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Articles by Evan E. Eichler
Androgens mediate sexual dimorphism in Pilarowski-Bjornsson syndrome
Keywords CHD1 Mendelian disease sex differences neurodevelopmental disorder Introduction Traditionally, autosomal-dominant disorders have been considered to have limited sex differences, unlike X-linked disorders defined by this feature.
Complete chromosome 21 centromere sequencing of families with Down syndrome
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Results To study the chr21 centromeres in individuals with T21, we initially sequenced the DNA of a proband (AG16777) (maternal age at childbirth, 29 years) using both PacBio HiFi sequence data (59×) and UL-ONT sequence data (23×). We used Verkko, a hybrid genome assembly workflow,42 to assemble all proband chr21 centromere haplotypes (total genome assembly size = 6.118 Gbp, number of contigs = 3,466, contig N50 = 7.72 Mbp).
By F. Kumara Mastrorosa, Alessia Daponte, Luciana de Gennaro, Shu-Cheng Chuang, Jiadong Lin, Yang Sui, David Porubsky, Keisuke K. Oshima, Julie Wertz, Allison N Rozanski, William Harvey, Yanni Wang, Tiffany Y. Leung, Daniel Chan, Weiya He, Jordan Knuth, Gage H. Garcia, Katherine Munson, Kendra Hoekzema, Peter M. Lansdorp, Claudia Rita Catacchio, Mario Ventura, Stephanie Sherman, Emily Allen, Tracie C Rosser, Glennis A. Logsdon, Evan E. Eichler, Marcelo Ayllon
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The American Journal of Human Genetics
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A global map for introgressed structural variation and selection in humans
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Editor’s summary Structured Abstract Abstract Results Discussion Materials and methods Acknowledgments Supplementary Materials References and Notes Information & Authors Metrics & Citations View Options References Figures Tables Media Share Editor’s summary Between 2 and 5% of modern Eurasian genomes are derived from admixture with Neanderthals and Denisovans, with Papua New Guineans bearing the largest fractions.
By Patrick Reilly, Ke-Ting Shin, Justin Stewart, Natthapon Soisangwan, DAVID GORDON, William Harvey, David Porubsky, Kendra Hoekzema, Carl Baker, Katherine Munson, Christopher Kinipi, Matthew Leavesley, Nicolas Brucato, Murray P. Cox, Irene Gallego Romero, Evan E. Eichler, Athef Javidh, François‐X Ricaut
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Science Magazine
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Population differences of chromosome 22q11.2 duplication structure predispose differentially to microdeletion and inversion
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Abstract Chromosome 22q11.2 microdeletion syndrome (22q11.2DS) is mediated by high-identity polymorphic low-copy repeats (LCRA-to-D) that have been challenging to sequence characterize. We sequence-resolved 135 chromosome 22q11.2 haplotypes from diverse humans and define 63 distinct structural configurations differing in size by 11-fold for LCRA.
By David Porubsky, DongAhn Yoo, Nidhi Koundinya, Erika Souche, Philip C. Dishuck, Nicolas Dierckxsens, William Harvey, Katherine Munson, Kendra Hoekzema, Daniel Chan, Marta Santos, Senne Meynants, Ann Swillen, Jeroen Breckpot, Patrick Hasenfeld, Jan Korbel, Peter M. Lansdorp, Joris R. Vermeesch, Evan E. Eichler, Tiffany Y. Leung, Vasiliki Tsapalou
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Nature
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Long-read sequencing of families reveals increased germline and postzygotic mutation rates in repetitive DNA
Abstract Long-read sequencing improves sensitivity to discover variation in complex repetitive regions, assign parent-of-origin, and distinguish germline from postzygotic mutations. We applied Illumina, Oxford Nanopore Technologies, and PacBio sequencing to discover and validate de novo mutations in 73 children from 42 autism families (157 individuals).
Epigenetic and evolutionary features of ape subterminal heterochromatin
1,2 1Department of Genome Sciences, University of Washington School of Medicine, Seattle, Washington 98195, USA; 2Howard Hughes Medical Institute, University of Washington, Seattle, Washington 98195, USA Corresponding author: ee3{at}uw.edu Footnotes [Supplemental material is available for this article.] Article published online before print. Article, supplemental material, and publication date are at https://www.genome.org/cgi/doi/10.1101/gr.280987.125.
GREGoR: accelerating genomics for rare diseases - Nature
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Abstract Rare diseases are collectively common, affecting approximately 1 in 20 individuals worldwide. In recent years, rapid progress has been made in rare disease diagnostics due to advances in next-generation sequencing, development of new computational and functional genomics approaches to prioritize genes and variants and increased global sharing of clinical and genetic data. However, more than half of individuals suspected to have a rare disease lack a genetic diagnosis.
By Moez Dawood, Ben Heavner, Rachel A Ungar, Laurens Wiel, Seth Berger, Jonathan Bernstein, Jessica X. Chong, Evan E. Eichler, James R. Lupski, Michael E. Talkowski, Alex Wagner, Chia-Lin Wei, Christopher N. Wellington, Matthew Wheeler, Casey A. Gifford, Danny Miller, Kaitlin E. Samocha, Fritz J Sedlazeck, Anne H. O’Donnell-Luria, Stephen Montgomery
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Nature
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Locityper enables targeted genotyping of complex polymorphic genes - Nature Genetics
Abstract The human genome contains many structurally variable polymorphic loci, including several hundred disease-associated genes, almost inaccessible for accurate variant calling. Here we present Locityper, a tool capable of genotyping such challenging genes using short-read and long-read whole-genome sequencing.
Author Correction: Complex genetic variation in nearly complete human genomes - Nature
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Correction to: Nature https://doi.org/10.1038/s41586-025-09140-6 Published online 23 July 2025 In the version of the article initially published, the x-axis label for Fig. 4f was “Position (Mb)” and has now been corrected to “Position (kb)” in the HTML and PDF versions of the article.
By Glennis A. Logsdon, Peter J. R. Ebert, Peter A. Audano, Mark Loftus, David Porubsky, Feyza Yilmaz, Pille Hallast, Timofey Prodanov, DongAhn Yoo, Katherine Munson, Chen-Shan Chin, Haoyu Cheng, Zechen Chong, Jonathan Crabtree, Mark Gerstein, Patrick Hasenfeld, Glenn Hickey, Sarah Hunt, Yunzhe Jiang, Sergey Koren, Youngjun Kwon, Chong Li, Heng Li, Jiaqi Li, Paul Norman, Benedict Paten, Adam M. Phillippy, Nicholas Pollock, Tobias Rausch, Yuwei Song, Likhitha Surapaneni, Weichen Zhou, Michael C. Zody, Ryan Mills, Mark J. P. Chaisson, Miriam K. Konkel, Jan Korbel, Charles Lee, Christine R. Beck, Evan E. Eichler
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Nature
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The Platinum Pedigree: a long-read benchmark for genetic variants - Nature Methods
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Abstract Recent advances in genome sequencing have improved variant calling in complex regions of the human genome. However, it is difficult to quantify variant calling performance because existing standards often focus on specificity, neglecting completeness in difficult-to-analyze regions.
By Zev Kronenberg, David Porubsky, Tom Mokveld, William J Rowell, Pi-Chuan Chang, James Holt, Christopher Saunders, Nathan Olson, Andrea Guarracino, Nidhi Koundinya, Katherine Munson, Xiao Chen, Harriet Dashnow, Erik Garrison, Peter M. Lansdorp, Justin Zook, Andrew Carroll, Aaron R Quinlan, Evan E. Eichler
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Nature
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The Somatic Mosaicism across Human Tissues Network - Nature
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Abstract From fertilization onwards, the cells of the human body acquire variations in their DNA sequence, known as somatic mutations. These postzygotic mutations arise from intrinsic errors in DNA replication and repair, as well as from exposure to mutagens. Somatic mutations have been implicated in some diseases, but a fundamental understanding of the frequency, type and patterns of mutations across healthy human tissues has been limited.
By Yujin Choi, Boxun Zhao, Alexej Abyzov, James Bennett, Bradley E. Bernstein, Alan Boyle Verified, Jason D. Buenrostro, Kathleen Burns, fei chen, Rui Chen, Evan E. Eichler, Gilad D. Evrony, Manuel Garber, Nils Gehlenborg, Soren Germer, Gad Getz, Fulai Jin, Po-Ru Loh, Gabor Marth, Ryan Mills, Stephen Montgomery, Peter J. Park, Rahul Satija, Fritz J Sedlazeck, Diane Shao, Hui Shen, Andrew Stergachis, Alexander E. Urban, Christopher Walsh, Ting Wang, Tao Wu, Chenghang Zong, Eunjung Lee, Flora M. Vaccarino, Harsha V. Doddapaneni
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Nature
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A near telomere-to-telomere phased reference assembly for the male mountain gorilla - Scientific Data
Abstract The endangered mountain gorilla, Gorilla beringei beringei, faces numerous threats to its survival, highlighting the urgent need for genomic resources to aid conservation efforts. Here, we present a near telomere-to-telomere, haplotype-phased reference genome assembly for a male mountain gorilla generated using PacBio HiFi (26.77× ave. coverage) and Oxford Nanopore Technologies (52.87× ave. coverage) data.
Near-complete Middle Eastern genomes refine autozygosity and enhance disease-causing and population-specific variant discovery - Nature Genetics
Abstract Advances in long-read sequencing have enabled routine complete assembly of human genomes, but much remains to be done to represent broader populations and show impact on disease-gene discovery. Here, we report highly accurate, near-complete and phased genomes from six Middle Eastern (ME) family trios (n = 18) with neurodevelopmental conditions, representing ancestries from Sudan, Jordan, Syria, Qatar and Afghanistan.
Reconstruction of the human amylase locus reveals ancient duplications seeding modern-day variation
Abstract Previous studies suggested that the copy number of the human salivary amylase gene, AMY1, correlates with starch-rich diets. However, evolutionary analyses are hampered by the absence of accurate, sequence-resolved haplotype variation maps. We identified 30 structurally distinct haplotypes at nucleotide resolution among 98 present-day humans, revealing that the coding sequences of AMY1 copies are evolving under negative selection.
A 25-year odyssey of genomic technology advances and structural variant discovery
A rapid banding technique for human chromosomes. Lancet. 1971; 2: 971-972 Specific banding patterns of human chromosomes. Proc. Natl. Acad. Sci. USA. 1971; 68: 2073-2077 Sumner A.T. Evans H.J. Buckland R.A. New technique for distinguishing between human chromosomes. Nat. New Biol. 1971; 232: 31-32 Mechanisms involved in the banding of chromosomes with guinacrine and Giems. II. The interaction of the dyes with the chromosomal components. Exp. Cell Res.
Effects of parental age and polymer composition on short tandem repeat de novo mutation rates
Abstract Short tandem repeats (STRs) are hotspots of genomic variability in the human germline because of their high mutation rates, which have long been attributed largely to polymerase slippage during DNA replication. This model suggests that STR mutation rates should scale linearly with a father's age, as progenitor cells continually divide after puberty.
Envisioning a new era: Complete genetic information from routine, telomere-to-telomere genomes
Summary Advances in long-read sequencing and assembly now mean that individual labs can generate phased genomes that are more accurate and more contiguous than the original human reference genome. With declining costs and increasing democratization of technology, we suggest that complete genome assemblies, where both parental haplotypes are phased telomere to telomere, will become standard in human genetics.
Assembly of 43 human Y chromosomes reveals extensive complexity and variation - Nature
Abstract The prevalence of highly repetitive sequences within the human Y chromosome has prevented its complete assembly to date1 and led to its systematic omission from genomic analyses. Here we present de novo assemblies of 43 Y chromosomes spanning 182,900 years of human evolution and report considerable diversity in size and structure.
The complete sequence of a human Y chromosome - Nature
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Abstract The human Y chromosome has been notoriously difficult to sequence and assemble because of its complex repeat structure that includes long palindromes, tandem repeats and segmental duplications1,2,3. As a result, more than half of the Y chromosome is missing from the GRCh38 reference sequence and it remains the last human chromosome to be finished4,5.
By Arang Rhie, Savannah Hoyt, Dylan Taylor, Nicolas Altemose, Paul W. Hook, Sergey Koren, Jamie Allen, Andrey Bzikadze, Chen-Shan Chin, Mark Diekhans, Arkarachai Fungtammasan, Erik Garrison, Jennifer L. Gerton, Andrea Guarracino, Nancy Hansen, Marina Haukness, Thibaut Hourlier, Sarah Hunt, Miten Jain, Glennis A. Logsdon, Wojciech Makalowski, Fergal J. Martin, Rajiv C. McCoy, Katherine Munson, Terence Murphy, Luis F. Paulin, David Porubsky, Tamara A. Potapova, Fedor Ryabov, Steven Salzberg, Fritz J Sedlazeck, Kishwar Shafin, Francoise Thibaud-Nissen, Winston Timp, Marta Tomaszkiewicz, Mitchell R. Vollger, Brian P. Walenz, Samantha Zarate, Justin Zook, Evan E. Eichler, Rachel O’Neill, Michael C Schatz, Karen H Miga
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Nature
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A draft human pangenome reference - Nature
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Abstract Here the Human Pangenome Reference Consortium presents a first draft of the human pangenome reference. The pangenome contains 47 phased, diploid assemblies from a cohort of genetically diverse individuals1. These assemblies cover more than 99% of the expected sequence in each genome and are more than 99% accurate at the structural and base pair levels.
By Wen-Wei Liao, Daniel Doerr, Marina Haukness, Shuangjia Lu, Vincenza Colonna, Andrea Guarracino, Kerstin Howe, Miten Jain, Tsung-Yu Lu, Fergal J. Martin, Matthew Mitchell, Katherine Munson, Adam Novak, David Porubsky, Pjotr Prins, Jouni Sirén, Chad Tomlinson, Flavia Villani, Mitchell R. Vollger, Konstantinos Billis, Omar E Cornejo, Mark Diekhans, Peter J. R. Ebert, Olivier Fedrigo, Giulio Formenti, Nanibaa’ A. Garrison, Richard Green, Thibaut Hourlier, Hanlee P. Ji, Jan Korbel, Sergey Koren, Hojoon Lee, Hugo Magalhães, Santiago Marco-Sola, Jennifer McDaniel, Jacquelyn Mountcastle, Nathan Olson, Arang Rhie, Kishwar Shafin, Francoise Thibaud-Nissen, Francesca Floriana Tricomi, Brian P. Walenz, Guillaume Bourque, Mark J. P. Chaisson, Paul Flicek, Adam M. Phillippy, Justin Zook, Evan E. Eichler, David Haussler, Ting Wang, Erich D. Jarvis, Karen H Miga, Erik Garrison, Tobias Marschall, Ira M. Hall, Heng Li
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Nature
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Estimating the Prevalence of De Novo Monogenic Neurodevelopmental Disorders from Large Cohort Studies
Abstract : Rare diseases impact up to 400 million individuals globally. Of the thousands of known rare diseases, many are rare neurodevelopmental disorders (RNDDs) impacting children. RNDDs have proven to be difficult to assess epidemiologically for several reasons.
A predictive ensemble classifier for the gene expression diagnosis of ASD at ages 1 to 4 years - Molecular Psychiatry
Participant recruitment and clinical evaluation Participants in this study included 240 male toddlers ages 1–4 years (Table 1, Supplementary Table 1). About 70% of toddlers were recruited from the general population using an early screening, detection, and diagnosis strategy called the Get SET Early procedure [50].
Semi-automated assembly of high-quality diploid human reference genomes - Nature
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Cell lines The GM24385 (RRID:CVCL_1C78) EBV-immortalized LCL of HG002 was obtained from the National Institute for General Medical Sciences (NIGMS) Human Genetic Cell Repository at the Coriell Institute for Medical Research. This cell line was used to generate the Oxford Nanopore sequencing and Bionano mapping data.
By Erich D. Jarvis, Giulio Formenti, Andrea Guarracino, Jonathan Wood, Alan Tracey, Francoise Thibaud-Nissen, Mitchell R. Vollger, David Porubsky, Glennis A. Logsdon, Mark J. P. Chaisson, Peter J. R. Ebert, Merly Escalona, Olivier Fedrigo, Jennifer L. Gerton, Richard Green, Patrick Hasenfeld, Marina Haukness, Mikhail Kolmogorov, Jan Korbel, Sergey Koren, Jonas Korlach, Joyce Lee Verified, Daofeng Li, Feng Luo, Tobias Marschall, Jennifer McDaniel, Nathan Olson, Kishwar Shafin, Nathan O Stitziel, Jianxin Wang, Chuanle Xiao, Guojie Zhang, Ting Wang, Heng Li, David Haussler, Evan E. Eichler, Adam M. Phillippy, Kerstin Howe
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Nature
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GAVISUNK: Genome assembly validation via inter-SUNK distances in Oxford Nanopore reads
Thank you for your interest in spreading the word about bioRxiv. NOTE: Your email address is requested solely to identify you as the sender of this article. Your Email * Your Name * Send To * Enter multiple addresses on separate lines or separate them with commas. Message Subject (Your Name) has forwarded a page to you from bioRxiv Message Body (Your Name) thought you would like to see this page from the bioRxiv website.
The Human Pangenome Project: a global resource to map genomic diversity - Nature
Abstract The human reference genome is the most widely used resource in human genetics and is due for a major update. Its current structure is a linear composite of merged haplotypes from more than 20 people, with a single individual comprising most of the sequence. It contains biases and errors within a framework that does not represent global human genomic variation.
Pangenome-based genome inference allows efficient and accurate genotyping across a wide spectrum of variant classes - Nature Genetics
Abstract Typical genotyping workflows map reads to a reference genome before identifying genetic variants. Generating such alignments introduces reference biases and comes with substantial computational burden. Furthermore, short-read lengths limit the ability to characterize repetitive genomic regions, which are particularly challenging for fast k-mer-based genotypers.
Remembering Steve Warren (1953-2021): A giant in the field of genetics
Joseph Cubells Associate professor, Emory University Evan Eichler Professor, University of Washington James Sutcliffe Associate professor, Vanderbilt University Huda Zoghbi Director, Jan and Dan Duncan Neurological Research Institute Steve Warren, a giant in the field of human genetics, died in June at age 67.
Characterizing nucleotide variation and expansion dynamics in human-specific variable number tandem repeats
Meredith M. Course1, Arvis Sulovari2, Kathryn Gudsnuk1, Evan E. Eichler2,3 and Paul N.
Mining the gaps of chromosome 8
RESEARCH SUMMARY 14 May 2021 The first gapless, telomere-to-telomere sequence of a human autosome, chromosome 8, is complete. Sequencing and assembly of the corresponding centromere in the chimpanzee, orangutan and macaque reveals details of its rapid evolution over the past 25 million years. Glennis A. Logsdon Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA, USA. You can also search for this author in PubMed Google Scholar Evan E.
20th Anniversary
October 2020 marks the 20th anniversary of the launch of Nature Reviews Genetics. To celebrate this milestone, we have delved into our archives to curate a Collection of cutting-edge articles, historical pieces and thought-provoking commentaries and opinions. Featuring a range of article types, including Reviews, Perspectives, Viewpoints and Comments, this Collection provides a glimpse of the genetics and genomics field over the past two decades.
An evolutionary driver of interspersed segmental duplications in primates
Stuart Cantsilieris1,2, Susan M. Sunkin3, Matthew E. Johnson4, Fabio Anaclerio5, John Huddleston6,7, Carl Baker1, Max L. Dougherty1, Jason G. Underwood8, Arvis Sulovari1, PingHsun Hsieh1, Yafei Mao1, 5, Maika Malig1,9,10, AnneMarie E. Welch1,11, Melanie Sorensen1, Katherine M. Munson1, Weihong Jiang12, Santhosh Girirajan13, Mario Ventura5, Bruce T. Lamb14, Ronald A. Conlon12 & Evan E.
Long-read human genome sequencing and its applications - Nature Reviews Genetics
van Dijk, E. L., Jaszczyszyn, Y., Naquin, D. & Thermes, C. The third revolution in sequencing technology. Trends Genet. 34, 666–681 (2018). PubMed Google Scholar Shendure, J. et al. DNA sequencing at 40: past, present and future. Nature 550, 345–353 (2017). CAS Article Google Scholar Sudmant, P. H. et al. An integrated map of structural variation in 2,504 human genomes. Nature 526, 75–81 (2015). CAS PubMed PubMed Central Google Scholar Sudmant, P. H. et al.
Long-read assembly of the Chinese rhesus macaque genome and identification of ape-specific structural variants
Abstract We present a high-quality de novo genome assembly (rheMacS) of the Chinese rhesus macaque (Macaca mulatta) using long-read sequencing and multiplatform scaffolding approaches. Compared to the current Indian rhesus macaque reference genome (rheMac8), rheMacS increases sequence contiguity 75-fold, closing 21,940 of the remaining assembly gaps (60.8 Mbp).
Genetic Variation, Comparative Genomics, and the Diagnosis of Disease
logo-32 logo-40 logo-60 This article is available to subscribers. Subscribe now. Already have an account? Sign in Review ArticleFrontiers in MedicineFree Preview Evan E. Eichler, Ph.D. Audio Interview Interview with Dr. Evan E. Eichler on genetic variation, comparative genomics, and the diagnosis of disease. (07:53)Download The genome is not akin to a string of fixed length. Many large segments of DNA may be present or absent — a major contributor to pathogenic genomic variation.
The Role of De Novo Noncoding Regulatory Mutations in Neurodevelopmental Disorders
Highlights Recent sequencing advances have allowed whole-genome sequencing (WGS) of large numbers of individuals with autism. WGS data are beginning to provide insight into the potential contribution of noncoding variants in neurodevelopmental disorders. A trend has been observed for an excess of de novo variants in conserved noncoding regions among autism patients with no obvious genic cause. The noncoding de novo mutation signature is stronger near genes already implicated in autism.
Properties and rates of germline mutations in humans
Trends Genet. Author manuscript; available in PMC 2014 Apr 1. Published in final edited form as: PMCID: PMC3785239 NIHMSID: NIHMS481698 Properties and rates of germline mutations in humans Catarina D. Campbell 1Department of Genome Sciences, University of Washington, Seattle, WA 98195 Evan E.
Comorbid symptoms of inattention, autism, and executive cognition in youth with putative genetic risk
Symptoms of autism spectrum disorder (ASD) and inattention (IA) are highly comorbid and associated with deficits in executive cognition. Cognitive deficits have been posited as candidate endophenotypes of psychiatric traits, but few studies have conceptualized cognitive deficits as psychiatric comorbidities.
Characterizing nucleotide variation and expansion dynamics in human-specific variable number tandem repeats
Meredith M. Course1, Arvis Sulovari2, Kathryn Gudsnuk1, Evan E. Eichler2,3 and Paul N.
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