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

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 · see citing works

BEDTools: a flexible suite of utilities for comparing genomic features

Quinlan, A. R., & Hall, I. M. (2010) · Bioinformatics · doi:10.1093/bioinformatics/btq033 · Cited by 27,437 · see citing works

The Human Genome Browser at UCSC

Kent, W. J., Sugnet, C. W., Furey, T. S., Roskin, K. M., Pringle, T. H., Zahler, A. M., & Haussler, A. D. (2002) · Genome Research · doi:10.1101/gr.229102 · Cited by 10,400 · see citing works

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

Exome Aggregation Consortium, Lek, M., Karczewski, K. J., Minikel, E. V., Samocha, K. E., Banks, E., Fennell, T., O’Donnell-Luria, A. H., Ware, J. S., Hill, A. J., et al. (2016) · Nature · doi:10.1038/nature19057 · Cited by 9,587 · see citing works

Biological insights from 108 schizophrenia-associated genetic loci

Schizophrenia Working Group of the Psychiatric Genomics Consortium (2014) · Nature · doi:10.1038/nature13595 · Cited by 7,577 · see citing works

Topological domains in mammalian genomes identified by analysis of chromatin interactions

Dixon, J. R., Selvaraj, S., Yue, F., Kim, A., Li, Y., Shen, Y., Hu, M., Liu, J. S., & Ren, B. (2012) · Nature · doi:10.1038/nature11082 · Cited by 6,829 · see citing works

Integrative analysis of 111 reference human epigenomes

Roadmap Epigenomics Consortium, Kundaje, A., Meuleman, W., Ernst, J., Bilenky, M., Yen, A., Heravi-Moussavi, A., Kheradpour, P., Zhang, Z., Wang, J., et al. (2015) · Nature · doi:10.1038/nature14248 · Cited by 6,368 · see citing works

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 6,283 · see citing works

GENCODE: The reference human genome annotation for The ENCODE Project

Harrow, J., Frankish, A., Gonzalez, J. M., Tapanari, E., Diekhans, M., Kokocinski, F., Aken, B. L., Barrell, D., Zadissa, A., Searle, S., et al. (2012) · Genome Research · doi:10.1101/gr.135350.111 · Cited by 4,585 · see citing works

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

Siepel, A., Bejerano, G., Pedersen, J. S., Hinrichs, A. S., Hou, M., Rosenbloom, K., Clawson, H., Spieth, J., Hillier, L. W., Richards, S., et al. (2005) · Genome Research · doi:10.1101/gr.3715005 · Cited by 4,408 · see citing works

Genome-wide association studies for common diseases and complex traits

Hirschhorn, J. N., & Daly, M. J. (2005) · Nature Reviews Genetics · doi:10.1038/nrg1521 · Cited by 2,852 · see citing works

The contribution of de novo coding mutations to autism spectrum disorder

Iossifov, I., O’Roak, B. J., Sanders, S. J., Ronemus, M., Krumm, N., Levy, D., Stessman, H. A., Witherspoon, K. T., Vives, L., Patterson, K. E., et al. (2014) · Nature · doi:10.1038/nature13908 · Cited by 2,585 · see citing works

An atlas of active enhancers across human cell types and tissues

The FANTOM Consortium, Andersson, R., Gebhard, C., Miguel-Escalada, I., Hoof, I., Bornholdt, J., Boyd, M., Chen, Y., Zhao, X., Schmidl, C., et al. (2014) · Nature · doi:10.1038/nature12787 · Cited by 2,550 · see citing works

ChromHMM: automating chromatin-state discovery and characterization

Ernst, J., & Kellis, M. (2012) · Nature Methods · doi:10.1038/nmeth.1906 · Cited by 2,489 · see citing works

DELLY: structural variant discovery by integrated paired-end and split-read analysis

Rausch, T., Zichner, T., Schlattl, A., Stütz, A. M., Beneš, V., & Korbel, J. O. (2012) · Bioinformatics · doi:10.1093/bioinformatics/bts378 · Cited by 2,384 · see citing works

An integrated map of structural variation in 2,504 human genomes

Sudmant, P. H., Rausch, T., Gardner, E. J., Handsaker, R. E., Abyzov, A., Huddleston, J., Zhang, Y., Ye, K., Jun, G., Hsi-Yang Fritz, M., et al. (2015) · Nature · doi:10.1038/nature15394 · Cited by 2,354 · see citing works

Detection of nonneutral substitution rates on mammalian phylogenies

Pollard, K. S., Hubisz, M. J., Rosenbloom, K. R., & Siepel, A. (2010) · Genome Research · doi:10.1101/gr.097857.109 · Cited by 2,353 · see citing works

Manta: rapid detection of structural variants and indels for germline and cancer sequencing applications

(2015) · doi:10.1093/bioinformatics/btv710 · Cited by 2,234 · see citing works

Sporadic autism exomes reveal a highly interconnected protein network of de novo mutations

O’Roak, B. J., Vives, L., Girirajan, S., Karakoc, E., Krumm, N., Coe, B. P., Levy, R., Ko, A., Lee, C., Smith, J. D., et al. (2012) · Nature · doi:10.1038/nature10989 · Cited by 2,165 · see citing works

The new NHGRI-EBI Catalog of published genome-wide association studies (GWAS Catalog)

MacArthur, J., Bowler, E., Cerezo, M., Gil, L., Hall, P., Hastings, E., Junkins, H., McMahon, A., Milano, A., Morales, J., et al. (2017) · Nucleic Acids Research · doi:10.1093/nar/gkw1133 · Cited by 2,161 · see citing works

Rate of de novo mutations and the importance of father’s age to disease risk

Kong, A., Frigge, M. L., Masson, G., Besenbacher, S., Sulem, P., Magnusson, G., Gudjonsson, S. A., Sigurdsson, A., Jonasdottir, A., Jonasdottir, A., et al. (2012) · Nature · doi:10.1038/nature11396 · Cited by 2,134 · see citing works

De novo mutations revealed by whole-exome sequencing are strongly associated with autism

Sanders, S. J., Murtha, M. T., Gupta, A. R., Murdoch, J. D., Raubeson, M. J., Willsey, A. J., Ercan-Sencicek, A. G., DiLullo, N. M., Parikshak, N. N., Stein, J. L., et al. (2012) · Nature · doi:10.1038/nature10945 · Cited by 2,084 · see citing works

FMRP Stalls Ribosomal Translocation on mRNAs Linked to Synaptic Function and Autism

Darnell, J. C., Van Driesche, S. J., Zhang, C., Hung, K. Y. S., Mele, A., Fraser, C. E., Stone, E. F., Chen, C., Fak, J. J., Chi, S. W., et al. (2011) · Cell · doi:10.1016/j.cell.2011.06.013 · Cited by 2,072 · see citing works

Genetic diagnosis of developmental disorders in the DDD study: a scalable analysis of genome-wide research data

Wright, C., Fitzgerald, T. W., Jones, W., Clayton, S., McRae, J., van Kogelenberg, M., King, D. A., Ambridge, K., Barrett, D. M., Bayzetinova, T., et al. (2015) · The Lancet · doi:10.1016/s0140-6736(14)61705-0 · Cited by 1,794 · see citing works

Patterns and rates of exonic de novo mutations in autism spectrum disorders

Neale, B. M., Kou, Y., Liu, L., Ma’ayan, A., Samocha, K. E., Sabo, A., Lin, C.-F., Stevens, C., Wang, L.-S., Makarov, V., et al. (2012) · Nature · doi:10.1038/nature11011 · Cited by 1,734 · see citing works

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 · see citing works

ChIP-seq accurately predicts tissue-specific activity of enhancers

Visel, A., Blow, M. J., Li, Z., Zhang, T., Akiyama, J. A., Holt, A., Plajzer-Frick, I., Shoukry, M., Wright, C., Chen, F., et al. (2009) · Nature · doi:10.1038/nature07730 · Cited by 1,639 · see citing works

LUMPY: a probabilistic framework for structural variant discovery

Layer, R. M., Chiang, C., Quinlan, A. R., & Hall, I. M. (2014) · Genome biology · doi:10.1186/gb-2014-15-6-r84 · Cited by 1,510 · see citing works

Why Most Discovered True Associations Are Inflated

Ioannidis, J. P. A. (2008) · Epidemiology · doi:10.1097/ede.0b013e31818131e7 · Cited by 1,495 · see citing works

Prevalence and architecture of de novo mutations in developmental disorders

Study, D. D. D. (2017) · Nature · doi:10.1038/nature21062 · Cited by 1,480 · see citing works

Genome-wide association study implicates immune activation of multiple integrin genes in inflammatory bowel disease

de Lange, K. M., Moutsianas, L., Lee, J. C., Lamb, C. A., Luo, Y., Kennedy, N. A., Jostins, L., Rice, D. L., Gutierrez-Achury, J., Ji, S.-G., et al. (2017) · Nature Genetics · doi:10.1038/ng.3760 · Cited by 1,445 · see citing works

Insights into autism spectrum disorder genomic architecture and biology from 71 risk loci

Sanders, S. J., He, X., Willsey, A. J., Ercan-Sencicek, A. G., Samocha, K. E., Cicek, A. E., Murtha, M. T., Bal, V. H., Bishop, S. L., Dong, S., et al. (2015) · Neuron · doi:10.1016/j.neuron.2015.09.016 · Cited by 1,430 · see citing works

A polygenic burden of rare disruptive mutations in schizophrenia

Purcell, S. M., Moran, J. L., Fromer, M., Ruderfer, D., Solovieff, N., Roussos, P., O’Dushlaine, C., Chambert, K., Bergen, S. E., Kähler, A., et al. (2014) · Nature · doi:10.1038/nature12975 · Cited by 1,385 · see citing works

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

Astle, W. J., Elding, H., Jiang, T., Allen, D., Ruklisa, D., Mann, A. L., Mead, D., Bouman, H., Riveros-Mckay, F., Kostadima, M. A., et al. (2016) · Cell · doi:10.1016/j.cell.2016.10.042 · Cited by 1,224 · see citing works

VISTA Enhancer Browser—a database of tissue-specific human enhancers

Visel, A., Minovitsky, S., Dubchak, I., & Pennacchio, L. A. (2007) · Nucleic Acids Research · doi:10.1093/nar/gkl822 · Cited by 1,080 · see citing works

Contribution of copy number variants to schizophrenia from a genome-wide study of 41,321 subjects

Marshall, C. R., Howrigan, D. P., Merico, D., Thiruvahindrapuram, B., Wu, W., Greer, D. S., Antaki, D., Shetty, A., Holmans, P. A., Pinto, D., et al. (2017) · Nature Genetics · doi:10.1038/ng.3725 · Cited by 1,058 · see citing works

VarDict: a novel and versatile variant caller for next-generation sequencing in cancer research

Lai, Z., Markovets, A. A., Ahdesmaki, M. J., Chapman, B., Hofmann, O., McEwen, R. K., Johnson, J., Dougherty, B. A., Barrett, J. C., & Dry, J. R. (2016) · Nucleic Acids Research · doi:10.1093/nar/gkw227 · Cited by 971 · see citing works

Coexpression networks implicate human midfetal deep cortical projection neurons in the pathogenesis of autism

Willsey, A. J., Sanders, S. J., Li, M., Dong, S., Tebbenkamp, A. T., Muhle, R. A., Reilly, S. K., Lin, L., Fertuzinhos, S., Miller, J. A., et al. (2013) · Cell · doi:10.1016/j.cell.2013.10.020 · Cited by 934 · see citing works

Toward better understanding of artifacts in variant calling from high-coverage samples

Li, H. (2014) · Bioinformatics · doi:10.1093/bioinformatics/btu356 · Cited by 896 · see citing works

Contribution of rare inherited and de novo variants in 2,871 congenital heart disease probands

Jin, S. C., Homsy, J., Zaidi, S., Lu, Q., Morton, S., DePalma, S. R., Zeng, X., Qi, H., Chang, W., Sierant, M. C., et al. (2017) · Nature Genetics · doi:10.1038/ng.3970 · Cited by 875 · see citing works

Genomic variant annotation and prioritization with ANNOVAR and wANNOVAR

Yang, H., & Wang, K. (2015) · Nature Protocols · doi:10.1038/nprot.2015.105 · Cited by 845 · see citing works

Improving genetic diagnosis in Mendelian disease with transcriptome sequencing

Cummings, B. B., Marshall, J. L., Tukiainen, T., Lek, M., Donkervoort, S., Foley, A. R., Bolduc, V., Waddell, L. B., Sandaradura, S. A., O’Grady, G. L., et al. (2017) · Science Translational Medicine · doi:10.1126/scitranslmed.aal5209 · Cited by 831 · see citing works

The Cellular and Molecular Landscapes of the Developing Human Central Nervous System

Silbereis, J. C., Pochareddy, S., Zhu, Y., Li, M., & Sestan, N. (2016) · Neuron · doi:10.1016/j.neuron.2015.12.008 · Cited by 818 · see citing works

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 · see citing works

The Simons Simplex Collection: a resource for identification of autism genetic risk factors

Fischbach, G. D., & Lord, C. (2010) · Neuron · doi:10.1016/j.neuron.2010.10.006 · Cited by 725 · see citing works

Systematic dissection and optimization of inducible enhancers in human cells using a massively parallel reporter assay

Melnikov, A., Murugan, A., Zhang, X., Tesileanu, T., Wang, L., Rogov, P., Feizi, S., Gnirke, A., Callan, C. G., Kinney, J. B., et al. (2012) · Nature Biotechnology · doi:10.1038/nbt.2137 · Cited by 711 · see citing works

Estimation of significance thresholds for genomewide association scans

Dudbridge, F., & Gusnanto, A. (2008) · Genetic Epidemiology · doi:10.1002/gepi.20297 · Cited by 703 · see citing works

Sequencing Chromosomal Abnormalities Reveals Neurodevelopmental Loci that Confer Risk across Diagnostic Boundaries

Talkowski, M. E., Rosenfeld, J. A., Blumenthal, I., Pillalamarri, V., Chiang, C., Heilbut, A., Ernst, C., Hanscom, C., Rossin, E., Lindgren, A. M., et al. (2012) · Cell · doi:10.1016/j.cell.2012.03.028 · Cited by 577 · see citing works

Integrating sequencing datasets to form highly confident SNP and indel genotype calls for a whole human genomePreprint

Zook, J. M., Chapman, B., Wang, J. J., et al. (2013) · arXiv (Cornell University) · doi:10.48550/arxiv.1307.4661 · Cited by 551 · see citing works

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 · see citing works

Characterization of the proteome, diseases and evolution of the human postsynaptic density

Bayés, À., van de Lagemaat, L. N., Collins, M. O., Croning, M. D. R., Whittle, I. R., Choudhary, J. S., & Grant, S. G. N. (2011) · Nature Neuroscience · doi:10.1038/nn.2719 · Cited by 499 · see citing works

Hi-C: A Method to Study the Three-dimensional Architecture of Genomes.

van Berkum, N. L., Aiden, E. L., Williams, L., Imakaev, M., Gnirke, A., Mirny, L. A., Dekker, J., & Lander, E. S. (2010) · Journal of Visualized Experiments · doi:10.3791/1869 · Cited by 474 · see citing works

The PsychENCODE project

Akbarian, S., Liu, C., Knowles, J. A., Vaccarino, F. M., Farnham, P. J., Crawford, G. E., Jaffe, A. E., Pinto, D., Dracheva, S., Geschwind, D. H., et al. (2015) · Nature Neuroscience · doi:10.1038/nn.4156 · Cited by 451 · see citing works

Increased burden of ultra-rare protein-altering variants among 4,877 individuals with schizophrenia

Genovese, G., Fromer, M., Stahl, E. A., Ruderfer, D. M., Chambert, K., Landén, M., Moran, J. L., Purcell, S. M., Sklar, P., Sullivan, P. F., et al. (2016) · Nature Neuroscience · doi:10.1038/nn.4402 · Cited by 444 · see citing works

cn.MOPS: mixture of Poissons for discovering copy number variations in next-generation sequencing data with a low false discovery rate

Klambauer, G., Schwarzbauer, K., Mayr, A., Clevert, D.-A., Mitterecker, A., Bodenhofer, U., & Hochreiter, S. (2012) · Nucleic Acids Research · doi:10.1093/nar/gks003 · Cited by 440 · see citing works

Large multiallelic copy number variations in humans

Handsaker, R. E., Doren, V. V., Berman, J. R., Genovese, G., Kashin, S., Boettger, L. M., & McCarroll, S. A. (2015) · Nature Genetics · doi:10.1038/ng.3200 · Cited by 382 · see citing works

The Mobile Element Locator Tool (MELT): population-scale mobile element discovery and biologyPreprint

Gardner, E. J., Lam, V. K. L., Harris, D., Chuang, N. T., Scott, E., Pittard, W. S., Mills, R. E., & Devine, S. E. (2017) · Genome Research · doi:10.1101/gr.218032.116 · Cited by 371 · see citing works

The autism-associated chromatin modifier CHD8 regulates other autism risk genes during human neurodevelopment

Cotney, J., Muhle, R. A., Sanders, S. J., Liu, L., Willsey, A. J., Niu, W., Liu, W., Klei, L., Lei, J., Yin, J., et al. (2015) · Nature Communications · doi:10.1038/ncomms7404 · Cited by 350 · see citing works

<i>CHD8</i> regulates neurodevelopmental pathways associated with autism spectrum disorder in neural progenitors

Sugathan, A., Biagioli, M., Golzio, C., Erdin, S., Blumenthal, I., Manavalan, P., Ragavendran, A., Brand, H., Lucente, D., Miles, J., et al. (2014) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1405266111 · Cited by 342 · see citing works

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 342 · see citing works

Fecundity of patients with schizophrenia, autism, bipolar disorder, depression, anorexia nervosa, or substance abuse vs their unaffected siblings

Power, R. A., Kyaga, S., Uher, R., MacCabe, J. H., Långström, N., Landen, M., McGuffin, P., Lewis, C. M., Lichtenstein, P., & Svensson, A. C. (2013) · JAMA Psychiatry · doi:10.1001/jamapsychiatry.2013.268 · Cited by 336 · see citing works

The genomic landscape of balanced cytogenetic abnormalities associated with human congenital anomalies

Redin, C., Brand, H., Collins, R. L., Kammin, T., Mitchell, E., Hodge, J. C., Hanscom, C., Pillalamarri, V., Seabra, C. M., Abbott, M.-A., et al. (2017) · Nature Genetics · doi:10.1038/ng.3720 · Cited by 334 · see citing works

Genomic Patterns of De Novo Mutation in Simplex Autism

Turner, T. N., Coe, B. P., Dickel, D. E., Hoekzema, K., Nelson, B. J., Zody, M. C., Kronenberg, Z. N., Hormozdiari, F., Raja, A. N., Pennacchio, L. A., et al. (2017) · Cell · doi:10.1016/j.cell.2017.08.047 · Cited by 330 · see citing works

Evaluating historical candidate genes for schizophrenia

Farrell, M. S., Werge, T., Sklar, P., Owen, M. J., Ophoff, R. A., O'Donovan, M. C., Corvin, A., Cichon, S., & Sullivan, P. F. (2015) · Molecular Psychiatry · doi:10.1038/mp.2015.16 · Cited by 315 · see citing works

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. S., Kuderna, L. F. K., Zhang, W., Fu, S., Vieira, F. G., et al. (2017) · GigaScience · doi:10.1093/gigascience/gix049 · Cited by 314 · see citing works

Genome Sequencing of Autism-Affected Families Reveals Disruption of Putative Noncoding Regulatory DNA

Turner, T. N., Hormozdiari, F., Duyzend, M., McClymont, S. A., Hook, P. W., Iossifov, I. H., Raja, A. N., Baker, C. A., Hoekzema, K., Stessman, H. A. F., et al. (2015) · The American Journal of Human Genetics · doi:10.1016/j.ajhg.2015.11.023 · Cited by 263 · see citing works

Accurate de novo and transmitted indel detection in exome-capture data using microassembly

Narzisi, G., O'Rawe, J., Iossifov, I. H., Fang, H., Lee, Y.-H., Wang, Z., Wu, Y., Lyon, G. J., Wigler, M. H., & Schatz, M. C. (2014) · Nature Methods · doi:10.1038/nmeth.3069 · Cited by 216 · see citing works

Paternally inherited cis-regulatory structural variants are associated with autism

Brandler, W. M., Antaki, D., Gujral, M., Kleiber, M. L., Whitney, J., Maile, M. S., Hong, O., Chapman, T. R., Tan, S., Tandon, P., et al. (2018) · Science · doi:10.1126/science.aan2261 · Cited by 209 · see citing works

Defining the diverse spectrum of inversions, complex structural variation, and chromothripsis in the morbid human genome

Collins, R. L., Brand, H., Redin, C. E., Hanscom, C., Antolik, C. W., Stone, M. R., Glessner, J., Mason, T., Pregno, G., Dorrani, N., et al. (2017) · Genome biology · doi:10.1186/s13059-017-1158-6 · Cited by 203 · see citing works

No Evidence That Schizophrenia Candidate Genes Are More Associated With Schizophrenia Than Noncandidate Genes

Johnson, E. C., Border, R., Melroy-Greif, W. E., de Leeuw, C., Ehringer, M. A., & Keller, M. C. (2017) · Biological Psychiatry · doi:10.1016/j.biopsych.2017.06.033 · Cited by 201 · see citing works

DeNovoGear: de novo indel and point mutation discovery and phasing

Ramu, A., Noordam, M. J., Schwartz, R. S., Wüster, A., Hurles, M. E., Cartwright, R. A., & Conrad, D. F. (2013) · Nature Methods · doi:10.1038/nmeth.2611 · Cited by 172 · see citing works

Improving genetic diagnosis in Mendelian disease with transcriptome sequencingPreprint

Cummings, B. B., Marshall, J. L., Tukiainen, T., et al. (2016) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/074153 · Cited by 153 · see citing works

Sequential Translation of Trinucleotide Codons for the Initiation and Termination of Protein Synthesis

Caskey, C. T., Tompkins, R. K., Scolnick, E. M., Caryk, T. M., & Nirenberg, M. (1968) · Science · doi:10.1126/science.162.3849.135 · Cited by 152 · see citing works

A Genome-wide Association Study of Autism Using the Simons Simplex Collection: Does Reducing Phenotypic Heterogeneity in Autism Increase Genetic Homogeneity?

Chaste, P., Klei, L., Sanders, S. J., Hus, V., Murtha, M. T., Lowe, J. K., Willsey, A. J., Moreno-De-Luca, D., Yu, T. W., Fombonne, E., et al. (2015) · Biological Psychiatry · doi:10.1016/j.biopsych.2014.09.017 · Cited by 144 · see citing works

Wham: Identifying Structural Variants of Biological Consequence

Kronenberg, Z. N., Osborne, E. J., Cone, K. R., Kennedy, B., Domyan, E. T., Shapiro, M. D., Elde, N. C., & Yandell, M. D. (2015) · PLoS Computational Biology · doi:10.1371/journal.pcbi.1004572 · Cited by 135 · see citing works

Whole genome sequencing in psychiatric disorders: the WGSPD consortium

(WGSPD), W. G. S. F. P. D., Sanders, S., Neale, B. M., Huang, H., Werling, D. M., An, J., Dong, S., Abecasis, G. R., Arguello, P. A., Blangero, J., et al. (2017) · Nature Neuroscience · doi:10.1038/s41593-017-0017-9 · Cited by 125 · see citing works

From trans to cis: transcriptional regulatory networks in neocortical development

Shibata, M., Gulden, F. O., & Sestan, N. (2015) · Trends in Genetics · doi:10.1016/j.tig.2014.12.004 · Cited by 109 · see citing works

A Bayesian framework for de novo mutation calling in parents-offspring trios

Wei, Q., Zhan, X., Zhong, X. Y., Liu, Y., Han, Y., Chen, W., & Li, B. (2014) · Bioinformatics · doi:10.1093/bioinformatics/btu839 · Cited by 97 · see citing works

Paired-Duplication Signatures Mark Cryptic Inversions and Other Complex Structural Variation

Brand, H., Collins, R. L., Hanscom, C., Rosenfeld, J. A., Pillalamarri, V., Stone, M. R., Kelley, F., Mason, T., Margolin, L., Eggert, S., et al. (2015) · The American Journal of Human Genetics · doi:10.1016/j.ajhg.2015.05.012 · Cited by 76 · see citing works

Indexcov: fast coverage quality control for whole-genome sequencing

Pedersen, B. S., Collins, R. L., Talkowski, M. E., & Quinlan, A. R. (2017) · GigaScience · doi:10.1093/gigascience/gix090 · Cited by 44 · see citing works

Whole Genome Sequencing in Psychiatric Disorders: the WGSPD ConsortiumPreprint

Sanders, S., Neale, B. M., Huang, H., et al. (2017) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/160499 · Cited by 36 · see citing works

Paternally inherited noncoding structural variants contribute to autismPreprint

Brandler, W. M., Antaki, D., Gujral, M., et al. (2017) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/102327 · Cited by 11 · see citing works

De novo indels within introns contribute to ASD incidencePreprint

Muñoz, A., Yamrom, B., Lee, Y.-H., Andrews, P., Marks, S., Lin, K., Wang, Z., Krainer, A. R., Darnell, R. B., Wigler, M. H., et al. (2017) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/137471 · Cited by 3 · see citing works

Large-Scale Exome Sequencing Study Implicates Both Developmental and Functional Changes in the Neurobiology of Autism

Satterstrom, F. K., Kosmicki, J. A., Wang, J., Breen, M. S., De Rubeis, S., An, J.-Y., Peng, M., Collins, R., Grove, J., Klei, L., et al. (2020) · Cell · doi:10.1016/j.cell.2019.12.036 · Cited by 2,321 · see citing works

High-coverage whole-genome sequencing of the expanded 1000 Genomes Project cohort including 602 trios

Byrska-Bishop, M., Evani, U. S., Zhao, X., Basile, A. O., Abel, H. J., Regier, A. A., Corvelo, A., Clarke, W. E., Musunuri, R., Nagulapalli, K., et al. (2022) · Cell · doi:10.1016/j.cell.2022.08.004 · Cited by 1,094 · see citing works

A structural variation reference for medical and population genetics

Collins, R. L., Brand, H., Karczewski, K. J., Zhao, X., Alföldi, J., Francioli, L. C., Khera, A. V., Lowther, C., Gauthier, L. D., Wang, H., et al. (2020) · Nature · doi:10.1038/s41586-020-2287-8 · Cited by 1,037 · see citing works

Rare coding variation provides insight into the genetic architecture and phenotypic context of autism

Fu, J. M., Satterstrom, F. K., Peng, M., Brand, H., Collins, R. L., Dong, S., Wamsley, B., Klei, L., Wang, L., Hao, S. P., et al. (2022) · Nature Genetics · doi:10.1038/s41588-022-01104-0 · Cited by 640 · see citing works

Structural variation in the sequencing era

Ho, S. S., Urban, A. E., & Mills, R. E. (2019) · Nature Reviews Genetics · doi:10.1038/s41576-019-0180-9 · Cited by 608 · see citing works

Comprehensive evaluation of structural variation detection algorithms for whole genome sequencing

Kosugi, S., Momozawa, Y., Liu, X., Terao, C. C., Kubo, M., & Kamatani, Y. (2019) · Genome biology · doi:10.1186/s13059-019-1720-5 · Cited by 502 · see citing works

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 · see citing works

Integrating de novo and inherited variants in 42,607 autism cases identifies mutations in new moderate-risk genes

Zhou, X., Feliciano, P., Shu, C., Wang, T., Astrovskaya, I., Hall, J. B., Obiajulu, J. U., Wright, J. R., Murali, S. C., Xu, S. X., et al. (2022) · Nature Genetics · doi:10.1038/s41588-022-01148-2 · Cited by 453 · see citing works

Insights into clonal haematopoiesis from 8,342 mosaic chromosomal alterations

Loh, P.-R., Genovese, G., Handsaker, R. E., Finucane, H. K., Reshef, Y. A., Palamara, P. F., Birmann, B. M., Talkowski, M. E., Bakhoum, S. F., McCarroll, S. A., et al. (2018) · Nature · doi:10.1038/s41586-018-0321-x · Cited by 423 · see citing works

A cross-disorder dosage sensitivity map of the human genome

Collins, R. L., Glessner, J., Porcu, E., Lepamets, M., Brandon, R. C., Lauricella, C., Han, L., Morley, T. J., Niestroj, L., Ulirsch, J. C., et al. (2022) · Cell · doi:10.1016/j.cell.2022.06.036 · Cited by 377 · see citing works

Genome-wide de novo risk score implicates promoter variation in autism spectrum disorder

An, J.-Y., Lin, K., Zhu, L., Werling, D. M., Dong, S., Brand, H., Wang, H. Z., Zhao, X., Schwartz, G. B., Collins, R. L., et al. (2018) · Science · doi:10.1126/science.aat6576 · Cited by 316 · see citing works

Mapping and characterization of structural variation in 17,795 human genomes

Genomics, N. C. F. C. D., Abel, H. J., Larson, D. E., Regier, A. A., Chiang, C., Das, I., Kanchi, K. L., Layer, R. M., Neale, B. M., Salerno, W. J., et al. (2020) · Nature · doi:10.1038/s41586-020-2371-0 · Cited by 310 · see citing works

Whole-Genome Sequencing to Characterize Monogenic and Polygenic Contributions in Patients Hospitalized With Early-Onset Myocardial Infarction

Khera, A. V., Chaffin, M., Zekavat, S. M., Collins, R. L., Roselli, C., Natarajan, P., Lichtman, J. H., D’Onofrio, G., Mattera, J., Dreyer, R., et al. (2019) · Circulation · doi:10.1161/circulationaha.118.035658 · Cited by 315 · see citing works

Transcriptome and epigenome landscape of human cortical development modeled in organoids

Amiri, A., Coppola, G., Scuderi, S., Wu, F., Roychowdhury, T., Liu, F., Pochareddy, S., Shin, Y., Safi, A., Song, L., et al. (2018) · Science · doi:10.1126/science.aat6720 · Cited by 302 · see citing works

Whole-genome deep-learning analysis identifies contribution of noncoding mutations to autism risk

Zhou, J., Park, C. Y., Theesfeld, C. L., Wong, A. K., Yuan, Y., Scheckel, C., Fak, J. J., Funk, J., Yao, K., Tajima, Y., et al. (2019) · Nature Genetics · doi:10.1038/s41588-019-0420-0 · Cited by 287 · see citing works

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 277 · see citing works

Signalling pathways in autism spectrum disorder: mechanisms and therapeutic implications

Jiang, C.-C., Lin, L., Long, S., Ke, X., Fukunaga, K., Lu, Y., & Han, F. (2022) · Signal Transduction and Targeted Therapy · doi:10.1038/s41392-022-01081-0 · Cited by 272 · see citing works

A map of constrained coding regions in the human genome

Havrilla, J. M., Pedersen, B. S., Layer, R. M., & Quinlan, A. R. (2018) · Nature Genetics · doi:10.1038/s41588-018-0294-6 · Cited by 230 · see citing works

Genome-wide detection of tandem DNA repeats that are expanded in autism

Trost, B., Engchuan, W., Nguyen, C. M., Thiruvahindrapuram, B., Dolzhenko, E., Backstrom, I., Mirceta, M., Mojarad, B. A., Yin, Y., Dov, A., et al. (2020) · Nature · doi:10.1038/s41586-020-2579-z · Cited by 238 · see citing works

Genomics, convergent neuroscience and progress in understanding autism spectrum disorder

Willsey, H. R., Willsey, A. J., Wang, B., & State, M. W. (2022) · Nature reviews. Neuroscience · doi:10.1038/s41583-022-00576-7 · Cited by 229 · see citing works

Patterns of de novo tandem repeat mutations and their role in autism

Mitra, I., Huang, B., Mousavi, N., Ma, N., Lamkin, M., Yanicky, R., Shleizer-Burko, S., Lohmueller, K. E., & Gymrek, M. (2021) · Nature · doi:10.1038/s41586-020-03078-7 · Cited by 194 · see citing works

SUPERGNOVA: local genetic correlation analysis reveals heterogeneous etiologic sharing of complex traits

Zhang, Y., Lu, Q., Ye, Y., Huang, K., Liu, W., Wu, Y., Zhong, X., Li, B., Yu, Z., Travers, B. G., et al. (2021) · Genome biology · doi:10.1186/s13059-021-02478-w · Cited by 198 · see citing works

Genomic analyses implicate noncoding de novo variants in congenital heart disease

Richter, F., Morton, S. U., Kim, S. W., Kitaygorodsky, A., Wasson, L. K., Chen, K., Zhou, J., Qi, H., Patel, N., DePalma, S. R., et al. (2020) · Nature Genetics · doi:10.1038/s41588-020-0652-z · Cited by 174 · see citing works

Genetic Advances in Autism

Thapar, A., & Rutter, M. L. (2020) · Journal of Autism and Developmental Disorders · doi:10.1007/s10803-020-04685-z · Cited by 174 · see citing works

Best practices for the interpretation and reporting of clinical whole genome sequencing

Austin-Tse, C. A., Jobanputra, V., Perry, D., Bick, D. P., Taft, R. J., Venner, E., Gibbs, R. A., Young, E. J., Barnett, S., Belmont, J. W., et al. (2022) · npj Genomic Medicine · doi:10.1038/s41525-022-00295-z · Cited by 164 · see citing works

Genotype-phenotype correlations in <i>SCN8A</i> -related disorders reveal prognostic and therapeutic implications

Johannesen, K. M., Liu, Y., Koko, M., Gjerulfsen, C. E., Sonnenberg, L., Schubert, J., Fenger, C. D., Eltokhi, A., Rannap, M., Koch, N. A., et al. (2022) · Brain · doi:10.1093/brain/awab321 · Cited by 147 · see citing works

Autism Spectrum Disorder Genetics and the Search for Pathological Mechanisms

Manoli, D. S., & State, M. W. (2021) · American Journal of Psychiatry · doi:10.1176/appi.ajp.2020.20111608 · Cited by 151 · see citing works

Whole-Genome and RNA Sequencing Reveal Variation and Transcriptomic Coordination in the Developing Human Prefrontal Cortex

Werling, D. M., Pochareddy, S., Choi, J., An, J., Sheppard, B. K., Peng, M., Li, Z., Dastmalchi, C., Santpere, G., Sousa, A. M. M., et al. (2020) · Cell Reports · doi:10.1016/j.celrep.2020.03.053 · Cited by 133 · see citing works

A framework for an evidence-based gene list relevant to autism spectrum disorder

Schaaf, C. P., Betancur, C., Yuen, R. K. C., Parr, J. R., Skuse, D., Gallagher, L., Bernier, R., Buchanan, J. A., Buxbaum, J. D., Chen, C., et al. (2020) · Nature Reviews Genetics · doi:10.1038/s41576-020-0231-2 · Cited by 137 · see citing works

Impaired neurodevelopmental pathways in autism spectrum disorder: a review of signaling mechanisms and crosstalk

Kumar, S., Reynolds, K., Ji, Y., Gu, R., Rai, S., & Zhou, C. J. (2019) · Journal of Neurodevelopmental Disorders · doi:10.1186/s11689-019-9268-y · Cited by 142 · see citing works

Expectations and blind spots for structural variation detection from long-read assemblies and short-read genome sequencing technologies

Zhao, X., Collins, R. L., Lee, W.-P., Weber, A. M., Jun, Y., Zhu, Q., Weisburd, B., Huang, Y., Audano, P. A., Wang, H., et al. (2021) · The American Journal of Human Genetics · doi:10.1016/j.ajhg.2021.03.014 · Cited by 132 · see citing works

Lost in Translation: Traversing the Complex Path from Genomics to Therapeutics in Autism Spectrum Disorder

Sestan, N., & State, M. W. (2018) · Neuron · doi:10.1016/j.neuron.2018.10.015 · Cited by 127 · see citing works

The contributions of rare inherited and polygenic risk to ASD in multiplex families

Cirnigliaro, M., Chang, T. S., Arteaga, S. A., Pérez‐Cano, L., Ruzzo, E. K., Gordon, A., Bicks, L. K., Jung, J.-Y., Lowe, J. K., Wall, D. P., et al. (2023) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.2215632120 · Cited by 120 · see citing works

GATK-gCNV enables the discovery of rare copy number variants from exome sequencing data

Babadi, M., Fu, J. M., Lee, S. K., Smirnov, A. N., Gauthier, L. D., Walker, M., Benjamin, D. I., Zhao, X., Karczewski, K. J., Wong, I., et al. (2023) · Nature Genetics · doi:10.1038/s41588-023-01449-0 · Cited by 128 · see citing works

Pedigree-based estimation of human mobile element retrotransposition ratesPreprint

Feusier, J. E., Watkins, W. S., Thomas, J., Farrell, A., Witherspoon, D. J., Baird, L. M., Ha, H., Xing, J., & Jorde, L. B. (2019) · Genome Research · doi:10.1101/gr.247965.118 · Cited by 113 · see citing works

Opportunities and limitations of genetically modified nonhuman primate models for neuroscience research

Feng, G., Jensen, F. E., Greely, H. T., Okano, H., Treue, S., Roberts, A., Fox, J. G., Caddick, S. J., Poo, M.-M., Newsome, W. T., et al. (2020) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.2006515117 · Cited by 118 · see citing works

Accelerating Medicines Partnership: Parkinson's Disease. Genetic Resource

Iwaki, H., Leonard, H. L., Makarious, M. B., Bookman, M., Landin, B., Vismer, D., Casey, B. H., Gibbs, J. R., Hernandez, D. G., Blauwendraat, C., et al. (2021) · Movement Disorders · doi:10.1002/mds.28549 · Cited by 105 · see citing works

De novo structural mutation rates and gamete-of-origin biases revealed through genome sequencing of 2,396 families

Belyeu, J. R., Brand, H., Wang, H., Zhao, X., Pedersen, B. S., Feusier, J. E., Gupta, M., Nicholas, T. J., Brown, J., Baird, L. M., et al. (2021) · The American Journal of Human Genetics · doi:10.1016/j.ajhg.2021.02.012 · Cited by 105 · see citing works

Decomposition of phenotypic heterogeneity in autism reveals underlying genetic programs

Litman, A., Sauerwald, N., Snyder, L. G., Foss‐Feig, J. H., Park, C. Y., Hao, Y., Dinstein, I., Theesfeld, C. L., & Troyanskaya, O. G. (2025) · Nature Genetics · doi:10.1038/s41588-025-02224-z · Cited by 116 · see citing works

Neurobiological functions of transcriptional enhancers

Nord, A. S., & West, A. E. (2019) · Nature Neuroscience · doi:10.1038/s41593-019-0538-5 · Cited by 100 · see citing works

A Chromatin Accessibility Atlas of the Developing Human Telencephalon

Markenscoff-Papadimitriou, E., Whalen, S., Przytycki, P. F., Thomas, R., Binyameen, F., Nowakowski, T. J., Kriegstein, A. R., Sanders, S., State, M. W., Pollard, K. S., et al. (2020) · Cell · doi:10.1016/j.cell.2020.06.002 · Cited by 87 · see citing works

Closing in on Mechanisms of Open Neural Tube Defects

Lee, S., & Gleeson, J. G. (2020) · Trends in Neurosciences · doi:10.1016/j.tins.2020.04.009 · Cited by 97 · see citing works

Developmental isoform diversity in the human neocortex informs neuropsychiatric risk mechanisms

Patowary, A., Zhang, P., Jops, C. T., Vuong, C. K., Ge, X., Hou, K., Kim, M., Gong, N. N., Margolis, M. P., Vo, D., et al. (2024) · Science · doi:10.1126/science.adh7688 · Cited by 87 · see citing works

De novo and recessive forms of congenital heart disease have distinct genetic and phenotypic landscapes

Watkins, W. S., Hernandez, E. J., Wesołowski, S., Bisgrove, B. W., Sunderland, R. T., Lin, E., Lemmon, G., Demarest, B. L., Miller, T. A., Bernstein, D., et al. (2019) · Nature Communications · doi:10.1038/s41467-019-12582-y · Cited by 82 · see citing works

Increased burden of ultra-rare structural variants localizing to boundaries of topologically associated domains in schizophrenia

Halvorsen, M., Huh, R., Oskolkov, N., Wen, J., Netotea, S., Giusti‐Rodríguez, P., Karlsson, R., Bryois, J., Nystedt, B., Ameur, A., et al. (2020) · Nature Communications · doi:10.1038/s41467-020-15707-w · Cited by 81 · see citing works

Genetic architecture of autism spectrum disorder: Lessons from large-scale genomic studies

Choi, L., & An, J. (2021) · Neuroscience & Biobehavioral Reviews · doi:10.1016/j.neubiorev.2021.06.028 · Cited by 80 · see citing works

Understanding autism spectrum disorders with animal models: applications, insights, and perspectives

Zhu, L., 昆明650500，中国, 云., Zhu, Y., Gu, L., & Cheng, Y. (2021) · 动物学研究 · doi:10.24272/j.issn.2095-8137.2021.251 · Cited by 84 · see citing works

De novo mutations from whole exome sequencing in neurodevelopmental and psychiatric disorders: From discovery to application

Wang, W., Corominas, R., & Lin, G. N. (2019) · Frontiers in Genetics · doi:10.3389/fgene.2019.00258 · Cited by 70 · see citing works

The Genetics of Intellectual Disability

Jansen, S., Vissers, L. E. L. M., & de Vries, B. B. A. (2023) · Brain Sciences · doi:10.3390/brainsci13020231 · Cited by 81 · see citing works

Genetic testing for kidney disease of unknown etiology

Hays, T., Groopman, E., & Gharavi, A. G. (2020) · Kidney International · doi:10.1016/j.kint.2020.03.031 · Cited by 73 · see citing works

Systematic phenomics analysis of autism-associated genes reveals parallel networks underlying reversible impairments in habituation

McDiarmid, T. A., Belmadani, M., Liang, J., Meili, F., Mathews, E., Mullen, G. P., Hendi, A., Wong, W.-R., Rand, J. B., Mizumoto, K., et al. (2019) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1912049116 · Cited by 67 · see citing works

Genomic Diagnosis for Pediatric Disorders: Revolution and Evolution

Lalonde, E., Rentas, S., Lin, F., Dulik, M. C., Skraban, C. M., & Spinner, N. B. (2020) · Frontiers in Pediatrics · doi:10.3389/fped.2020.00373 · Cited by 69 · see citing works

The Role of De Novo Noncoding Regulatory Mutations in Neurodevelopmental Disorders

Turner, T. N., & Eichler, E. E. (2018) · Trends in Neurosciences · doi:10.1016/j.tins.2018.11.002 · Cited by 69 · see citing works

Diversity and consequences of structural variation in the human genome

Collins, R. L., & Talkowski, M. E. (2025) · Nature Reviews Genetics · doi:10.1038/s41576-024-00808-9 · Cited by 71 · see citing works

De novo Mutations (DNMs) in Autism Spectrum Disorder (ASD): Pathway and Network Analysis

Alonso-González, A., Rodriguez‐Fontenla, C., & Carracedo, Á. (2018) · Frontiers in Genetics · doi:10.3389/fgene.2018.00406 · Cited by 65 · see citing works

Functional interpretation of genetic variants using deep learning predicts impact on chromatin accessibility and histone modification

Hoffman, G. E., Bendl, J. M., Girdhar, K., Schadt, E. E., & Roussos, P. (2019) · Nucleic Acids Research · doi:10.1093/nar/gkz808 · Cited by 62 · see citing works

An open resource of structural variation for medical and population geneticsPreprint

Collins, R. L., Brand, H., Karczewski, K. J., Zhao, X., Alföldi, J., Francioli, L. C., Khera, A. V., Lowther, C., Gauthier, L. D., Wang, H., et al. (2019) · bioRxiv (Cold Spring Harbor Laboratory) · doi:10.1101/578674 · Cited by 61 · see citing works

Systematic evaluation of genome sequencing for the diagnostic assessment of autism spectrum disorder and fetal structural anomalies

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. (2023) · The American Journal of Human Genetics · doi:10.1016/j.ajhg.2023.07.010 · Cited by 68 · see citing works

Contribution of retrotransposition to developmental disorders

Gardner, E. J., Prigmore, E., Gallone, G., Danecek, P., Samocha, K. E., Handsaker, J., Gerety, S. S., Ironfield, H., Short, P., Sifrim, A., et al. (2019) · Nature Communications · doi:10.1038/s41467-019-12520-y · Cited by 58 · see citing works

A white paper on a neurodevelopmental framework for drug discovery in autism and other neurodevelopmental disorders

Díaz‐Caneja, C. M., State, M. W., Hagerman, R. J., Jacquemont, S., Marín, Ó., Bagni, C., Umbricht, D., Simonoff, E. A., Andres-Trelles, F., Kaale, A., et al. (2021) · European Neuropsychopharmacology · doi:10.1016/j.euroneuro.2021.02.020 · Cited by 54 · see citing works

Genetic mechanisms of regression in autism spectrum disorder

Tammimies, K. (2019) · Neuroscience & Biobehavioral Reviews · doi:10.1016/j.neubiorev.2019.04.022 · Cited by 53 · see citing works

Leveraging large genomic datasets to illuminate the pathobiology of autism spectrum disorders

Searles, V. B., Wang, B., & State, M. W. (2020) · Neuropsychopharmacology · doi:10.1038/s41386-020-0768-y · Cited by 52 · see citing works

Recent Advances in Understanding the Genetic Architecture of Autism

Dias, C., & Walsh, C. A. (2020) · Annual Review of Genomics and Human Genetics · doi:10.1146/annurev-genom-121219-082309 · Cited by 53 · see citing works

A genome-wide scan statistic framework for whole-genome sequence data analysis

He, Z., Xu, B., Buxbaum, J. D., & Ionita‐Laza, I. (2019) · Nature Communications · doi:10.1038/s41467-019-11023-0 · Cited by 50 · see citing works

Perfect and imperfect views of ultraconserved sequences

Snetkova, V., Pennacchio, L. A., Visel, A., & Dickel, D. E. (2021) · Nature Reviews Genetics · doi:10.1038/s41576-021-00424-x · Cited by 45 · see citing works

Towards understanding sex differences in autism spectrum disorders

Leow, K. Q., Tonta, M. A., Lü, J., Coleman, H. A., & Parkington, H. C. (2024) · Brain Research · doi:10.1016/j.brainres.2024.148877 · Cited by 50 · see citing works

Advances in Biomarker Studies in Autism Spectrum Disorders

Shen, L., Zhao, Y., Zhang, H., Feng, C., Gao, Y. L., Zhao, D., Xia, S., Qi, H., Iqbal, J., Liu, X., et al. (2019) · Advances in experimental medicine and biology · doi:10.1007/978-3-030-05542-4_11 · Cited by 48 · see citing works

Functional annotation of rare structural variation in the human brain

Han, L., Zhao, X., Benton, M. L., Perumal, T. M., Collins, R. L., Hoffman, G. E., Johnson, J., Sloofman, L. G., Wang, H. Z., Stone, M. R., et al. (2020) · Nature Communications · doi:10.1038/s41467-020-16736-1 · Cited by 43 · see citing works

New gene discoveries highlight functional convergence in autism and related neurodevelopmental disorders

Moysés‐Oliveira, M., Yadav, R., Erdin, S., & Talkowski, M. E. (2020) · Current Opinion in Genetics & Development · doi:10.1016/j.gde.2020.07.001 · Cited by 45 · see citing works

Large-scale discovery of novel neurodevelopmental disorder-related genes through a unified analysis of single-nucleotide and copy number variants

Hamanaka, K., Miyake, N., Mizuguchi, T., Miyatake, S., Uchiyama, Y., Tsuchida, N., Sekiguchi, F., Mitsuhashi, S., Tsurusaki, Y., Nakashima, M., et al. (2022) · Genome Medicine · doi:10.1186/s13073-022-01042-w · Cited by 46 · see citing works

Points to consider in the detection of germline structural variants using next-generation sequencing: A statement of the American College of Medical Genetics and Genomics (ACMG)

Raca, G., Astbury, C., Behlmann, A., Castro, M. J. D., Hickey, S. E., Karaca, E., Lowther, C., Riggs, E. R., Seifert, B. A., Thorland, E. C., et al. (2022) · Genetics in Medicine · doi:10.1016/j.gim.2022.09.017 · Cited by 47 · see citing works

Functional characterization of rare NRXN1 variants identified in autism spectrum disorders and schizophrenia

Ishizuka, K., Yoshida, T., Kawabata, T., Imai, A., Mori, H., Kimura, H., Inada, T., Okahisa, Y., Egawa, J., Usami, M., et al. (2020) · Journal of Neurodevelopmental Disorders · doi:10.1186/s11689-020-09325-2 · Cited by 45 · see citing works

Dissecting the genetic basis of comorbid epilepsy phenotypes in neurodevelopmental disorders

Chow, J. C., Jensen, M., Amini, H., Hormozdiari, F., Penn, O., Shifman, S., Girirajan, S., & Hormozdiari, F. (2019) · Genome Medicine · doi:10.1186/s13073-019-0678-y · Cited by 44 · see citing works

Nucleosome positioning stability is a modulator of germline mutation rate variation across the human genome

Li, C., & Luscombe, N. (2020) · Nature Communications · doi:10.1038/s41467-020-15185-0 · Cited by 38 · see citing works

Three decades of ASD genetics: building a foundation for neurobiological understanding and treatment

Eyring, K. W., & Geschwind, D. H. (2021) · Human Molecular Genetics · doi:10.1093/hmg/ddab176 · Cited by 41 · see citing works

Thousands of high-quality sequencing samples fail to show meaningful correlation between 5S and 45S ribosomal DNA arrays in humans

Hall, A. N., Turner, T. N., & Queitsch, C. (2021) · Scientific Reports · doi:10.1038/s41598-020-80049-y · Cited by 43 · see citing works

Rates of contributory de novo mutation in high and low-risk autism families

Yoon, S. C., Muñoz, A., Yamrom, B., Lee, Y.-H., Andrews, P., Marks, S., Wang, Z., Reeves, C., Winterkorn, L. H., Krieger, A. Μ., et al. (2021) · Communications Biology · doi:10.1038/s42003-021-02533-z · Cited by 42 · see citing works

Characterizing mobile element insertions in 5675 genomes

Niu, Y., Teng, X., Zhou, H., Shi, Y., Li, Y., Tang, Y., Zhang, P., Luo, H., Kang, Q., Xu, T., et al. (2022) · Nucleic Acids Research · doi:10.1093/nar/gkac128 · Cited by 45 · see citing works

PTEN mutations in autism spectrum disorder and congenital hydrocephalus: developmental pleiotropy and therapeutic targets

DeSpenza, T., Carlson, M., Panchagnula, S., Robert, S. M., Duy, P. Q., Mermin‐Bunnell, K., Reeves, B. C., Kundishora, A. J., Elsamadicy, A. A., Smith, H. L., et al. (2021) · Trends in Neurosciences · doi:10.1016/j.tins.2021.08.007 · Cited by 40 · see citing works

The state of research on the genetics of autism spectrum disorder: methodological, clinical and conceptual progress

Arnett, A. B., Trinh, S., & Bernier, R. (2018) · Current Opinion in Psychology · doi:10.1016/j.copsyc.2018.07.004 · Cited by 39 · see citing works

Applicability of the Mutation–Selection Balance Model to Population Genetics of Heterozygous Protein-Truncating Variants in Humans

Weghorn, D., Balick, D. J., Cassa, C. A., Kosmicki, J. A., Daly, M. J., Beier, D. R., & Sunyaev, S. R. (2019) · Molecular Biology and Evolution · doi:10.1093/molbev/msz092 · Cited by 39 · see citing works

Estimating the Prevalence of De Novo Monogenic Neurodevelopmental Disorders from Large Cohort Studies

Gillentine, M. A., Wang, T., & Eichler, E. E. (2022) · Biomedicines · doi:10.3390/biomedicines10112865 · Cited by 40 · see citing works

Causal and Candidate Gene Variants in a Large Cohort of Women With Primary Ovarian Insufficiency

Gorsi, B., Hernandez, E. J., Moore, M. B., Moriwaki, M., Chow, C. Y., Coelho, E., Taylor, E., Lu, C., Walker, A. M., Touraine, P. A., et al. (2021) · The Journal of Clinical Endocrinology & Metabolism · doi:10.1210/clinem/dgab775 · Cited by 39 · see citing works

Focus on your locus with a massively parallel reporter assay

McAfee, J. C., Bell, J., Krupa, O., Matoba, N., Stein, J. L., & Won, H. (2022) · Journal of Neurodevelopmental Disorders · doi:10.1186/s11689-022-09461-x · Cited by 39 · see citing works

Genome‐Wide Analysis of Structural Variants in Parkinson Disease

Billingsley, K. J., Ding, J., Jerez, P. Á., Illarionova, A., Levine, K. S., Grenn, F. P., Makarious, M. B., Moore, A. K., Vitale, D., Reed, X., et al. (2023) · Annals of Neurology · doi:10.1002/ana.26608 · Cited by 40 · see citing works

Chromosomal Instability in Genome Evolution: From Cancer to Macroevolution

Comaills, V., & Castellano‐Pozo, M. (2023) · Biology · doi:10.3390/biology12050671 · Cited by 37 · see citing works

De novo variation in bipolar disorder

Goes, F. S., Pirooznia, M., Tehan, M., Zandi, P. P., McGrath, J. A., Wolyniec, P. S., Nestadt, G., & Pulver, A. E. (2019) · Molecular Psychiatry · doi:10.1038/s41380-019-0611-1 · Cited by 37 · see citing works

Long genes linked to autism spectrum disorders harbor broad enhancer-like chromatin domainsPreprint

Zhao, Y.-T., Kwon, D. Y., Johnson, B. S., Fasolino, M., Lamonica, J. M., Kim, Y. J., Zhao, B. S., He, C., Vahedi, G., Kim, T. H., et al. (2018) · Genome Research · doi:10.1101/gr.233775.117 · Cited by 35 · see citing works

Genetic landscape of autism spectrum disorder in Vietnamese children

Kiên, T. T., Le, V. S., Bui, H. T. P., Do, D. H., Ly, H. T. T., Nguyen, H. T., Dao, L. T. M., Nguyen, T. H., Vu, D. M., Ha, L. T., et al. (2020) · Scientific Reports · doi:10.1038/s41598-020-61695-8 · Cited by 35 · see citing works

Likely damaging de novo variants in congenital diaphragmatic hernia patients are associated with worse clinical outcomes

Qiao, L., Wynn, J., Yu, L., Hernan, R., Zhou, X., Duron, V., Aspelund, G., Farkouh‐Karoleski, C., Zygumunt, A., Krishnan, U., et al. (2020) · Genetics in Medicine · doi:10.1038/s41436-020-0908-0 · Cited by 35 · see citing works

Decoding microRNAs in autism spectrum disorder

Li, J., Xu, X., Liu, J., Zhang, S., Tan, X., Li, Z., Zhang, J., & Wang, Z. (2022) · Molecular Therapy — Nucleic Acids · doi:10.1016/j.omtn.2022.11.005 · Cited by 38 · see citing works

Transcriptional and functional consequences of alterations to MEF2C and its topological organization in neuronal models

Mohajeri, K., Yadav, R., D’haene, E., Boone, P. M., Erdin, S., Gao, D., Moysés‐Oliveira, M., Bhavsar, R., Currall, B., O’Keefe, K., et al. (2022) · The American Journal of Human Genetics · doi:10.1016/j.ajhg.2022.09.015 · Cited by 34 · see citing works

Inflammation and the Potential Implication of Macrophage-Microglia Polarization in Human ASD: An Overview

Lampiasi, N., Bonaventura, R., Deidda, I., Zito, F., & Russo, R. (2023) · International Journal of Molecular Sciences · doi:10.3390/ijms24032703 · Cited by 39 · see citing works

Maternal paracetamol (acetaminophen) use during pregnancy and risk of autism spectrum disorder and attention deficit/hyperactivity disorder in offspring: umbrella review of systematic reviews

Sheikh, J., Allotey, J., Sobhy, S., Plana, M. N., Martinez-Barros, H., Naidu, H., Junaid, F., Sofat, R., Mol, B. W., Kenny, L. C., et al. (2025) · BMJ · doi:10.1136/bmj-2025-088141 · Cited by 33 · see citing works

Single cell epigenomic atlas of the developing human brain and organoids

Ziffra, R. S., Kim, C. N., Wilfert, A., Turner, T. N., Haeussler, M., Casella, A. M., Przytycki, P. F., Kreimer, A., Pollard, K. S., Ament, S. A., et al. (2019) · doi:10.1101/2019.12.30.891549 · Cited by 33 · see citing works

Whole genome sequencing analysis identifies sex differences of familial pattern contributing to phenotypic diversity in autism

Kim, S.-W., Lee, H., Song, D. Y., Lee, G., Ji, J., Park, J. W., Han, J. H., Lee, J., Byun, H. J., Son, J. H., et al. (2024) · Genome Medicine · doi:10.1186/s13073-024-01385-6 · Cited by 32 · see citing works

Whole-genome analysis reveals the contribution of non-coding de novo transposon insertions to autism spectrum disorder

Borges-Monroy, R., Chu, C., Dias, C., Choi, J., Lee, S., Gao, Y., Shin, T., Park, P. J., Walsh, C. A., & Lee, E. A. (2021) · Mobile DNA · doi:10.1186/s13100-021-00256-w · Cited by 33 · see citing works

Unified inference of missense variant effects and gene constraints in the human genome

Huang, Y.-F. (2020) · PLoS Genetics · doi:10.1371/journal.pgen.1008922 · Cited by 31 · see citing works

Overlapping Molecular Pathways Leading to Autism Spectrum Disorders, Fragile X Syndrome, and Targeted Treatments

Salcedo‐Arellano, M. J., Cabal-Herrera, A. M., Punatar, R., Clark, C. J., Romney, C. A., & Hagerman, R. J. (2020) · Neurotherapeutics · doi:10.1007/s13311-020-00968-6 · Cited by 30 · see citing works

Developmental convergence and divergence in human stem cell models of autism

Gordon, A., Yoon, S., Bicks, L. K., Martín, J. M., Pintacuda, G., Arteaga, S. A., Wamsley, B., Guo, Q., Elahi, L. S., Dolmetsch, R. E., et al. (2026) · Nature · doi:10.1038/s41586-025-10047-5 · Cited by 41 · see citing works

LIMITED CONTRIBUTION OF RARE, NONCODING VARIATION TO AUTISM SPECTRUM DISORDER FROM SEQUENCING OF 2,076 GENOMES IN QUARTET FAMILIES

Werling, D. M., Brand, H., An, J., Stone, M. R., Glessner, J., Zhu, L., Collins, R. L., Dong, S., Layer, R. M., Markenscoff-Papadimitriou, E., et al. (2019) · European Neuropsychopharmacology · doi:10.1016/j.euroneuro.2017.08.010 · Cited by 20 · see citing works

Genomic architecture of Autism Spectrum Disorder from comprehensive whole-genome sequence annotationPreprint

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) · medRxiv · doi:10.1101/2022.05.05.22274031 · Cited by 3 · see citing works

Identifying associations of de novo noncoding variants with autism through integration of gene expression, sequence, and sex information

Li, R., & Ernst, J. (2025) · Genome biology · doi:10.1186/s13059-025-03619-1 · Cited by 1 · see citing works

Analysis of recent shared ancestry in a familial cohort identifies coding and noncoding autism spectrum disorder variants

Tuncay, İ. O., Parmalee, N. L., Khalil, R., Kaur, K. J., Kumar, A., Jimale, M., Howe, J., Goodspeed, K., Evans, P., Alzghoul, L., et al. (2022) · npj Genomic Medicine · doi:10.1038/s41525-022-00284-2 · Cited by 38 · see citing works

Detection of Clinically Relevant Genetic Variants in Autism Spectrum Disorder by Whole-Genome Sequencing

Jiang, Y.-H., Yuen, R. K. C., Jin, X., Wang, M., Chen, N., Wu, X., Ju, J., Mei, J., Shi, Y., He, M., et al. (2013) · The American Journal of Human Genetics · doi:10.1016/j.ajhg.2013.06.012 · Cited by 474 · see citing works