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1. The variation and evolution of complete human centromeres

Author

Logsdon, Glennis A., Rozanski, Allison N., Ryabov, Fedor, Potapova, Tamara, Shepelev, Valery A., Catacchio, Claudia R., Porubsky, David, Mao, Yafei, Yoo, DongAhn, Rautiainen, Mikko, Koren, Sergey, Nurk, Sergey, Lucas, Julian K., Hoekzema, Kendra, Munson, Katherine M., Gerton, Jennifer L., Phillippy, Adam M., Ventura, Mario, Alexandrov, Ivan A., and Eichler, Evan E.

Published
2024
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2. Increased mutation and gene conversion within human segmental duplications

Author

Vollger, Mitchell R, Dishuck, Philip C, Harvey, William T, DeWitt, William S, Guitart, Xavi, Goldberg, Michael E, Rozanski, Allison N, Lucas, Julian, Asri, Mobin, Munson, Katherine M, Lewis, Alexandra P, Hoekzema, Kendra, Logsdon, Glennis A, Porubsky, David, Paten, Benedict, Harris, Kelley, Hsieh, PingHsun, and Eichler, Evan E

Subjects
Biological Sciences, Bioinformatics and Computational Biology, Genetics, 2.1 Biological and endogenous factors, Humans, Gene Conversion, Genome, Human, Mutation, Segmental Duplications, Genomic, Polymorphism, Single Nucleotide, Haplotypes, Exons, Cytosine, Guanine, CpG Islands, Human Pangenome Reference Consortium, General Science & Technology
Abstract

Single-nucleotide variants (SNVs) in segmental duplications (SDs) have not been systematically assessed because of the limitations of mapping short-read sequencing data1,2. Here we constructed 1:1 unambiguous alignments spanning high-identity SDs across 102 human haplotypes and compared the pattern of SNVs between unique and duplicated regions3,4. We find that human SNVs are elevated 60% in SDs compared to unique regions and estimate that at least 23% of this increase is due to interlocus gene conversion (IGC) with up to 4.3 megabase pairs of SD sequence converted on average per human haplotype. We develop a genome-wide map of IGC donors and acceptors, including 498 acceptor and 454 donor hotspots affecting the exons of about 800 protein-coding genes. These include 171 genes that have 'relocated' on average 1.61 megabase pairs in a subset of human haplotypes. Using a coalescent framework, we show that SD regions are slightly evolutionarily older when compared to unique sequences, probably owing to IGC. SNVs in SDs, however, show a distinct mutational spectrum: a 27.1% increase in transversions that convert cytosine to guanine or the reverse across all triplet contexts and a 7.6% reduction in the frequency of CpG-associated mutations when compared to unique DNA. We reason that these distinct mutational properties help to maintain an overall higher GC content of SD DNA compared to that of unique DNA, probably driven by GC-biased conversion between paralogous sequences5,6.

Published
2023

3. Semi-automated assembly of high-quality diploid human reference genomes

Author

Jarvis, Erich D, Formenti, Giulio, Rhie, Arang, Guarracino, Andrea, Yang, Chentao, Wood, Jonathan, Tracey, Alan, Thibaud-Nissen, Francoise, Vollger, Mitchell R, Porubsky, David, Cheng, Haoyu, Asri, Mobin, Logsdon, Glennis A, Carnevali, Paolo, Chaisson, Mark JP, Chin, Chen-Shan, Cody, Sarah, Collins, Joanna, Ebert, Peter, Escalona, Merly, Fedrigo, Olivier, Fulton, Robert S, Fulton, Lucinda L, Garg, Shilpa, Gerton, Jennifer L, Ghurye, Jay, Granat, Anastasiya, Green, Richard E, Harvey, William, Hasenfeld, Patrick, Hastie, Alex, Haukness, Marina, Jaeger, Erich B, Jain, Miten, Kirsche, Melanie, Kolmogorov, Mikhail, Korbel, Jan O, Koren, Sergey, Korlach, Jonas, Lee, Joyce, Li, Daofeng, Lindsay, Tina, Lucas, Julian, Luo, Feng, Marschall, Tobias, Mitchell, Matthew W, McDaniel, Jennifer, Nie, Fan, Olsen, Hugh E, Olson, Nathan D, Pesout, Trevor, Potapova, Tamara, Puiu, Daniela, Regier, Allison, Ruan, Jue, Salzberg, Steven L, Sanders, Ashley D, Schatz, Michael C, Schmitt, Anthony, Schneider, Valerie A, Selvaraj, Siddarth, Shafin, Kishwar, Shumate, Alaina, Stitziel, Nathan O, Stober, Catherine, Torrance, James, Wagner, Justin, Wang, Jianxin, Wenger, Aaron, Xiao, Chuanle, Zimin, Aleksey V, Zhang, Guojie, Wang, Ting, Li, Heng, Garrison, Erik, Haussler, David, Hall, Ira, Zook, Justin M, Eichler, Evan E, Phillippy, Adam M, Paten, Benedict, Howe, Kerstin, and Miga, Karen H

Subjects
Genetics, Human Genome, Biotechnology, Generic health relevance, Humans, Chromosome Mapping, Diploidy, Genome, Human, Haplotypes, High-Throughput Nucleotide Sequencing, Sequence Analysis, DNA, Reference Standards, Genomics, Chromosomes, Human, Genetic Variation, Human Pangenome Reference Consortium, General Science & Technology
Abstract

The current human reference genome, GRCh38, represents over 20 years of effort to generate a high-quality assembly, which has benefitted society1,2. However, it still has many gaps and errors, and does not represent a biological genome as it is a blend of multiple individuals3,4. Recently, a high-quality telomere-to-telomere reference, CHM13, was generated with the latest long-read technologies, but it was derived from a hydatidiform mole cell line with a nearly homozygous genome5. To address these limitations, the Human Pangenome Reference Consortium formed with the goal of creating high-quality, cost-effective, diploid genome assemblies for a pangenome reference that represents human genetic diversity6. Here, in our first scientific report, we determined which combination of current genome sequencing and assembly approaches yield the most complete and accurate diploid genome assembly with minimal manual curation. Approaches that used highly accurate long reads and parent-child data with graph-based haplotype phasing during assembly outperformed those that did not. Developing a combination of the top-performing methods, we generated our first high-quality diploid reference assembly, containing only approximately four gaps per chromosome on average, with most chromosomes within ±1% of the length of CHM13. Nearly 48% of protein-coding genes have non-synonymous amino acid changes between haplotypes, and centromeric regions showed the highest diversity. Our findings serve as a foundation for assembling near-complete diploid human genomes at scale for a pangenome reference to capture global genetic variation from single nucleotides to structural rearrangements.

Published
2022

5. Assembly of 43 human Y chromosomes reveals extensive complexity and variation

Author

Hallast, Pille, Ebert, Peter, Loftus, Mark, Yilmaz, Feyza, Audano, Peter A., Logsdon, Glennis A., Bonder, Marc Jan, Zhou, Weichen, Höps, Wolfram, Kim, Kwondo, Li, Chong, Hoyt, Savannah J., Dishuck, Philip C., Porubsky, David, Tsetsos, Fotios, Kwon, Jee Young, Zhu, Qihui, Munson, Katherine M., Hasenfeld, Patrick, Harvey, William T., Lewis, Alexandra P., Kordosky, Jennifer, Hoekzema, Kendra, O’Neill, Rachel J., Korbel, Jan O., Tyler-Smith, Chris, Eichler, Evan E., Shi, Xinghua, Beck, Christine R., Marschall, Tobias, Konkel, Miriam K., and Lee, Charles

Published
2023
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6. The complete sequence of a human Y chromosome

Author

Rhie, Arang, Nurk, Sergey, Cechova, Monika, Hoyt, Savannah J., Taylor, Dylan J., Altemose, Nicolas, Hook, Paul W., Koren, Sergey, Rautiainen, Mikko, Alexandrov, Ivan A., Allen, Jamie, Asri, Mobin, Bzikadze, Andrey V., Chen, Nae-Chyun, Chin, Chen-Shan, Diekhans, Mark, Flicek, Paul, Formenti, Giulio, Fungtammasan, Arkarachai, Garcia Giron, Carlos, Garrison, Erik, Gershman, Ariel, Gerton, Jennifer L., Grady, Patrick G. S., Guarracino, Andrea, Haggerty, Leanne, Halabian, Reza, Hansen, Nancy F., Harris, Robert, Hartley, Gabrielle A., Harvey, William T., Haukness, Marina, Heinz, Jakob, Hourlier, Thibaut, Hubley, Robert M., Hunt, Sarah E., Hwang, Stephen, Jain, Miten, Kesharwani, Rupesh K., Lewis, Alexandra P., Li, Heng, Logsdon, Glennis A., Lucas, Julian K., Makalowski, Wojciech, Markovic, Christopher, Martin, Fergal J., Mc Cartney, Ann M., McCoy, Rajiv C., McDaniel, Jennifer, McNulty, Brandy M., Medvedev, Paul, Mikheenko, Alla, Munson, Katherine M., Murphy, Terence D., Olsen, Hugh E., Olson, Nathan D., Paulin, Luis F., Porubsky, David, Potapova, Tamara, Ryabov, Fedor, Salzberg, Steven L., Sauria, Michael E. G., Sedlazeck, Fritz J., Shafin, Kishwar, Shepelev, Valery A., Shumate, Alaina, Storer, Jessica M., Surapaneni, Likhitha, Taravella Oill, Angela M., Thibaud-Nissen, Françoise, Timp, Winston, Tomaszkiewicz, Marta, Vollger, Mitchell R., Walenz, Brian P., Watwood, Allison C., Weissensteiner, Matthias H., Wenger, Aaron M., Wilson, Melissa A., Zarate, Samantha, Zhu, Yiming, Zook, Justin M., Eichler, Evan E., O’Neill, Rachel J., Schatz, Michael C., Miga, Karen H., Makova, Kateryna D., and Phillippy, Adam M.

Published
2023
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7. Neurodevelopmental copy-number variants: A roadmap to improving outcomes by uniting patient advocates, researchers, and clinicians for collective impact

Author

Variants, Commission on Novel Technologies for Neurodevelopmental Copy Number, Buttermore, Elizabeth, Chamberlain, Stormy, Cody, Jannine, Costain, Gregory, Dang, Louis, DeWoody, Andrew, DeWoody, Yssa, Dies, Kira, Eichler, Evan, Girirajan, Santhosh, Gramm, Marie, Halladay, Alycia, Lal, Dennis, Lalli, Matthew, Levy, Tess, Logsdon, Glennis, Lowenstein, Daniel, Mefford, Heather, Mulle, Jennifer, Muotri, Alysson, Murphy, Melissa, Palma, Eduardo Perez, Pinter, Stefan, Pollak, Rebecca, Purcell, Ryan, Samaco, Rodney, Shah, Bina, Singh, Karun, So, Joyce, Sundberg, Maria, Veeraragavan, Surabi, Vogel-Farley, Vanessa, and Wynshaw-Boris, Anthony

Subjects
Biological Sciences, Biomedical and Clinical Sciences, Genetics, Human Genome, Intellectual and Developmental Disabilities (IDD), Neurosciences, Brain Disorders, DNA Copy Number Variations, Genome, Humans, Neurodevelopmental Disorders, Patient Advocacy, Phenotype, Commission on Novel Technologies for Neurodevelopmental Copy Number Variants, CNVs, biobank, community engagement, copy-number variants, genomic disorders, iPSCs, inclusion, infrastructure, long-read sequencing, neurodevelopment, neurological, patient centered, patient led, structural variants, systematic phenotyping, team science, Medical and Health Sciences, Genetics & Heredity, Biological sciences, Biomedical and clinical sciences, Health sciences
Abstract

Copy-number variants and structural variants (CNVs/SVs) drive many neurodevelopmental-related disorders. While many neurodevelopmental-related CNVs/SVs give rise to complex phenotypes, the overlap in phenotypic presentation between independent CNVs can be extensive and provides a motivation for shared approaches. This confluence at the level of clinical phenotype implies convergence in at least some aspects of the underlying genomic mechanisms. With this perspective, our Commission on Novel Technologies for Neurodevelopmental CNVs asserts that the time has arrived to approach neurodevelopmental-related CNVs/SVs as a class of disorders that can be identified, investigated, and treated on the basis of shared mechanisms and/or pathways (e.g., molecular, neurological, or developmental). To identify common etiologic mechanisms among uncommon neurodevelopmental-related disorders and to potentially identify common therapies, it is paramount for teams of scientists, clinicians, and patients to unite their efforts. We bring forward novel, collaborative, and integrative strategies to translational CNV/SV research that engages diverse stakeholders to help expedite therapeutic outcomes. We articulate a clear vision for piloted roadmap strategies to reduce patient/caregiver burden and redundancies, increase efficiency, avoid siloed data, and accelerate translational discovery across CNV/SV-based syndromes.

Published
2022

8. Epigenetic patterns in a complete human genome

Author

Gershman, Ariel, Sauria, Michael EG, Guitart, Xavi, Vollger, Mitchell R, Hook, Paul W, Hoyt, Savannah J, Jain, Miten, Shumate, Alaina, Razaghi, Roham, Koren, Sergey, Altemose, Nicolas, Caldas, Gina V, Logsdon, Glennis A, Rhie, Arang, Eichler, Evan E, Schatz, Michael C, O'Neill, Rachel J, Phillippy, Adam M, Miga, Karen H, and Timp, Winston

Subjects
Biological Sciences, Bioinformatics and Computational Biology, Genetics, Human Genome, 1.1 Normal biological development and functioning, Underpinning research, Generic health relevance, Centromere, CpG Islands, DNA Methylation, Disease, Epigenesis, Genetic, Genetic Loci, Genome, Human, Genomics, Humans, Reference Standards, Sequence Analysis, DNA, General Science & Technology
Abstract

The completion of a telomere-to-telomere human reference genome, T2T-CHM13, has resolved complex regions of the genome, including repetitive and homologous regions. Here, we present a high-resolution epigenetic study of previously unresolved sequences, representing entire acrocentric chromosome short arms, gene family expansions, and a diverse collection of repeat classes. This resource precisely maps CpG methylation (32.28 million CpGs), DNA accessibility, and short-read datasets (166,058 previously unresolved chromatin immunoprecipitation sequencing peaks) to provide evidence of activity across previously unidentified or corrected genes and reveals clinically relevant paralog-specific regulation. Probing CpG methylation across human centromeres from six diverse individuals generated an estimate of variability in kinetochore localization. This analysis provides a framework with which to investigate the most elusive regions of the human genome, granting insights into epigenetic regulation.

Published
2022

9. Complete genomic and epigenetic maps of human centromeres

Author

Altemose, Nicolas, Logsdon, Glennis A, Bzikadze, Andrey V, Sidhwani, Pragya, Langley, Sasha A, Caldas, Gina V, Hoyt, Savannah J, Uralsky, Lev, Ryabov, Fedor D, Shew, Colin J, Sauria, Michael EG, Borchers, Matthew, Gershman, Ariel, Mikheenko, Alla, Shepelev, Valery A, Dvorkina, Tatiana, Kunyavskaya, Olga, Vollger, Mitchell R, Rhie, Arang, McCartney, Ann M, Asri, Mobin, Lorig-Roach, Ryan, Shafin, Kishwar, Lucas, Julian K, Aganezov, Sergey, Olson, Daniel, de Lima, Leonardo Gomes, Potapova, Tamara, Hartley, Gabrielle A, Haukness, Marina, Kerpedjiev, Peter, Gusev, Fedor, Tigyi, Kristof, Brooks, Shelise, Young, Alice, Nurk, Sergey, Koren, Sergey, Salama, Sofie R, Paten, Benedict, Rogaev, Evgeny I, Streets, Aaron, Karpen, Gary H, Dernburg, Abby F, Sullivan, Beth A, Straight, Aaron F, Wheeler, Travis J, Gerton, Jennifer L, Eichler, Evan E, Phillippy, Adam M, Timp, Winston, Dennis, Megan Y, O'Neill, Rachel J, Zook, Justin M, Schatz, Michael C, Pevzner, Pavel A, Diekhans, Mark, Langley, Charles H, Alexandrov, Ivan A, and Miga, Karen H

Subjects
Biological Sciences, Bioinformatics and Computational Biology, Genetics, Human Genome, Generic health relevance, Centromere, Chromosome Mapping, Epigenesis, Genetic, Evolution, Molecular, Genome, Human, Genomics, Humans, Repetitive Sequences, Nucleic Acid, General Science & Technology
Abstract

Existing human genome assemblies have almost entirely excluded repetitive sequences within and near centromeres, limiting our understanding of their organization, evolution, and functions, which include facilitating proper chromosome segregation. Now, a complete, telomere-to-telomere human genome assembly (T2T-CHM13) has enabled us to comprehensively characterize pericentromeric and centromeric repeats, which constitute 6.2% of the genome (189.9 megabases). Detailed maps of these regions revealed multimegabase structural rearrangements, including in active centromeric repeat arrays. Analysis of centromere-associated sequences uncovered a strong relationship between the position of the centromere and the evolution of the surrounding DNA through layered repeat expansions. Furthermore, comparisons of chromosome X centromeres across a diverse panel of individuals illuminated high degrees of structural, epigenetic, and sequence variation in these complex and rapidly evolving regions.

Published
2022

10. The complete sequence of a human genome

Author

Nurk, Sergey, Koren, Sergey, Rhie, Arang, Rautiainen, Mikko, Bzikadze, Andrey V, Mikheenko, Alla, Vollger, Mitchell R, Altemose, Nicolas, Uralsky, Lev, Gershman, Ariel, Aganezov, Sergey, Hoyt, Savannah J, Diekhans, Mark, Logsdon, Glennis A, Alonge, Michael, Antonarakis, Stylianos E, Borchers, Matthew, Bouffard, Gerard G, Brooks, Shelise Y, Caldas, Gina V, Chen, Nae-Chyun, Cheng, Haoyu, Chin, Chen-Shan, Chow, William, de Lima, Leonardo G, Dishuck, Philip C, Durbin, Richard, Dvorkina, Tatiana, Fiddes, Ian T, Formenti, Giulio, Fulton, Robert S, Fungtammasan, Arkarachai, Garrison, Erik, Grady, Patrick GS, Graves-Lindsay, Tina A, Hall, Ira M, Hansen, Nancy F, Hartley, Gabrielle A, Haukness, Marina, Howe, Kerstin, Hunkapiller, Michael W, Jain, Chirag, Jain, Miten, Jarvis, Erich D, Kerpedjiev, Peter, Kirsche, Melanie, Kolmogorov, Mikhail, Korlach, Jonas, Kremitzki, Milinn, Li, Heng, Maduro, Valerie V, Marschall, Tobias, McCartney, Ann M, McDaniel, Jennifer, Miller, Danny E, Mullikin, James C, Myers, Eugene W, Olson, Nathan D, Paten, Benedict, Peluso, Paul, Pevzner, Pavel A, Porubsky, David, Potapova, Tamara, Rogaev, Evgeny I, Rosenfeld, Jeffrey A, Salzberg, Steven L, Schneider, Valerie A, Sedlazeck, Fritz J, Shafin, Kishwar, Shew, Colin J, Shumate, Alaina, Sims, Ying, Smit, Arian FA, Soto, Daniela C, Sović, Ivan, Storer, Jessica M, Streets, Aaron, Sullivan, Beth A, Thibaud-Nissen, Françoise, Torrance, James, Wagner, Justin, Walenz, Brian P, Wenger, Aaron, Wood, Jonathan MD, Xiao, Chunlin, Yan, Stephanie M, Young, Alice C, Zarate, Samantha, Surti, Urvashi, McCoy, Rajiv C, Dennis, Megan Y, Alexandrov, Ivan A, Gerton, Jennifer L, O’Neill, Rachel J, Timp, Winston, Zook, Justin M, Schatz, Michael C, Eichler, Evan E, Miga, Karen H, and Phillippy, Adam M

Subjects
Biological Sciences, Bioinformatics and Computational Biology, Genetics, Human Genome, 1.1 Normal biological development and functioning, Underpinning research, Generic health relevance, Cell Line, Chromosomes, Artificial, Bacterial, Chromosomes, Human, Genome, Human, Human Genome Project, Humans, Reference Values, Sequence Analysis, DNA, General Science & Technology
Abstract

Since its initial release in 2000, the human reference genome has covered only the euchromatic fraction of the genome, leaving important heterochromatic regions unfinished. Addressing the remaining 8% of the genome, the Telomere-to-Telomere (T2T) Consortium presents a complete 3.055 billion-base pair sequence of a human genome, T2T-CHM13, that includes gapless assemblies for all chromosomes except Y, corrects errors in the prior references, and introduces nearly 200 million base pairs of sequence containing 1956 gene predictions, 99 of which are predicted to be protein coding. The completed regions include all centromeric satellite arrays, recent segmental duplications, and the short arms of all five acrocentric chromosomes, unlocking these complex regions of the genome to variational and functional studies.

Published
2022

11. Structurally divergent and recurrently mutated regions of primate genomes

Author

Mao, Yafei, Harvey, William T., Porubsky, David, Munson, Katherine M., Hoekzema, Kendra, Lewis, Alexandra P., Audano, Peter A., Rozanski, Allison, Yang, Xiangyu, Zhang, Shilong, Yoo, DongAhn, Gordon, David S., Fair, Tyler, Wei, Xiaoxi, Logsdon, Glennis A., Haukness, Marina, Dishuck, Philip C., Jeong, Hyeonsoo, del Rosario, Ricardo, Bauer, Vanessa L., Fattor, Will T., Wilkerson, Gregory K., Mao, Yuxiang, Shi, Yongyong, Sun, Qiang, Lu, Qing, Paten, Benedict, Bakken, Trygve E., Pollen, Alex A., Feng, Guoping, Sawyer, Sara L., Warren, Wesley C., Carbone, Lucia, and Eichler, Evan E.

Published
2024
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12. Telomere-to-telomere assembly of a complete human X chromosome

Author

Miga, Karen H, Koren, Sergey, Rhie, Arang, Vollger, Mitchell R, Gershman, Ariel, Bzikadze, Andrey, Brooks, Shelise, Howe, Edmund, Porubsky, David, Logsdon, Glennis A, Schneider, Valerie A, Potapova, Tamara, Wood, Jonathan, Chow, William, Armstrong, Joel, Fredrickson, Jeanne, Pak, Evgenia, Tigyi, Kristof, Kremitzki, Milinn, Markovic, Christopher, Maduro, Valerie, Dutra, Amalia, Bouffard, Gerard G, Chang, Alexander M, Hansen, Nancy F, Wilfert, Amy B, Thibaud-Nissen, Françoise, Schmitt, Anthony D, Belton, Jon-Matthew, Selvaraj, Siddarth, Dennis, Megan Y, Soto, Daniela C, Sahasrabudhe, Ruta, Kaya, Gulhan, Quick, Josh, Loman, Nicholas J, Holmes, Nadine, Loose, Matthew, Surti, Urvashi, Risques, Rosa ana, Graves Lindsay, Tina A, Fulton, Robert, Hall, Ira, Paten, Benedict, Howe, Kerstin, Timp, Winston, Young, Alice, Mullikin, James C, Pevzner, Pavel A, Gerton, Jennifer L, Sullivan, Beth A, Eichler, Evan E, and Phillippy, Adam M

Subjects
Biological Sciences, Bioinformatics and Computational Biology, Genetics, Bioengineering, Nanotechnology, Human Genome, Generic health relevance, Centromere, Chromosomes, Human, X, CpG Islands, DNA Methylation, DNA, Satellite, Female, Genome, Human, Humans, Hydatidiform Mole, Male, Pregnancy, Reproducibility of Results, Telomere, Testis, General Science & Technology
Abstract

After two decades of improvements, the current human reference genome (GRCh38) is the most accurate and complete vertebrate genome ever produced. However, no single chromosome has been finished end to end, and hundreds of unresolved gaps persist1,2. Here we present a human genome assembly that surpasses the continuity of GRCh382, along with a gapless, telomere-to-telomere assembly of a human chromosome. This was enabled by high-coverage, ultra-long-read nanopore sequencing of the complete hydatidiform mole CHM13 genome, combined with complementary technologies for quality improvement and validation. Focusing our efforts on the human X chromosome3, we reconstructed the centromeric satellite DNA array (approximately 3.1 Mb) and closed the 29 remaining gaps in the current reference, including new sequences from the human pseudoautosomal regions and from cancer-testis ampliconic gene families (CT-X and GAGE). These sequences will be integrated into future human reference genome releases. In addition, the complete chromosome X, combined with the ultra-long nanopore data, allowed us to map methylation patterns across complex tandem repeats and satellite arrays. Our results demonstrate that finishing the entire human genome is now within reach, and the data presented here will facilitate ongoing efforts to complete the other human chromosomes.

Published
2020

13. Chasing perfection: validation and polishing strategies for telomere-to-telomere genome assemblies

Author

Mc Cartney, Ann M., Shafin, Kishwar, Alonge, Michael, Bzikadze, Andrey V., Formenti, Giulio, Fungtammasan, Arkarachai, Howe, Kerstin, Jain, Chirag, Koren, Sergey, Logsdon, Glennis A., Miga, Karen H., Mikheenko, Alla, Paten, Benedict, Shumate, Alaina, Soto, Daniela C., Sović, Ivan, Wood, Jonathan M. D., Zook, Justin M., Phillippy, Adam M., and Rhie, Arang

Published
2022
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14. Phosphorylation of CENP-A on serine 7 does not control centromere function.

Author

Barra, Viviana, Logsdon, Glennis A, Scelfo, Andrea, Hoffmann, Sebastian, Hervé, Solène, Aslanian, Aaron, Nechemia-Arbely, Yael, Cleveland, Don W, Black, Ben E, and Fachinetti, Daniele

Subjects
Hela Cells, Centromere, Humans, Phosphorylation, Gene Editing, Centromere Protein A, HeLa Cells
Abstract

CENP-A is the histone H3 variant necessary to specify the location of all eukaryotic centromeres via its CENP-A targeting domain and either one of its terminal regions. In humans, several post-translational modifications occur on CENP-A, but their role in centromere function remains controversial. One of these modifications of CENP-A, phosphorylation on serine 7, has been proposed to control centromere assembly and function. Here, using gene targeting at both endogenous CENP-A alleles and gene replacement in human cells, we demonstrate that a CENP-A variant that cannot be phosphorylated at serine 7 maintains correct CENP-C recruitment, faithful chromosome segregation and long-term cell viability. Thus, we conclude that phosphorylation of CENP-A on serine 7 is dispensable to maintain correct centromere dynamics and function.

Published
2019

15. Neurodevelopmental copy-number variants: A roadmap to improving outcomes by uniting patient advocates, researchers, and clinicians for collective impact

Author

Buttermore, Elizabeth, Chamberlain, Stormy, Cody, Jannine, Costain, Gregory, Dang, Louis, DeWoody, Andrew, DeWoody, Yssa, Dies, Kira, Eichler, Evan, Girirajan, Santhosh, Gramm, Marie, Halladay, Alycia, Lal, Dennis, Lalli, Matthew, Levy, Tess, Logsdon, Glennis, Lowenstein, Daniel, Mefford, Heather, Mulle, Jennifer, Muotri, Alysson, Murphy, Melissa, Perez Palma, Eduardo, Pinter, Stefan, Pollak, Rebecca, Purcell, Ryan, Samaco, Rodney, Shah, Bina, Singh, Karun, So, Joyce, Sundberg, Maria, Veeraragavan, Surabi, Vogel-Farley, Vanessa, and Wynshaw-Boris, Anthony

Published
2022
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16. Centromeres are maintained by fastening CENP-A to DNA and directing an arginine anchor-dependent nucleosome transition.

Author

Guo, Lucie Y, Allu, Praveen Kumar, Zandarashvili, Levani, McKinley, Kara L, Sekulic, Nikolina, Dawicki-McKenna, Jennine M, Fachinetti, Daniele, Logsdon, Glennis A, Jamiolkowski, Ryan M, Cleveland, Don W, Cheeseman, Iain M, and Black, Ben E

Subjects
Centromere, Nucleosomes, Animals, Humans, Mice, Arginine, Chromosomal Proteins, Non-Histone, DNA, Protein Binding, Female, Male, Protein Domains, Centromere Protein A, Chromosomal Proteins, Non-Histone
Abstract

Maintaining centromere identity relies upon the persistence of the epigenetic mark provided by the histone H3 variant, centromere protein A (CENP-A), but the molecular mechanisms that underlie its remarkable stability remain unclear. Here, we define the contributions of each of the three candidate CENP-A nucleosome-binding domains (two on CENP-C and one on CENP-N) to CENP-A stability using gene replacement and rapid protein degradation. Surprisingly, the most conserved domain, the CENP-C motif, is dispensable. Instead, the stability is conferred by the unfolded central domain of CENP-C and the folded N-terminal domain of CENP-N that becomes rigidified 1,000-fold upon crossbridging CENP-A and its adjacent nucleosomal DNA. Disrupting the 'arginine anchor' on CENP-C for the nucleosomal acidic patch disrupts the CENP-A nucleosome structural transition and removes CENP-A nucleosomes from centromeres. CENP-A nucleosome retention at centromeres requires a core centromeric nucleosome complex where CENP-C clamps down a stable nucleosome conformation and CENP-N fastens CENP-A to the DNA.

Published
2017

17. CENP-A Modifications on Ser68 and Lys124 Are Dispensable for Establishment, Maintenance, and Long-Term Function of Human Centromeres

Author

Fachinetti, Daniele, Logsdon, Glennis A, Abdullah, Amira, Selzer, Evan B, Cleveland, Don W, and Black, Ben E

Subjects
Biochemistry and Cell Biology, Biological Sciences, Genetics, Cancer, Underpinning research, 1.1 Normal biological development and functioning, Generic health relevance, Autoantigens, Cell Line, Centromere, Centromere Protein A, Chromosomal Proteins, Non-Histone, Genetic Loci, Humans, Lysine, Protein Processing, Post-Translational, Serine, CENP-A, CRISPR, auxin, centromere, chromatin assembly, epigenetics, histone, histone variants, kinetochore, mitosis, Medical and Health Sciences, Developmental Biology, Biochemistry and cell biology
Abstract

CENP-A is a histone H3 variant key to epigenetic specification of mammalian centromeres. Using transient overexpression of CENP-A mutants, two recent reports in Developmental Cell proposed essential centromere functions for post-translational modifications of human CENP-A. Phosphorylation at Ser68 was proposed to have an essential role in CENP-A deposition at centromeres. Blockage of ubiquitination at Lys124 was proposed to abrogate localization of CENP-A to the centromere. Following gene inactivation and replacement in human cells, we demonstrate that CENP-A mutants that cannot be phosphorylated at Ser68 or ubiquitinated at Lys124 assemble efficiently at centromeres during G1, mediate early events in centromere establishment at an ectopic chromosomal locus, and maintain centromere function indefinitely. Thus, neither Ser68 nor Lys124 post-translational modification is essential for long-term centromere identity, propagation, cell-cycle-dependent deposition, maintenance, function, or mediation of early steps in centromere establishment.

Published
2017

18. The structure, function and evolution of a complete human chromosome 8

Author

Logsdon, Glennis A., Vollger, Mitchell R., Hsieh, PingHsun, Mao, Yafei, Liskovykh, Mikhail A., Koren, Sergey, Nurk, Sergey, Mercuri, Ludovica, Dishuck, Philip C., Rhie, Arang, de Lima, Leonardo G., Dvorkina, Tatiana, Porubsky, David, Harvey, William T., Mikheenko, Alla, Bzikadze, Andrey V., Kremitzki, Milinn, Graves-Lindsay, Tina A., Jain, Chirag, Hoekzema, Kendra, Murali, Shwetha C., Munson, Katherine M., Baker, Carl, Sorensen, Melanie, Lewis, Alexandra M., Surti, Urvashi, Gerton, Jennifer L., Larionov, Vladimir, Ventura, Mario, Miga, Karen H., Phillippy, Adam M., and Eichler, Evan E.

Published
2021
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23. Centromere innovations within a mouse species

Author

Gambogi, Craig W., primary, Pandey, Nootan, additional, Dawicki-McKenna, Jennine M., additional, Arora, Uma P., additional, Liskovykh, Mikhail A., additional, Ma, Jun, additional, Lamelza, Piero, additional, Larionov, Vladimir, additional, Lampson, Michael A., additional, Logsdon, Glennis A., additional, Dumont, Beth L., additional, and Black, Ben E., additional

Published
2023
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25. Characterization of large-scale genomic differences in the first complete human genome

Author

Yang, Xiangyu, primary, Wang, Xuankai, additional, Zou, Yawen, additional, Zhang, Shilong, additional, Xia, Manying, additional, Fu, Lianting, additional, Vollger, Mitchell R., additional, Chen, Nae-Chyun, additional, Taylor, Dylan J., additional, Harvey, William T., additional, Logsdon, Glennis A., additional, Meng, Dan, additional, Shi, Junfeng, additional, McCoy, Rajiv C., additional, Schatz, Michael C., additional, Li, Weidong, additional, Eichler, Evan E., additional, Lu, Qing, additional, and Mao, Yafei, additional

Published
2023
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27. Conservation of chromatin organization within human and primate centromeres

Author

Dubocanin, Danilo, primary, Cortes, Adriana E. Sedeno, additional, Hartley, Gabrielle A., additional, Ranchalis, Jane E., additional, Agarwal, Aman, additional, Logsdon, Glennis, additional, Munson, Katherine M., additional, Real, Taylor D., additional, Mallory, Benjamin J., additional, Eichler, Evan E., additional, O'Neill, Rachel J, additional, and Stergachis, Andrew Ben, additional

Published
2023
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28. Structurally divergent and recurrently mutated regions of primate genomes

Author

Mao, Yafei, primary, Harvey, William T., additional, Porubsky, David, additional, Munson, Katherine M., additional, Hoekzema, Kendra, additional, Lewis, Alexandra P., additional, Audano, Peter A., additional, Rozanski, Allison, additional, Yang, Xiangyu, additional, Zhang, Shilong, additional, Gordon, David S., additional, Wei, Xiaoxi, additional, Logsdon, Glennis A., additional, Haukness, Marina, additional, Dishuck, Philip C., additional, Jeong, Hyeonsoo, additional, del Rosario, Ricardo, additional, Bauer, Vanessa L., additional, Fattor, Will T., additional, Wilkerson, Gregory K., additional, Lu, Qing, additional, Paten, Benedict, additional, Feng, Guoping, additional, Sawyer, Sara L., additional, Warren, Wesley C., additional, Carbone, Lucia, additional, and Eichler, Evan E., additional

Published
2023
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29. Increased mutation and gene conversion within human segmental duplications.

Author

Vollger, Mitchell, Vollger, Mitchell, Dishuck, Philip, Harvey, William, DeWitt, William, Guitart, Xavi, Goldberg, Michael, Rozanski, Allison, Lucas, Julian, Asri, Mobin, Munson, Katherine, Lewis, Alexandra, Hoekzema, Kendra, Logsdon, Glennis, Porubsky, David, Paten, Benedict, Harris, Kelley, Hsieh, PingHsun, Eichler, Evan, Vollger, Mitchell, Vollger, Mitchell, Dishuck, Philip, Harvey, William, DeWitt, William, Guitart, Xavi, Goldberg, Michael, Rozanski, Allison, Lucas, Julian, Asri, Mobin, Munson, Katherine, Lewis, Alexandra, Hoekzema, Kendra, Logsdon, Glennis, Porubsky, David, Paten, Benedict, Harris, Kelley, Hsieh, PingHsun, and Eichler, Evan

Abstract

Single-nucleotide variants (SNVs) in segmental duplications (SDs) have not been systematically assessed because of the limitations of mapping short-read sequencing data1,2. Here we constructed 1:1 unambiguous alignments spanning high-identity SDs across 102 human haplotypes and compared the pattern of SNVs between unique and duplicated regions3,4. We find that human SNVs are elevated 60% in SDs compared to unique regions and estimate that at least 23% of this increase is due to interlocus gene conversion (IGC) with up to 4.3 megabase pairs of SD sequence converted on average per human haplotype. We develop a genome-wide map of IGC donors and acceptors, including 498 acceptor and 454 donor hotspots affecting the exons of about 800 protein-coding genes. These include 171 genes that have relocated on average 1.61 megabase pairs in a subset of human haplotypes. Using a coalescent framework, we show that SD regions are slightly evolutionarily older when compared to unique sequences, probably owing to IGC. SNVs in SDs, however, show a distinct mutational spectrum: a 27.1% increase in transversions that convert cytosine to guanine or the reverse across all triplet contexts and a 7.6% reduction in the frequency of CpG-associated mutations when compared to unique DNA. We reason that these distinct mutational properties help to maintain an overall higher GC content of SD DNA compared to that of unique DNA, probably driven by GC-biased conversion between paralogous sequences5,6.

Published
2023

31. A refined characterization of large-scale genomic differences in the first complete human genome

Author

Yang, Xiangyu, primary, Wang, Xuankai, additional, Zou, Yawen, additional, Zhang, Shilong, additional, Xia, Manying, additional, Vollger, Mitchell R., additional, Chen, Nae-Chyun, additional, Taylor, Dylan J., additional, Harvey, William T., additional, Logsdon, Glennis A., additional, Meng, Dan, additional, Shi, Junfeng, additional, McCoy, Rajiv C., additional, Schatz, Michael C., additional, Li, Weidong, additional, Eichler, Evan E., additional, Lu, Qing, additional, and Mao, Yafei, additional

Published
2022
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32. The complete sequence of a human Y chromosome

Author

Rhie, Arang, primary, Nurk, Sergey, additional, Cechova, Monika, additional, Hoyt, Savannah J., additional, Taylor, Dylan J., additional, Altemose, Nicolas, additional, Hook, Paul W., additional, Koren, Sergey, additional, Rautiainen, Mikko, additional, Alexandrov, Ivan A., additional, Allen, Jamie, additional, Asri, Mobin, additional, Bzikadze, Andrey V., additional, Chen, Nae-Chyun, additional, Chin, Chen-Shan, additional, Diekhans, Mark, additional, Flicek, Paul, additional, Formenti, Giulio, additional, Fungtammasan, Arkarachai, additional, Garcia Giron, Carlos, additional, Garrison, Erik, additional, Gershman, Ariel, additional, Gerton, Jennifer L., additional, Grady, Patrick G.S., additional, Guarracino, Andrea, additional, Haggerty, Leanne, additional, Halabian, Reza, additional, Hansen, Nancy F., additional, Harris, Robert, additional, Hartley, Gabrielle A., additional, Harvey, William T., additional, Haukness, Marina, additional, Heinz, Jakob, additional, Hourlier, Thibaut, additional, Hubley, Robert M., additional, Hunt, Sarah E., additional, Hwang, Stephen, additional, Jain, Miten, additional, Kesharwani, Rupesh K., additional, Lewis, Alexandra P., additional, Li, Heng, additional, Logsdon, Glennis A., additional, Lucas, Julian K., additional, Makalowski, Wojciech, additional, Markovic, Christopher, additional, Martin, Fergal J., additional, Mc Cartney, Ann M., additional, McCoy, Rajiv C., additional, McDaniel, Jennifer, additional, McNulty, Brandy M., additional, Medvedev, Paul, additional, Mikheenko, Alla, additional, Munson, Katherine M., additional, Murphy, Terence D., additional, Olsen, Hugh E., additional, Olson, Nathan D., additional, Paulin, Luis F., additional, Porubsky, David, additional, Potapova, Tamara, additional, Ryabov, Fedor, additional, Salzberg, Steven L., additional, Sauria, Michael E.G., additional, Sedlazeck, Fritz J., additional, Shafin, Kishwar, additional, Shepelev, Valery A., additional, Shumate, Alaina, additional, Storer, Jessica M., additional, Surapaneni, Likhitha, additional, Taravella Oill, Angela M., additional, Thibaud-Nissen, Françoise, additional, Timp, Winston, additional, Tomaszkiewicz, Marta, additional, Vollger, Mitchell R., additional, Walenz, Brian P., additional, Watwood, Allison C., additional, Weissensteiner, Matthias H., additional, Wenger, Aaron M., additional, Wilson, Melissa A., additional, Zarate, Samantha, additional, Zhu, Yiming, additional, Zook, Justin M., additional, Eichler, Evan E., additional, O’Neill, Rachel J., additional, Schatz, Michael C., additional, Miga, Karen H., additional, Makova, Kateryna D., additional, and Phillippy, Adam M., additional

Published
2022
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33. Additional file 3 of Characterization of large-scale genomic differences in the first complete human genome

Author

Yang, Xiangyu, Wang, Xuankai, Zou, Yawen, Zhang, Shilong, Xia, Manying, Fu, Lianting, Vollger, Mitchell R., Chen, Nae-Chyun, Taylor, Dylan J., Harvey, William T., Logsdon, Glennis A., Meng, Dan, Shi, Junfeng, McCoy, Rajiv C., Schatz, Michael C., Li, Weidong, Eichler, Evan E., Lu, Qing, and Mao, Yafei

Abstract

Additional file 3. Review history.

Published
2023
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34. Additional file 1 of Characterization of large-scale genomic differences in the first complete human genome

Author

Yang, Xiangyu, Wang, Xuankai, Zou, Yawen, Zhang, Shilong, Xia, Manying, Fu, Lianting, Vollger, Mitchell R., Chen, Nae-Chyun, Taylor, Dylan J., Harvey, William T., Logsdon, Glennis A., Meng, Dan, Shi, Junfeng, McCoy, Rajiv C., Schatz, Michael C., Li, Weidong, Eichler, Evan E., Lu, Qing, and Mao, Yafei

Abstract

Additional file 1: Fig. S1. The visualization of four discrepant regions bydotplot. Fig. S2. Comparison of the gene length of CR1 in long-read human genome assemblies. Fig. S3. Gene structure differences in the discrepant regions. Fig. S4. The discrepant region contains CFHR1 and CFHR3. Fig. S5. The number of gene difference in deletions (total N = 68) and insertions (total N = 87) between GRCh38 and T2T-CHM13. Fig. S6. The distribution of the median CN s.d. Fig. S7.The distribution of intersected disease-related CNVs. Fig. S8. The SGPD read-depth genotyping of KLRC2 in different human populations. Fig. S9. The haplotype structure of living human populations in T2T-CHM13. Fig. S10. SNV distribution in T2T-CHM13 and GRCh38 of two chromosome regions. Fig.S11. CN of KLRC2 and KLRC3 for NHP population level. Fig. S12. The syntenic relationship of KLRC gene cluster region between human and different apes. Fig. S13. The syntenic relationship of KLRC gene cluster region between human and monkey genomes. Fig. S14. The phylogenetic tree of KLRC2 and KLRC3 with mouse lemur as outgroup. Fig. S15. The pi diversity of the KLRC gene cluster based on the 94 long-read genome assemblies. Fig. S16. Selection pressure testing using aBSREL on KLRC3 clade. Fig. S17.Comparison of the genomic region of the inversion containing a gap in GRCh38. Fig. S18. The syntenic relationship of GSTM gene cluster region between human and NHPs. Fig. S19. The phylogenetic tree of GSTM in primates. Fig. S20. The CN of KLRC3 in different human populations.

Published
2023
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37. Alpha Satellite Insertion Close to an Ancestral Centromeric Region

Author

Giannuzzi, Giuliana, Logsdon, Glennis A, Chatron, Nicolas, Miller, Danny E, Reversat, Julie, Munson, Katherine M, Hoekzema, Kendra, Bonnet-Dupeyron, Marie-Noëlle, Rollat-Farnier, Pierre-Antoine, Baker, Carl A, Sanlaville, Damien, Eichler, Evan E, Schluth-Bolard, Caroline, and Reymond, Alexandre

Subjects
Chromosomal Proteins, Non-Histone, ancestral centromere, Centromere, AcademicSubjects/SCI01130, structural variation, Humans, alpha satellite, DNA, Satellite, AcademicSubjects/SCI01180, Centromere Protein B, Discoveries, In Situ Hybridization, Fluorescence
Abstract

Human centromeres are mainly composed of alpha satellite DNA hierarchically organized as higher-order repeats (HORs). Alpha satellite dynamics is shown by sequence homogenization in centromeric arrays and by its transfer to other centromeric locations, for example, during the maturation of new centromeres. We identified during prenatal aneuploidy diagnosis by fluorescent in situ hybridization a de novo insertion of alpha satellite DNA from the centromere of chromosome 18 (D18Z1) into cytoband 15q26. Although bound by CENP-B, this locus did not acquire centromeric functionality as demonstrated by the lack of constriction and the absence of CENP-A binding. The insertion was associated with a 2.8-kbp deletion and likely occurred in the paternal germline. The site was enriched in long terminal repeats and located ∼10 Mbp from the location where a centromere was ancestrally seeded and became inactive in the common ancestor of humans and apes 20–25 million years ago. Long-read mapping to the T2T-CHM13 human genome assembly revealed that the insertion derives from a specific region of chromosome 18 centromeric 12-mer HOR array in which the monomer size follows a regular pattern. The rearrangement did not directly disrupt any gene or predicted regulatory element and did not alter the methylation status of the surrounding region, consistent with the absence of phenotypic consequences in the carrier. This case demonstrates a likely rare but new class of structural variation that we name “alpha satellite insertion.” It also expands our knowledge on alphoid DNA dynamics and conveys the possibility that alphoid arrays can relocate near vestigial centromeric sites.

Published
2021

39. Semi-automated assembly of high-quality diploid human reference genomes

Author

Jarvis, Erich D., Formenti, Giulio, Rhie, Arang, Guarracino, Andrea, Yang, Chentao, Wood, Jonathan, Tracey, Alan, Thibaud-Nissen, Francoise, Vollger, Mitchell R., Porubsky, David, Cheng, Haoyu, Asri, Mobin, Logsdon, Glennis A., Carnevali, Paolo, Chaisson, Mark J.P., Chin, Chen Shan, Cody, Sarah, Collins, Joanna, Ebert, Peter, Escalona, Merly, Fedrigo, Olivier, Fulton, Robert S., Fulton, Lucinda L., Garg, Shilpa, Gerton, Jennifer L., Ghurye, Jay, Granat, Anastasiya, Green, Richard E., Harvey, William, Hasenfeld, Patrick, Hastie, Alex, Haukness, Marina, Jaeger, Erich B., Jain, Miten, Kirsche, Melanie, Kolmogorov, Mikhail, Korbel, Jan O., Koren, Sergey, Korlach, Jonas, Lee, Joyce, Li, Daofeng, Lindsay, Tina, Lucas, Julian, Luo, Feng, Marschall, Tobias, Mitchell, Matthew W., McDaniel, Jennifer, Nie, Fan, Zhang, Guojie, Li, Heng, Jarvis, Erich D., Formenti, Giulio, Rhie, Arang, Guarracino, Andrea, Yang, Chentao, Wood, Jonathan, Tracey, Alan, Thibaud-Nissen, Francoise, Vollger, Mitchell R., Porubsky, David, Cheng, Haoyu, Asri, Mobin, Logsdon, Glennis A., Carnevali, Paolo, Chaisson, Mark J.P., Chin, Chen Shan, Cody, Sarah, Collins, Joanna, Ebert, Peter, Escalona, Merly, Fedrigo, Olivier, Fulton, Robert S., Fulton, Lucinda L., Garg, Shilpa, Gerton, Jennifer L., Ghurye, Jay, Granat, Anastasiya, Green, Richard E., Harvey, William, Hasenfeld, Patrick, Hastie, Alex, Haukness, Marina, Jaeger, Erich B., Jain, Miten, Kirsche, Melanie, Kolmogorov, Mikhail, Korbel, Jan O., Koren, Sergey, Korlach, Jonas, Lee, Joyce, Li, Daofeng, Lindsay, Tina, Lucas, Julian, Luo, Feng, Marschall, Tobias, Mitchell, Matthew W., McDaniel, Jennifer, Nie, Fan, Zhang, Guojie, and Li, Heng

Abstract

The current human reference genome, GRCh38, represents over 20 years of effort to generate a high-quality assembly, which has benefitted society1,2. However, it still has many gaps and errors, and does not represent a biological genome as it is a blend of multiple individuals3,4. Recently, a high-quality telomere-to-telomere reference, CHM13, was generated with the latest long-read technologies, but it was derived from a hydatidiform mole cell line with a nearly homozygous genome5. To address these limitations, the Human Pangenome Reference Consortium formed with the goal of creating high-quality, cost-effective, diploid genome assemblies for a pangenome reference that represents human genetic diversity6. Here, in our first scientific report, we determined which combination of current genome sequencing and assembly approaches yield the most complete and accurate diploid genome assembly with minimal manual curation. Approaches that used highly accurate long reads and parent–child data with graph-based haplotype phasing during assembly outperformed those that did not. Developing a combination of the top-performing methods, we generated our first high-quality diploid reference assembly, containing only approximately four gaps per chromosome on average, with most chromosomes within ±1% of the length of CHM13. Nearly 48% of protein-coding genes have non-synonymous amino acid changes between haplotypes, and centromeric regions showed the highest diversity. Our findings serve as a foundation for assembling near-complete diploid human genomes at scale for a pangenome reference to capture global genetic variation from single nucleotides to structural rearrangements.

Published
2022

40. Centromere Innovations with a Mouse Species

Author

Pandey, Nootan, primary, Gambogi, Craig, additional, Dawicki‐McKenna, Jennine, additional, Arora, Uma, additional, Logsdon, Glennis, additional, Ma, Jun, additional, Lamelza, Piero, additional, Lampson, Michael A., additional, Dumont, Beth, additional, and Black, Ben E., additional

Published
2022
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43. The Dynamic Structure and Rapid Evolution of Human Centromeric Satellite DNA.

Author

Logsdon, Glennis A. and Eichler, Evan E.

Subjects
*SATELLITE DNA, *CHROMOSOME segregation, *HUMAN chromosomes, *HUMAN evolution, *HUMAN biology, *HUMAN DNA
Abstract

The complete sequence of a human genome provided our first comprehensive view of the organization of satellite DNA associated with heterochromatin. We review how our understanding of the genetic architecture and epigenetic properties of human centromeric DNA have advanced as a result. Preliminary studies of human and nonhuman ape centromeres reveal complex, saltatory mutational changes organized around distinct evolutionary layers. Pockets of regional hypomethylation within higher-order α-satellite DNA, termed centromere dip regions, appear to define the site of kinetochore attachment in all human chromosomes, although such epigenetic features can vary even within the same chromosome. Sequence resolution of satellite DNA is providing new insights into centromeric function with potential implications for improving our understanding of human biology and health. [ABSTRACT FROM AUTHOR]

Published
2023
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46. Chasing perfection: validation and polishing strategies for telomere-to-telomere genome assemblies

Author

Rhie, Arang, primary, Cartney, Ann Mc, additional, Shafin, Kishwar, additional, Alonge, Michael, additional, Bzikadze, Andrey, additional, Formenti, Giulio, additional, Fungtammasan, Arkarachai, additional, Howe, Kerstin, additional, Jain, Chirag, additional, Koren, Sergey, additional, Logsdon, Glennis, additional, Miga, Karen, additional, Mikheenko, Alla, additional, Paten, Benedict, additional, Shumate, Alaina, additional, Soto, Daniela, additional, Sović, Ivan, additional, Wood, Jonathan, additional, Zook, Justin, additional, and Phillippy, Adam, additional

Published
2021
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47. Complete genomic and epigenetic maps of human centromeres

Author

Altemose, Nicolas, primary, Logsdon, Glennis A., additional, Bzikadze, Andrey V., additional, Sidhwani, Pragya, additional, Langley, Sasha A., additional, Caldas, Gina V., additional, Hoyt, Savannah J., additional, Uralsky, Lev, additional, Ryabov, Fedor D., additional, Shew, Colin J., additional, Sauria, Michael E.G., additional, Borchers, Matthew, additional, Gershman, Ariel, additional, Mikheenko, Alla, additional, Shepelev, Valery A., additional, Dvorkina, Tatiana, additional, Kunyavskaya, Olga, additional, Vollger, Mitchell R., additional, Rhie, Arang, additional, McCartney, Ann M., additional, Asri, Mobin, additional, Lorig-Roach, Ryan, additional, Shafin, Kishwar, additional, Aganezov, Sergey, additional, Olson, Daniel, additional, de Lima, Leonardo Gomes, additional, Potapova, Tamara, additional, Hartley, Gabrielle A., additional, Haukness, Marina, additional, Kerpedjiev, Peter, additional, Gusev, Fedor, additional, Tigyi, Kristof, additional, Brooks, Shelise, additional, Young, Alice, additional, Nurk, Sergey, additional, Koren, Sergey, additional, Salama, Sofie R., additional, Paten, Benedict, additional, Rogaev, Evgeny I., additional, Streets, Aaron, additional, Karpen, Gary H., additional, Dernburg, Abby F., additional, Sullivan, Beth A., additional, Straight, Aaron F., additional, Wheeler, Travis J., additional, Gerton, Jennifer L., additional, Eichler, Evan E., additional, Phillippy, Adam M., additional, Timp, Winston, additional, Dennis, Megan Y., additional, O’Neill, Rachel J., additional, Zook, Justin M., additional, Schatz, Michael C., additional, Pevzner, Pavel A., additional, Diekhans, Mark, additional, Langley, Charles H., additional, Alexandrov, Ivan A., additional, and Miga, Karen H., additional

Published
2021
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48. Chasing perfection: validation and polishing strategies for telomere-to-telomere genome assemblies

Author

Cartney, Ann M. Mc, primary, Shafin, Kishwar, additional, Alonge, Michael, additional, Bzikadze, Andrey V., additional, Formenti, Giulio, additional, Fungtammasan, Arkarachai, additional, Howe, Kerstin, additional, Jain, Chirag, additional, Koren, Sergey, additional, Logsdon, Glennis A., additional, Miga, Karen H., additional, Mikheenko, Alla, additional, Paten, Benedict, additional, Shumate, Alaina, additional, Soto, Daniela C., additional, Sović, Ivan, additional, Wood, Jonathan MD, additional, Zook, Justin M., additional, Phillippy, Adam M., additional, and Rhie, Arang, additional

Published
2021
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49. Epigenetic Patterns in a Complete Human Genome

Author

Gershman, Ariel, primary, Sauria, Michael E.G., additional, Hook, Paul W., additional, Hoyt, Savannah J., additional, Razaghi, Roham, additional, Koren, Sergey, additional, Altemose, Nicolas, additional, Caldas, Gina V., additional, Vollger, Mitchell R., additional, Logsdon, Glennis A., additional, Rhie, Arang, additional, Eichler, Evan E., additional, Schatz, Michael C., additional, O’Neill, Rachel J., additional, Phillippy, Adam M., additional, Miga, Karen H., additional, and Timp, Winston, additional

Published
2021
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50. The complete sequence of a human genome

Author

Nurk, Sergey, primary, Koren, Sergey, additional, Rhie, Arang, additional, Rautiainen, Mikko, additional, Bzikadze, Andrey V., additional, Mikheenko, Alla, additional, Vollger, Mitchell R., additional, Altemose, Nicolas, additional, Uralsky, Lev, additional, Gershman, Ariel, additional, Aganezov, Sergey, additional, Hoyt, Savannah J., additional, Diekhans, Mark, additional, Logsdon, Glennis A., additional, Alonge, Michael, additional, Antonarakis, Stylianos E., additional, Borchers, Matthew, additional, Bouffard, Gerard G., additional, Brooks, Shelise Y., additional, Caldas, Gina V., additional, Cheng, Haoyu, additional, Chin, Chen-Shan, additional, Chow, William, additional, de Lima, Leonardo G., additional, Dishuck, Philip C., additional, Durbin, Richard, additional, Dvorkina, Tatiana, additional, Fiddes, Ian T., additional, Formenti, Giulio, additional, Fulton, Robert S., additional, Fungtammasan, Arkarachai, additional, Garrison, Erik, additional, Grady, Patrick G.S., additional, Graves-Lindsay, Tina A., additional, Hall, Ira M., additional, Hansen, Nancy F., additional, Hartley, Gabrielle A., additional, Haukness, Marina, additional, Howe, Kerstin, additional, Hunkapiller, Michael W., additional, Jain, Chirag, additional, Jain, Miten, additional, Jarvis, Erich D., additional, Kerpedjiev, Peter, additional, Kirsche, Melanie, additional, Kolmogorov, Mikhail, additional, Korlach, Jonas, additional, Kremitzki, Milinn, additional, Li, Heng, additional, Maduro, Valerie V., additional, Marschall, Tobias, additional, McCartney, Ann M., additional, McDaniel, Jennifer, additional, Miller, Danny E., additional, Mullikin, James C., additional, Myers, Eugene W., additional, Olson, Nathan D., additional, Paten, Benedict, additional, Peluso, Paul, additional, Pevzner, Pavel A., additional, Porubsky, David, additional, Potapova, Tamara, additional, Rogaev, Evgeny I., additional, Rosenfeld, Jeffrey A., additional, Salzberg, Steven L., additional, Schneider, Valerie A., additional, Sedlazeck, Fritz J., additional, Shafin, Kishwar, additional, Shew, Colin J., additional, Shumate, Alaina, additional, Sims, Yumi, additional, Smit, Arian F. A., additional, Soto, Daniela C., additional, Sović, Ivan, additional, Storer, Jessica M., additional, Streets, Aaron, additional, Sullivan, Beth A., additional, Thibaud-Nissen, Françoise, additional, Torrance, James, additional, Wagner, Justin, additional, Walenz, Brian P., additional, Wenger, Aaron, additional, Wood, Jonathan M. D., additional, Xiao, Chunlin, additional, Yan, Stephanie M., additional, Young, Alice C., additional, Zarate, Samantha, additional, Surti, Urvashi, additional, McCoy, Rajiv C., additional, Dennis, Megan Y., additional, Alexandrov, Ivan A., additional, Gerton, Jennifer L., additional, O’Neill, Rachel J., additional, Timp, Winston, additional, Zook, Justin M., additional, Schatz, Michael C., additional, Eichler, Evan E., additional, Miga, Karen H., additional, and Phillippy, Adam M., additional

Published
2021
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