dbSNP: the NCBI database of genetic variation

Prospects for whole-genome linkage disequilibrium mapping of common disease genes

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Signatures of mutational processes in human cancer

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The Ensembl Variant Effect Predictor

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From FastQ data to high confidence variant calls: the Genome Analysis Toolkit best practices pipeline

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The International HapMap Project

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High-throughput droplet digital PCR system for absolute quantitation of DNA copy number

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HaploReg: a resource for exploring chromatin states, conservation, and regulatory motif alterations within sets of genetically linked variants

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Development and validation of a clinical cancer genomic profiling test based on massively parallel DNA sequencing

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COSMIC: somatic cancer genetics at high-resolution

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A living biobank of breast cancer organoids captures disease heterogeneity

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Fast and SNP-tolerant detection of complex variants and splicing in short reads

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Universal Patterns of Selection in Cancer and Somatic Tissues

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The landscape of genomic alterations across childhood cancers

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A large genome-wide association study of age-related macular degeneration highlights contributions of rare and common variants

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The origin and evolution of mutations in acute myeloid leukemia

Welch, J. S., Ley, T. J., Link, D. C., Miller, C. A., Larson, D. E., Koboldt, D. C., Wartman, L. D., Lamprecht, T. L., Liu, F., Xia, J., et al. (2012) · Cell · doi:10.1016/j.cell.2012.06.023 · Cited by 1,575

PhenoScanner: a database of human genotype-phenotype associations.

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Human primary liver cancer–derived organoid cultures for disease modeling and drug screening

Broutier, L., Mastrogiovanni, G., Verstegen, M. M., Francies, H. E., Gavarró, L. M., Bradshaw, C. R., Allen, G. E., Arnes-Benito, R., Sidorova, O., Gaspersz, M. P., et al. (2017) · Nature Medicine · doi:10.1038/nm.4438 · Cited by 1,471

The Allelic Landscape of Human Blood Cell Trait Variation and Links to Common Complex Disease

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Genotype and SNP calling from next-generation sequencing data

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DNABERT: pre-trained bidirectional encoder representations from transformers model for DNA-language in genome

Ji, Y., Zhou, Z., Liu, H., & Davuluri, R. V. (2021) · Bioinformatics · doi:10.1093/bioinformatics/btab083 · Cited by 1,303

Loss of IFN-γ pathway genes in tumor cells as a mechanism of resistance to anti-CTLA-4 therapy

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NCBI Reference Sequences (RefSeq): current status, new features and genome annotation policy

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Single-Cell RNA-Seq Reveals Lineage and X Chromosome Dynamics in Human Preimplantation Embryos

Petropoulos, S., Edsgärd, D., Reinius, B., Deng, Q., Panula, S. P., Codeluppi, S., Plaza Reyes, A., Linnarsson, S., Sandberg, R., & Lanner, F. (2016) · Cell · doi:10.1016/j.cell.2016.03.023 · Cited by 1,063

Mutational signatures associated with tobacco smoking in human cancer

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The whole-genome landscape of medulloblastoma subtypes

Northcott, P. A., Buchhalter, I., Morrissy, A. S., Hovestadt, V., Weischenfeldt, J., Ehrenberger, T., Gröbner, S., Segura-Wang, M., Zichner, T., Rudneva, V. A., et al. (2017) · Nature · doi:10.1038/nature22973 · Cited by 1,112

Long‐term expanding human airway organoids for disease modeling

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Database resources of the National Center for Biotechnology Information

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Insights into human genetic variation and population history from 929 diverse genomes

Bergström, A., McCarthy, S. A., Hui, R., Almarri, M. A., Ayub, Q., Danecek, P., Chen, Y., Felkel, S., Hallast, P., Kamm, J., et al. (2020) · Science · doi:10.1126/science.aay5012 · Cited by 1,020

Upstream open reading frames cause widespread reduction of protein expression and are polymorphic among humans

Calvo, S. E., Pagliarini, D. J., & Mootha, V. K. (2009) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.0810916106 · Cited by 914

The power of genetic diversity in genome-wide association studies of lipids

Graham, S. E., Clarke, S. L., Wu, K.-H. H., Kanoni, S., Zajac, G. J. M., Ramdas, S., Surakka, I., Ntalla, I., Vedantam, S., Winkler, T. W., et al. (2021) · Nature · doi:10.1038/s41586-021-04064-3 · Cited by 972

The diploid genome sequence of an Asian individual

Wang, J., Wang, W., Li, R., Li, Y., Tian, G., Goodman, L., Fan, W., Zhang, J., Li, J., Zhang, J., et al. (2008) · Nature · doi:10.1038/nature07484 · Cited by 924

Recurrent R-spondin fusions in colon cancer

Seshagiri, S., Stawiski, E. W., Durinck, S., Modrusan, Z., Storm, E. E., Conboy, C. B., Chaudhuri, S., Guan, Y., Janakiraman, V., Jaiswal, B. S., et al. (2012) · Nature · doi:10.1038/nature11282 · Cited by 960

SNP detection for massively parallel whole-genome resequencing

Li, R., Li, Y., Fang, X., Yang, H., Wang, J., Kristiansen, K., & Wang, J. (2009) · Genome Research · doi:10.1101/gr.088013.108 · Cited by 944

Tissue-specific mutation accumulation in human adult stem cells during life

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Inferring the molecular and phenotypic impact of amino acid variants with MutPred2

Pejaver, V., Urresti, J., Lugo-Martinez, J., Pagel, K. A., Lin, G. N., Nam, H.-J., Mort, M., Cooper, D. N., Sebat, J., Iakoucheva, L. M., et al. (2020) · Nature Communications · doi:10.1038/s41467-020-19669-x · Cited by 923

The Human Gene Mutation Database: 2008 update

Stenson, P. D., Mort, M., Ball, E. V., Howells, K., Phillips, A. D., Thomas, N. S., & Cooper, D. N. (2009) · Genome Medicine · doi:10.1186/gm13 · Cited by 873

Proteogenomic Analysis of Human Colon Cancer Reveals New Therapeutic Opportunities

Vasaikar, S., Huang, C., Wang, X., Petyuk, V. A., Savage, S. R., Wen, B., Dou, Y., Zhang, Y., Shi, Z., Arshad, O. A., et al. (2019) · Cell · doi:10.1016/j.cell.2019.03.030 · Cited by 799

Genomic data in the all of us research program

The All of Us Research Program Genomics Investigators, Manuscript Writing Group, Bick, A. G., Metcalf, G. A., Mayo, K. R., Lichtenstein, L., Rura, S., Carroll, R. J., Musick, A., Linder, J. E., et al. (2024) · Nature · doi:10.1038/s41586-023-06957-x · Cited by 829

CIRCLE-Seq: A highly sensitive in vitro screen for genome-wide CRISPR-cas9 nuclease off-targets

Tsai, S. Q., Nguyen, N. T., Malagon-Lopez, J., Topkar, V. V., Aryee, M. J., & Joung, J. K. (2017) · Nature Methods · doi:10.1038/nmeth.4278 · Cited by 814

STrengthening the REporting of Genetic Association Studies (STREGA)— An Extension of the STROBE Statement

Little, J., Higgins, J. P. T., Ioannidis, J. P. A., Moher, D., Gagnon, F., von Elm, E., Khoury, M. J., Cohen, B., Davey-Smith, G., Grimshaw, J., et al. (2009) · PLoS Medicine · doi:10.1371/journal.pmed.1000022 · Cited by 811

Genetic Misdiagnoses and the Potential for Health Disparities

Manrai, A. K., Funke, B. H., Rehm, H. L., Olesen, M. S., Maron, B. A., Szolovits, P., Margulies, D. M., Loscalzo, J., & Kohane, I. S. (2016) · New England Journal of Medicine · doi:10.1056/nejmsa1507092 · Cited by 808

Large-scale whole-genome sequencing of the Icelandic population

Gudbjartsson, D. F., Helgason, H., Gudjonsson, S. A., Zink, F., Oddson, A., Gylfason, A., Besenbacher, S., Magnusson, G., Halldorsson, B. V., Hjartarson, E., et al. (2015) · Nature Genetics · doi:10.1038/ng.3247 · Cited by 791

Database resources of the National Center for Biotechnology Information

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Genome-wide Association Study Identifies 27 Loci Influencing Concentrations of Circulating Cytokines and Growth Factors

Ahola-Olli, A. V., Würtz, P., Havulinna, A. S., Aalto, K., Pitkänen, N., Lehtimäki, T., Kähönen, M., Lyytikäinen, L.-P., Raitoharju, E., Seppälä, I., et al. (2017) · The American Journal of Human Genetics · doi:10.1016/j.ajhg.2016.11.007 · Cited by 628

Induction of resistance to chimeric antigen receptor T cell therapy by transduction of a single leukemic B cell

Ruella, M., Xu, J., Barrett, D. M., Fraietta, J. A., Reich, T. J., Ambrose, D. E., Klichinsky, M., Shestova, O., Patel, P. R., Kulikovskaya, I., et al. (2018) · Nature Medicine · doi:10.1038/s41591-018-0201-9 · Cited by 659

Establishing Cerebral Organoids as Models of Human-Specific Brain Evolution

Pollen, A. A., Bhaduri, A., Andrews, M. G., Nowakowski, T. J., Meyerson, O. S., Mostajo-Radji, M. A., Di Lullo, E., Alvarado, B., Bedolli, M., Dougherty, M. L., et al. (2019) · Cell · doi:10.1016/j.cell.2019.01.017 · Cited by 600

Aging and neurodegeneration are associated with increased mutations in single human neurons

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Most Rare Missense Alleles Are Deleterious in Humans: Implications for Complex Disease and Association Studies

Kryukov, G. V., Pennacchio, L. A., & Sunyaev, S. R. (2007) · The American Journal of Human Genetics · doi:10.1086/513473 · Cited by 598

Characterizing the Major Structural Variant Alleles of the Human Genome

Audano, P. A., Sulovari, A., Graves-Lindsay, T. A., Cantsilieris, S., Sorensen, M., Welch, A. E., Dougherty, M. L., Nelson, B. J., Shah, A., Dutcher, S. K., et al. (2019) · Cell · doi:10.1016/j.cell.2018.12.019 · Cited by 492

Gene Expression Regulation by Upstream Open Reading Frames and Human Disease

Barbosa, C., Peixeiro, I., & Romão, L. (2013) · PLoS Genetics · doi:10.1371/journal.pgen.1003529 · Cited by 525

Human pluripotent stem cells recurrently acquire and expand dominant negative P53 mutations

Merkle, F. T., Ghosh, S., Kamitaki, N., Mitchell, J., Avior, Y., Mello, C., Kashin, S., Mekhoubad, S., Ilic, D., Charlton, M., et al. (2017) · Nature · doi:10.1038/nature22312 · Cited by 506

Neurobiology of intelligence: science and ethics

Gray, J. R., & Thompson, P. M. (2004) · Nature Reviews Neuroscience · doi:10.1038/nrn1405 · Cited by 479

The HIrisPlex system for simultaneous prediction of hair and eye colour from DNA

Walsh, S., Liu, F., Wollstein, A., Kovatsi, L., Ralf, A., Kosiniak-Kamysz, A., Branicki, W., & Kayser, M. (2013) · Forensic Science International Genetics · doi:10.1016/j.fsigen.2012.07.005 · Cited by 428

Genome graphs and the evolution of genome inference

Paten, B., Novak, A. M., Eizenga, J. M., & Garrison, E. (2017) · Genome Research · doi:10.1101/gr.214155.116 · Cited by 351

The evaluation of tools used to predict the impact of missense variants is hindered by two types of circularity

Grimm, D. G., Azencott, C., Aicheler, F., Gieraths, U., MacArthur, D. G., Samocha, K. E., Cooper, D. N., Stenson, P. D., Daly, M. J., Smoller, J. W., et al. (2015) · Human Mutation · doi:10.1002/humu.22768 · Cited by 356

Gaining comprehensive biological insight into the transcriptome by performing a broad-spectrum RNA-seq analysis

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Whole Genome Sequencing Defines the Genetic Heterogeneity of Familial Pancreatic Cancer

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Improved exome prioritization of disease genes through cross-species phenotype comparison

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Definition And Clinical Importance Of Haplotypes.

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Shifting Paradigm of Association Studies: Value of Rare Single-Nucleotide Polymorphisms

Gorlov, I. P., Gorlova, O. Y., Sunyaev, S. R., Spitz, M. R., & Amos, C. I. (2008) · The American Journal of Human Genetics · doi:10.1016/j.ajhg.2007.09.006 · Cited by 338

Integrative analysis of the melanoma transcriptome

Berger, M. F., Levin, J. Z., Vijayendran, K., Sivachenko, A., Adiconis, X., Maguire, J., Johnson, L. A., Robinson, J., Verhaak, R. G., Sougnez, C., et al. (2010) · Genome Research · doi:10.1101/gr.103697.109 · Cited by 305

Evaluation of DNA from the Papanicolaou test to detect ovarian and endometrial cancers.

Kinde, I., Bettegowda, C., Wang, Y., Wu, J., Agrawal, N., Shih, I.-M., Kurman, R., Dao, F., Levine, D. A., Giuntoli, R., et al. (2013) · Science Translational Medicine · doi:10.1126/scitranslmed.3004952 · Cited by 327

Organoid Cultures as Preclinical Models of Non–Small Cell Lung Cancer

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Prevalence of Germline Mutations in Cancer Predisposition Genes in Patients With Pancreatic Cancer

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Gut microbiota diversity across ethnicities in the United States

Brooks, A. W., Priya, S., Blekhman, R., & Bordenstein, S. R. (2018) · PLOS Biology · doi:10.1371/journal.pbio.2006842 · Cited by 304

The National Institutes of Health Undiagnosed Diseases Program: insights into rare diseases

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Exome Sequencing and the Management of Neurometabolic Disorders

Tarailo-Graovac, M., Shyr, C., Ross, C. J., Horvath, G. A., Salvarinova, R., Ye, X. C., Zhang, L.-H., Bhavsar, A. P., Lee, J. J. Y., Drögemöller, B. I., et al. (2016) · New England Journal of Medicine · doi:10.1056/nejmoa1515792 · Cited by 281

Pangenome-based genome inference allows efficient and accurate genotyping across a wide spectrum of variant classes

Ebler, J., Ebert, P., Clarke, W. E., Rausch, T., Audano, P. A., Houwaart, T., Mao, Y., Korbel, J. O., Eichler, E. E., Zody, M. C., et al. (2022) · Nature Genetics · doi:10.1038/s41588-022-01043-w · Cited by 277

False-positive results released by direct-to-consumer genetic tests highlight the importance of clinical confirmation testing for appropriate patient care

Tandy-Connor, S., Guiltinan, J., Krempely, K., LaDuca, H., Reineke, P., Gutierrez, S., Gray, P., & Tippin Davis, B. (2018) · Genetics in Medicine · doi:10.1038/gim.2018.38 · Cited by 273

MirSNP, a database of polymorphisms altering miRNA target sites, identifies miRNA-related SNPs in GWAS SNPs and eQTLs

Liu, C., Zhang, F., Li, T., Lu, M., Wang, L., Yue, W., & Zhang, D. (2012) · BMC Genomics · doi:10.1186/1471-2164-13-661 · Cited by 264

Computational identification of gene–social environment interaction at the human IL6 locus

Cole, S. W., Arevalo, J. M. G., Takahashi, R., Sloan, E. K., Lutgendorf, S. K., Sood, A. K., Sheridan, J. F., & Seeman, T. E. (2010) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.0911515107 · Cited by 256

Identification of a large set of rare complete human knockouts

Sulem, P., Helgason, H., Oddson, A., Stefansson, H., Gudjonsson, S. A., Zink, F., Hjartarson, E., Sigurdsson, G. T., Jonasdottir, A., Jonasdottir, A., et al. (2015) · Nature Genetics · doi:10.1038/ng.3243 · Cited by 220

Interaction between CRHR1 gene and stressful life events predicts adolescent heavy alcohol use

Blomeyer, D., Treutlein, J., Esser, G., Schmidt, M. H., Schumann, G., & Laucht, M. (2008) · Biological Psychiatry · doi:10.1016/j.biopsych.2007.04.026 · Cited by 211

Genomic insights into population history and biological adaptation in Oceania

Choin, J., Mendoza-Revilla, J., Arauna, L. R., Cuadros-Espinoza, S., Cassar, O., Larena, M., Ko, A. M.-S., Harmant, C., Laurent, R., Verdu, P., et al. (2021) · Nature · doi:10.1038/s41586-021-03236-5 · Cited by 208

Informed Consent in Genomics and Genetic Research

McGuire, A. L., & Beskow, L. M. (2010) · Annual Review of Genomics and Human Genetics · doi:10.1146/annurev-genom-082509-141711 · Cited by 204

Genetic association of the human corticotropin releasing hormone receptor 1 (CRHR1) with binge drinking and alcohol intake patterns in two independent samples

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Contribution to Alzheimer's disease risk of rare variants in TREM2, SORL1, and ABCA7 in 1779 cases and 1273 controls

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A second X chromosome contributes to resilience in a mouse model of Alzheimer’s disease

Davis, E. J., Broestl, L., Abdulai-Saiku, S., Worden, K., Bonham, L. W., Miñones-Moyano, E., Moreno, A. J., Wang, D., Chang, K., Williams, G., et al. (2020) · Science Translational Medicine · doi:10.1126/scitranslmed.aaz5677 · Cited by 176

How far from the SNP may the causative genes be?

Brodie, A., Azaria, J. R., & Ofran, Y. (2016) · Nucleic Acids Research · doi:10.1093/nar/gkw500 · Cited by 172

Comprehensive detection of germline variants by MSK-IMPACT, a clinical diagnostic platform for solid tumor molecular oncology and concurrent cancer predisposition testing

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