An analytical framework for whole-genome sequence association studies and its implications for autism spectrum disorder

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

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The Human Genome Browser at UCSC

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Analysis of protein-coding genetic variation in 60,706 humans

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Biological insights from 108 schizophrenia-associated genetic loci

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Topological domains in mammalian genomes identified by analysis of chromatin interactions

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

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Integrative analysis of 111 reference human epigenomes

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GENCODE: The reference human genome annotation for The ENCODE Project

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Evolutionarily conserved elements in vertebrate, insect, worm, and yeast genomes

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Recent genetic and functional insights in autism spectrum disorder

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Genome-wide structural variant analysis identifies risk loci for non-Alzheimer’s dementias

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A Cre-dependent massively parallel reporter assay allows for cell-type specific assessment of the functional effects of non-coding elements in vivo

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De novo mutations identified by whole-genome sequencing implicate chromatin modifications in obsessive-compulsive disorder

Lin, G. N., Song, W., Wang, W., Wang, P., Yu, H., Cai, W., Jiang, X., Huang, W., Qian, W., Chen, Y., et al. (2022) · Science Advances · doi:10.1126/sciadv.abi6180 · Cited by 30

Biological implications of genetic variations in autism spectrum disorders from genomics studies

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Kevlar: A Mapping-Free Framework for Accurate Discovery of De Novo Variants

Standage, D., Brown, C. T., & Hormozdiari, F. (2019) · iScience · doi:10.1016/j.isci.2019.07.032 · Cited by 28

Key Synaptic Pathology in Autism Spectrum Disorder: Genetic Mechanisms and Recent Advances

Zhang, Y., Tang, R., Hu, Z., Wang, X., Gao, X., Wang, T., & Tang, M. X. (2024) · Journal of Integrative Neuroscience · doi:10.31083/j.jin2310184 · Cited by 30

Rare germline structural variants increase risk for pediatric solid tumors

Gillani, R., Collins, R. L., Crowdis, J., Garza, A., Jones, J. K., Walker, M., Sanchis-Juan, A., Whelan, C., Pierce‐Hoffman, E., Talkowski, M. E., et al. (2025) · Science · doi:10.1126/science.adq0071 · Cited by 28

Genetic testing for unexplained perinatal disorders

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Coding and noncoding variants in EBF3 are involved in HADDS and simplex autism

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Next-Generation Sequencing in Autism Spectrum DisorderPreprint

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CellWalker integrates single-cell and bulk data to resolve regulatory elements across cell types in complex tissues

Przytycki, P. F., & Pollard, K. S. (2021) · Genome biology · doi:10.1186/s13059-021-02279-1 · Cited by 25

A Population-Specific Major Allele Reference Genome From The United Arab Emirates Population

Elbait, G. D., Henschel, A., Tay, G. K., & AlSafar, H. S. (2021) · Frontiers in Genetics · doi:10.3389/fgene.2021.660428 · Cited by 23

A comprehensive benchmarking of WGS-based deletion structural variant callers

Sarwal, V., Niehus, S., Ayyala, R., Kim, M., Sarkar, A. P., Chang, S., Lu, A., Rajkumar, N., Darci-Maher, N., Littman, R., et al. (2022) · Briefings in Bioinformatics · doi:10.1093/bib/bbac221 · Cited by 28

A recurrent SHANK3 frameshift variant in Autism Spectrum Disorder

Loureiro, L. O., Howe, J., Reuter, M. S., Iaboni, A., Calli, K., Roshandel, D., Pritišanac, I., Moses, A. M., Forman-Kay, J. D., Trost, B., et al. (2021) · npj Genomic Medicine · doi:10.1038/s41525-021-00254-0 · Cited by 30

Estimating contribution of rare non‐coding variants to neuropsychiatric disorders

Takata, A. (2018) · Psychiatry and Clinical Neurosciences · doi:10.1111/pcn.12774 · Cited by 24

Origins and Long-Term Patterns of Copy-Number Variation in Rhesus Macaques

Thomas, G. W. C., Wang, R. J., Nguyen, J., Harris, R. A., Raveendran, M., Rogers, J., & Hahn, M. W. (2020) · Molecular Biology and Evolution · doi:10.1093/molbev/msaa303 · Cited by 21

Non-coding de novo mutations in chromatin interactions are implicated in autism spectrum disorder

Kim, I. B., Lee, T., Lee, J., Kim, J., Lee, S., Koh, I. G., Kim, J. H., An, J., Lee, H., Kim, W. K., et al. (2022) · Molecular Psychiatry · doi:10.1038/s41380-022-01697-2 · Cited by 27

Transcriptome-wide transmission disequilibrium analysis identifies novel risk genes for autism spectrum disorder

Huang, K., Wu, Y., Shin, J., Zheng, Y., Siahpirani, A. F., Lin, Y., Ni, Z., Chen, J., You, J., Keleş, S., et al. (2021) · PLoS Genetics · doi:10.1371/journal.pgen.1009309 · Cited by 23

Molecular Dysregulation in Autism Spectrum Disorder

Gill, P. S., Clothier, J. L., Veerapandiyan, A., Dweep, H., Porter-Gill, P. A., & Schaefer, G. B. (2021) · Journal of Personalized Medicine · doi:10.3390/jpm11090848 · Cited by 22

Mapping and characterization of structural variation in 17,795 deeply sequenced human genomesPreprint

Abel, H., Larson, D. E., Chiang, C., Das, I., Kanchi, K., Layer, R. M., Neale, B. M., Salerno, W. J., Reeves, C., Buyske, S. G., et al. (2018) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/508515 · Cited by 22

MicroRNA Expression Profiles in Autism Spectrum Disorder: Role for miR-181 in Immunomodulation

Frye, R. E., Rose, S., McCullough, S. S., Bennuri, S. C., Porter-Gill, P. A., Dweep, H., & Gill, P. S. (2021) · Journal of Personalized Medicine · doi:10.3390/jpm11090922 · Cited by 22

Rare variants found in clinical gene panels illuminate the genetic and allelic architecture of orofacial clefting

Perez, K. K. D., Curtis, S. W., Sanchis‐Juan, A., Zhao, X., Head, S. T., Ho, S., Carter, B., McHenry, T. G., Bishop, M. R., Valencia‐Ramirez, L. C., et al. (2023) · Genetics in Medicine · doi:10.1016/j.gim.2023.100918 · Cited by 21

Gene therapy for polygenic or complex diseases

Wu, T., Hu, Y., & Tang, L. V. (2024) · Biomarker Research · doi:10.1186/s40364-024-00618-5 · Cited by 24

FunSPU: A versatile and adaptive multiple functional annotation-based association test of whole-genome sequencing data

Ma, Y., & Wei, P. (2019) · PLoS Genetics · doi:10.1371/journal.pgen.1008081 · Cited by 19

Detection of trait-associated structural variations using short-read sequencing

Kosugi, S., Kamatani, Y., Harada, K., Tomizuka, K., Momozawa, Y., Morisaki, T., & Terao, C. (2023) · Cell Genomics · doi:10.1016/j.xgen.2023.100328 · Cited by 19

de novo variant calling identifies cancer mutation signatures in the 1000 Genomes Project

Ng, J. K., Vats, P., Fritz‐Waters, E., Sarkar, S., Sams, E. I., Padhi, E. M., Payne, Z. L., Leonard, S., West, M. A., Prince, C., et al. (2022) · Human Mutation · doi:10.1002/humu.24455 · Cited by 17

A Comparison of Structural Variant Calling from Short-Read and Nanopore-Based Whole-Genome Sequencing Using Optical Genome Mapping as a Benchmark

Pei, Y., Tanguy, M., Giess, A. P., Dixit, A., Wilson, L. C., Gibbons, R. J., Twigg, S. R. F., Elgar, G., & Wilkie, A. O. M. (2024) · Genes · doi:10.3390/genes15070925 · Cited by 18

Genetic modifiers and ascertainment drive variable expressivity of complex disorders

Jensen, M., Smolen, C., Tyryshkina, A., Pizzo, L., Sun, J., Noss, S., Banerjee, D., Oetjens, M. T., Shimelis, H., Taylor, C. M., et al. (2025) · Cell · doi:10.1016/j.cell.2025.09.012 · Cited by 21

CWAS-Plus: estimating category-wide association of rare noncoding variation from whole-genome sequencing data with cell-type-specific functional data

Kim, Y., Jeong, M., Koh, I. G., Kim, C., Lee, H., Kim, J. H., Yurko, R., Kim, I. B., Park, J., Werling, D. M., et al. (2024) · Briefings in Bioinformatics · doi:10.1093/bib/bbae323 · Cited by 18

Prenatal Neuropathologies in Autism Spectrum Disorder and Intellectual Disability: The Gestation of a Comprehensive Zebrafish Model

Kozol, R. A. (2018) · Journal of Developmental Biology · doi:10.3390/jdb6040029 · Cited by 18

PsyMuKB: An Integrative De Novo Variant Knowledge Base for Developmental Disorders

Lin, G. N., Guo, S., Xian, T., Wang, W., Qian, W., Song, W., Wang, J., Yu, S., Wang, Z., Cui, D., et al. (2019) · Genomics Proteomics & Bioinformatics · doi:10.1016/j.gpb.2019.10.002 · Cited by 16

Introduction of genomics into prenatal diagnostics

Talkowski, M. E., & Rehm, H. L. (2019) · The Lancet · doi:10.1016/s0140-6736(19)30193-x · Cited by 18

Topologically associating domains define the impact of de novo promoter variants on autism spectrum disorder risk

Nakamura, T., Ueda, J., Mizuno, S., Honda, K., Kazuno, A., Yamamoto, H., Hara, T., & Takata, A. (2024) · Cell Genomics · doi:10.1016/j.xgen.2024.100488 · Cited by 17

The Importance of Large-Scale Genomic Studies to Unravel Genetic Risk Factors for Autism

Nóbrega, I. D. S., Silva, A. L. T. E., Yokota-Moreno, B. Y., & Sertie, A. L. (2024) · International Journal of Molecular Sciences · doi:10.3390/ijms25115816 · Cited by 18

Autism spectrum disorder genomics: The progress and potential of genomic technologies

Ghrálaigh, F. N., Gallagher, L., & Lopez, L. M. (2020) · Genomics · doi:10.1016/j.ygeno.2020.09.022 · Cited by 14

Phenotype based prediction of exome sequencing outcome using machine learning for neurodevelopmental disorders

Dingemans, A. J. M., Hinne, M., Jansen, S., van Reeuwijk, J., de Leeuw, N., Pfundt, R., van Bon, B. W. M., Silfhout, A. T. V., Kleefstra, T., Koolen, D. A., et al. (2021) · Genetics in Medicine · doi:10.1016/j.gim.2021.10.019 · Cited by 16

Delineation of a novel neurodevelopmental syndrome associated with PAX5 haploinsufficiency

Gofin, Y., Wang, T., Gillentine, M. A., Scott, T. M., Berry, A. M., Azamian, M. S., Genetti, C. A., Agrawal, P. B., Picker, J. D., Wojcik, M. H., et al. (2022) · Human Mutation · doi:10.1002/humu.24332 · Cited by 15

Integrating Genetic Structural Variations and Whole-Genome Sequencing Into Clinical Neurology

Lin, X., Yang, Y., Melton, P. E., Singh, V., Simpson, S., Burdon, K. P., Taylor, B. V., & Zhou, Y. (2022) · Neurology Genetics · doi:10.1212/nxg.0000000000200005 · Cited by 16

Whole-genome sequencing in a family with twin boys with autism and intellectual disability suggests multimodal polygenic riskPreprint

McKenna, B. G., Koomar, T., Vervier, K., Kremsreiter, J. L., & Michaelson, J. J. (2018) · Molecular Case Studies · doi:10.1101/mcs.a003285 · Cited by 15

Characterization of De Novo Promoter Variants in Autism Spectrum Disorder with Massively Parallel Reporter Assays

Koesterich, J., An, J., Inoue, F., Sohota, A., Ahituv, N., Sanders, S., & Kreimer, A. (2023) · International Journal of Molecular Sciences · doi:10.3390/ijms24043509 · Cited by 13

Intellectual Disability and Behavioral Deficits Linked to CYFIP1 Missense Variants Disrupting Actin Polymerization

Mariano, V., Kanellopoulos, A. K., Ricci, C., Di Marino, D., Borrie, S. C., Dupraz, S., Bradke, F., Achsel, T., Legius, E., Odent, S., et al. (2024) · Biological Psychiatry · doi:10.1016/j.biopsych.2023.08.027 · Cited by 14

HAT: de novo variant calling for highly accurate short-read and long-read sequencing data

Ng, J. K., & Turner, T. N. (2024) · Bioinformatics · doi:10.1093/bioinformatics/btad775 · Cited by 12

Trends and cross-country inequalities in the global burden of neurodevelopmental disorders among children aged 0–14 from 1990 to 2021

Jia, T., Kong, Y., Zhao, G., & Wang, Y. (2025) · Frontiers in Public Health · doi:10.3389/fpubh.2025.1609254 · Cited by 16

Single-neuron whole genome sequencing identifies increased somatic mutation burden in Alzheimer's disease related genes

Li, Z., Min, S., Alliey‐Rodriguez, N., Giase, G. M., Cheng, L., Craig, D. W., Faulkner, G. J., Asif, H., Liu, C., & Gershon, E. S. (2022) · Neurobiology of Aging · doi:10.1016/j.neurobiolaging.2022.12.002 · Cited by 14

Short tandem repeat expansions in cortical layer‐specific genes implicate in phenotypic severity and adaptability of autism spectrum disorder

Kim, J. H., Koh, I. G., Lee, H., Lee, G., Song, D., Kim, S., Kim, Y., Han, J. H., Bong, G., Lee, J., et al. (2024) · Psychiatry and Clinical Neurosciences · doi:10.1111/pcn.13676 · Cited by 13

Systematic evaluation of genome sequencing for the assessment of fetal structural anomaliesPreprint

Lowther, C., Valkanas, E., Giordano, J. L., Wang, H. Z., Currall, B., O’Keefe, K., Pierce‐Hoffman, E., Kurtas, N. E., Whelan, C. W., Hao, S. P., et al. (2020) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2020.08.12.248526 · Cited by 13

Epistasis between mutator alleles contributes to germline mutation spectrum variability in laboratory mice

Sasani, T. A., Quinlan, A. R., & Harris, K. (2023) · eLife · doi:10.7554/elife.89096 · Cited by 12

The Genetic Control of Stoichiometry Underlying Autism

Darnell, R. B. (2020) · Annual Review of Neuroscience · doi:10.1146/annurev-neuro-100119-024851 · Cited by 12

GATK-gCNV: A Rare Copy Number Variant Discovery Algorithm and Its Application to Exome Sequencing in the UK BiobankPreprint

Babadi, M., Fu, J. M., Lee, S. K., Smirnov, A. N., Gauthier, L. D., Walker, M., Benjamin, D. I., Karczewski, K. J., Wong, I., Collins, R. L., et al. (2022) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2022.08.25.504851 · Cited by 12

The Landscape of Structural Variation in Aye-Ayes (Daubentonia madagascariensis)

Versoza, C. J., Jensen, J. D., & Pfeifer, S. P. (2025) · Genome Biology and Evolution · doi:10.1093/gbe/evaf167 · Cited by 11

Sizing up whole-genome sequencing studies of common diseases

Wray, N. R., & Gratten, J. (2018) · Nature Genetics · doi:10.1038/s41588-018-0113-0 · Cited by 12

Outgroup Machine Learning Approach Identifies Single Nucleotide Variants in Noncoding DNA Associated with Autism Spectrum Disorder

Varma, M., Paskov, K. M., Jung, J.-Y., Chrisman, B., Stockham, N., Washington, P. Y., & Wall, D. P. (2018) · Pacific Symposium on Biocomputing (PSB) · doi:10.1142/9789813279827_0024 · Cited by 12

De novo mutation of cancer-related genes associates with particular neurodevelopmental disorders

Li, B., Li, K., Tian, D., Zhou, Q., Xie, Y., Fang, Z., Wang, X., Luo, T., Wang, Z., Zhang, Y., et al. (2020) · Journal of Molecular Medicine · doi:10.1007/s00109-020-01991-y · Cited by 10

Integrated Functional Analysis Implicates Syndromic and Rare Copy Number Variation Genes as Prominent Molecular Players in Pathogenesis of Autism Spectrum Disorders

Ashitha, S. N. M., & Ramachandra, N. B. (2020) · Neuroscience · doi:10.1016/j.neuroscience.2020.04.051 · Cited by 10

From genetics to biology: advancing mental health research in the Genomics ERA

Arguello, P. A., Addington, A. M., Borja, S. E., Brady, L. S., Dutka, T., Gitik, M., Koester, S. E., Meinecke, D. L., Merikangas, K. R., McMahon, F. J., et al. (2019) · Molecular Psychiatry · doi:10.1038/s41380-019-0445-x · Cited by 11

ParseCNV2: efficient sequencing tool for copy number variation genome-wide association studies

Glessner, J., Li, J., Liu, Y., Khan, M., Chang, X., Abou‐Sleiman, P. M., & Hakonarson, H. H. (2022) · European Journal of Human Genetics · doi:10.1038/s41431-022-01222-7 · Cited by 9

Overview of structural variation calling: Simulation, identification, and visualization

Lei, Y., Meng, Y., Guo, X., Ning, K., Bian, Y., Li, L., Hu, Z., Anashkina, A. A., Jiang, Q., Dong, Y., et al. (2022) · Computers in Biology and Medicine · doi:10.1016/j.compbiomed.2022.105534 · Cited by 12

Developmental convergence and divergence in human stem cell models of autism spectrum disorderPreprint

Gordon, A., Yoon, S., Bicks, L. K., Martín, J. M., Pintacuda, G., Arteaga, S., Wamsley, B., Guo, Q., Elahi, L. S., Dolmetsch, R. E., et al. (2024) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2024.04.01.587492 · Cited by 10

Balanced chromosomal rearrangements offer insights into coding and noncoding genomic features associated with developmental disordersPreprint

Lowther, C., Mehrjouy, M. M., Collins, R. L., Bak, M., Dudchenko, O., Brand, H., Dong, Z., Rasmussen, M. B., Gu, H., Weisz, D., et al. (2022) · medRxiv · doi:10.1101/2022.02.15.22270795 · Cited by 7

Advances and challenges in quantitative delineation of the genetic architecture of complex traits

Tang, H., & He, Z. (2021) · Quantitative Biology · doi:10.15302/j-qb-021-0249 · Cited by 9

The genetic landscape of early‐onset Alzheimer's disease in China

Qin, W. D., Li, F., Liu, W., Li, Y., Cao, S., Wei, Y., Li, Y., Wang, Y., Wang, Q., & Jia, J. (2025) · Alzheimer s & Dementia · doi:10.1002/alz.14486 · Cited by 9

Neurodevelopmental impact of CNV models in ASD: Recent advances and future directions

Tamada, K., & Takumi, T. (2025) · Current Opinion in Neurobiology · doi:10.1016/j.conb.2025.103001 · Cited by 10

Whole-genome sequencing analyses suggest novel genetic factors associated with Alzheimer’s disease and a cumulative effects model for risk liability

Kim, J. P., Cho, M., Kim, C., Lee, H., Jang, B., Jung, S., Kim, Y., Koh, I. G., Kim, S., Shin, D., et al. (2025) · Nature Communications · doi:10.1038/s41467-025-59949-y · Cited by 10

Real‐life Progression of the Use of a Genetic Panel in to Diagnose Neonatal Cholestasis

Ito, S., Togawa, T., Imagawa, K., Ito, K., Endo, T., Sugiura, T., & Saitoh, S. (2022) · JPGN Reports · doi:10.1097/pg9.0000000000000196 · Cited by 8

Advancing precision diagnosis in autism: Insights from large-scale genomic studies

Kim, S.-W., & An, J. (2025) · Molecules and Cells · doi:10.1016/j.mocell.2025.100248 · Cited by 10

Molecular and Genetic Mechanisms in Autism Spectrum Disorder

Pruitt, A., Gupta, A. R., & Hoffman, E. J. (2025) · Annals of Neurology · doi:10.1002/ana.70013 · Cited by 11

Spatio-Temporal Roles of ASD-Associated Variants in Human Brain Development

Kim, Y., & An, J. (2020) · Genes · doi:10.3390/genes11050535 · Cited by 8

Investigation of Chromosomal Structural Abnormalities in Patients With Undiagnosed Neurodevelopmental Disorders

Cao, Y., Luk, H., Zhang, Y., Chau, M. H. K., Xue, S., Cheng, S. S. W., Li, A. M., Chong, J. S. C., Leung, T. Y., Dong, Z., et al. (2022) · Frontiers in Genetics · doi:10.3389/fgene.2022.803088 · Cited by 8

Genetic Determinants and Pharmacogenetics of Osteoporosis and Osteoporotic Fracture

Hsu, Y., Xu, X., & Jeong, S. (2020) · Contemporary Endocrinology · doi:10.1007/978-3-319-69287-6_25 · Cited by 8

Functional annotation of rare structural variation in the human brainPreprint

Han, L., Zhao, X., Benton, M. L., Perumal, T. M., Collins, R. L., Hoffman, G. E., Johnson, J., Sloofman, L. G., Wang, H. Z., Brennand, K., et al. (2019) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/711754 · Cited by 8

de novo variant calling identifies cancer mutation profiles in the 1000 Genomes ProjectPreprint

Ng, J. K., Vats, P., Fritz‐Waters, E., Sarkar, S., Sams, E. I., Padhi, E. M., Payne, Z. L., Leonard, S., West, M. A., Prince, C., et al. (2021) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/2021.05.27.445979 · Cited by 8

Complex de novo structural variants are an underestimated cause of rare disorders

Jung, H., Yang, T.-P., Walker, S., Danecek, P., Garcia-Salinas, O. I., Neville, M. D. C., Christopher, J., Cortés‐Ciriano, I., Firth, H. V., Scally, A., et al. (2025) · Nature Communications · doi:10.1038/s41467-025-64722-2 · Cited by 8

A Map of 3′ DNA Transduction Variants Mediated by Non-LTR Retroelements on 3202 Human Genomes

Halabian, R., & Makałowski, W. (2022) · Biology · doi:10.3390/biology11071032 · Cited by 6

Neuroscience and the Future of Psychiatry

Travis, M. J. (2019) · FOCUS The Journal of Lifelong Learning in Psychiatry · doi:10.1176/appi.focus.20180032 · Cited by 7

Discovery of rare variants implicated in schizophrenia using next-generation sequencing

Rhoades, R. E., Jackson, F. L. C., & Teng, S. (2019) · Journal of Translational Genetics and Genomics · doi:10.20517/jtgg.2018.26 · Cited by 8

Whole genome sequencing in multiplex families reveals novel inherited and de novo genetic risk in autismPreprint

Ruzzo, E. K., Pérez‐Cano, L., Jung, J.-Y., Wang, L.-K., Kashef-Haghighi, D., Hartl, C., Hoekstra, J. N., Leventhal, O., Gandal, M. J., Paskov, K. M., et al. (2018) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/338855 · Cited by 7

Evaluation of familial phenotype deviation to measure the impact of de novo mutations in autism

Kim, S.-W., Lee, H., Song, D. Y., Lee, G., Han, J. H., Lee, J., Byun, H. J., Son, J. H., Kim, Y. R., Lee, Y., et al. (2025) · Genome Medicine · doi:10.1186/s13073-025-01532-7 · Cited by 7

Clinical Targeted Panel Sequencing Analysis in Clinical Evaluation of Children with Autism Spectrum Disorder in China

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Regulatory de novo mutations underlying intellectual disability

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Co-occurrence of rare variants implicates gene pairs in cytoskeletal pathways and is associated with increased severity in autism spectrum disorder

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