Structural variation in the human genome

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

Detection of large-scale variation in the human genome

Iafrate, A. J., Feuk, L., Rivera, M. N., Listewnik, M. L., Donahoe, P. K., Qi, Y., Scherer, S. W., & Lee, C. (2004) · Nature Genetics · doi:10.1038/ng1416 · Cited by 2,892

Initial sequence of the chimpanzee genome and comparison with the human genome

The Chimpanzee Sequencing and Analysis Consortium (2005) · Nature · doi:10.1038/nature04072 · Cited by 2,459

Common deletion polymorphisms in the human genome

McCarroll, S. A., Hadnott, T. N., Perry, G. H., Sabeti, P. C., Zody, M. C., Barrett, J. C., Dallaire, S., Gabriel, S. B., Lee, C., Daly, M. J., et al. (2006) · Nature Genetics · doi:10.1038/ng1696 · Cited by 701

A genome-wide comparison of recent chimpanzee and human segmental duplications

Cheng, Z., Ventura, M., She, X., Khaitovich, P., Graves, T., Osoegawa, K., Church, D., DeJong, P., Wilson, R. K., Pääbo, S., et al. (2005) · Nature · doi:10.1038/nature04000 · Cited by 398

Common deletions and SNPs are in linkage disequilibrium in the human genome

Hinds, D. A., Kloek, A. P., Jen, M., Chen, X., & Frazer, K. A. (2006) · Nature Genetics · doi:10.1038/ng1695 · Cited by 372

A 1.5 million–base pair inversion polymorphism in families with Williams-Beuren syndrome

Osborne, L. R., Li, M., Pober, B., Chitayat, D., Bodurtha, J., Mandel, A., Costa, T., Grebe, T., Cox, S., Tsui, L.-C., et al. (2001) · Nature Genetics · doi:10.1038/ng753 · Cited by 344

Comparison of the genomes of human and mouse lays the foundation of genome zoology

Emes, R. D. (2003) · Human Molecular Genetics · doi:10.1093/hmg/ddg078 · Cited by 220

Identification and analysis of functional elements in 1% of the human genome by the ENCODE pilot project

The ENCODE Project Consortium (2007) · Nature · doi:10.1038/nature05874 · Cited by 5,223

Consensus Statement: Chromosomal Microarray Is a First-Tier Clinical Diagnostic Test for Individuals with Developmental Disabilities or Congenital Anomalies

Miller, D. T., Adam, M. P., Aradhya, S., Biesecker, L. G., Brothman, A. R., Carter, N. P., Church, D. M., Crolla, J. A., Eichler, E. E., Epstein, C. J., et al. (2010) · The American Journal of Human Genetics · doi:10.1016/j.ajhg.2010.04.006 · Cited by 2,882

Strong association of de novo copy number mutations with autism

Sebat, J., Lakshmi, B., Malhotra, D., Troge, J., Lese-Martin, C., Walsh, T., Yamrom, B., Yoon, S., Krasnitz, A., Kendall, J., et al. (2007) · Science · doi:10.1126/science.1138659 · Cited by 2,795

Structural Variation of Chromosomes in Autism Spectrum Disorder

Marshall, C. R., Noor, A., Vincent, J. B., Lionel, A. C., Feuk, L., Skaug, J., Shago, M., Moessner, R., Pinto, D., Ren, Y., et al. (2008) · The American Journal of Human Genetics · doi:10.1016/j.ajhg.2007.12.009 · Cited by 1,815

PennCNV: An integrated hidden Markov model designed for high-resolution copy number variation detection in whole-genome SNP genotyping data

Wang, K., Li, M., Hadley, D., Liu, R., Glessner, J., Grant, S. F. A., Hakonarson, H., & Bucan, M. (2007) · Genome Research · doi:10.1101/gr.6861907 · Cited by 1,792

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

Genome structural variation discovery and genotyping

Alkan, C., Coe, B. P., & Eichler, E. E. (2011) · Nature Reviews Genetics · doi:10.1038/nrg2958 · Cited by 1,630

CNVnator: An approach to discover, genotype, and characterize typical and atypical CNVs from family and population genome sequencing

Abyzov, A., Urban, A. E., Snyder, M., & Gerstein, M. (2011) · Genome Research · doi:10.1101/gr.114876.110 · Cited by 1,658

Ovarian aging: mechanisms and clinical consequences

Broekmans, F. J., Soules, M. R., & Fauser, B. C. (2009) · Endocrine Reviews · doi:10.1210/er.2009-0006 · Cited by 1,248

Copy number variation in human health, disease, and evolution

Zhang, F., Gu, W., Hurles, M. E., & Lupski, J. R. (2009) · Annual Review of Genomics and Human Genetics · doi:10.1146/annurev.genom.9.081307.164217 · Cited by 1,207

Human genetic variation and its contribution to complex traits

Frazer, K. A., Murray, S. S., Schork, N. J., & Topol, E. J. (2009) · Nature Reviews Genetics · doi:10.1038/nrg2554 · Cited by 1,073

A copy number variation map of the human genome

Zarrei, M., MacDonald, J. R., Merico, D., & Scherer, S. W. (2015) · Nature Reviews Genetics · doi:10.1038/nrg3871 · Cited by 921

The UCSC genome browser and associated tools

Kuhn, R. M., Haussler, D., & Kent, W. J. (2013) · Briefings in Bioinformatics · doi:10.1093/bib/bbs038 · Cited by 883

Detecting Natural Selection in Genomic Data

Vitti, J. J., Grossman, S. R., & Sabeti, P. C. (2013) · Annual Review of Genetics · doi:10.1146/annurev-genet-111212-133526 · Cited by 694

Copy-number variations associated with neuropsychiatric conditions

Cook Jr, E. H., & Scherer, S. W. (2008) · Nature · doi:10.1038/nature07458 · Cited by 659

QuantiSNP: an Objective Bayes Hidden-Markov Model to detect and accurately map copy number variation using SNP genotyping data

Colella, S., Yau, C., Taylor, J. M., Mirza, G., Butler, H., Clouston, P., Bassett, A. S., Seller, A., Holmes, C. C., & Ragoussis, J. (2007) · Nucleic Acids Research · doi:10.1093/nar/gkm076 · Cited by 616

Population analysis of large copy number variants and hotspots of human genetic disease

Itsara, A., Cooper, G. M., Baker, C., Girirajan, S., Li, J., Absher, D., Krauss, R. M., Myers, R. M., Ridker, P. M., Chasman, D. I., et al. (2009) · The American Journal of Human Genetics · doi:10.1016/j.ajhg.2008.12.014 · Cited by 591

Single nucleotide polymorphism arrays: a decade of biological, computational and technological advances

LaFramboise, T. (2009) · Nucleic Acids Research · doi:10.1093/nar/gkp552 · Cited by 467

Female reproductive ageing: current knowledge and future trends

Broekmans, F. J., Knauff, E. A. H., te Velde, E. R., Macklon, N. S., & Fauser, B. C. (2007) · Trends in Endocrinology & Metabolism · doi:10.1016/j.tem.2007.01.004 · Cited by 427

Copy number variations and clinical cytogenetic diagnosis of constitutional disorders

Lee, C., Iafrate, A. J., & Brothman, A. R. (2007) · Nature Genetics · doi:10.1038/ng2092 · Cited by 388

Copy number variations and cancer

Shlien, A., & Malkin, D. (2009) · Genome Medicine · doi:10.1186/gm62 · Cited by 386

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

A roadmap for understanding the evolutionary significance of structural genomic variation

Mérot, C., Oomen, R. A., Tigano, A., & Wellenreuther, M. (2020) · Trends in Ecology & Evolution · doi:10.1016/j.tree.2020.03.002 · Cited by 357

Gene Copy-Number Alterations: A Cost-Benefit Analysis

Tang, Y.-C., & Amon, A. (2013) · Cell · doi:10.1016/j.cell.2012.11.043 · Cited by 348

New Gene Evolution: Little Did We Know

Long, M., VanKuren, N. W., Chen, S., & Vibranovski, M. D. (2013) · Annual Review of Genetics · doi:10.1146/annurev-genet-111212-133301 · Cited by 307

ADHD and autism: differential diagnosis or overlapping traits? A selective review

Taurines, R., Schwenck, C., Westerwald, E., Sachse, M., Siniatchkin, M., & Freitag, C. (2012) · ADHD Attention Deficit and Hyperactivity Disorders · doi:10.1007/s12402-012-0086-2 · Cited by 301

Rare structural variants in schizophrenia: one disorder, multiple mutations; one mutation, multiple disorders

Sebat, J., Levy, D. L., & McCarthy, S. E. (2009) · Trends in Genetics · doi:10.1016/j.tig.2009.10.004 · Cited by 260

An epigenetic framework for neurodevelopmental disorders: From pathogenesis to potential therapy

Millan, M. J. (2013) · Neuropharmacology · doi:10.1016/j.neuropharm.2012.11.015 · Cited by 229

Cognitive Performance Among Carriers of Pathogenic Copy Number Variants: Analysis of 152,000 UK Biobank Subjects

Kendall, K. M., Rees, E., Escott-Price, V., Einon, M., Thomas, R., Hewitt, J., O’Donovan, M. C., Owen, M. J., Walters, J. T. R., & Kirov, G. (2017) · Biological Psychiatry · doi:10.1016/j.biopsych.2016.08.014 · Cited by 226

A Comprehensive Workflow for Read Depth-Based Identification of Copy-Number Variation from Whole-Genome Sequence Data

Trost, B., Walker, S., Wang, Z., Thiruvahindrapuram, B., MacDonald, J. R., Sung, W. W. L., Pereira, S. L., Whitney, J., Chan, A. J. S., Pellecchia, G., et al. (2018) · The American Journal of Human Genetics · doi:10.1016/j.ajhg.2017.12.007 · Cited by 191

The genetics of Tourette syndrome: A review

O'Rourke, J. A., Scharf, J. M., Yu, D., & Pauls, D. L. (2009) · Journal of Psychosomatic Research · doi:10.1016/j.jpsychores.2009.06.006 · Cited by 212

SNPnexus: a web database for functional annotation of newly discovered and public domain single nucleotide polymorphisms

Chelala, C., Khan, A., & Lemoine, N. R. (2009) · Bioinformatics · doi:10.1093/bioinformatics/btn653 · Cited by 200

Genetic association analysis of copy-number variation (CNV) in human disease pathogenesis

Ionita-Laza, I., Rogers, A. J., Lange, C., Raby, B. A., & Lee, C. (2009) · Genomics · doi:10.1016/j.ygeno.2008.08.012 · Cited by 198

Paragraph: a graph-based structural variant genotyper for short-read sequence data

Chen, S., Krusche, P., Dolzhenko, E., Sherman, R. M., Petrovski, R., Schlesinger, F., Kirsche, M., Bentley, D. R., Schatz, M. C., Sedlazeck, F. J., et al. (2019) · Genome Biology · doi:10.1186/s13059-019-1909-7 · Cited by 196

Genomic copy number variation, human health, and disease

Wain, L. V., Armour, J. A., & Tobin, M. D. (2009) · The Lancet · doi:10.1016/s0140-6736(09)60249-x · Cited by 196

Applications of transformer-based language models in bioinformatics: a survey

Zhang, S., Fan, R., Liu, Y., Chen, S., Liu, Q., & Zeng, W. (2023) · Bioinformatics Advances · doi:10.1093/bioadv/vbad001 · Cited by 176

Current status of structural variation studies in plants

Yuan, Y., Bayer, P. E., Batley, J., & Edwards, D. (2021) · Plant Biotechnology Journal · doi:10.1111/pbi.13646 · Cited by 163

Male-biased autosomal effect of 16p13.11 copy number variation in neurodevelopmental disorders

Tropeano, M., Ahn, J. W., Dobson, R. J. B., Breen, G., Rucker, J., Dixit, A., Pal, D. K., McGuffin, P., Farmer, A., White, P. S., et al. (2013) · PLoS ONE · doi:10.1371/journal.pone.0061365 · Cited by 154

Identification of FOXP1 deletions in three unrelated patients with mental retardation and significant speech and language deficits

Horn, D., Kapeller, J., Rivera-Brugués, N., Moog, U., Lorenz-Depiereux, B., Eck, S., Hempel, M., Wagenstaller, J., Gawthrope, A., Monaco, A. P., et al. (2010) · Human Mutation · doi:10.1002/humu.21362 · Cited by 140

Advances in genomics for adapting crops to climate change

Scheben, A., Yuan, Y., & Edwards, D. (2016) · Current Plant Biology · doi:10.1016/j.cpb.2016.09.001 · Cited by 117

Somatic Mutagenesis in Mammals and Its Implications for Human Disease and Aging

Zhang, L., & Vijg, J. (2018) · Annual Review of Genetics · doi:10.1146/annurev-genet-120417-031501 · Cited by 108

Studying copy number variations using a nanofluidic platform

Qin, J., Jones, R. C., & Ramakrishnan, R. (2008) · Nucleic Acids Research · doi:10.1093/nar/gkn518 · Cited by 102

Rare autosomal copy number variations in early-onset familial Alzheimer’s disease

Hooli, B. V., Kovacs-Vajna, Z. M., Mullin, K., Blumenthal, M. A., Mattheisen, M., Zhang, C., Lange, C., Mohapatra, G., Bertram, L., & Tanzi, R. E. (2014) · Molecular Psychiatry · doi:10.1038/mp.2013.77 · Cited by 100

Evolving Role of MeCP2 in Rett syndrome and Autism

LaSalle, J. M., & Yasui, D. H. (2009) · Epigenomics · doi:10.2217/epi.09.13 · Cited by 98

Molecular, genetic and evolutionary analysis of a paracentric inversion in Arabidopsis thaliana

Fransz, P., Linc, G., Lee, C., Aflitos, S. A., Lasky, J. R., Toomajian, C., Ali, H., Peters, J., van Dam, P., Ji, X., et al. (2016) · The Plant Journal · doi:10.1111/tpj.13262 · Cited by 94

Analysis of deletion breakpoints from 1,092 humans reveals details of mutation mechanisms

Abyzov, A., Li, S., Kim, D. R., Mohiyuddin, M., Stütz, A. M., Parrish, N. F., Mu, X. J., Clark, W., Chen, K., Hurles, M., et al. (2015) · Nature Communications · doi:10.1038/ncomms8256 · Cited by 91

Association of common copy number variants at the glutathione S-transferase genes and rare novel genomic changes with schizophrenia

Rodríguez-Santiago, B., Brunet, A., Sobrino, B., Serra-Juhé, C., Flores, R., Armengol, L., Vilella, E., Gabau, E., Guitart, M., Guillamat, R., et al. (2010) · Molecular Psychiatry · doi:10.1038/mp.2009.53 · Cited by 88

Reciprocal white matter alterations due to 16p11.2 chromosomal deletions versus duplications

Chang, Y. S., Owen, J. P., Pojman, N. J., Thieu, T., Bukshpun, P., Wakahiro, M. L. J., Marco, E. J., Berman, J. I., Spiro, J. E., Chung, W. K., et al. (2016) · Human Brain Mapping · doi:10.1002/hbm.23211 · Cited by 81

Copy Number Variation in Familial Parkinson Disease

Pankratz, N., Dumitriu, A., Hetrick, K. N., Sun, M., Latourelle, J. C., Wilk, J. B., Halter, C., Doheny, K. F., Gusella, J. F., Nichols, W. C., et al. (2011) · PLoS ONE · doi:10.1371/journal.pone.0020988 · Cited by 81

Detection of a novel familial deletion of four genes between BP1 and BP2 of the Prader-Willi/Angelman syndrome critical region by oligo-array CGH in a child with neurological disorder and speech impairment

Murthy, S. K., Nygren, A. O. H., El Shakankiry, H. M., Schouten, J. P., Al Khayat, A. I., Ridha, A., & Al Ali, M. T. (2007) · Cytogenetic and Genome Research · doi:10.1159/000097433 · Cited by 79

Autism: the quest for the genes

Sykes, N. H., & Lamb, J. A. (2007) · Expert Reviews in Molecular Medicine · doi:10.1017/s1462399407000452 · Cited by 58

Rare CNVs and Tag SNPs at 15q11.2 are associated with schizophrenia in the Han Chinese population

Zhao, Q., Li, T., Zhao, X., Huang, K., Wang, T., Li, Z., Ji, J., Zeng, Z., Zhang, Z., Li, K., et al. (2013) · Schizophrenia Bulletin · doi:10.1093/schbul/sbr197 · Cited by 58

Genome-wide association analysis of copy number variation in recurrent depressive disorder

Rucker, J. J. H., Breen, G., Pinto, D., Pedroso, I., Lewis, C. M., Cohen-Woods, S., Uher, R., Schosser, A., Rivera, M., Aitchison, K. J., et al. (2013) · Molecular Psychiatry · doi:10.1038/mp.2011.144 · Cited by 51

Human 45,X fibroblast transcriptome reveals distinct differentially expressed genes including long noncoding RNAs potentially associated with the pathophysiology of Turner syndrome

Rajpathak, S. N., Vellarikkal, S. K., Patowary, A., Scaria, V., Sivasubbu, S., & Deobagkar, D. D. (2014) · PLoS ONE · doi:10.1371/journal.pone.0100076 · Cited by 51

Analysis of genetic deletions and duplications in the University College London bipolar disorder case control sample

McQuillin, A., Bass, N., Anjorin, A., Lawrence, J., Kandaswamy, R., Lydall, G., Moran, J., Sklar, P., Purcell, S., & Gurling, H. (2011) · European Journal of Human Genetics · doi:10.1038/ejhg.2010.221 · Cited by 47

Genomic Disorders in Psychiatry-What Does the Clinician Need to Know?

Lowther, C., Costain, G., Baribeau, D. A., & Bassett, A. S. (2017) · Current Psychiatry Reports · doi:10.1007/s11920-017-0831-5 · Cited by 41

Untitled work

(2007) · Cited by 33

Structure and evolution of the filaggrin gene repeated region in primates

Romero, V., Hosomichi, K., Nakaoka, H., Shibata, H., & Inoue, I. (2017) · BMC Evolutionary Biology · doi:10.1186/s12862-016-0851-5 · Cited by 11

A Pilot Detection and Associate Study of Gene Presence-Absence Variation in Holstein Cattle

Boschiero, C., Neupane, M., Yang, L., Schroeder, S. G., Tuo, W., Ma, L., Baldwin, R. L., Van Tassell, C. P., & Liu, G. E. (2024) · Animals · doi:10.3390/ani14131921 · Cited by 5