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1. Chromosome level genome assembly of the Etruscan shrew Suncus etruscus

Author

Bukhman, Yury V., Meyer, Susanne, Chu, Li-Fang, Abueg, Linelle, Antosiewicz-Bourget, Jessica, Balacco, Jennifer, Brecht, Michael, Dinatale, Erica, Fedrigo, Olivier, Formenti, Giulio, Fungtammasan, Arkarachai, Giri, Swagarika Jaharlal, Hiller, Michael, Howe, Kerstin, Kihara, Daisuke, Mamott, Daniel, Mountcastle, Jacquelyn, Pelan, Sarah, Rabbani, Keon, Sims, Ying, Tracey, Alan, Wood, Jonathan M. D., Jarvis, Erich D., Thomson, James A., Chaisson, Mark J. P., and Stewart, Ron

Published
2024
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2. Reversible median nerve neuropathy and local muscle irritation resulting from blind removal attempts of etonogestrel contraceptive implant: a case report

Author

Siraphat Fungtammasan, Natchanika Sinthuchai, Kawee Pataradool, Unnop Jaisamrarn, and Somsook Santibenchakul

Subjects
Etonogestrel contraceptive implant, Deep insertion, Median nerve neuropathy, Difficult removal, Case report, Gynecology and obstetrics, RG1-991
Abstract

Abstract Nexplanon is an etonogestrel contraceptive implant that comes with an applicator, making it easier to insert and remove. Complications related to insertion and removal procedures, such as neural-vascular injuries, are rare. We describe a case of reversible median nerve neuropathy and local muscle irritation resulting from blind removal attempts of an iatrogenically migrated implant. The patient presented with an unusual pain at the surgical site along with abnormal sensations and numbness in her left hand that worsened after blind attempts to remove the implant. Radiographs revealed that the rod was 3 cm from her insertion scar and deeply embedded in her left arm. The patient then underwent left arm exploration and implant removal under fluoroscopic guidance by an orthopedic surgeon. The rod was placed intramuscularly, adjacent to the median nerve under the basilic vein. The abnormal sensations and numbness in her left hand could be attributed to median nerve involvement, while the atypical pain at the surgical site could be a result of local irritation from the intramuscularly migrated implant from attempts at removal. The symptoms gradually resolved after surgery. This indicates that patients with impalpable contraceptive implants should be referred for implant removal by specialists familiar with the procedure to prevent further deterioration of adjacent structures from iatrogenic implant migration.

Published
2023
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3. 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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4. Benchmarking challenging small variants with linked and long reads.

Author

Wagner, Justin, Olson, Nathan, Harris, Lindsay, Khan, Ziad, Farek, Jesse, Mahmoud, Medhat, Stankovic, Ana, Kovacevic, Vladimir, Yoo, Byunggil, Miller, Neil, Rosenfeld, Jeffrey, Ni, Bohan, Zarate, Samantha, Kirsche, Melanie, Aganezov, Sergey, Schatz, Michael, Narzisi, Giuseppe, Byrska-Bishop, Marta, Clarke, Wayne, Evani, Uday, Markello, Charles, Shafin, Kishwar, Zhou, Xin, Sidow, Arend, Bansal, Vikas, Ebert, Peter, Marschall, Tobias, Lansdorp, Peter, Hanlon, Vincent, Mattsson, Carl-Adam, Barrio, Alvaro, Fiddes, Ian, Xiao, Chunlin, Fungtammasan, Arkarachai, Chin, Chen-Shan, Wenger, Aaron, Rowell, William, Sedlazeck, Fritz, Carroll, Andrew, Salit, Marc, and Zook, Justin

Abstract

Genome in a Bottle benchmarks are widely used to help validate clinical sequencing pipelines and develop variant calling and sequencing methods. Here we use accurate linked and long reads to expand benchmarks in 7 samples to include difficult-to-map regions and segmental duplications that are challenging for short reads. These benchmarks add more than 300,000 SNVs and 50,000 insertions or deletions (indels) and include 16% more exonic variants, many in challenging, clinically relevant genes not covered previously, such as PMS2. For HG002, we include 92% of the autosomal GRCh38 assembly while excluding regions problematic for benchmarking small variants, such as copy number variants, that should not have been in the previous version, which included 85% of GRCh38. It identifies eight times more false negatives in a short read variant call set relative to our previous benchmark. We demonstrate that this benchmark reliably identifies false positives and false negatives across technologies, enabling ongoing methods development.

Published
2022

5. 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, 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

7. Reference genome and demographic history of the most endangered marine mammal, the vaquita

Author

Morin, Phillip A, Archer, Frederick I, Avila, Catherine D, Balacco, Jennifer R, Bukhman, Yury V, Chow, William, Fedrigo, Olivier, Formenti, Giulio, Fronczek, Julie A, Fungtammasan, Arkarachai, Gulland, Frances MD, Haase, Bettina, Heide‐Jorgensen, Mads Peter, Houck, Marlys L, Howe, Kerstin, Misuraca, Ann C, Mountcastle, Jacquelyn, Musser, Whitney, Paez, Sadye, Pelan, Sarah, Phillippy, Adam, Rhie, Arang, Robinson, Jacqueline, Rojas‐Bracho, Lorenzo, Rowles, Teri K, Ryder, Oliver A, Smith, Cynthia R, Stevenson, Sacha, Taylor, Barbara L, Teilmann, Jonas, Torrance, James, Wells, Randall S, Westgate, Andrew J, and Jarvis, Erich D

Subjects
Genetics, Human Genome, 2.1 Biological and endogenous factors, Aetiology, Generic health relevance, Life on Land, Animals, Chromosomes, Endangered Species, Female, Genetics, Population, Genome, Phocoena, Conservation genomics, genome diversity, historical demography, Phocoena sinus, porpoise, Vertebrate Genomes Project, Biological Sciences, Evolutionary Biology
Abstract

The vaquita is the most critically endangered marine mammal, with fewer than 19 remaining in the wild. First described in 1958, the vaquita has been in rapid decline for more than 20 years resulting from inadvertent deaths due to the increasing use of large-mesh gillnets. To understand the evolutionary and demographic history of the vaquita, we used combined long-read sequencing and long-range scaffolding methods with long- and short-read RNA sequencing to generate a near error-free annotated reference genome assembly from cell lines derived from a female individual. The genome assembly consists of 99.92% of the assembled sequence contained in 21 nearly gapless chromosome-length autosome scaffolds and the X-chromosome scaffold, with a scaffold N50 of 115 Mb. Genome-wide heterozygosity is the lowest (0.01%) of any mammalian species analysed to date, but heterozygosity is evenly distributed across the chromosomes, consistent with long-term small population size at genetic equilibrium, rather than low diversity resulting from a recent population bottleneck or inbreeding. Historical demography of the vaquita indicates long-term population stability at less than 5,000 (Ne) for over 200,000 years. Together, these analyses indicate that the vaquita genome has had ample opportunity to purge highly deleterious alleles and potentially maintain diversity necessary for population health.

Published
2021

8. Towards complete and error-free genome assemblies of all vertebrate species

Author

Rhie, Arang, McCarthy, Shane A, Fedrigo, Olivier, Damas, Joana, Formenti, Giulio, Koren, Sergey, Uliano-Silva, Marcela, Chow, William, Fungtammasan, Arkarachai, Kim, Juwan, Lee, Chul, Ko, Byung June, Chaisson, Mark, Gedman, Gregory L, Cantin, Lindsey J, Thibaud-Nissen, Francoise, Haggerty, Leanne, Bista, Iliana, Smith, Michelle, Haase, Bettina, Mountcastle, Jacquelyn, Winkler, Sylke, Paez, Sadye, Howard, Jason, Vernes, Sonja C, Lama, Tanya M, Grutzner, Frank, Warren, Wesley C, Balakrishnan, Christopher N, Burt, Dave, George, Julia M, Biegler, Matthew T, Iorns, David, Digby, Andrew, Eason, Daryl, Robertson, Bruce, Edwards, Taylor, Wilkinson, Mark, Turner, George, Meyer, Axel, Kautt, Andreas F, Franchini, Paolo, Detrich, H William, Svardal, Hannes, Wagner, Maximilian, Naylor, Gavin JP, Pippel, Martin, Malinsky, Milan, Mooney, Mark, Simbirsky, Maria, Hannigan, Brett T, Pesout, Trevor, Houck, Marlys, Misuraca, Ann, Kingan, Sarah B, Hall, Richard, Kronenberg, Zev, Sović, Ivan, Dunn, Christopher, Ning, Zemin, Hastie, Alex, Lee, Joyce, Selvaraj, Siddarth, Green, Richard E, Putnam, Nicholas H, Gut, Ivo, Ghurye, Jay, Garrison, Erik, Sims, Ying, Collins, Joanna, Pelan, Sarah, Torrance, James, Tracey, Alan, Wood, Jonathan, Dagnew, Robel E, Guan, Dengfeng, London, Sarah E, Clayton, David F, Mello, Claudio V, Friedrich, Samantha R, Lovell, Peter V, Osipova, Ekaterina, Al-Ajli, Farooq O, Secomandi, Simona, Kim, Heebal, Theofanopoulou, Constantina, Hiller, Michael, Zhou, Yang, Harris, Robert S, Makova, Kateryna D, Medvedev, Paul, Hoffman, Jinna, Masterson, Patrick, Clark, Karen, Martin, Fergal, Howe, Kevin, Flicek, Paul, Walenz, Brian P, Kwak, Woori, and Clawson, Hiram

Subjects
Biological Sciences, Bioinformatics and Computational Biology, Genetics, Human Genome, Biotechnology, Generic health relevance, Animals, Birds, Gene Library, Genome, Genome Size, Genome, Mitochondrial, Genomics, Haplotypes, High-Throughput Nucleotide Sequencing, Molecular Sequence Annotation, Sequence Alignment, Sequence Analysis, DNA, Sex Chromosomes, Vertebrates, General Science & Technology
Abstract

High-quality and complete reference genome assemblies are fundamental for the application of genomics to biology, disease, and biodiversity conservation. However, such assemblies are available for only a few non-microbial species1-4. To address this issue, the international Genome 10K (G10K) consortium5,6 has worked over a five-year period to evaluate and develop cost-effective methods for assembling highly accurate and nearly complete reference genomes. Here we present lessons learned from generating assemblies for 16 species that represent six major vertebrate lineages. We confirm that long-read sequencing technologies are essential for maximizing genome quality, and that unresolved complex repeats and haplotype heterozygosity are major sources of assembly error when not handled correctly. Our assemblies correct substantial errors, add missing sequence in some of the best historical reference genomes, and reveal biological discoveries. These include the identification of many false gene duplications, increases in gene sizes, chromosome rearrangements that are specific to lineages, a repeated independent chromosome breakpoint in bat genomes, and a canonical GC-rich pattern in protein-coding genes and their regulatory regions. Adopting these lessons, we have embarked on the Vertebrate Genomes Project (VGP), an international effort to generate high-quality, complete reference genomes for all of the roughly 70,000 extant vertebrate species and to help to enable a new era of discovery across the life sciences.

Published
2021

9. Shotgun transcriptome, spatial omics, and isothermal profiling of SARS-CoV-2 infection reveals unique host responses, viral diversification, and drug interactions

Author

Butler, Daniel, Mozsary, Christopher, Meydan, Cem, Foox, Jonathan, Rosiene, Joel, Shaiber, Alon, Danko, David, Afshinnekoo, Ebrahim, MacKay, Matthew, Sedlazeck, Fritz J, Ivanov, Nikolay A, Sierra, Maria, Pohle, Diana, Zietz, Michael, Gisladottir, Undina, Ramlall, Vijendra, Sholle, Evan T, Schenck, Edward J, Westover, Craig D, Hassan, Ciaran, Ryon, Krista, Young, Benjamin, Bhattacharya, Chandrima, Ng, Dianna L, Granados, Andrea C, Santos, Yale A, Servellita, Venice, Federman, Scot, Ruggiero, Phyllis, Fungtammasan, Arkarachai, Chin, Chen-Shan, Pearson, Nathaniel M, Langhorst, Bradley W, Tanner, Nathan A, Kim, Youngmi, Reeves, Jason W, Hether, Tyler D, Warren, Sarah E, Bailey, Michael, Gawrys, Justyna, Meleshko, Dmitry, Xu, Dong, Couto-Rodriguez, Mara, Nagy-Szakal, Dorottya, Barrows, Joseph, Wells, Heather, O’Hara, Niamh B, Rosenfeld, Jeffrey A, Chen, Ying, Steel, Peter AD, Shemesh, Amos J, Xiang, Jenny, Thierry-Mieg, Jean, Thierry-Mieg, Danielle, Iftner, Angelika, Bezdan, Daniela, Sanchez, Elizabeth, Campion, Thomas R, Sipley, John, Cong, Lin, Craney, Arryn, Velu, Priya, Melnick, Ari M, Shapira, Sagi, Hajirasouliha, Iman, Borczuk, Alain, Iftner, Thomas, Salvatore, Mirella, Loda, Massimo, Westblade, Lars F, Cushing, Melissa, Wu, Shixiu, Levy, Shawn, Chiu, Charles, Schwartz, Robert E, Tatonetti, Nicholas, Rennert, Hanna, Imielinski, Marcin, and Mason, Christopher E

Subjects
Biological Sciences, Biomedical and Clinical Sciences, Clinical Sciences, Infectious Diseases, Vaccine Related, Biodefense, Rare Diseases, Emerging Infectious Diseases, Clinical Research, Prevention, Lung, Pneumonia & Influenza, Aetiology, Development of treatments and therapeutic interventions, 2.1 Biological and endogenous factors, 5.1 Pharmaceuticals, Infection, Good Health and Well Being, Adult, Aged, Angiotensin Receptor Antagonists, Angiotensin-Converting Enzyme Inhibitors, Antiviral Agents, COVID-19, COVID-19 Nucleic Acid Testing, Drug Interactions, Female, Gene Expression Profiling, Genome, Viral, HLA Antigens, Host Microbial Interactions, Humans, Male, Middle Aged, Molecular Diagnostic Techniques, New York City, Nucleic Acid Amplification Techniques, Pandemics, RNA-Seq, SARS-CoV-2, COVID-19 Drug Treatment
Abstract

In less than nine months, the Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) killed over a million people, including >25,000 in New York City (NYC) alone. The COVID-19 pandemic caused by SARS-CoV-2 highlights clinical needs to detect infection, track strain evolution, and identify biomarkers of disease course. To address these challenges, we designed a fast (30-minute) colorimetric test (LAMP) for SARS-CoV-2 infection from naso/oropharyngeal swabs and a large-scale shotgun metatranscriptomics platform (total-RNA-seq) for host, viral, and microbial profiling. We applied these methods to clinical specimens gathered from 669 patients in New York City during the first two months of the outbreak, yielding a broad molecular portrait of the emerging COVID-19 disease. We find significant enrichment of a NYC-distinctive clade of the virus (20C), as well as host responses in interferon, ACE, hematological, and olfaction pathways. In addition, we use 50,821 patient records to find that renin-angiotensin-aldosterone system inhibitors have a protective effect for severe COVID-19 outcomes, unlike similar drugs. Finally, spatial transcriptomic data from COVID-19 patient autopsy tissues reveal distinct ACE2 expression loci, with macrophage and neutrophil infiltration in the lungs. These findings can inform public health and may help develop and drive SARS-CoV-2 diagnostic, prevention, and treatment strategies.

Published
2021

10. Reference genome and demographic history of the most endangered marine mammal, the vaquita

Author

Morin, Phillip A, Archer, Frederick I, Avila, Catherine D, Balacco, Jennifer R, Bukhman, Yury V, Chow, William, Fedrigo, Olivier, Formenti, Giulio, Fronczek, Julie A, Fungtammasan, Arkarachai, Gulland, Frances MD, Haase, Bettina, Heide-Jorgensen, Mads Peter, Houck, Marlys L, Howe, Kerstin, Misuraca, Ann C, Mountcastle, Jacquelyn, Musser, Whitney, Paez, Sadye, Pelan, Sarah, Phillippy, Adam, Rhie, Arang, Robinson, Jacqueline, Rojas-Bracho, Lorenzo, Rowles, Teri K, Ryder, Oliver A, Smith, Cynthia R, Stevenson, Sacha, Taylor, Barbara L, Teilmann, Jonas, Torrance, James, Wells, Randall S, Westgate, Andrew, and Jarvis, Erich D

Subjects
Human Genome, Genetics, Generic health relevance, Life on Land
Abstract

AbstractThe vaquita is the most critically endangered marine mammal, with fewer than 19 remaining in the wild. First described in 1958, the vaquita has been in rapid decline resulting from inadvertent deaths due to the increasing use of large-mesh gillnets for more than 20 years. To understand the evolutionary and demographic history of the vaquita, we used combined long-read sequencing and long-range scaffolding methods with long- and short-read RNA sequencing to generate a near error-free annotated reference genome assembly from cell lines derived from a female individual. The genome assembly consists of 99.92% of the assembled sequence contained in 21 nearly gapless chromosome-length autosome scaffolds and the X-chromosome scaffold, with a scaffold N50 of 115 Mb. Genome-wide heterozygosity is the lowest (0.01%) of any mammalian species analyzed to date, but heterozygosity is evenly distributed across the chromosomes, consistent with long-term small population size at genetic equilibrium, rather than low diversity resulting from a recent population bottleneck or inbreeding. Historical demography of the vaquita indicates long-term population stability at less than 5000 (Ne) for over 200,000 years. Together, these analyses indicate that the vaquita genome has had ample opportunity to purge highly deleterious alleles and potentially maintain diversity necessary for population health.

Published
2020

12. A chromosome-level reference genome and pangenome for barn swallow population genomics

Author

Secomandi, Simona, Gallo, Guido R., Sozzoni, Marcella, Iannucci, Alessio, Galati, Elena, Abueg, Linelle, Balacco, Jennifer, Caprioli, Manuela, Chow, William, Ciofi, Claudio, Collins, Joanna, Fedrigo, Olivier, Ferretti, Luca, Fungtammasan, Arkarachai, Haase, Bettina, Howe, Kerstin, Kwak, Woori, Lombardo, Gianluca, Masterson, Patrick, Messina, Graziella, Møller, Anders P., Mountcastle, Jacquelyn, Mousseau, Timothy A., Ferrer Obiol, Joan, Olivieri, Anna, Rhie, Arang, Rubolini, Diego, Saclier, Marielle, Stanyon, Roscoe, Stucki, David, Thibaud-Nissen, Françoise, Torrance, James, Torroni, Antonio, Weber, Kristina, Ambrosini, Roberto, Bonisoli-Alquati, Andrea, Jarvis, Erich D., Gianfranceschi, Luca, and Formenti, Giulio

Published
2023
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14. 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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15. Curated variation benchmarks for challenging medically relevant autosomal genes

Author

Wagner, Justin, Olson, Nathan D., Harris, Lindsay, McDaniel, Jennifer, Cheng, Haoyu, Fungtammasan, Arkarachai, Hwang, Yih-Chii, Gupta, Richa, Wenger, Aaron M., Rowell, William J., Khan, Ziad M., Farek, Jesse, Zhu, Yiming, Pisupati, Aishwarya, Mahmoud, Medhat, Xiao, Chunlin, Yoo, Byunggil, Sahraeian, Sayed Mohammad Ebrahim, Miller, Danny E., Jáspez, David, Lorenzo-Salazar, José M., Muñoz-Barrera, Adrián, Rubio-Rodríguez, Luis A., Flores, Carlos, Narzisi, Giuseppe, Evani, Uday Shanker, Clarke, Wayne E., Lee, Joyce, Mason, Christopher E., Lincoln, Stephen E., Miga, Karen H., Ebbert, Mark T. W., Shumate, Alaina, Li, Heng, Chin, Chen-Shan, Zook, Justin M., and Sedlazeck, Fritz J.

Published
2022
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16. A strategy for building and using a human reference pangenome.

Author

Llamas, Bastien, Narzisi, Giuseppe, Schneider, Valerie, Audano, Peter, Biederstedt, Evan, Blauvelt, Lon, Bradbury, Peter, Chang, Xian, Chin, Chen-Shan, Fungtammasan, Arkarachai, Clarke, Wayne, Cleary, Alan, Ebler, Jana, Eizenga, Jordan, Sibbesen, Jonas, Markello, Charles, Garrison, Erik, Garg, Shilpa, Hickey, Glenn, Lazo, Gerard, Lin, Michael, Mahmoud, Medhat, Marschall, Tobias, Minkin, Ilia, Musunuri, Rajeeva, Sagayaradj, Sagayamary, Novak, Adam, Rautiainen, Mikko, Regier, Allison, Sedlazeck, Fritz, Siren, Jouni, Souilmi, Yassine, Wagner, Justin, Wrightsman, Travis, Yokoyama, Toshiyuki, Zeng, Qiandong, Zook, Justin, Paten, Benedict, Busby, Ben, and Monlong, Jean

Abstract

In March 2019, 45 scientists and software engineers from around the world converged at the University of California, Santa Cruz for the first pangenomics codeathon. The purpose of the meeting was to propose technical specifications and standards for a usable human pangenome as well as to build relevant tools for genome graph infrastructures. During the meeting, the group held several intense and productive discussions covering a diverse set of topics, including advantages of graph genomes over a linear reference representation, design of new methods that can leverage graph-based data structures, and novel visualization and annotation approaches for pangenomes. Additionally, the participants self-organized themselves into teams that worked intensely over a three-day period to build a set of pipelines and tools for specific pangenomic applications. A summary of the questions raised and the tools developed are reported in this manuscript.

Published
2019

17. Complete vertebrate mitogenomes reveal widespread repeats and gene duplications

Author

Giulio Formenti, Arang Rhie, Jennifer Balacco, Bettina Haase, Jacquelyn Mountcastle, Olivier Fedrigo, Samara Brown, Marco Rosario Capodiferro, Farooq O. Al-Ajli, Roberto Ambrosini, Peter Houde, Sergey Koren, Karen Oliver, Michelle Smith, Jason Skelton, Emma Betteridge, Jale Dolucan, Craig Corton, Iliana Bista, James Torrance, Alan Tracey, Jonathan Wood, Marcela Uliano-Silva, Kerstin Howe, Shane McCarthy, Sylke Winkler, Woori Kwak, Jonas Korlach, Arkarachai Fungtammasan, Daniel Fordham, Vania Costa, Simon Mayes, Matteo Chiara, David S. Horner, Eugene Myers, Richard Durbin, Alessandro Achilli, Edward L. Braun, Adam M. Phillippy, Erich D. Jarvis, and The Vertebrate Genomes Project Consortium

Subjects
Mitochondrial DNA, Vertebrate, Assembly, Long reads, Sequencing, Duplications, Biology (General), QH301-705.5, Genetics, QH426-470
Abstract

Abstract Background Modern sequencing technologies should make the assembly of the relatively small mitochondrial genomes an easy undertaking. However, few tools exist that address mitochondrial assembly directly. Results As part of the Vertebrate Genomes Project (VGP) we develop mitoVGP, a fully automated pipeline for similarity-based identification of mitochondrial reads and de novo assembly of mitochondrial genomes that incorporates both long (> 10 kbp, PacBio or Nanopore) and short (100–300 bp, Illumina) reads. Our pipeline leads to successful complete mitogenome assemblies of 100 vertebrate species of the VGP. We observe that tissue type and library size selection have considerable impact on mitogenome sequencing and assembly. Comparing our assemblies to purportedly complete reference mitogenomes based on short-read sequencing, we identify errors, missing sequences, and incomplete genes in those references, particularly in repetitive regions. Our assemblies also identify novel gene region duplications. The presence of repeats and duplications in over half of the species herein assembled indicates that their occurrence is a principle of mitochondrial structure rather than an exception, shedding new light on mitochondrial genome evolution and organization. Conclusions Our results indicate that even in the “simple” case of vertebrate mitogenomes the completeness of many currently available reference sequences can be further improved, and caution should be exercised before claiming the complete assembly of a mitogenome, particularly from short reads alone.

Published
2021
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18. Shotgun transcriptome, spatial omics, and isothermal profiling of SARS-CoV-2 infection reveals unique host responses, viral diversification, and drug interactions

Author

Daniel Butler, Christopher Mozsary, Cem Meydan, Jonathan Foox, Joel Rosiene, Alon Shaiber, David Danko, Ebrahim Afshinnekoo, Matthew MacKay, Fritz J. Sedlazeck, Nikolay A. Ivanov, Maria Sierra, Diana Pohle, Michael Zietz, Undina Gisladottir, Vijendra Ramlall, Evan T. Sholle, Edward J. Schenck, Craig D. Westover, Ciaran Hassan, Krista Ryon, Benjamin Young, Chandrima Bhattacharya, Dianna L. Ng, Andrea C. Granados, Yale A. Santos, Venice Servellita, Scot Federman, Phyllis Ruggiero, Arkarachai Fungtammasan, Chen-Shan Chin, Nathaniel M. Pearson, Bradley W. Langhorst, Nathan A. Tanner, Youngmi Kim, Jason W. Reeves, Tyler D. Hether, Sarah E. Warren, Michael Bailey, Justyna Gawrys, Dmitry Meleshko, Dong Xu, Mara Couto-Rodriguez, Dorottya Nagy-Szakal, Joseph Barrows, Heather Wells, Niamh B. O’Hara, Jeffrey A. Rosenfeld, Ying Chen, Peter A. D. Steel, Amos J. Shemesh, Jenny Xiang, Jean Thierry-Mieg, Danielle Thierry-Mieg, Angelika Iftner, Daniela Bezdan, Elizabeth Sanchez, Thomas R. Campion, John Sipley, Lin Cong, Arryn Craney, Priya Velu, Ari M. Melnick, Sagi Shapira, Iman Hajirasouliha, Alain Borczuk, Thomas Iftner, Mirella Salvatore, Massimo Loda, Lars F. Westblade, Melissa Cushing, Shixiu Wu, Shawn Levy, Charles Chiu, Robert E. Schwartz, Nicholas Tatonetti, Hanna Rennert, Marcin Imielinski, and Christopher E. Mason

Subjects
Science
Abstract

Here, using clinical samples and autopsy tissues, the authors combine fast-colorimetric test (LAMP) for SARS-CoV-2 infection and large-scale shotgun metatranscriptomics for host, viral, and microbial profiling and provide a map of the viral genetic features of the New York City outbreak and associate specific host responses and gene expression perturbations with SARS-CoV-2 infection.

Published
2021
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20. Chromosome-scale, haplotype-resolved assembly of human genomes

Author

Garg, Shilpa, Fungtammasan, Arkarachai, Carroll, Andrew, Chou, Mike, Schmitt, Anthony, Zhou, Xiang, Mac, Stephen, Peluso, Paul, Hatas, Emily, Ghurye, Jay, Maguire, Jared, Mahmoud, Medhat, Cheng, Haoyu, Heller, David, Zook, Justin M., Moemke, Tobias, Marschall, Tobias, Sedlazeck, Fritz J., Aach, John, Chin, Chen-Shan, Church, George M., and Li, Heng

Published
2021
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21. A diploid assembly-based benchmark for variants in the major histocompatibility complex

Author

Chen-Shan Chin, Justin Wagner, Qiandong Zeng, Erik Garrison, Shilpa Garg, Arkarachai Fungtammasan, Mikko Rautiainen, Sergey Aganezov, Melanie Kirsche, Samantha Zarate, Michael C. Schatz, Chunlin Xiao, William J. Rowell, Charles Markello, Jesse Farek, Fritz J. Sedlazeck, Vikas Bansal, Byunggil Yoo, Neil Miller, Xin Zhou, Andrew Carroll, Alvaro Martinez Barrio, Marc Salit, Tobias Marschall, Alexander T. Dilthey, and Justin M. Zook

Subjects
Science
Abstract

Accurate, phased assemblies are a key tool in understanding the human genome, particularly in highly polymorphic regions like the medically important MHC. Here the authors provide an assembly-based benchmark for this difficult-to-characterize region.

Published
2020
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22. Effect of sequence depth and length in long-read assembly of the maize inbred NC358

Author

Shujun Ou, Jianing Liu, Kapeel M. Chougule, Arkarachai Fungtammasan, Arun S. Seetharam, Joshua C. Stein, Victor Llaca, Nancy Manchanda, Amanda M. Gilbert, Sharon Wei, Chen-Shan Chin, David E. Hufnagel, Sarah Pedersen, Samantha J. Snodgrass, Kevin Fengler, Margaret Woodhouse, Brian P. Walenz, Sergey Koren, Adam M. Phillippy, Brett T. Hannigan, R. Kelly Dawe, Candice N. Hirsch, Matthew B. Hufford, and Doreen Ware

Subjects
Science
Abstract

Sequence depth and read length determine the quality of genome assembly. Here, the authors leverage a set of PacBio reads to develop guidelines for sequencing and assembly of complex plant genomes in order to allocate finite resources using maize as an example.

Published
2020
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24. A strategy for building and using a human reference pangenome [version 2; peer review: 2 approved]

Author

Bastien Llamas, Giuseppe Narzisi, Valerie Schneider, Peter A. Audano, Evan Biederstedt, Lon Blauvelt, Peter Bradbury, Xian Chang, Chen-Shan Chin, Arkarachai Fungtammasan, Wayne E. Clarke, Alan Cleary, Jana Ebler, Jordan Eizenga, Jonas A. Sibbesen, Charles J. Markello, Erik Garrison, Shilpa Garg, Glenn Hickey, Gerard R. Lazo, Michael F. Lin, Medhat Mahmoud, Tobias Marschall, Ilia Minkin, Jean Monlong, Rajeeva L. Musunuri, Sagayamary Sagayaradj, Adam M. Novak, Mikko Rautiainen, Allison Regier, Fritz J. Sedlazeck, Jouni Siren, Yassine Souilmi, Justin Wagner, Travis Wrightsman, Toshiyuki T. Yokoyama, Qiandong Zeng, Justin M. Zook, Benedict Paten, and Ben Busby

Subjects
Software Tool Article, Articles, Hackathon, Pangenome, Graph Genome, RNAseq, Structural Variant
Abstract

In March 2019, 45 scientists and software engineers from around the world converged at the University of California, Santa Cruz for the first pangenomics codeathon. The purpose of the meeting was to propose technical specifications and standards for a usable human pangenome as well as to build relevant tools for genome graph infrastructures. During the meeting, the group held several intense and productive discussions covering a diverse set of topics, including advantages of graph genomes over a linear reference representation, design of new methods that can leverage graph-based data structures, and novel visualization and annotation approaches for pangenomes. Additionally, the participants self-organized themselves into teams that worked intensely over a three-day period to build a set of pipelines and tools for specific pangenomic applications. A summary of the questions raised and the tools developed are reported in this manuscript.

Published
2021
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27. Methods developed during the first National Center for Biotechnology Information Structural Variation Codeathon at Baylor College of Medicine [version 1; peer review: 1 approved, 1 approved with reservations]

Author

Medhat Mahmoud, Alejandro Rafael Gener, Michael M. Khayat, Adam C. English, Advait Balaji, Anbo Zhou, Andreas Hehn, Arkarachai Fungtammasan, Brianna Sierra Chrisman, Chen-Shan Chin, Chiao-Feng Lin, Chun-Hsuan Lo, Chunxiao Liao, Claudia M. B. Carvalho, Colin Diesh, David E. Symer, Divya Kalra, Dreycey Albin, Elbay Aliyev, Eric T. Dawson, Eric Venner, Fernanda Foertter, Gigon Bae, Haowei Du, Joyjit Daw, Junzhou Wang, Keiko Akagi, Lon Phan, Michael Jochum, Mohammadamin Edrisi, Nirav N. Shah, Qi Wang, Robert Fullem, Rong Zheng, Sara E Kalla, Shakuntala Mitra, Todd J. Treangen, Vaidhyanathan Mahaganapathy, Venkat Sai Malladi, Vipin K Menon, Yilei Fu, Yongze Yin, Yuanqing Feng, Tim Hefferon, Fritz J. Sedlazeck, and Ben Busby

Subjects
Software Tool Article, Articles, Structural Variant, Graph Genome, Human Genomics, Clinical Annotation, Quality Control, Codeathon
Abstract

In October 2019, 46 scientists from around the world participated in the first National Center for Biotechnology Information (NCBI) Structural Variation (SV) Codeathon at Baylor College of Medicine. The charge of this first annual working session was to identify ongoing challenges around the topics of SV and graph genomes, and in response to design reliable methods to facilitate their study. Over three days, seven working groups each designed and developed new open-sourced methods to improve the bioinformatic analysis of genomic SVs represented in next-generation sequencing (NGS) data. The groups’ approaches addressed a wide range of problems in SV detection and analysis, including quality control (QC) assessments of metagenome assemblies and population-scale VCF files, de novo copy number variation (CNV) detection based on continuous long sequence reads, the representation of sequence variation using graph genomes, and the development of an SV annotation pipeline. A summary of the questions and developments that arose during the daily discussions between groups is outlined. The new methods are publicly available at https://github.com/NCBI-Codeathons/, and demonstrate that a codeathon devoted to SV analysis can produce valuable new insights both for participants and for the broader research community.

Published
2020
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28. Accurate circular consensus long-read sequencing improves variant detection and assembly of a human genome

Author

Wenger, Aaron M., Peluso, Paul, Rowell, William J., Chang, Pi-Chuan, Hall, Richard J., Concepcion, Gregory T., Ebler, Jana, Fungtammasan, Arkarachai, Kolesnikov, Alexey, Olson, Nathan D., Töpfer, Armin, Alonge, Michael, Mahmoud, Medhat, Qian, Yufeng, Chin, Chen-Shan, Phillippy, Adam M., Schatz, Michael C., Myers, Gene, DePristo, Mark A., Ruan, Jue, Marschall, Tobias, Sedlazeck, Fritz J., Zook, Justin M., Li, Heng, Koren, Sergey, Carroll, Andrew, Rank, David R., and Hunkapiller, Michael W.

Published
2019
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29. The effect of Moringa oleifera capsule in increasing breastmilk volume in early postpartum patients: A double-blind, randomized controlled trial.

Author

Siraphat Fungtammasan and Vorapong Phupong

Subjects
Medicine, Science
Abstract

Moringa oleifera is an herbal galactagogue that has been used to increase the volume of breastmilk. Few studies have evaluated the effect of Moringa oleifera in breastfeeding. There are conflicting data whether it can increase the volume of breastmilk or not. Thus, the objective of this study is to evaluate the efficacy of Moringa oleifera leaves in increasing the volume of breastmilk in early postpartum mothers. A randomized, double-blind, placebo-controlled trial will be conducted. The outcomes of this study will provide the data of Moringa oleifera as an herbal medication to increase the volume of breastmilk. This information will be used to increase the rate of exclusive breastfeeding for the first 6 months as recommended by the World Health Organization. Clinical trial registration This clinical trial was registered at ClinicalTrials.gov (Clinical trials registration: NCT04487613).

Published
2021
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31. The complete sequence of a human genome

Author

Sergey Nurk, Sergey Koren, Arang Rhie, Mikko Rautiainen, Andrey V. Bzikadze, Alla Mikheenko, Mitchell R. Vollger, Nicolas Altemose, Lev Uralsky, Ariel Gershman, Sergey Aganezov, Savannah J. Hoyt, Mark Diekhans, Glennis A. Logsdon, Michael Alonge, Stylianos E. Antonarakis, Matthew Borchers, Gerard G. Bouffard, Shelise Y. Brooks, Gina V. Caldas, Nae-Chyun Chen, Haoyu Cheng, Chen-Shan Chin, William Chow, Leonardo G. de Lima, Philip C. Dishuck, Richard Durbin, Tatiana Dvorkina, Ian T. Fiddes, Giulio Formenti, Robert S. Fulton, Arkarachai Fungtammasan, Erik Garrison, Patrick G. S. Grady, Tina A. Graves-Lindsay, Ira M. Hall, Nancy F. Hansen, Gabrielle A. Hartley, Marina Haukness, Kerstin Howe, Michael W. Hunkapiller, Chirag Jain, Miten Jain, Erich D. Jarvis, Peter Kerpedjiev, Melanie Kirsche, Mikhail Kolmogorov, Jonas Korlach, Milinn Kremitzki, Heng Li, Valerie V. Maduro, Tobias Marschall, Ann M. McCartney, Jennifer McDaniel, Danny E. Miller, James C. Mullikin, Eugene W. Myers, Nathan D. Olson, Benedict Paten, Paul Peluso, Pavel A. Pevzner, David Porubsky, Tamara Potapova, Evgeny I. Rogaev, Jeffrey A. Rosenfeld, Steven L. Salzberg, Valerie A. Schneider, Fritz J. Sedlazeck, Kishwar Shafin, Colin J. Shew, Alaina Shumate, Ying Sims, Arian F. A. Smit, Daniela C. Soto, Ivan Sović, Jessica M. Storer, Aaron Streets, Beth A. Sullivan, Françoise Thibaud-Nissen, James Torrance, Justin Wagner, Brian P. Walenz, Aaron Wenger, Jonathan M. D. Wood, Chunlin Xiao, Stephanie M. Yan, Alice C. Young, Samantha Zarate, Urvashi Surti, Rajiv C. McCoy, Megan Y. Dennis, Ivan A. Alexandrov, Jennifer L. Gerton, Rachel J. O’Neill, Winston Timp, Justin M. Zook, Michael C. Schatz, Evan E. Eichler, Karen H. Miga, Adam M. Phillippy, Nurk, Sergey [0000-0003-1301-5749], Koren, Sergey [0000-0002-1472-8962], Rhie, Arang [0000-0002-9809-8127], Rautiainen, Mikko [0000-0003-2971-267X], Bzikadze, Andrey V [0000-0002-7928-7950], Vollger, Mitchell R [0000-0002-8651-1615], Altemose, Nicolas [0000-0002-7231-6026], Uralsky, Lev [0000-0002-5565-7961], Gershman, Ariel [0000-0001-8899-8781], Aganezov, Sergey [0000-0003-2458-8323], Hoyt, Savannah J [0000-0001-7804-3236], Diekhans, Mark [0000-0002-0430-0989], Logsdon, Glennis A [0000-0003-2396-0656], Alonge, Michael [0000-0002-3692-1819], Antonarakis, Stylianos E [0000-0001-8907-5823], Borchers, Matthew [0000-0001-5903-3489], Bouffard, Gerard G [0000-0001-8744-6440], Chen, Nae-Chyun [0000-0002-4140-4568], Cheng, Haoyu [0000-0002-9209-5793], Chin, Chen-Shan [0000-0003-4394-2455], Chow, William [0000-0002-9056-201X], de Lima, Leonardo G [0000-0001-6340-6065], Dishuck, Philip C [0000-0003-2223-9787], Durbin, Richard [0000-0002-9130-1006], Fiddes, Ian T [0000-0002-1580-7443], Formenti, Giulio [0000-0002-7554-5991], Fungtammasan, Arkarachai [0000-0003-2398-0358], Garrison, Erik [0000-0003-3821-631X], Grady, Patrick GS [0000-0003-0180-7810], Graves-Lindsay, Tina A [0000-0002-0409-891X], Hall, Ira M [0000-0003-4442-6655], Hansen, Nancy F [0000-0002-0950-0699], Haukness, Marina [0000-0001-9991-8089], Howe, Kerstin [0000-0003-2237-513X], Jain, Miten [0000-0002-4571-3982], Jarvis, Erich D [0000-0001-8931-5049], Kirsche, Melanie [0000-0002-6631-4761], Kolmogorov, Mikhail [0000-0002-5489-9045], Korlach, Jonas [0000-0003-3047-4250], Kremitzki, Milinn [0000-0001-7980-3153], Li, Heng [0000-0003-4874-2874], Maduro, Valerie V [0000-0001-8250-9844], Marschall, Tobias [0000-0002-9376-1030], McDaniel, Jennifer [0000-0003-1987-0914], Miller, Danny E [0000-0001-6096-8601], Mullikin, James C [0000-0003-0825-3750], Myers, Eugene W [0000-0002-6580-7839], Olson, Nathan D [0000-0003-2585-3037], Paten, Benedict [0000-0001-8863-3539], Pevzner, Pavel A [0000-0002-0418-165X], Porubsky, David [0000-0001-8414-8966], Potapova, Tamara [0000-0003-2761-1795], Rosenfeld, Jeffrey A [0000-0002-8750-2841], Salzberg, Steven L [0000-0002-8859-7432], Sedlazeck, Fritz J [0000-0001-6040-2691], Shafin, Kishwar [0000-0001-5252-3434], Shumate, Alaina [0000-0002-4450-1857], Smit, Arian FA [0000-0003-2088-3165], Soto, Daniela C [0000-0002-6292-655X], Sović, Ivan [0000-0002-5900-4319], Storer, Jessica M [0000-0002-9619-5265], Streets, Aaron [0000-0002-3909-8389], Sullivan, Beth A [0000-0001-5216-4603], Thibaud-Nissen, Françoise [0000-0003-4957-7807], Torrance, James [0000-0002-6117-8190], Walenz, Brian P [0000-0001-8431-1428], Wenger, Aaron [0000-0003-1183-0432], Wood, Jonathan MD [0000-0002-7545-2162], Xiao, Chunlin [0000-0001-8702-4889], Yan, Stephanie M [0000-0002-6880-465X], Young, Alice C [0000-0003-0549-9261], Zarate, Samantha [0000-0001-5570-2059], McCoy, Rajiv C [0000-0003-0615-146X], Dennis, Megan Y [0000-0002-8502-5420], Alexandrov, Ivan A [0000-0003-4342-2003], Gerton, Jennifer L [0000-0003-0743-3637], O'Neill, Rachel J [0000-0002-1525-6821], Timp, Winston [0000-0003-2083-6027], Zook, Justin M [0000-0003-2309-8402], Schatz, Michael C [0000-0002-4118-4446], Eichler, Evan E [0000-0002-8246-4014], Miga, Karen H [0000-0001-9709-4565], Phillippy, Adam M [0000-0003-2983-8934], and Apollo - University of Cambridge Repository

Subjects
Chromosomes, Artificial, Bacterial, Genome, Multidisciplinary, General Science & Technology, Genome, Human, 1.1 Normal biological development and functioning, Human Genome, Bacterial, DNA, Sequence Analysis, DNA, Chromosomes, Cell Line, Underpinning research, Reference Values, Artificial, Human Genome Project, Genetics, Chromosomes, Human, Humans, Generic health relevance, Sequence Analysis, Human
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
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32. A strategy for building and using a human reference pangenome [version 1; peer review: 1 approved, 1 approved with reservations]

Author

Bastien Llamas, Giuseppe Narzisi, Valerie Schneider, Peter A. Audano, Evan Biederstedt, Lon Blauvelt, Peter Bradbury, Xian Chang, Chen-Shan Chin, Arkarachai Fungtammasan, Wayne E. Clarke, Alan Cleary, Jana Ebler, Jordan Eizenga, Jonas A. Sibbesen, Charles J. Markello, Erik Garrison, Shilpa Garg, Glenn Hickey, Gerard R. Lazo, Michael F. Lin, Medhat Mahmoud, Tobias Marschall, Ilia Minkin, Jean Monlong, Rajeeva L. Musunuri, Sagayamary Sagayaradj, Adam M. Novak, Mikko Rautiainen, Allison Regier, Fritz J. Sedlazeck, Jouni Siren, Yassine Souilmi, Justin Wagner, Travis Wrightsman, Toshiyuki T. Yokoyama, Qiandong Zeng, Justin M. Zook, Benedict Paten, and Ben Busby

Subjects
Software Tool Article, Articles, Hackathon, Pangenome, Graph Genome, RNAseq, Structural Variant
Abstract

In March 2019, 45 scientists and software engineers from around the world converged at the University of California, Santa Cruz for the first pangenomics codeathon. The purpose of the meeting was to propose technical specifications and standards for a usable human pangenome as well as to build relevant tools for genome graph infrastructures. During the meeting, the group held several intense and productive discussions covering a diverse set of topics, including advantages of graph genomes over a linear reference representation, design of new methods that can leverage graph-based data structures, and novel visualization and annotation approaches for pangenomes. Additionally, the participants self-organized themselves into teams that worked intensely over a three-day period to build a set of pipelines and tools for specific pangenomic applications. A summary of the questions raised and the tools developed are reported in this manuscript.

Published
2019
Full Text
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37. A chromosome-level reference genome and pangenome for barn swallow population genomics

Author

Secomandi, S., Gallo, G.R., Sozzoni, M., Iannucci, A., Galati, E., Abueg, L., Balacco, J., Caprioli, M., Chow, W., Ciofi, C., Collins, J., Fedrigo, O., Ferretti, L., Fungtammasan, A., Haase, B., Howe, K., Kwak, W., Lombardo, G., Masterson, P., Messina, G., Møller, A.P., Mountcastle, J., Mousseau, T.A., Ferrer Obiol, J., Olivieri, A., Rhie, A., Rubolini, D., Saclier, M., Stanyon, R., Stucki, D., Thibaud-Nissen, F., Torrance, J., Torroni, A., Weber, K., Ambrosini, R., Bonisoli-Alquati, A., Jarvis, E.D., Gianfranceschi, L., and Formenti, G.

Subjects
Settore BIO/07 - Ecologia, population genomics, CP: Molecular biology, barn swallow, comparative genomics, genetic marker catalog, genome assembly, linkage disequilibrium, pangenome graph, pangenomics, reference genome, synanthropy, Settore BIO/11 - Biologia Molecolare, Settore BIO/18 - Genetica
Published
2023

39. Benchmarking challenging small variants with linked and long reads

Author

Justin Wagner, Nathan D. Olson, Lindsay Harris, Ziad Khan, Jesse Farek, Medhat Mahmoud, Ana Stankovic, Vladimir Kovacevic, Byunggil Yoo, Neil Miller, Jeffrey A. Rosenfeld, Bohan Ni, Samantha Zarate, Melanie Kirsche, Sergey Aganezov, Michael C. Schatz, Giuseppe Narzisi, Marta Byrska-Bishop, Wayne Clarke, Uday S. Evani, Charles Markello, Kishwar Shafin, Xin Zhou, Arend Sidow, Vikas Bansal, Peter Ebert, Tobias Marschall, Peter Lansdorp, Vincent Hanlon, Carl-Adam Mattsson, Alvaro Martinez Barrio, Ian T. Fiddes, Chunlin Xiao, Arkarachai Fungtammasan, Chen-Shan Chin, Aaron M. Wenger, William J. Rowell, Fritz J. Sedlazeck, Andrew Carroll, Marc Salit, and Justin M. Zook

Abstract

Genome in a Bottle benchmarks are widely used to help validate clinical sequencing pipelines and develop variant calling and sequencing methods. Here we use accurate linked and long reads to expand benchmarks in 7 samples to include difficult-to-map regions and segmental duplications that are challenging for short reads. These benchmarks add more than 300,000 SNVs and 50,000 insertions or deletions (indels) and include 16% more exonic variants, many in challenging, clinically relevant genes not covered previously, such as

Published
2022

40. The complete sequence of a human Y chromosome

Author

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

Abstract

The human Y chromosome has been notoriously difficult to sequence and assemble because of its complex repeat structure including long palindromes, tandem repeats, and segmental duplications. 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 finished. Here, the Telomere-to-Telomere (T2T) consortium presents the complete 62,460,029 base pair sequence of a human Y chromosome from the HG002 genome (T2T-Y) that corrects multiple errors in GRCh38-Y and adds over 30 million base pairs of sequence to the reference, revealing the complete ampliconic structures ofTSPY, DAZ, andRBMY; 42 additional protein-coding genes, mostly from theTSPYgene family; and an alternating pattern of human satellite 1 and 3 blocks in the heterochromatic Yq12 region. We have combined T2T-Y with a prior assembly of the CHM13 genome and mapped available population variation, clinical variants, and functional genomics data to produce a complete and comprehensive reference sequence for all 24 human chromosomes.

Published
2022
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42. 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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43. Hi‐C scaffolded short‐ and long‐read genome assemblies of the California sea lion are broadly consistent for syntenic inference across 45 million years of evolution

Author

Jochen B. W. Wolf, Alan Tracey, Matthew Breen, Saurabh D. Pophaly, Claire R. Peart, Jonathan Wood, Christina L. Williams, Bee Ling Ng, Benjamin A. Neely, David J. Adams, James Torrance, Jeremy A. Johnson, Arkarachai Fungtammasan, Joanna Collins, Kerstin Howe, William Cheng, Olivier Fedrigo, Arang Rhie, Bettina Haase, Ying Sims, Frances M. D. Gulland, Erich D. Jarvis, Joseph I. Hoffman, Michael E. Goebel, Jacquelyn Mountcastle, and Giulio Formenti

Subjects
0106 biological sciences, 0301 basic medicine, Genome evolution, X Chromosome, Sequence assembly, Biology, Synteny, 010603 evolutionary biology, 01 natural sciences, Genome, 03 medical and health sciences, Dogs, Genetics, Animals, Ecology, Evolution, Behavior and Systematics, X chromosome, Genomic organization, Bacterial artificial chromosome, Ferrets, Chromosome, Sea Lions, 030104 developmental biology, Evolutionary biology, Biotechnology
Abstract

With the advent of chromatin-interaction maps, chromosome-level genome assemblies have become a reality for a wide range of organisms. Scaffolding quality is, however, difficult to judge. To explore this gap, we generated multiple chromosome-scale genome assemblies of an emerging wild animal model for carcinogenesis, the California sea lion (Zalophus californianus). Short-read assemblies were scaffolded with two independent chromatin interaction mapping data sets (Hi-C and Chicago), and long-read assemblies with three data types (Hi-C, optical maps and 10X linked reads) following the "Vertebrate Genomes Project (VGP)" pipeline. In both approaches, 18 major scaffolds recovered the karyotype (2n = 36), with scaffold N50s of 138 and 147 Mb, respectively. Synteny relationships at the chromosome level with other pinniped genomes (2n = 32-36), ferret (2n = 34), red panda (2n = 36) and domestic dog (2n = 78) were consistent across approaches and recovered known fissions and fusions. Comparative chromosome painting and multicolour chromosome tiling with a panel of 264 genome-integrated single-locus canine bacterial artificial chromosome probes provided independent evaluation of genome organization. Broad-scale discrepancies between the approaches were observed within chromosomes, most commonly in translocations centred around centromeres and telomeres, which were better resolved in the VGP assembly. Genomic and cytological approaches agreed on near-perfect synteny of the X chromosome, and in combination allowed detailed investigation of autosomal rearrangements between dog and sea lion. This study presents high-quality genomes of an emerging cancer model and highlights that even highly fragmented short-read assemblies scaffolded with Hi-C can yield reliable chromosome-level scaffolds suitable for comparative genomic analyses.

Published
2021
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44. 2019 Novel Coronavirus (SARS-CoV-2)

Author

Jochum, Michael, Lee, Michael, Yin, Yongze, Taylor, Deanne, Meller, Rob, Fisch, Katie, Vitalis, Elizabeth, Fungtammasan, Chai, Zaksas, Viktorija, Chin, Jason, Sipahioglu, Carla, Li, Winifred, Curry, Kristen, Kille, Bryce, Treangen, Todd, and Ternus, Krista

Subjects
ComputingMethodologies_PATTERNRECOGNITION
Abstract

This project includes the analysis of public COVID-19 sequence datasets with a variety of open source bioinformatics tools.

Published
2022
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46. Reference genome and demographic history of the most endangered marine mammal, the vaquita

Author

Bettina Haase, Yury V Bukhman, Julie A Fronczek, Mads Peter Heide-Jørgensen, Sacha Stevenson, Sarah Pelan, Randall S. Wells, Whitney B. Musser, Lorenzo Rojas-Bracho, Kerstin Howe, Oliver A. Ryder, William Chow, Marlys L. Houck, Adam M. Phillippy, Andrew J. Westgate, Catherine D Avila, Jennifer Balacco, Sadye Paez, Phillip A. Morin, Ann C Misuraca, Jacqueline Robinson, Arang Rhie, Teri Rowles, Arkarachai Fungtammasan, James Torrance, Olivier Fedrigo, Cynthia R. Smith, Erich D. Jarvis, Frances M. D. Gulland, Jonas Teilmann, Jacquelyn Mountcastle, Giulio Formenti, Barbara L. Taylor, and Frederick I. Archer

Subjects
0106 biological sciences, 0301 basic medicine, Vaquita, Demographic history, Biology, historical demography, Genome, 010603 evolutionary biology, 01 natural sciences, Chromosomes, 03 medical and health sciences, Critically endangered, biology.animal, Phocoena, Genetics, Animals, porpoise, Ecology, Evolution, Behavior and Systematics, Phocoena sinus, Endangered Species, Small population size, biology.organism_classification, From the Cover, 030104 developmental biology, Population bottleneck, genome diversity, Vertebrate Genomes Project, Genetics, Population, Evolutionary biology, Conservation genomics, Female, Inbreeding, Porpoise, Biotechnology, Reference genome
Abstract

The vaquita is the most critically endangered marine mammal, with fewer than 19 remaining in the wild. First described in 1958, the vaquita has been in rapid decline for more than 20 years resulting from inadvertent deaths due to the increasing use of large‐mesh gillnets. To understand the evolutionary and demographic history of the vaquita, we used combined long‐read sequencing and long‐range scaffolding methods with long‐ and short‐read RNA sequencing to generate a near error‐free annotated reference genome assembly from cell lines derived from a female individual. The genome assembly consists of 99.92% of the assembled sequence contained in 21 nearly gapless chromosome‐length autosome scaffolds and the X‐chromosome scaffold, with a scaffold N50 of 115 Mb. Genome‐wide heterozygosity is the lowest (0.01%) of any mammalian species analysed to date, but heterozygosity is evenly distributed across the chromosomes, consistent with long‐term small population size at genetic equilibrium, rather than low diversity resulting from a recent population bottleneck or inbreeding. Historical demography of the vaquita indicates long‐term population stability at less than 5,000 (Ne) for over 200,000 years. Together, these analyses indicate that the vaquita genome has had ample opportunity to purge highly deleterious alleles and potentially maintain diversity necessary for population health., see also the Perspective by Annabel Whibley

Published
2020
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47. Effect of sequence depth and length in long-read assembly of the maize inbred NC358

Author

R. Kelly Dawe, Jianing Liu, Kapeel Chougule, Adam M. Phillippy, Chen-Shan Chin, Sharon Wei, Brian P. Walenz, Sergey Koren, Samantha J. Snodgrass, Brett T. Hannigan, Joshua C. Stein, Arkarachai Fungtammasan, Nancy Manchanda, Arun S. Seetharam, Margaret R. Woodhouse, Kevin Fengler, Sarah Pedersen, Candice N. Hirsch, Shujun Ou, Matthew B. Hufford, Doreen Ware, Victor Llaca, Amanda M. Gilbert, and David E. Hufnagel

Subjects
0301 basic medicine, 0106 biological sciences, Transposable element, Agricultural genetics, Computer science, Heterochromatin, Science, General Physics and Astronomy, Sequence assembly, Computational biology, Biology, 01 natural sciences, Genome, Zea mays, General Biochemistry, Genetics and Molecular Biology, Article, 03 medical and health sciences, Centromere, Genome assembly algorithms, Resource allocation (computer), Inbreeding, lcsh:Science, Gene, 030304 developmental biology, Sequence (medicine), Repetitive Sequences, Nucleic Acid, 2. Zero hunger, 0303 health sciences, Multidisciplinary, Base Sequence, High-Throughput Nucleotide Sequencing, General Chemistry, 030104 developmental biology, DNA Transposable Elements, lcsh:Q, Line (text file), Limited resources, Genome, Plant, 010606 plant biology & botany
Abstract

Improvements in long-read data and scaffolding technologies have enabled rapid generation of reference-quality assemblies for complex genomes. Still, an assessment of critical sequence depth and read length is important for allocating limited resources. To this end, we have generated eight assemblies for the complex genome of the maize inbred line NC358 using PacBio datasets ranging from 20 to 75 × genomic depth and with N50 subread lengths of 11–21 kb. Assemblies with ≤30 × depth and N50 subread length of 11 kb are highly fragmented, with even low-copy genic regions showing degradation at 20 × depth. Distinct sequence-quality thresholds are observed for complete assembly of genes, transposable elements, and highly repetitive genomic features such as telomeres, heterochromatic knobs, and centromeres. In addition, we show high-quality optical maps can dramatically improve contiguity in even our most fragmented base assembly. This study provides a useful resource allocation reference to the community as long-read technologies continue to mature., Sequence depth and read length determine the quality of genome assembly. Here, the authors leverage a set of PacBio reads to develop guidelines for sequencing and assembly of complex plant genomes in order to allocate finite resources using maize as an example.

Published
2020

48. Pangenomics provides insights into the role of synanthropy in barn swallow evolution

Author

Simona Secomandi, Guido Roberto Gallo, Marcella Sozzoni, Alessio Iannucci, Elena Galati, Linelle Abueg, Jennifer Balacco, Manuela Caprioli, William Chow, Claudio Ciofi, Joanna Collins, Olivier Fedrigo, Luca Ferretti, Arkarachai Fungtammasan, Bettina Haase, Kerstin Howe, Woori Kwak, Gianluca Lombardo, Patrick Masterson, Graziella Messina, Anders Pape Møller, Jacquelyn Mountcastle, Timothy A. Mousseau, Joan Ferrer-Obiol, Anna Olivieri, Arang Rhie, Diego Rubolini, Marielle Saclier, Roscoe Stanyon, David Stucki, Françoise Thibaud-Nissen, James Torrance, Antonio Torroni, Kristina Weber, Roberto Ambrosini, Andrea Bonisoli-Alquati, Erich D. Jarvis, Luca Gianfranceschi, and Giulio Formenti

Abstract

Insights into the evolution of non-model organisms are often limited by the lack of reference genomes. As part of the Vertebrate Genomes Project, we present a new reference genome and a pangenome produced with High-Fidelity long reads for the barn swallow Hirundo rustica. We then generated a reference-free multialignment with other bird genomes to identify genes under selection. Conservation analyses pointed at genes enriched for transcriptional regulation and neurodevelopment. The most conserved gene is CAMK2N2, with a potential role in fear memory formation. In addition, using all publicly available data, we generated a comprehensive catalogue of genetic markers. Genome-wide linkage disequilibrium scans identified potential selection signatures at multiple loci. The top candidate region comprises several genes and includes BDNF, a gene involved in stress response, fear memory formation, and tameness. We propose that the strict association with humans in this species is linked with the evolution of pathways typically under selection in domesticated taxa.

Published
2022
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