science.1254806 · Cited by 1,243

The genetic landscape of high-risk neuroblastoma

Pugh, T. J., Morozova, O., Attiyeh, E. F., Asgharzadeh, S., Wei, J. S., Auclair, D., Carter, S. L., Cibulskis, K., Hanna, M., Kieżun, A., et al. (2013) · Nature Genetics · doi:10.1038/ng.2529 · Cited by 1,198

Uncovering the roles of rare variants in common disease through whole-genome sequencing

Cirulli, E. T., & Goldstein, D. B. (2010) · Nature Reviews Genetics · doi:10.1038/nrg2779 · Cited by 1,136

Genome sequencing identifies major causes of severe intellectual disability

Gilissen, C., Hehir-Kwa, J. Y., Thung, D. T., van de Vorst, M., van Bon, B. W. M., Willemsen, M. H., Kwint, M., Janssen, I. M., Hoischen, A., Schenck, A., et al. (2014) · Nature · doi:10.1038/nature13394 · Cited by 1,125

Advances in understanding cancer genomes through second-generation sequencing

Meyerson, M. M., Gabriel, S., & Getz, G. A. (2010) · Nature Reviews Genetics · doi:10.1038/nrg2841 · Cited by 1,142

DNA sequencing at 40: past, present and future

Shendure, J., Balasubramanian, S., Church, G. M., Gilbert, W., Rogers, J., Schloss, J. A., & Waterston, R. (2017) · Nature · doi:10.1038/nature24286 · Cited by 1,166

Analysis of Genetic Inheritance in a Family Quartet by Whole-Genome Sequencing

Roach, J. C., Glusman, G., Smit, A. F. A., Huff, C. D., Hubley, R., Shannon, P. T., Rowen, L., Pant, K. P., Goodman, N., Bamshad, M., et al. (2010) · Science · doi:10.1126/science.1186802 · Cited by 1,084

Inferring human population size and separation history from multiple genome sequences

Schiffels, S., & Durbin, R. (2014) · Nature Genetics · doi:10.1038/ng.3015 · Cited by 1,073

Metagenomics - a guide from sampling to data analysis

Thomas, T., Gilbert, J. A., & Meyer, F. (2012) · Microbial Informatics and Experimentation · doi:10.1186/2042-5783-2-3 · Cited by 1,114

Germline mutations affecting the proofreading domains of POLE and POLD1 predispose to colorectal adenomas and carcinomas

Palles, C., Cazier, J., Howarth, K. M., Domingo, E., Jones, A. M., Broderick, P., Kemp, Z., Spain, S. L., Guarino, E., Salguero, I., et al. (2012) · Nature Genetics · doi:10.1038/ng.2503 · Cited by 1,008

Characterizing and measuring bias in sequence data

Ross, M. G., Russ, C., Costello, M., Hollinger, A., Lennon, N. J., Hegarty, R., Nusbaum, C., & Jaffe, D. B. (2013) · Genome Biology · doi:10.1186/gb-2013-14-5-r51 · Cited by 909

Extensive sequencing of seven human genomes to characterize benchmark reference materials

Zook, J. M., Catoe, D., McDaniel, J., Vang, L., Spies, N., Sidow, A., Weng, Z., Liu, Y., Mason, C. E., Alexander, N., et al. (2016) · Scientific Data · doi:10.1038/sdata.2016.25 · Cited by 811

Highly Multiplexed Subcellular RNA Sequencing in Situ

Lee, J. H., Daugharthy, E. R., Scheiman, J., Kalhor, R., Yang, J. L., Ferrante, T. C., Terry, R., Jeanty, S. S. F., Li, C., Amamoto, R., et al. (2014) · Science · doi:10.1126/science.1250212 · Cited by 973

Upper Palaeolithic Siberian genome reveals dual ancestry of Native Americans

Raghavan, M., Skoglund, P., Graf, K. E., Metspalu, M., Albrechtsen, A., Moltke, I., Rasmussen, S., Stafford Jr, T. W., Orlando, L., Metspalu, E., et al. (2014) · Nature · doi:10.1038/nature12736 · Cited by 963

A window into third-generation sequencing

Schadt, E. E., Turner, S., & Kasarskis, A. (2010) · Human Molecular Genetics · doi:10.1093/hmg/ddq416 · Cited by 1,026

Robust and scalable inference of population history from hundreds of unphased whole genomes

Terhorst, J., Kamm, J., & Song, Y. S. (2016) · Nature Genetics · doi:10.1038/ng.3748 · Cited by 950

In situ sequencing for RNA analysis in preserved tissue and cells

Ke, R., Mignardi, M., Pacureanu, A., Svedlund, J., Botling, J., Wählby, C., & Nilsson, M. (2013) · Nature Methods · doi:10.1038/nmeth.2563 · Cited by 934

Pan-cancer genome and transcriptome analyses of 1,699 paediatric leukaemias and solid tumours

Ma, X., Liu, Y., Liu, Y., Alexandrov, L. B., Edmonson, M. N., Gawad, C., Zhou, X., Li, Y., Rusch, M. C., Easton, J., et al. (2018) · Nature · doi:10.1038/nature25795 · Cited by 901

Sequencing of neuroblastoma identifies chromothripsis and defects in neuritogenesis genes

Molenaar, J. J., Köster, J., Zwijnenburg, D. A., Sluis, P. V., Valentijn, L. J., van der Ploeg, I., Hamdi, M., van Nes, J., Westerman, B. A., van Arkel, J., et al. (2012) · Nature · doi:10.1038/nature10910 · Cited by 873

The molecular landscape of pediatric acute myeloid leukemia reveals recurrent structural alterations and age-specific mutational interactions

Bolouri, H., Farrar, J. E., Triche, T. J., Ries, R. E., Lim, E. L., Alonzo, T. A., Ma, Y. P., Moore, R. A., Mungall, A. J. J., Marra, M. A., et al. (2017) · Nature Medicine · doi:10.1038/nm.4439 · Cited by 869

Ancient human genome sequence of an extinct Palaeo-Eskimo

Rasmussen, M., Li, Y., Lindgreen, S., Pedersen, J. S., Albrechtsen, A., Moltke, I., Metspalu, M., Metspalu, E., Kivisild, T., Gupta, R., et al. (2010) · Nature · doi:10.1038/nature08835 · Cited by 849

Integrating human sequence data sets provides a resource of benchmark SNP and indel genotype calls

Zook, J. M., Chapman, B., Wang, J., Mittelman, D., Hofmann, O., Hide, W., & Salit, M. (2014) · Nature Biotechnology · doi:10.1038/nbt.2835 · Cited by 800

An expansive human regulatory lexicon encoded in transcription factor footprints

Neph, S. J., Vierstra, J. D., Stergachis, A. B., Reynolds, A. P., Haugen, E., Vernot, B., Thurman, R. E., John, S., Sandstrom, R. S., Johnson, A., et al. (2012) · Nature · doi:10.1038/nature11212 · Cited by 760

Comprehensive Genomic Analysis of Rhabdomyosarcoma Reveals a Landscape of Alterations Affecting a Common Genetic Axis in Fusion-Positive and Fusion-Negative Tumors

Shern, J. F., Chen, L., Chmielecki, J., Wei, J. S., Patidar, R., Rosenberg, M. W., Ambrogio, L., Auclair, D., Wang, J., Song, Y. K., et al. (2014) · Cancer Discovery · doi:10.1158/2159-8290.cd-13-0639 · Cited by 753

Carrier testing for severe childhood recessive diseases by next-generation sequencing

Bell, C. J., Dinwiddie, D. L., Miller, N. A., Hateley, S. L., Ganusova, E. E., Mudge, J., Langley, R. J., Zhang, L., Lee, C. C., Schilkey, F. D., et al. (2011) · Science Translational Medicine · doi:10.1126/scitranslmed.3001756 · Cited by 706

A scalable, fully automated process for construction of sequence-ready human exome targeted capture libraries

Fisher, S., Barry, A. J., Abreu, J., Minie, B., Nolan, J., Delorey, T. M., Young, G., Fennell, T. J., Allen, A., Ambrogio, L., et al. (2011) · Genome biology · doi:10.1186/gb-2011-12-1-r1 · Cited by 676

Single cell analysis: the new frontier in 'Omics'

Wang, D., & Bodovitz, S. (2010) · Trends in biotechnology · doi:10.1016/j.tibtech.2010.03.002 · Cited by 678

High‐throughput DNA sequencing – concepts and limitations

Kircher, M., & Kelso, J. F. (2010) · BioEssays · doi:10.1002/bies.200900181 · Cited by 706

A comprehensive transcriptional portrait of human cancer cell lines

Klijn, C. N., Durinck, S., Stawiski, E. W., Haverty, P. M., Jiang, Z., Liu, H., Degenhardt, J. D., Mayba, O., Gnad, F., Liu, J., et al. (2014) · Nature Biotechnology · doi:10.1038/nbt.3080 · Cited by 669

Whole-genome sequence variation, population structure and demographic history of the Dutch population

Francioli, L. C., Menelaou, A., Pulit, S. L., Elbers, C. C., Kloosterman, W. P., van Setten, J., Nijman, I. J., Renkens, I., de Bakker, P. I. W., van Dijk, F., et al. (2014) · Nature Genetics · doi:10.1038/ng.3021 · Cited by 651

A C9orf72 promoter repeat expansion in a Flanders-Belgian cohort with disorders of the frontotemporal lobar degeneration-amyotrophic lateral sclerosis spectrum: a gene identification study

Gijselinck, I., Langenhove, T. V., van der Zee, J., Sleegers, K., Philtjens, S., Kleinberger, G., Janssens, J., Bettens, K., Cauwenberghe, C. V., Pereson, S., et al. (2011) · The Lancet Neurology · doi:10.1016/s1474-4422(11)70261-7 · Cited by 655

Computational solutions to large‐scale data management and analysis

Schadt, E. E., Linderman, M. D., Sorenson, J., Lee, L., & Nolan, G. P. (2010) · Nature Reviews Genetics · doi:10.1038/nrg2857 · Cited by 631

Advancements in Next-Generation Sequencing

Levy, S., & Myers, R. (2016) · Annual Review of Genomics and Human Genetics · doi:10.1146/annurev-genom-083115-022413 · Cited by 630

Nanopore DNA sequencing with MspA

Derrington, I. M., Butler, T. Z., Collins, M. D., Manrao, E. A., Pavlenok, M., Niederweis, M., & Gundlach, J. H. (2010) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1001831107 · Cited by 586

Identifying Mendelian disease genes with the Variant Effect Scoring Tool

Carter, H. K., Douville, C. B., Stenson, P. D., Cooper, D. N., & Karchin, R. (2013) · BMC Genomics · doi:10.1186/1471-2164-14-s3-s3 · Cited by 593

Genome dynamics of the human embryonic kidney 293 lineage in response to cell biology manipulations

Lin, Y., Boone, M., Meuris, L., Lemmens, I. H., Roy, N. V., Soete, A., Reumers, J., Moisse, M., Plaisance, S., Drmanac, R., et al. (2014) · Nature Communications · doi:10.1038/ncomms5767 · Cited by 590

Whole-genome sequencing of quartet families with autism spectrum disorder

Yuen, R. K. C., Thiruvahindrapuram, B., Merico, D., Walker, S., Tammimies, K., Hoang, N., Chrysler, C., Nalpathamkalam, T., Pellecchia, G., Liu, Y., et al. (2015) · Nature Medicine · doi:10.1038/nm.3792 · Cited by 514

Relapsed neuroblastomas show frequent RAS-MAPK pathway mutations

Eleveld, T. F., Oldridge, D. A., Bernard, V., Köster, J., Daage, L. C., Diskin, S. J., Schild, L. G., Bessoltane, N., Bellini, A., Chicard, M., et al. (2015) · Nature Genetics · doi:10.1038/ng.3333 · Cited by 536

Fluorescent in situ sequencing (FISSEQ) of RNA for gene expression profiling in intact cells and tissues

Lee, J. H., Daugharthy, E. R., Scheiman, J., Kalhor, R., Ferrante, T. C., Terry, R., Turczyk, B. M., Yang, J. L., Lee, H. S., Aach, J., et al. (2015) · Nature Protocols · doi:10.1038/nprot.2014.191 · Cited by 529

Big Data Analytics in Healthcare

Belle, A., Thiagarajan, R., Soroushmehr, S. M. R., Navidi, F., Beard, D. A., & Najarian, K. (2015) · BioMed Research International · doi:10.1155/2015/370194 · Cited by 580

Tracking the clonal origin of lethal prostate cancer

Haffner, M. C., Mosbruger, T. L., Esopi, D., Fedor, H. L., Heaphy, C. M., Walker, D. A., Adejola, N., Gurel, M., Hicks, J. L., Meeker, A. K., et al. (2013) · Journal of Clinical Investigation · doi:10.1172/jci70354 · Cited by 506

The mutation spectrum revealed by paired genome sequences from a lung cancer patient

Lee, W., Jiang, Z., Liu, J., Haverty, P. M., Guan, Y., Stinson, J., Yue, P., Zhang, Y., Pant, K. P., Bhatt, D., et al. (2010) · Nature · doi:10.1038/nature09004 · Cited by 492

A novel recurrent mutation in MITF predisposes to familial and sporadic melanoma

Yokoyama, S., Woods, S. L., Boyle, G. M., Aoude, L. G., MacGregor, S., Zismann, V., Gartside, M. G., Cust, A. E., Haq, R., Harland, M., et al. (2011) · Nature · doi:10.1038/nature10630 · Cited by 498

A recent bottleneck of Y chromosome diversity coincides with a global change in culturePreprint

Karmin, M., Saag, L., Vicente, M., Sayres, M. A. W., Järve, M., Talas, U. G., Rootsi, S., Ilumäe, A.-M., Mägi, R., Mitt, M., et al. (2015) · Genome Research · doi:10.1101/gr.186684.114 · Cited by 480

Assuring the quality of next-generation sequencing in clinical laboratory practice

Gargis, A. S., Kalman, L. V., Berry, M. W., Bick, D. P., Dimmock, D., Hambuch, T. M., Lu, F., Lyon, E., Voelkerding, K. V., Zehnbauer, B. A., et al. (2012) · Nature Biotechnology · doi:10.1038/nbt.2403 · Cited by 460

Inherited and de novo genetic risk for autism impacts shared networks

Ruzzo, E. K., Pérez-Cano, L., Jung, J.-Y., Wang, L.-K., Kashef-Haghighi, D., Hartl, C., Singh, C., Xu, J., Hoekstra, J. N., Leventhal, O., et al. (2019) · Cell · doi:10.1016/j.cell.2019.07.015 · Cited by 457

Genomic analyses inform on migration events during the peopling of Eurasia

Pagani, L., Lawson, D. J., Jagoda, E., Mörseburg, A., Eriksson, A., Mitt, M., Clemente, F., Hudjashov, G., DeGiorgio, M., Saag, L., et al. (2016) · Nature · doi:10.1038/nature19792 · Cited by 459

Next-Generation Sequencing in Oncology: Genetic Diagnosis, Risk Prediction and Cancer Classification

Kamps, R., Brandão, R. D., van den Bosch, B. J. C., Paulussen, A. D. C., Xanthoulea, S., Blok, M. J., & Romano, A. (2017) · International Journal of Molecular Sciences · doi:10.3390/ijms18020308 · Cited by 472

Clinical Interpretation and Implications of Whole-Genome Sequencing

Dewey, F., Grove, M. E., Pan, C., Goldstein, B., Bernstein, J., Chaib, H., Merker, J., Goldfeder, R., Enns, G., David, S., et al. (2014) · Journal of the American Medical Association (JAMA) · doi:10.1001/jama.2014.1717 · Cited by 456

Low concordance of multiple variant-calling pipelines: practical implications for exome and genome sequencing

O'Rawe, J., Jiang, T., Sun, G., Wu, Y., Wang, W., Hu, J., Bodily, P., Tian, L., Hakonarson, H. H., Johnson, W. E., et al. (2013) · Genome Medicine · doi:10.1186/gm432 · Cited by 443

De Novo Pathogenic SCN8A Mutation Identified by Whole-Genome Sequencing of a Family Quartet Affected by Infantile Epileptic Encephalopathy and SUDEP

Veeramah, K. R., O'Brien, J. E., Meisler, M. H., Cheng, X., Dib-Hajj, S. D., Waxman, S. G., Talwar, D., Girirajan, S., Eichler, E. E., Restifo, L. L., et al. (2012) · The American Journal of Human Genetics · doi:10.1016/j.ajhg.2012.01.006 · Cited by 438

The Genomic Landscape of the Ewing Sarcoma Family of Tumors Reveals Recurrent STAG2 Mutation

Brohl, A. S., Solomon, D. A., Chang, W., Wang, J., Song, Y., Sindiri, S., Patidar, R., Hurd, L., Chen, L., Shern, J. F., et al. (2014) · PLoS Genetics · doi:10.1371/journal.pgen.1004475 · Cited by 440

Noncanonical Self-Assembly of Multifunctional DNA Nanoflowers for Biomedical Applications

Zhu, G., Hu, R., Zhao, Z., Chen, Z., Zhang, X., & Tan, W. (2013) · Journal of the American Chemical Society · doi:10.1021/ja406115e · Cited by 433

High-throughput bacterial genome sequencing: an embarrassment of choice, a world of opportunity

Loman, N. J., Constantinidou, C., Chan, J. Z.-M., Halachev, M. R., Sergeant, M. J., Penn, C. W., Robinson, E., & Pallen, M. J. (2012) · Nature Reviews Microbiology · doi:10.1038/nrmicro2850 · Cited by 426

A genetic mechanism for Tibetan high-altitude adaptation

Lorenzo, F., Huff, C. D., Myllymäki, M., Olenchock, B. A., Swierczek, S. I., Tashi, T., Gordeuk, V. R., Wuren, T., Ge, R., McClain, D. A., et al. (2014) · Nature Genetics · doi:10.1038/ng.3067 · Cited by 429

The emerging landscape of spatial profiling technologies

Moffitt, J. R., Lundberg, E., & Heyn, H. (2022) · Nature Reviews Genetics · doi:10.1038/s41576-022-00515-3 · Cited by 419

Strategies for enhancing the sensitivity of plasmonic nanosensors

Guo, L., Jackman, J. A., Yang, H., Chen, P., Cho, N., & Kim, D. (2015) · Nano Today · doi:10.1016/j.nantod.2015.02.007 · Cited by 412

SNP ascertainment bias in population genetic analyses: Why it is important, and how to correct it

Lachance, J., & Tishkoff, S. A. (2013) · BioEssays · doi:10.1002/bies.201300014 · Cited by 425

Characterizing Mutational Signatures in Human Cancer Cell Lines Reveals Episodic APOBEC Mutagenesis

Petljak, M., Alexandrov, L. B., Brammeld, J. S., Price, S., Wedge, D. C., Großmann, S., Dawson, K. J., Ju, Y. S., Iorio, F., Tubío, J. M. C., et al. (2019) · Cell · doi:10.1016/j.cell.2019.02.012 · Cited by 407

An open resource for accurately benchmarking small variant and reference calls

Zook, J. M., McDaniel, J., Olson, N. D., Wagner, J., Parikh, H. M., Heaton, H., Irvine, S. A., Trigg, L., Truty, R., McLean, C. Y., et al. (2019) · Nature Biotechnology · doi:10.1038/s41587-019-0074-6 · Cited by 404

Exploring single-sample SNP and INDEL calling with whole-genomede novoassembly

Li, H. (2012) · Bioinformatics · doi:10.1093/bioinformatics/bts280 · Cited by 398

ARMC5 Mutations in Macronodular Adrenal Hyperplasia with Cushing's Syndrome

Assié, G., Libé, R., Espiard, S., Rizk-Rabin, M., Guimier, A., Luscap, W., Barreau, O., Lefèvre, L., Sibony, M., Guignat, L., et al. (2013) · New England Journal of Medicine · doi:10.1056/nejmoa1304603 · Cited by 395

Allele-specific methylation is prevalent and is contributed by CpG-SNPs in the human genome

Shoemaker, R., Deng, J., Wang, W., & Zhang, K. (2010) · Genome Research · doi:10.1101/gr.104695.109 · Cited by 380

Landscape of Next-Generation Sequencing Technologies

Niedringhaus, T. P., Milanova, D., Kerby, M. B., Snyder, M. P., & Barron, A. E. (2011) · Analytical Chemistry · doi:10.1021/ac2010857 · Cited by 399

Exome sequencing and the genetic basis of complex traits

Kiezun, A., Garimella, K., Do, R., Stitziel, N. O., Neale, B. M., McLaren, P. J., Gupta, N., Sklar, P., Sullivan, P. F., Moran, J. L., et al. (2012) · Nature Genetics · doi:10.1038/ng.2303 · Cited by 372

Tracking the origins and drivers of subclonal metastatic expansion in prostate cancer

Hong, M. K. H., Macintyre, G., Wedge, D. C., Loo, P. V., Patel, K., Lunke, S., Alexandrov, L. B., Sloggett, C., Cmero, M., Marass, F., et al. (2015) · Nature Communications · doi:10.1038/ncomms7605 · Cited by 367

A Children's Oncology Group and TARGET initiative exploring the genetic landscape of Wilms tumor

Gadd, S., Huff, V., Walz, A. L., Ooms, A. H. A. G., Armstrong, A. E., Gerhard, D. S., Smith, M. A., Auvil, J. M. G., Meerzaman, D. M., Chen, Q.-R., et al. (2017) · Nature Genetics · doi:10.1038/ng.3940 · Cited by 369

Genome-Wide Inference of Ancestral Recombination Graphs

Rasmussen, M. D., Hubisz, M. J., Gronau, I., & Siepel, A. (2014) · PLoS Genetics · doi:10.1371/journal.pgen.1004342 · Cited by 371

Whole-genome sequencing expands diagnostic utility and improves clinical management in paediatric medicine

Stavropoulos, D. J., Merico, D., Jobling, R. K., Bowdin, S. C., Monfared, N., Thiruvahindrapuram, B., Nalpathamkalam, T., Pellecchia, G., Yuen, R. K. C., Szego, M. J., et al. (2016) · npj Genomic Medicine · doi:10.1038/npjgenmed.2015.12 · Cited by 366

Integrative Annotation of Variants from 1092 Humans: Application to Cancer Genomics

Khurana, E., Fu, Y., Colonna, V., Mu, X. J., Kang, H. M., Lappalainen, T., Sboner, A., Lochovsky, L., Chen, J., Harmanci, A. O., et al. (2013) · Science · doi:10.1126/science.1235587 · Cited by 368

Systems Pharmacology: Network Analysis to Identify Multiscale Mechanisms of Drug Action

Zhao, S., & Iyengar, R. (2011) · The Annual Review of Pharmacology and Toxicology · doi:10.1146/annurev-pharmtox-010611-134520 · Cited by 366

A reference data set of 5.4 million phased human variants validated by genetic inheritance from sequencing a three-generation 17-member pedigreePreprint

Eberle, M. A., Fritzilas, E., Krusche, P., Källberg, M., Moore, B. L., Bekritsky, M. A., Iqbal, Z., Chuang, H., Humphray, S., Halpern, A. L., et al. (2016) · Genome Research · doi:10.1101/gr.210500.116 · Cited by 356

Mutations in Human Accelerated Regions Disrupt Cognition and Social Behavior

Doan, R. N., Bae, B.-I., Cubelos, B., Chang, C. Y., Hossain, A. A., Al-Saad, S., Mukaddes, N. M., Öner, Ö., Al‐Saffar, M., Balkhy, S., et al. (2016) · Cell · doi:10.1016/j.cell.2016.08.071 · Cited by 357

Evolutionary History and Adaptation from High-Coverage Whole-Genome Sequences of Diverse African Hunter-Gatherers

Lachance, J., Vernot, B., Elbers, C. C., Ferwerda, B., Froment, A., Bodo, J.-M., Lema, G., Fu, W., Nyambo, T., Rebbeck, T. R., et al. (2012) · Cell · doi:10.1016/j.cell.2012.07.009 · Cited by 343

VariantAnnotation : a Bioconductor package for exploration and annotation of genetic variants

Obenchain, V., Lawrence, M. F., Carey, V. J., Gogarten, S. M., Shannon, P. T., & Morgan, M. T. (2014) · Bioinformatics · doi:10.1093/bioinformatics/btu168 · Cited by 340

Making sense of cancer genomic dataPreprint

Chin, L., Hahn, W. C., Getz, G. A., & Meyerson, M. M. (2011) · Genes & Development · doi:10.1101/gad.2017311 · Cited by 344

Parent-of-origin-specific signatures of de novo mutations

Goldmann, J. M., Wong, W. S. W., Pinelli, M., Farrah, T., Bodian, D. L., Stittrich, A., Glusman, G., Vissers, L. E. L. M., Hoischen, A., Roach, J. C., et al. (2016) · Nature Genetics · doi:10.1038/ng.3597 · Cited by 340

Towards a comprehensive structural variation map of an individual human genome

Pang, A. W., MacDonald, J. R., Pinto, D., Wei, J., Rafiq, M. A., Conrad, D. F., Park, H., Hurles, M. E., Lee, C., Venter, J. C., et al. (2010) · Genome Biology · doi:10.1186/gb-2010-11-5-r52 · Cited by 335

In Brief

(2009) · Nature Reviews Genetics · doi:10.1038/nrg2713

Complete Human Genome Sequencing for Large-Scale Human Disease Studies

Drmanac, R. (2010) · PubMed Central

Accurate Whole Genome Sequencing as the Ultimate Genetic Test

Drmanac, R., Peters, B. A., Church, G. M., Reid, C. A., & Xu, X. (2014) · Clinical Chemistry · doi:10.1373/clinchem.2014.224907 · Cited by 6

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

Drmanac, R., Sparks, A. B., Callow, M. J., Halpern, A. L., Burns, N. L., Kermani, B. G., Carnevali, P., Nazarenko, I., Nilsen, G. B., Yeung, G., et al. (2010)

Genome sequencing on nanoballs

Porreca, G. J. (2010) · Nature Biotechnology · doi:10.1038/nbt0110-43 · Cited by 49